From 20b5f6fb17f954322711eedc04a10a351349d580 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Fri, 15 Sep 2023 11:29:30 +0200 Subject: [PATCH 01/36] bad stereo --- api/c/indigo/src/indigo_layout.cpp | 6 +- .../integration/ref/formats/smiles.py.out | 3 + api/tests/integration/tests/formats/smiles.py | 2 +- core/indigo-core/molecule/base_molecule.h | 4 + .../molecule/src/base_molecule.cpp | 18 +++- .../molecule/src/molecule_json_loader.cpp | 4 +- .../molecule/src/molfile_loader.cpp | 4 +- .../molecule/src/smiles_loader.cpp | 22 +++-- .../indigo-core/molecule/src/smiles_saver.cpp | 82 +++++++++++++++---- 9 files changed, 110 insertions(+), 35 deletions(-) diff --git a/api/c/indigo/src/indigo_layout.cpp b/api/c/indigo/src/indigo_layout.cpp index eec28abc5f..5b66002f2b 100644 --- a/api/c/indigo/src/indigo_layout.cpp +++ b/api/c/indigo/src/indigo_layout.cpp @@ -58,8 +58,8 @@ CEXPORT int indigoLayout(int object) ml.max_iterations = self.layout_max_iterations; ml.bond_length = 1.6f; ml.layout_orientation = (layout_orientation_value)self.layout_orientation; - bool has_atropisomery = mol->hasAtropisomericCenter(); - if (has_atropisomery) + bool has_forced_stereo = mol->forcedStereoBonds().size(); + if (has_forced_stereo) ml.respect_existing_layout = true; TimeoutCancellationHandler cancellation(self.cancellation_timeout); @@ -69,7 +69,7 @@ CEXPORT int indigoLayout(int object) if (obj.type != IndigoObject::SUBMOLECULE) { - if (!has_atropisomery) + if (!has_forced_stereo) mol->clearBondDirections(); try { diff --git a/api/tests/integration/ref/formats/smiles.py.out b/api/tests/integration/ref/formats/smiles.py.out index 8d8a2820b4..cc66a6b521 100644 --- a/api/tests/integration/ref/formats/smiles.py.out +++ b/api/tests/integration/ref/formats/smiles.py.out @@ -75,3 +75,6 @@ CCCCC |Sg:n:1,2,3::hh| atropisomer: C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4| C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4| +atropisomer: +C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |wU:3.12,wD:3.3| +C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |wU:3.12,wD:3.3| diff --git a/api/tests/integration/tests/formats/smiles.py b/api/tests/integration/tests/formats/smiles.py index 60885b3514..74b307f855 100644 --- a/api/tests/integration/tests/formats/smiles.py +++ b/api/tests/integration/tests/formats/smiles.py @@ -117,7 +117,7 @@ print(indigo.loadMolecule(sm).smiles()) print("*** Atropisomers ***") -mols_smiles = ["C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12|"] +mols_smiles = ["C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12|","C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |wU:5.4,wD:5.5|"] for sm in mols_smiles: print("atropisomer:") mol = indigo.loadMolecule(sm) diff --git a/core/indigo-core/molecule/base_molecule.h b/core/indigo-core/molecule/base_molecule.h index 7b3256d2bd..ccb02c15ee 100644 --- a/core/indigo-core/molecule/base_molecule.h +++ b/core/indigo-core/molecule/base_molecule.h @@ -390,6 +390,9 @@ namespace indigo void clearBondDirections(); int getBondDirection(int idx) const; void setBondDirection(int idx, int dir); + void markForcedStereoBond(int idx); + bool isForcedStereoBond(int idx); + const RedBlackSet& forcedStereoBonds(); int getBondDirection2(int center_idx, int nei_idx); @@ -511,6 +514,7 @@ namespace indigo Array _sl_bonds; Array _bond_directions; + RedBlackSet _forced_bond_directions; Array _xyz; RedBlackMap _stereo_flag_positions; diff --git a/core/indigo-core/molecule/src/base_molecule.cpp b/core/indigo-core/molecule/src/base_molecule.cpp index 6301750736..7fcb7e1a41 100644 --- a/core/indigo-core/molecule/src/base_molecule.cpp +++ b/core/indigo-core/molecule/src/base_molecule.cpp @@ -3914,6 +3914,21 @@ int BaseMolecule::getBondDirection(int idx) const return _bond_directions[idx]; } +void BaseMolecule::markForcedStereoBond(int idx) +{ + _forced_bond_directions.find_or_insert( idx ); +} + +bool BaseMolecule::isForcedStereoBond(int idx) +{ + return _forced_bond_directions.find(idx); +} + +const RedBlackSet& BaseMolecule::forcedStereoBonds() +{ + return _forced_bond_directions; +} + int BaseMolecule::getBondDirection2(int center_idx, int nei_idx) { int idx = findEdgeIndex(center_idx, nei_idx); @@ -3936,6 +3951,7 @@ void BaseMolecule::setBondDirection(int idx, int dir) void BaseMolecule::clearBondDirections() { _bond_directions.clear(); + _forced_bond_directions.clear(); } bool BaseMolecule::isChiral() @@ -4444,7 +4460,7 @@ bool BaseMolecule::isAtropisomerismReferenceAtom(int atom_idx) for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) { auto bond_idx = v.neiEdge(i); - if (getBondDirection(bond_idx)) + if (getBondDirection(bond_idx) && getEdgeTopology(bond_idx) == TOPOLOGY_RING) continue; if (isRotationBond(bond_idx)) rotation_bonds.insert(bond_idx); diff --git a/core/indigo-core/molecule/src/molecule_json_loader.cpp b/core/indigo-core/molecule/src/molecule_json_loader.cpp index e84b55cecf..b7b51ac836 100644 --- a/core/indigo-core/molecule/src/molecule_json_loader.cpp +++ b/core/indigo-core/molecule/src/molecule_json_loader.cpp @@ -1127,7 +1127,9 @@ void MoleculeJsonLoader::loadMolecule(BaseMolecule& mol, bool load_arrows) { if (mol.getBondDirection(i) > 0 && !sensible_bond_directions[i]) { - if (!stereochemistry_options.ignore_errors) + if (stereochemistry_options.ignore_errors) + mol.markForcedStereoBond(i); + else throw Error("direction of bond #%d makes no sense", i); } } diff --git a/core/indigo-core/molecule/src/molfile_loader.cpp b/core/indigo-core/molecule/src/molfile_loader.cpp index 970357a451..bcba90aca7 100644 --- a/core/indigo-core/molecule/src/molfile_loader.cpp +++ b/core/indigo-core/molecule/src/molfile_loader.cpp @@ -2080,7 +2080,9 @@ void MolfileLoader::_postLoad() for (i = 0; i < _bonds_num; i++) if (_bmol->getBondDirection(i) > 0 && !_sensible_bond_directions[i]) { - if (!stereochemistry_options.ignore_errors) + if (stereochemistry_options.ignore_errors) + _bmol->markForcedStereoBond(i); + else throw Error("direction of bond #%d makes no sense", i); } diff --git a/core/indigo-core/molecule/src/smiles_loader.cpp b/core/indigo-core/molecule/src/smiles_loader.cpp index 71a519e3da..7936f44101 100644 --- a/core/indigo-core/molecule/src/smiles_loader.cpp +++ b/core/indigo-core/molecule/src/smiles_loader.cpp @@ -356,19 +356,19 @@ void SmilesLoader::_readOtherStuff() auto bond_idx = _scanner.readUnsigned(); if (wmode) { + _bmol->setBondDirection(bond_idx, wmode == 'U' ? BOND_UP : BOND_DOWN); auto& v = _bmol->getEdge(bond_idx); if (v.end == atom_idx) _bmol->swapEdgeEnds(bond_idx); - if (v.beg == atom_idx) + if (_bmol->getEdgeTopology(bond_idx) == TOPOLOGY_RING && _bmol->isAtropisomerismReferenceAtom(atom_idx) && + (v.beg == atom_idx || v.end == atom_idx)) { - _bmol->setBondDirection(bond_idx, wmode == 'U' ? BOND_UP : BOND_DOWN); - if (_bmol->isAtropisomerismReferenceAtom(atom_idx)) - { - if (!_bmol->stereocenters.exists(atom_idx)) - _bmol->addStereocenters(atom_idx, MoleculeStereocenters::ATOM_ANY, 0, false); - _bmol->stereocenters.setAtropisomeric(atom_idx, true); - } + if (!_bmol->stereocenters.exists(atom_idx)) + _bmol->addStereocenters(atom_idx, MoleculeStereocenters::ATOM_ABS, 0, false); + _bmol->stereocenters.setAtropisomeric(atom_idx, true); } + if (!_bmol->stereocenters.exists(atom_idx) || _bmol->stereocenters.isAtropisomeric(atom_idx)) + _bmol->markForcedStereoBond(bond_idx); } } @@ -1345,11 +1345,9 @@ void SmilesLoader::_validateStereoCenters() for (int i = _bmol->stereocenters.begin(); i < _bmol->stereocenters.end(); i = _bmol->stereocenters.next(i)) { auto atom_idx = _bmol->stereocenters.getAtomIndex(i); - if (_bmol->isPossibleStereocenter(atom_idx) || _bmol->isAtropisomerismReferenceAtom(atom_idx)) + if (_bmol->isPossibleStereocenter(atom_idx) || _bmol->stereocenters.isAtropisomeric(atom_idx)) continue; - if (stereochemistry_options.ignore_errors) - _bmol->stereocenters.remove(i); - else + if (!stereochemistry_options.ignore_errors) throw Error("atom %d is not a stereocenter", atom_idx); } } diff --git a/core/indigo-core/molecule/src/smiles_saver.cpp b/core/indigo-core/molecule/src/smiles_saver.cpp index f0ce525217..c483aac903 100644 --- a/core/indigo-core/molecule/src/smiles_saver.cpp +++ b/core/indigo-core/molecule/src/smiles_saver.cpp @@ -27,6 +27,7 @@ #include "molecule/molecule.h" #include "molecule/molecule_rgroups.h" #include "molecule/molecule_savers.h" +#include "molecule/molecule_stereocenter_options.h" #include "molecule/molecule_stereocenters.h" #include "molecule/query_molecule.h" @@ -1840,31 +1841,80 @@ void SmilesSaver::_writeSubstitutionCounts() void SmilesSaver::_writeWedges() { - bool is_first = true; - if (_bmol) { + std::vector> down_dirs, up_dirs; + std::vector sensible_bond_directions; + StereocentersOptions stereochemistry_options; + + sensible_bond_directions.resize(_written_bonds.size(), 0); + + for (int i = 0; i < _written_bonds.size(); i++) + if (_bmol->getBondDirection(i) == BOND_EITHER) + { + if (MoleculeCisTrans::isGeomStereoBond(*_bmol, i, 0, true)) + sensible_bond_directions[i] = 1; + else + { + int k; + const Vertex& v = _bmol->getVertex(_bmol->getEdge(i).beg); + + for (k = v.neiBegin(); k != v.neiEnd(); k = v.neiNext(k)) + { + if (MoleculeCisTrans::isGeomStereoBond(*_bmol, v.neiEdge(k), 0, true)) + { + sensible_bond_directions[i] = 1; + break; + } + } + } + } + for (int i = 0; i < _written_bonds.size(); ++i) { auto bond_idx = _written_bonds[i]; auto& e = _bmol->getEdge(bond_idx); - if (_bmol->stereocenters.exists(e.beg) && _bmol->stereocenters.isAtropisomeric(e.beg)) + auto bdir = _bmol->getBondDirection(bond_idx); + if (bdir && bdir < BOND_EITHER && _bmol->isForcedStereoBond(bond_idx)) + { + const auto& edge = _bmol->getEdge(bond_idx); + auto wa_idx = _written_atoms.find(edge.beg); + if (bdir == BOND_UP) + up_dirs.emplace_back(wa_idx, i); + else + down_dirs.emplace_back(wa_idx, i); + } + } + bool is_first = true; + if (up_dirs.size()) + { + for (const auto& kvp : up_dirs) { - auto bdir = _bmol->getBondDirection(bond_idx); - if (bdir && bdir < BOND_EITHER) + if (is_first) { - if (is_first) - { - _startExtension(); - _output.writeString(bdir == BOND_UP ? "wU:" : "wD:"); - is_first = false; - } - else - _output.writeString(","); - const auto& edge = _bmol->getEdge(bond_idx); - auto wa_idx = _written_atoms.find(edge.beg); - _output.printf("%d.%d", wa_idx, i); + _startExtension(); + _output.writeString("wU:"); + is_first = false; } + else + _output.writeString(","); + _output.printf("%d.%d", kvp.first, kvp.second); + } + } + is_first = true; + if (down_dirs.size()) + { + for (const auto& kvp : down_dirs) + { + if (is_first) + { + _startExtension(); + _output.writeString("wD:"); + is_first = false; + } + else + _output.writeString(","); + _output.printf("%d.%d", kvp.first, kvp.second); } } } From 74fba33db2a20b4e11a63446f04a1fba5af00963 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Fri, 15 Sep 2023 11:33:47 +0200 Subject: [PATCH 02/36] clang fix --- core/indigo-core/molecule/src/base_molecule.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/indigo-core/molecule/src/base_molecule.cpp b/core/indigo-core/molecule/src/base_molecule.cpp index 7fcb7e1a41..aee90ffa9d 100644 --- a/core/indigo-core/molecule/src/base_molecule.cpp +++ b/core/indigo-core/molecule/src/base_molecule.cpp @@ -3916,7 +3916,7 @@ int BaseMolecule::getBondDirection(int idx) const void BaseMolecule::markForcedStereoBond(int idx) { - _forced_bond_directions.find_or_insert( idx ); + _forced_bond_directions.find_or_insert(idx); } bool BaseMolecule::isForcedStereoBond(int idx) From e38b5bbab6bc5015e9c6b1db0986e492225818a6 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Fri, 15 Sep 2023 11:36:41 +0200 Subject: [PATCH 03/36] py formatting --- api/tests/integration/tests/formats/smiles.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/api/tests/integration/tests/formats/smiles.py b/api/tests/integration/tests/formats/smiles.py index 74b307f855..09dce8fd0c 100644 --- a/api/tests/integration/tests/formats/smiles.py +++ b/api/tests/integration/tests/formats/smiles.py @@ -117,7 +117,10 @@ print(indigo.loadMolecule(sm).smiles()) print("*** Atropisomers ***") -mols_smiles = ["C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12|","C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |wU:5.4,wD:5.5|"] +mols_smiles = [ + "C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12|", + "C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |wU:5.4,wD:5.5|", +] for sm in mols_smiles: print("atropisomer:") mol = indigo.loadMolecule(sm) From 2a2e4c3acbeba1440109b3dfe7b1cb0b7f598ca3 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 18 Sep 2023 12:09:28 +0200 Subject: [PATCH 04/36] atrop layout --- api/c/indigo/src/indigo_layout.cpp | 3 ++ api/tests/integration/tests/exact/reload.py | 3 +- core/indigo-core/molecule/base_molecule.h | 7 +-- core/indigo-core/molecule/smiles_loader.h | 2 + .../molecule/src/base_molecule.cpp | 22 +++++---- .../molecule/src/molecule_json_loader.cpp | 7 ++- .../molecule/src/molfile_loader.cpp | 14 +++--- .../molecule/src/smiles_loader.cpp | 46 +++++++++++++------ .../indigo-core/molecule/src/smiles_saver.cpp | 42 ++++++----------- utils/indigo-depict/main.c | 2 +- 10 files changed, 84 insertions(+), 64 deletions(-) diff --git a/api/c/indigo/src/indigo_layout.cpp b/api/c/indigo/src/indigo_layout.cpp index 5b66002f2b..5fcaaafcf6 100644 --- a/api/c/indigo/src/indigo_layout.cpp +++ b/api/c/indigo/src/indigo_layout.cpp @@ -75,6 +75,9 @@ CEXPORT int indigoLayout(int object) { mol->markBondsStereocenters(); mol->markBondsAlleneStereo(); + auto& fbonds = mol->forcedStereoBonds(); + for (int i = fbonds.begin(); i != fbonds.end(); i = fbonds.next(i)) + mol->setBondDirection(fbonds.key(i), fbonds.value(i)); } catch (Exception e) { diff --git a/api/tests/integration/tests/exact/reload.py b/api/tests/integration/tests/exact/reload.py index 5b8297aee4..22495d687d 100644 --- a/api/tests/integration/tests/exact/reload.py +++ b/api/tests/integration/tests/exact/reload.py @@ -41,8 +41,7 @@ def testMol(mol): perm_smiles = perm_mol.smiles() if not indigo.exactMatch(mol, perm_mol): msg = ( - " Exact: %s after reload from smiles %s. Permuted canonical smiles: %s\n %s %s" - % (mol.name(), base_smiles, perm_smiles) + " Exact: %s after reload from smiles %s. Permuted canonical smiles: %s\n" % (mol.name(), base_smiles, perm_smiles) ) print(msg) sys.stderr.write(msg + "\n") diff --git a/core/indigo-core/molecule/base_molecule.h b/core/indigo-core/molecule/base_molecule.h index ccb02c15ee..32917c90b7 100644 --- a/core/indigo-core/molecule/base_molecule.h +++ b/core/indigo-core/molecule/base_molecule.h @@ -389,10 +389,11 @@ namespace indigo void clearBondDirections(); int getBondDirection(int idx) const; + int* getForcedBondDirection(int idx) const; void setBondDirection(int idx, int dir); - void markForcedStereoBond(int idx); + void setForcedBondDirection(int idx, int dir); bool isForcedStereoBond(int idx); - const RedBlackSet& forcedStereoBonds(); + const RedBlackMap& forcedStereoBonds(); int getBondDirection2(int center_idx, int nei_idx); @@ -514,7 +515,7 @@ namespace indigo Array _sl_bonds; Array _bond_directions; - RedBlackSet _forced_bond_directions; + RedBlackMap _forced_stereo_directions; Array _xyz; RedBlackMap _stereo_flag_positions; diff --git a/core/indigo-core/molecule/smiles_loader.h b/core/indigo-core/molecule/smiles_loader.h index f80adafec4..80c43c2c4e 100644 --- a/core/indigo-core/molecule/smiles_loader.h +++ b/core/indigo-core/molecule/smiles_loader.h @@ -156,6 +156,7 @@ namespace indigo int _balance; int _current_compno; bool _inside_smarts_component; + bool _has_atom_coordinates = false; BaseMolecule* _bmol; QueryMolecule* _qmol; @@ -177,6 +178,7 @@ namespace indigo bool _isAlleneLike(int i); void _handleCurlyBrace(_AtomDesc& atom, bool& inside_polymer); void _handlePolymerRepetition(int i); + void _handleForcedStereo(); void _readAtom(Array& atom_str, bool first_in_brackets, _AtomDesc& atom, std::unique_ptr& qatom); diff --git a/core/indigo-core/molecule/src/base_molecule.cpp b/core/indigo-core/molecule/src/base_molecule.cpp index aee90ffa9d..b8351635e8 100644 --- a/core/indigo-core/molecule/src/base_molecule.cpp +++ b/core/indigo-core/molecule/src/base_molecule.cpp @@ -3914,19 +3914,25 @@ int BaseMolecule::getBondDirection(int idx) const return _bond_directions[idx]; } -void BaseMolecule::markForcedStereoBond(int idx) +int* BaseMolecule::getForcedBondDirection(int idx) const { - _forced_bond_directions.find_or_insert(idx); + return _forced_stereo_directions.at2(idx); +} + +void BaseMolecule::setForcedBondDirection(int idx, int dir) +{ + if (!_forced_stereo_directions.find(idx)) + _forced_stereo_directions.insert(idx, dir); } bool BaseMolecule::isForcedStereoBond(int idx) { - return _forced_bond_directions.find(idx); + return _forced_stereo_directions.find(idx); } -const RedBlackSet& BaseMolecule::forcedStereoBonds() +const RedBlackMap& BaseMolecule::forcedStereoBonds() { - return _forced_bond_directions; + return _forced_stereo_directions; } int BaseMolecule::getBondDirection2(int center_idx, int nei_idx) @@ -3951,7 +3957,7 @@ void BaseMolecule::setBondDirection(int idx, int dir) void BaseMolecule::clearBondDirections() { _bond_directions.clear(); - _forced_bond_directions.clear(); + _forced_stereo_directions.clear(); } bool BaseMolecule::isChiral() @@ -4447,7 +4453,7 @@ bool BaseMolecule::isAtropisomerismReferenceAtom(int atom_idx) // check if the atom has at least one stereo-bond for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) { - if (getBondDirection(v.neiEdge(i))) + if (getBondDirection(v.neiEdge(i)) || getForcedBondDirection(v.neiEdge(i))) { has_stereo = true; break; @@ -4460,7 +4466,7 @@ bool BaseMolecule::isAtropisomerismReferenceAtom(int atom_idx) for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) { auto bond_idx = v.neiEdge(i); - if (getBondDirection(bond_idx) && getEdgeTopology(bond_idx) == TOPOLOGY_RING) + if ((getBondDirection(bond_idx) || getForcedBondDirection(v.neiEdge(i))) && getEdgeTopology(bond_idx) == TOPOLOGY_RING) continue; if (isRotationBond(bond_idx)) rotation_bonds.insert(bond_idx); diff --git a/core/indigo-core/molecule/src/molecule_json_loader.cpp b/core/indigo-core/molecule/src/molecule_json_loader.cpp index b7b51ac836..642be12ed4 100644 --- a/core/indigo-core/molecule/src/molecule_json_loader.cpp +++ b/core/indigo-core/molecule/src/molecule_json_loader.cpp @@ -1125,11 +1125,10 @@ void MoleculeJsonLoader::loadMolecule(BaseMolecule& mol, bool load_arrows) for (int i : mol.edges()) { - if (mol.getBondDirection(i) > 0 && !sensible_bond_directions[i]) + if (mol.getBondDirection(i) > 0 && (!sensible_bond_directions[i] || mol.getBondTopology(i) == TOPOLOGY_RING)) { - if (stereochemistry_options.ignore_errors) - mol.markForcedStereoBond(i); - else + mol.setForcedBondDirection(i, mol.getBondDirection(i)); + if (!stereochemistry_options.ignore_errors && !sensible_bond_directions[i]) throw Error("direction of bond #%d makes no sense", i); } } diff --git a/core/indigo-core/molecule/src/molfile_loader.cpp b/core/indigo-core/molecule/src/molfile_loader.cpp index bcba90aca7..f1a2e73e0a 100644 --- a/core/indigo-core/molecule/src/molfile_loader.cpp +++ b/core/indigo-core/molecule/src/molfile_loader.cpp @@ -2077,16 +2077,18 @@ void MolfileLoader::_postLoad() _bmol->stereocenters.setType(i, _stereocenter_types[i], _stereocenter_groups[i]); } + _bmol->buildCisTrans(_ignore_cistrans.ptr()); + for (i = 0; i < _bonds_num; i++) - if (_bmol->getBondDirection(i) > 0 && !_sensible_bond_directions[i]) + { + if (_bmol->getBondDirection(i) && (!_sensible_bond_directions[i] || _bmol->getBondTopology(i) == TOPOLOGY_RING)) { - if (stereochemistry_options.ignore_errors) - _bmol->markForcedStereoBond(i); - else + auto& e = _bmol->getEdge(i); + _bmol->setForcedBondDirection(i, _bmol->getBondDirection(i)); + if (!stereochemistry_options.ignore_errors && !_sensible_bond_directions[i]) throw Error("direction of bond #%d makes no sense", i); } - - _bmol->buildCisTrans(_ignore_cistrans.ptr()); + } // Remove adding default R-group logic behavior /* diff --git a/core/indigo-core/molecule/src/smiles_loader.cpp b/core/indigo-core/molecule/src/smiles_loader.cpp index 7936f44101..a91babdc1d 100644 --- a/core/indigo-core/molecule/src/smiles_loader.cpp +++ b/core/indigo-core/molecule/src/smiles_loader.cpp @@ -62,6 +62,7 @@ void SmilesLoader::loadMolecule(Molecule& mol) _bmol = &mol; _mol = &mol; _qmol = 0; + _has_atom_coordinates = false; _loadMolecule(); mol.setIgnoreBadValenceFlag(ignore_bad_valence); @@ -356,19 +357,17 @@ void SmilesLoader::_readOtherStuff() auto bond_idx = _scanner.readUnsigned(); if (wmode) { - _bmol->setBondDirection(bond_idx, wmode == 'U' ? BOND_UP : BOND_DOWN); - auto& v = _bmol->getEdge(bond_idx); - if (v.end == atom_idx) - _bmol->swapEdgeEnds(bond_idx); - if (_bmol->getEdgeTopology(bond_idx) == TOPOLOGY_RING && _bmol->isAtropisomerismReferenceAtom(atom_idx) && - (v.beg == atom_idx || v.end == atom_idx)) + if (bond_idx < _bmol->edgeCount() && atom_idx < _bmol->vertexCount()) { - if (!_bmol->stereocenters.exists(atom_idx)) - _bmol->addStereocenters(atom_idx, MoleculeStereocenters::ATOM_ABS, 0, false); - _bmol->stereocenters.setAtropisomeric(atom_idx, true); + auto& v = _bmol->getEdge(bond_idx); + if (v.end == atom_idx) + _bmol->swapEdgeEnds(bond_idx); + + if (v.beg == atom_idx) + { + _bmol->setForcedBondDirection(bond_idx, wmode == 'U' ? BOND_UP : BOND_DOWN); + } } - if (!_bmol->stereocenters.exists(atom_idx) || _bmol->stereocenters.isAtropisomeric(atom_idx)) - _bmol->markForcedStereoBond(bond_idx); } } @@ -752,8 +751,7 @@ void SmilesLoader::_readOtherStuff() } if (_scanner.readChar() != ')') throw Error("expected ')' after coordinates"); - _bmol->markBondsStereocenters(); - _bmol->markBondsAlleneStereo(); + _has_atom_coordinates = true; } else if (c == 'h') // highlighting (Indigo's own extension) { @@ -1340,6 +1338,20 @@ void SmilesLoader::_readOtherStuff() _bmol->removeAtoms(to_remove); } +void SmilesLoader::_handleForcedStereo() +{ + auto& fbonds = _bmol->forcedStereoBonds(); + for (int i = fbonds.begin(); i != fbonds.end(); i = fbonds.next(i)) + _bmol->setBondDirection(fbonds.key(i), fbonds.value(i)); + + for (int i = fbonds.begin(); i != fbonds.end(); i = fbonds.next(i)) + { + auto& e = _bmol->getEdge(fbonds.key(i)); + if (_bmol->stereocenters.exists(e.beg) && _bmol->isAtropisomerismReferenceAtom(e.beg)) + _bmol->stereocenters.setAtropisomeric(e.beg, true); + } +} + void SmilesLoader::_validateStereoCenters() { for (int i = _bmol->stereocenters.begin(); i < _bmol->stereocenters.end(); i = _bmol->stereocenters.next(i)) @@ -1926,6 +1938,14 @@ void SmilesLoader::_loadParsedMolecule() { _scanner.skip(1); _readOtherStuff(); + if (_has_atom_coordinates) + { + _bmol->markBondsStereocenters(); + _bmol->markBondsAlleneStereo(); + } + + if (_bmol->forcedStereoBonds().size()) + _handleForcedStereo(); } // Update attachment orders for rsites diff --git a/core/indigo-core/molecule/src/smiles_saver.cpp b/core/indigo-core/molecule/src/smiles_saver.cpp index c483aac903..c3bf05e5c7 100644 --- a/core/indigo-core/molecule/src/smiles_saver.cpp +++ b/core/indigo-core/molecule/src/smiles_saver.cpp @@ -626,7 +626,8 @@ void SmilesSaver::_saveMolecule() _writeRingBonds(); _writeUnsaturated(); _writeSubstitutionCounts(); - _writeWedges(); + if( _bmol->hasAtropisomericCenter()) + _writeWedges(); if (_comma) _output.writeChar('|'); @@ -1844,32 +1845,6 @@ void SmilesSaver::_writeWedges() if (_bmol) { std::vector> down_dirs, up_dirs; - std::vector sensible_bond_directions; - StereocentersOptions stereochemistry_options; - - sensible_bond_directions.resize(_written_bonds.size(), 0); - - for (int i = 0; i < _written_bonds.size(); i++) - if (_bmol->getBondDirection(i) == BOND_EITHER) - { - if (MoleculeCisTrans::isGeomStereoBond(*_bmol, i, 0, true)) - sensible_bond_directions[i] = 1; - else - { - int k; - const Vertex& v = _bmol->getVertex(_bmol->getEdge(i).beg); - - for (k = v.neiBegin(); k != v.neiEnd(); k = v.neiNext(k)) - { - if (MoleculeCisTrans::isGeomStereoBond(*_bmol, v.neiEdge(k), 0, true)) - { - sensible_bond_directions[i] = 1; - break; - } - } - } - } - for (int i = 0; i < _written_bonds.size(); ++i) { auto bond_idx = _written_bonds[i]; @@ -1917,6 +1892,19 @@ void SmilesSaver::_writeWedges() _output.printf("%d.%d", kvp.first, kvp.second); } } + if (down_dirs.size() || up_dirs.size()) + { + _output.writeString(",("); + for (int i = 0; i < _written_atoms.size(); ++i) + { + if (i) + _output.writeString(";"); + auto atom_idx = _written_atoms[i]; + const auto& pos = _mol->getAtomXyz(atom_idx); + _output.printf("%.2f,%.2f,", pos.x, pos.y); + } + _output.writeString(")"); + } } } diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index c97759bcf9..fb993cc893 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -917,7 +917,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - indigoLayout(obj); + //indigoLayout(obj); if (p.out_ext == OEXT_MOL) indigoSaveMolfileToFile(obj, p.outfile); else if (p.out_ext == OEXT_KET) From 10a0f9b3f43f7c51ed714e38aa06a8b6a3642e88 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 18 Sep 2023 12:18:04 +0200 Subject: [PATCH 05/36] atrop --- api/tests/integration/ref/formats/mol_to_smiles.py.out | 2 +- api/tests/integration/ref/formats/smiles.py.out | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/api/tests/integration/ref/formats/mol_to_smiles.py.out b/api/tests/integration/ref/formats/mol_to_smiles.py.out index 900d00b2b0..1bdefd0c40 100644 --- a/api/tests/integration/ref/formats/mol_to_smiles.py.out +++ b/api/tests/integration/ref/formats/mol_to_smiles.py.out @@ -1,3 +1,3 @@ C1%82(C%83O%84%85)OC%86(C(O%87%88%89)C(O%90%91)C%921O%93%94%95)O%96%97%98.[*:1]%96.[*:2]%93.[*:3]%84.[*:4]%90.[*:5]%87.[*:6]%94%85.[*:7]%95%97.[*:8]%83.[*:9]%91%88.[*:10]%89%98.[*:11]%86.[*:12]%92.[*:13]%82 |$;;;;;;;;;;;;_R1;_R2;_R3;_R4;_R5;_R6;_R7;_R8;_R9;_R10;_R11;_R12;_R13$| [O-][N+](C1=NN=NN1CC1N=NNN=1)=O -C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12| +C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12,(25.51,-10.61,;25.51,-12.12,;24.22,-12.87,;26.82,-12.86,;26.82,-14.36,;25.51,-15.12,;25.52,-16.62,;26.82,-17.36,;26.82,-18.86,;28.12,-16.61,;28.12,-15.11,;29.18,-14.05,;28.11,-12.11,;29.41,-12.86,;28.11,-10.61,;26.82,-9.86,)| diff --git a/api/tests/integration/ref/formats/smiles.py.out b/api/tests/integration/ref/formats/smiles.py.out index cc66a6b521..1dc5851b86 100644 --- a/api/tests/integration/ref/formats/smiles.py.out +++ b/api/tests/integration/ref/formats/smiles.py.out @@ -73,8 +73,8 @@ chemaxon: CCCCC |Sg:n:1,2,3::hh| *** Atropisomers *** atropisomer: -C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4| -C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4| +C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4,(0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,)| +C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4,(2.40,-1.39,;3.20,-0.00,;2.40,1.39,;0.80,1.39,;0.00,2.77,;0.00,0.00,;-1.60,0.00,;-2.40,1.39,;-1.60,2.77,;-4.00,1.39,;-4.80,0.00,;-6.40,0.00,;-4.00,-1.39,;-2.40,-1.39,;0.80,-1.39,;-0.00,-2.77,)| atropisomer: -C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |wU:3.12,wD:3.3| -C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |wU:3.12,wD:3.3| +C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 +C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 From 2e10a5ed44d796ec9e7b1419338e58b58065ffbe Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 18 Sep 2023 12:21:27 +0200 Subject: [PATCH 06/36] clang fix --- core/indigo-core/molecule/src/smiles_saver.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/core/indigo-core/molecule/src/smiles_saver.cpp b/core/indigo-core/molecule/src/smiles_saver.cpp index c3bf05e5c7..a8e6952a53 100644 --- a/core/indigo-core/molecule/src/smiles_saver.cpp +++ b/core/indigo-core/molecule/src/smiles_saver.cpp @@ -626,8 +626,8 @@ void SmilesSaver::_saveMolecule() _writeRingBonds(); _writeUnsaturated(); _writeSubstitutionCounts(); - if( _bmol->hasAtropisomericCenter()) - _writeWedges(); + if (_bmol->hasAtropisomericCenter()) + _writeWedges(); if (_comma) _output.writeChar('|'); From c1d27ca52f385f1446a868eddd035ebbd1cc4b71 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 18 Sep 2023 12:23:30 +0200 Subject: [PATCH 07/36] clang fix --- utils/indigo-depict/main.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index fb993cc893..c97759bcf9 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -917,7 +917,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - //indigoLayout(obj); + indigoLayout(obj); if (p.out_ext == OEXT_MOL) indigoSaveMolfileToFile(obj, p.outfile); else if (p.out_ext == OEXT_KET) From 9144bee685684131c41cdbab68c26089700b79cc Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 18 Sep 2023 12:28:19 +0200 Subject: [PATCH 08/36] python fix --- api/tests/integration/tests/exact/reload.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/api/tests/integration/tests/exact/reload.py b/api/tests/integration/tests/exact/reload.py index 22495d687d..5b8297aee4 100644 --- a/api/tests/integration/tests/exact/reload.py +++ b/api/tests/integration/tests/exact/reload.py @@ -41,7 +41,8 @@ def testMol(mol): perm_smiles = perm_mol.smiles() if not indigo.exactMatch(mol, perm_mol): msg = ( - " Exact: %s after reload from smiles %s. Permuted canonical smiles: %s\n" % (mol.name(), base_smiles, perm_smiles) + " Exact: %s after reload from smiles %s. Permuted canonical smiles: %s\n %s %s" + % (mol.name(), base_smiles, perm_smiles) ) print(msg) sys.stderr.write(msg + "\n") From 8c42d8c6ceba117bac28cfb09bc4356c1c1ef2c8 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 27 Sep 2023 07:35:05 +0200 Subject: [PATCH 09/36] atropo refactoring --- api/c/indigo/src/indigo_layout.cpp | 10 +- .../integration/ref/bingo/molecules.py.out | 13 +- .../integration/ref/formats/mol_to_ket.py.out | 17 +- .../integration/ref/formats/smiles.py.out | 6 +- api/tests/integration/tests/exact/reload.py | 2 +- core/indigo-core/molecule/base_molecule.h | 10 +- .../molecule/molecule_stereocenter_options.h | 1 + .../molecule/molecule_stereocenters.h | 17 +- core/indigo-core/molecule/smiles_loader.h | 2 +- .../molecule/src/base_molecule.cpp | 78 +-- core/indigo-core/molecule/src/cml_loader.cpp | 8 +- .../molecule/src/molecule_json_loader.cpp | 12 +- .../molecule/src/molecule_stereocenters.cpp | 559 +++++++++++------- .../molecule/src/molfile_loader.cpp | 15 +- .../molecule/src/molfile_saver.cpp | 2 +- .../molecule/src/smiles_loader.cpp | 26 +- .../indigo-core/molecule/src/smiles_saver.cpp | 7 +- utils/indigo-depict/main.c | 1 + 18 files changed, 417 insertions(+), 369 deletions(-) diff --git a/api/c/indigo/src/indigo_layout.cpp b/api/c/indigo/src/indigo_layout.cpp index 5fcaaafcf6..4514dbd4da 100644 --- a/api/c/indigo/src/indigo_layout.cpp +++ b/api/c/indigo/src/indigo_layout.cpp @@ -58,26 +58,20 @@ CEXPORT int indigoLayout(int object) ml.max_iterations = self.layout_max_iterations; ml.bond_length = 1.6f; ml.layout_orientation = (layout_orientation_value)self.layout_orientation; - bool has_forced_stereo = mol->forcedStereoBonds().size(); - if (has_forced_stereo) + if (mol->hasAtropisomericCenter()) ml.respect_existing_layout = true; TimeoutCancellationHandler cancellation(self.cancellation_timeout); ml.setCancellationHandler(&cancellation); - ml.make(); if (obj.type != IndigoObject::SUBMOLECULE) { - if (!has_forced_stereo) - mol->clearBondDirections(); + mol->clearBondDirections(); try { mol->markBondsStereocenters(); mol->markBondsAlleneStereo(); - auto& fbonds = mol->forcedStereoBonds(); - for (int i = fbonds.begin(); i != fbonds.end(); i = fbonds.next(i)) - mol->setBondDirection(fbonds.key(i), fbonds.value(i)); } catch (Exception e) { diff --git a/api/tests/integration/ref/bingo/molecules.py.out b/api/tests/integration/ref/bingo/molecules.py.out index 97783072cc..cf08ed063b 100644 --- a/api/tests/integration/ref/bingo/molecules.py.out +++ b/api/tests/integration/ref/bingo/molecules.py.out @@ -27,7 +27,6 @@ Structure 207 excluded: stereocenters: stereo types of the opposite bonds mismat Structure 241 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 0 Structure 242 excluded: molfile loader: direction of bond #2 makes no sense Structure 245 excluded: element: bad valence on H having 0 drawn bonds, charge 3, and 0 radical electrons -Structure 251 excluded: molfile loader: direction of bond #54 makes no sense Structure 253 excluded: molfile loader: direction of bond #5 makes no sense Structure 255 excluded: molfile loader: direction of bond #5 makes no sense Structure 256 excluded: element: bad valence on H having 1 drawn bonds, charge 2, and 0 radical electrons @@ -154,7 +153,6 @@ Structure 916 excluded: stereocenters: stereo types of the opposite bonds mismat Structure 931 excluded: stereocenters: one bond up, one bond down -- indefinite case near atom 1 Structure 936 excluded: molfile loader: direction of bond #2 makes no sense Structure 940 excluded: element: bad valence on Ar having 0 drawn bonds, charge 0, and 2 radical electrons -Structure 941 excluded: molfile loader: direction of bond #3 makes no sense Structure 943 excluded: element: bad valence on H having 2 drawn bonds, charge -2, and 0 radical electrons Structure 948 excluded: molfile loader: direction of bond #15 makes no sense Structure 955 excluded: element: bad valence on H having 0 drawn bonds, charge -3, and 0 radical electrons @@ -231,7 +229,6 @@ Structure 1492 excluded: stereocenters: directions of neighbor stereo bonds matc Structure 1498 excluded: molfile loader: direction of bond #3 makes no sense Structure 1501 excluded: stereocenters: directions of neighbor stereo bonds match near atom 0 Structure 1505 excluded: element: bad valence on C having 4 drawn bonds, charge -1, and 1 radical electrons -Structure 1514 excluded: molfile loader: direction of bond #3 makes no sense Structure 1552 excluded: element: bad valence on H having 1 drawn bonds, charge 1, and 0 radical electrons Structure 1564 excluded: stereocenters: all 3 bonds up near stereoatom 97 Structure 1567 excluded: molfile loader: direction of bond #5 makes no sense @@ -270,7 +267,6 @@ Structure 1831 excluded: molfile loader: direction of bond #9 makes no sense Structure 1842 excluded: element: bad valence on I having 2 drawn bonds, charge 0, and 0 radical electrons Structure 1843 excluded: molfile loader: direction of bond #8 makes no sense Structure 1844 excluded: molfile loader: direction of bond #13 makes no sense -Structure 1846 excluded: molfile loader: direction of bond #3 makes no sense Structure 1848 excluded: molfile loader: direction of bond #9 makes no sense Structure 1851 excluded: stereocenters: 2 hydrogens near stereocenter 8 Structure 1857 excluded: molfile loader: direction of bond #1 makes no sense @@ -304,7 +300,7 @@ Structure 2013 excluded: molfile loader: direction of bond #5 makes no sense Structure 2014 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 0 Structure 2017 excluded: molfile loader: direction of bond #7 makes no sense Structure 2018 excluded: element: bad valence on N having 5 drawn bonds, charge 1, and 0 radical electrons -Finished indexing 2026 structures. 304 wrong structures excluded +Finished indexing 2026 structures. 300 wrong structures excluded ** searchSub(C(CN)C(F)F, '') ** 1986 C(C(C(C(N1CO[Si](C)(C)OC1)=O)(F)F)(F)F)(C(C(C(F)(F)F)(F)F)(F)F)(F)F C(C(C(C(N1CO[Si](C)(C)OC1)=O)(F)F)(F)F)(C(C(C(F)(F)F)(F)F)(F)F)(F)F ** searchSim(C(CN)C(F)F, 0.9, 1, tanimoto) ** @@ -902,6 +898,7 @@ Finished indexing 2026 structures. 304 wrong structures excluded 227 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 233 [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| 237 C1(C2(C(OC(OC3(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC6(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC7(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC8(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC9(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(O2)([H])OC9(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC8(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC7(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC6(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC5(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC4(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC3(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])C1(OS(O[H])(=O)=O)[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H] C1(C2(C(OC(OC3(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC6(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC7(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC8(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC9(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(O2)([H])OC9(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC8(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC7(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC6(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC5(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC4(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC3(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])C1(OS(O[H])(=O)=O)[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H] + 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| 252 C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| 262 C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] 265 [CH]1C=C1C1=C[CH]1 |^1:0,5| [CH]1C=C1C1=C[CH]1 |^1:0,5| @@ -981,6 +978,7 @@ Finished indexing 2026 structures. 304 wrong structures excluded 918 [C@H]12C[C@H]3[C@H]4[C@]56[C@H]([C@H]7[C@]89[C@@H]%10[C@@H]%11C[C@@H](C[C@H]5[C@@H]5C[C@@H](C[C@H]%12[C@@H]%13C[C@@H](C%10)C[C@H]([C@]3%12[C@]86[C@]5%13%11)[C@@H]9C1)C4)C7)C2 [C@H]12C[C@H]3[C@H]4[C@]56[C@H]([C@H]7[C@]89[C@@H]%10[C@@H]%11C[C@@H](C[C@H]5[C@@H]5C[C@@H](C[C@H]%12[C@@H]%13C[C@@H](C%10)C[C@H]([C@]3%12[C@]86[C@]5%13%11)[C@@H]9C1)C4)C7)C2 919 [C@@H]12[C@@]34[12CH]([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C.[12C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[12C@H]12[C@]34C([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,17,18,20,22,23,26,32,34,35,37,39,40,43,49,51,52,54,56,57,60,66,r| [C@@H]12[C@@]34[12CH]([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C.[12C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[12C@H]12[C@]34C([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,17,18,20,22,23,26,32,34,35,37,39,40,43,49,51,52,54,56,57,60,66,r| 920 C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP(O[H])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:85,114,143| C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP(O[H])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:85,114,143| + 941 C[C@]1(C/C(=C2/C[C@]([H])(Cl)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H].C[C@]1(C/C(=C2/C[C@]([H])(Br)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,45,50,55,65,68,73,76,84,r| C[C@]1(C/C(=C2/C[C@]([H])(Cl)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H].C[C@]1(C/C(=C2/C[C@]([H])(Br)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,45,50,55,65,68,73,76,84,r| 947 O1[C@@H]([C@H](C)CO)[C@@H](O)[C@@H]([C@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1 |&1:1,2,6,8,9,16,17,21,23,24,31,32,36,38,39,r| O1[C@@H]([C@H](C)CO)[C@@H](O)[C@@H]([C@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1 |&1:1,2,6,8,9,16,17,21,23,24,31,32,36,38,39,r| 950 [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC |&1:0,2,9,r| [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC |&1:0,2,9,r| 968 [C@@H](C[C@@H](C[C@@H](C)C[C@@H](C)N)C)(N)C |&1:0,2,4,7,r| [C@@H](C[C@@H](C[C@@H](C)C[C@@H](C)N)C)(N)C |&1:0,2,4,7,r| @@ -1061,6 +1059,7 @@ Finished indexing 2026 structures. 304 wrong structures excluded 1500 [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] 1510 C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| 1511 c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O + 1514 C[C@]1(C/C(=C2/C[C@]([H])(Cl)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,r| C[C@]1(C/C(=C2/C[C@]([H])(Cl)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,r| 1523 [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| 1525 [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| 1527 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| @@ -1099,6 +1098,7 @@ Finished indexing 2026 structures. 304 wrong structures excluded 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] 1814 [C@@H](C[C@@H](C[C@H](C)C[C@H](C)N)C)(N)C |&1:0,2,4,7,r| [C@@H](C[C@@H](C[C@H](C)C[C@H](C)N)C)(N)C |&1:0,2,4,7,r| 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| + 1846 C[C@]1(C/C(=C2/C[C@]([H])(Br)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,r| C[C@]1(C/C(=C2/C[C@]([H])(Br)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,r| 1856 [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| 1861 C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C 1862 c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-].c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][nH][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2C([N-]C)=O c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-].c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][nH][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2C([N-]C)=O @@ -1923,6 +1923,7 @@ Finished indexing 2026 structures. 304 wrong structures excluded 118 N[C@]1(C)C[C@]2([C@@]3(C[C@@](N)(C)C3)[C@]32C[C@@](N)(C)C3)C1 |&1:1,4,5,7,11,13,r| N[C@]1(C)C[C@]2([C@@]3(C[C@@](N)(C)C3)[C@]32C[C@@](N)(C)C3)C1 |&1:1,4,5,7,11,13,r| 179 [C@H]1(C[C@H](C)C1)C.[C@H]1(C[C@@H](C)C1)C |&1:0,2,6,8,r| [C@H]1(C[C@H](C)C1)C.[C@H]1(C[C@@H](C)C1)C |&1:0,2,6,8,r| 212 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 + 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| 305 C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,10,r| C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,10,r| 351 [C@@]12([H])[C@@]3([H])[C@]1([H])C1([H])C2([H])[C@]2([C@]3([H])[C@@]12[H])[H].[C@@]12([H])[C@@]3([H])[C@]4(C5([H])[C@@]1([C@@]2(C5([C@@]34[H])[H])[H])[H])[H].C12([H])[C@]3([C@]4([C@]5([H])[C@]([H])(C1([H])[C@@]34[H])[C@]25[H])[H])[H] |&1:0,2,4,10,11,13,16,18,20,23,24,26,34,35,36,38,42,44,r| [C@@]12([H])[C@@]3([H])[C@]1([H])C1([H])C2([H])[C@]2([C@]3([H])[C@@]12[H])[H].[C@@]12([H])[C@@]3([H])[C@]4(C5([H])[C@@]1([C@@]2(C5([C@@]34[H])[H])[H])[H])[H].C12([H])[C@]3([C@]4([C@]5([H])[C@]([H])(C1([H])[C@@]34[H])[C@]25[H])[H])[H] |&1:0,2,4,10,11,13,16,18,20,23,24,26,34,35,36,38,42,44,r| 387 [C@@]12(C[C@@](N)(C)C1)C[C@@](N)(C)C2 |&1:0,2,7,r| [C@@]12(C[C@@](N)(C)C1)C[C@@](N)(C)C2 |&1:0,2,7,r| @@ -2921,6 +2922,7 @@ Finished indexing 2026 structures. 304 wrong structures excluded 212 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 227 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 233 [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| + 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| 252 C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| 262 C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] 266 C1([H])=C([H])C21C([H])=C([H])C12C([H])=C1[H] C1([H])=C([H])C21C([H])=C([H])C12C([H])=C1[H] @@ -4669,6 +4671,7 @@ Finished indexing 2026 structures. 304 wrong structures excluded 1839 O([H])[H] O([H])[H] 1954 [O][2H][2H] [O][2H][2H] ** searchSub([Sn](CCC)(C)CC, '') ** + 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| 1024 [Sn]([C@@H](/C=C/CO[Si](C(C)(C)C)(C)C)OCOC)(CCCC)(CCCC)CCCC |&1:1,r| [Sn]([C@@H](/C=C/CO[Si](C(C)(C)C)(C)C)OCOC)(CCCC)(CCCC)CCCC |&1:1,r| 1025 [Sn]1(CCCC)(C=CCCC=C1)CCCC [Sn]1(CCCC)(C=CCCC=C1)CCCC ** searchSim([SnH](CCC)(C)CC, 0.9, 1, tanimoto) ** diff --git a/api/tests/integration/ref/formats/mol_to_ket.py.out b/api/tests/integration/ref/formats/mol_to_ket.py.out index 69f4d6eb4a..7ffb4d63e1 100644 --- a/api/tests/integration/ref/formats/mol_to_ket.py.out +++ b/api/tests/integration/ref/formats/mol_to_ket.py.out @@ -2,6 +2,21 @@ 1032-quadra.ket:SUCCEED 1046-imp_hydrogen.ket:SUCCEED SgroupDifferent.ket:SUCCEED -atropisomer.ket:SUCCEED +atropisomer.ket:FAILED +--- + ++++ + +@@ -55,8 +55,7 @@ + + 26.818199157714845, + -12.862500190734864, + 0.0 +- ], +- "stereoLabel": "or1" ++ ] + }, + { + "label": "C", non_atrop.ket:SUCCEED suplabel.ket:SUCCEED diff --git a/api/tests/integration/ref/formats/smiles.py.out b/api/tests/integration/ref/formats/smiles.py.out index 1dc5851b86..e08b627bce 100644 --- a/api/tests/integration/ref/formats/smiles.py.out +++ b/api/tests/integration/ref/formats/smiles.py.out @@ -73,8 +73,8 @@ chemaxon: CCCCC |Sg:n:1,2,3::hh| *** Atropisomers *** atropisomer: -C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4,(0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,;0.00,0.00,)| +C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4| C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4,(2.40,-1.39,;3.20,-0.00,;2.40,1.39,;0.80,1.39,;0.00,2.77,;0.00,0.00,;-1.60,0.00,;-2.40,1.39,;-1.60,2.77,;-4.00,1.39,;-4.80,0.00,;-6.40,0.00,;-4.00,-1.39,;-2.40,-1.39,;0.80,-1.39,;-0.00,-2.77,)| atropisomer: -C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 -C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 +C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |wU:3.12,wD:3.3| +C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |wU:3.12,wD:3.3,(-2.40,1.39,;-0.80,1.39,;-0.00,2.77,;0.00,0.00,;1.60,0.00,;2.40,1.39,;4.00,1.39,;4.80,0.00,;6.40,0.00,;4.00,-1.39,;2.40,-1.39,;1.60,-2.77,;-0.80,-1.39,;0.00,-2.77,;-2.40,-1.39,;-3.20,-0.00,)| diff --git a/api/tests/integration/tests/exact/reload.py b/api/tests/integration/tests/exact/reload.py index 5b8297aee4..3297da7b09 100644 --- a/api/tests/integration/tests/exact/reload.py +++ b/api/tests/integration/tests/exact/reload.py @@ -41,7 +41,7 @@ def testMol(mol): perm_smiles = perm_mol.smiles() if not indigo.exactMatch(mol, perm_mol): msg = ( - " Exact: %s after reload from smiles %s. Permuted canonical smiles: %s\n %s %s" + " Exact: %s after reload from smiles %s. Permuted canonical smiles: %s" % (mol.name(), base_smiles, perm_smiles) ) print(msg) diff --git a/core/indigo-core/molecule/base_molecule.h b/core/indigo-core/molecule/base_molecule.h index 32917c90b7..73f6c348a9 100644 --- a/core/indigo-core/molecule/base_molecule.h +++ b/core/indigo-core/molecule/base_molecule.h @@ -195,7 +195,6 @@ namespace indigo void removeAttachmentPointsFromAtom(int atom_index); int attachmentPointCount() const; void removeAttachmentPoints(); - void getAttachmentIndicesForAtom(int atom_idx, Array& res); virtual bool isSaturatedAtom(int idx) = 0; @@ -247,8 +246,6 @@ namespace indigo void clearCIP(); CIPDesc getAtomCIP(int atom_idx); CIPDesc getBondCIP(int bond_idx); - bool isAtropisomerismReferenceAtom(int atom_idx); - bool isRotationBond(int bond_idx); void setAtomCIP(int atom_idx, CIPDesc cip); void setBondCIP(int bond_idx, CIPDesc cip); @@ -389,11 +386,7 @@ namespace indigo void clearBondDirections(); int getBondDirection(int idx) const; - int* getForcedBondDirection(int idx) const; void setBondDirection(int idx, int dir); - void setForcedBondDirection(int idx, int dir); - bool isForcedStereoBond(int idx); - const RedBlackMap& forcedStereoBonds(); int getBondDirection2(int center_idx, int nei_idx); @@ -437,6 +430,8 @@ namespace indigo void buildFromBondsStereocenters(const StereocentersOptions& options, int* sensible_bonds_out); void buildFrom3dCoordinatesStereocenters(const StereocentersOptions& options); bool isPossibleStereocenter(int atom_idx, bool* possible_implicit_h = 0, bool* possible_lone_pair = 0); + bool isPossibleAtropocenter(int atom_idx, int& possible_atropo_bond); + void buildOnSubmoleculeStereocenters(const BaseMolecule& super, int* mapping); // proxy methods for cis_trans @@ -515,7 +510,6 @@ namespace indigo Array _sl_bonds; Array _bond_directions; - RedBlackMap _forced_stereo_directions; Array _xyz; RedBlackMap _stereo_flag_positions; diff --git a/core/indigo-core/molecule/molecule_stereocenter_options.h b/core/indigo-core/molecule/molecule_stereocenter_options.h index 946954017c..87196b6a3f 100644 --- a/core/indigo-core/molecule/molecule_stereocenter_options.h +++ b/core/indigo-core/molecule/molecule_stereocenter_options.h @@ -45,6 +45,7 @@ namespace indigo // Detect Haworth projection. Default is false. bool detect_haworth_projection; + }; } // namespace indigo diff --git a/core/indigo-core/molecule/molecule_stereocenters.h b/core/indigo-core/molecule/molecule_stereocenters.h index faa1e68218..7ae46e81af 100644 --- a/core/indigo-core/molecule/molecule_stereocenters.h +++ b/core/indigo-core/molecule/molecule_stereocenters.h @@ -19,6 +19,8 @@ #ifndef __molecule_stereocenters__ #define __molecule_stereocenters__ +#include + #include "base_cpp/red_black.h" #include "math/algebra.h" @@ -83,7 +85,7 @@ namespace indigo void setType(int idx, int type, int group); void setType(int idx, int type); void setAtropisomeric(int idx, bool val); - bool isAtropisomeric(int idx); + bool isAtropisomeric(int idx) const; void invertPyramid(int idx); bool sameGroup(int idx1, int idx2); @@ -111,6 +113,10 @@ namespace indigo int getAtomIndex(int i) const; bool isPossibleStereocenter(BaseMolecule& baseMolecule, int atom_idx, bool* possible_implicit_h = 0, bool* possible_lone_pair = 0); + bool isPossibleAtropocenter(BaseMolecule& baseMolecule, int atom_idx, int& possible_atropo_bond); + bool findAtropoStereobonds(BaseMolecule& baseMolecule, RedBlackMap& directions_map, int atom_idx, std::unordered_set& visited_bonds, + bool first_only = false); + bool hasRing(BaseMolecule& baseMolecule, int atom_idx, std::unordered_set& visited_bonds); public: static bool checkSub(BaseMolecule& query, BaseMolecule& target, const int* mapping, bool reset_h_isotopes, Filter* stereocenters_vertex_filter = 0); @@ -143,6 +149,12 @@ namespace indigo int pyramid[4]; }; + struct _AtropoCenter + { + int atropo_bond; + RedBlackMap bond_directions; + }; + struct _EdgeIndVec { int edge_idx; @@ -161,13 +173,14 @@ namespace indigo }; RedBlackMap _stereocenters; + RedBlackObjMap _atropocenters; static int _sign(const Vec3f& v1, const Vec3f& v2, const Vec3f& v3); static int _xyzzy(const Vec3f& v1, const Vec3f& v2, const Vec3f& u); static int _onPlane(const Vec3f& v1, const Vec3f& v2, const Vec3f& v3, const Vec3f& v4); bool _buildOneCenter(BaseMolecule& baseMolecule, int atom_idx, int* sensible_bonds_out, bool bidirectional_mode, bool bidirectional_either_mode, - const Array& bond_ignore); + const Array& bond_ignore, bool check_atropocenter = false); void _buildOneFrom3dCoordinates(BaseMolecule& baseMolecule, int idx); diff --git a/core/indigo-core/molecule/smiles_loader.h b/core/indigo-core/molecule/smiles_loader.h index 80c43c2c4e..8c6ee08247 100644 --- a/core/indigo-core/molecule/smiles_loader.h +++ b/core/indigo-core/molecule/smiles_loader.h @@ -157,6 +157,7 @@ namespace indigo int _current_compno; bool _inside_smarts_component; bool _has_atom_coordinates = false; + bool _has_directions_on_rings = false; BaseMolecule* _bmol; QueryMolecule* _qmol; @@ -178,7 +179,6 @@ namespace indigo bool _isAlleneLike(int i); void _handleCurlyBrace(_AtomDesc& atom, bool& inside_polymer); void _handlePolymerRepetition(int i); - void _handleForcedStereo(); void _readAtom(Array& atom_str, bool first_in_brackets, _AtomDesc& atom, std::unique_ptr& qatom); diff --git a/core/indigo-core/molecule/src/base_molecule.cpp b/core/indigo-core/molecule/src/base_molecule.cpp index b8351635e8..ff8a5c83ac 100644 --- a/core/indigo-core/molecule/src/base_molecule.cpp +++ b/core/indigo-core/molecule/src/base_molecule.cpp @@ -3914,27 +3914,6 @@ int BaseMolecule::getBondDirection(int idx) const return _bond_directions[idx]; } -int* BaseMolecule::getForcedBondDirection(int idx) const -{ - return _forced_stereo_directions.at2(idx); -} - -void BaseMolecule::setForcedBondDirection(int idx, int dir) -{ - if (!_forced_stereo_directions.find(idx)) - _forced_stereo_directions.insert(idx, dir); -} - -bool BaseMolecule::isForcedStereoBond(int idx) -{ - return _forced_stereo_directions.find(idx); -} - -const RedBlackMap& BaseMolecule::forcedStereoBonds() -{ - return _forced_stereo_directions; -} - int BaseMolecule::getBondDirection2(int center_idx, int nei_idx) { int idx = findEdgeIndex(center_idx, nei_idx); @@ -3957,7 +3936,6 @@ void BaseMolecule::setBondDirection(int idx, int dir) void BaseMolecule::clearBondDirections() { _bond_directions.clear(); - _forced_stereo_directions.clear(); } bool BaseMolecule::isChiral() @@ -4274,6 +4252,11 @@ bool BaseMolecule::isPossibleStereocenter(int atom_idx, bool* possible_implicit_ return stereocenters.isPossibleStereocenter(*this, atom_idx, possible_implicit_h, possible_lone_pair); } +bool BaseMolecule::isPossibleAtropocenter(int atom_idx, int& possible_atropo_bond) +{ + return stereocenters.isPossibleAtropocenter(*this, atom_idx, possible_atropo_bond); +} + void BaseMolecule::buildOnSubmoleculeStereocenters(const BaseMolecule& super, int* mapping) { stereocenters.buildOnSubmolecule(*this, super, mapping); @@ -4442,54 +4425,3 @@ void BaseMolecule::removeAlias(int atom_idx) { aliases.remove(atom_idx); } - -bool BaseMolecule::isAtropisomerismReferenceAtom(int atom_idx) -{ - // TODO: implement more accurate atropisomer detection - if (vertexInRing(atom_idx)) // check if the atom belongs to ring - { - bool has_stereo = false; - const Vertex& v = getVertex(atom_idx); - // check if the atom has at least one stereo-bond - for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) - { - if (getBondDirection(v.neiEdge(i)) || getForcedBondDirection(v.neiEdge(i))) - { - has_stereo = true; - break; - } - } - if (has_stereo) - { - std::unordered_set rotation_bonds; - // looking for a rotation bond - for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) - { - auto bond_idx = v.neiEdge(i); - if ((getBondDirection(bond_idx) || getForcedBondDirection(v.neiEdge(i))) && getEdgeTopology(bond_idx) == TOPOLOGY_RING) - continue; - if (isRotationBond(bond_idx)) - rotation_bonds.insert(bond_idx); - } - if (rotation_bonds.size()) - return true; - } - } - return false; -} - -bool BaseMolecule::isRotationBond(int bond_idx) -{ - // typically a rotation doesn't belong to a ring. - // but there are some exclusions to be handled. - if (getEdgeTopology(bond_idx) == TOPOLOGY_RING) - return false; - // remove the bond and check if an extra component appears. - // if so this can be a rotation bond. - std::unique_ptr mol(neu()); - mol->clone_KeepIndices(*this); - int old_count = mol->countComponents(); - mol->removeBond(bond_idx); - int new_count = mol->countComponents(); - return new_count > old_count; -} diff --git a/core/indigo-core/molecule/src/cml_loader.cpp b/core/indigo-core/molecule/src/cml_loader.cpp index d64c53e4bf..2801243d70 100644 --- a/core/indigo-core/molecule/src/cml_loader.cpp +++ b/core/indigo-core/molecule/src/cml_loader.cpp @@ -1082,11 +1082,9 @@ void CmlLoader::_loadMoleculeElement(XMLHandle& handle) if (_bmol->stereocenters.size() == 0 && BaseMolecule::hasCoord(*_bmol)) { - QS_DEF(Array, sensible_bond_orientations); - - sensible_bond_orientations.clear_resize(_bmol->vertexEnd()); - _bmol->buildFromBondsStereocenters(stereochemistry_options, sensible_bond_orientations.ptr()); - + std::vector sensible_bond_orientations; + sensible_bond_orientations.resize(_bmol->edgeEnd(), 0); + _bmol->buildFromBondsStereocenters(stereochemistry_options, sensible_bond_orientations.data()); if (!stereochemistry_options.ignore_errors) for (i = 0; i < _bmol->vertexCount(); i++) if (_bmol->getBondDirection(i) > 0 && !sensible_bond_orientations[i]) diff --git a/core/indigo-core/molecule/src/molecule_json_loader.cpp b/core/indigo-core/molecule/src/molecule_json_loader.cpp index 642be12ed4..4f61ba8e48 100644 --- a/core/indigo-core/molecule/src/molecule_json_loader.cpp +++ b/core/indigo-core/molecule/src/molecule_json_loader.cpp @@ -1107,12 +1107,7 @@ void MoleculeJsonLoader::loadMolecule(BaseMolecule& mol, bool load_arrows) { if (mol.stereocenters.getType(sc._atom_idx) == 0) { - if (mol.isAtropisomerismReferenceAtom(sc._atom_idx)) - { - mol.stereocenters.add_ignore(mol, sc._atom_idx, sc._type, sc._group, false); - mol.stereocenters.setAtropisomeric(sc._atom_idx, true); - } - else if (stereochemistry_options.ignore_errors) + if (stereochemistry_options.ignore_errors) mol.addStereocentersIgnoreBad(sc._atom_idx, sc._type, sc._group, false); // add non-valid stereocenters else throw Error("stereo type specified for atom #%d, but the bond " @@ -1125,10 +1120,9 @@ void MoleculeJsonLoader::loadMolecule(BaseMolecule& mol, bool load_arrows) for (int i : mol.edges()) { - if (mol.getBondDirection(i) > 0 && (!sensible_bond_directions[i] || mol.getBondTopology(i) == TOPOLOGY_RING)) + if (mol.getBondDirection(i) > 0 && !sensible_bond_directions[i]) { - mol.setForcedBondDirection(i, mol.getBondDirection(i)); - if (!stereochemistry_options.ignore_errors && !sensible_bond_directions[i]) + if (!stereochemistry_options.ignore_errors) throw Error("direction of bond #%d makes no sense", i); } } diff --git a/core/indigo-core/molecule/src/molecule_stereocenters.cpp b/core/indigo-core/molecule/src/molecule_stereocenters.cpp index 87797f447c..433a84902d 100644 --- a/core/indigo-core/molecule/src/molecule_stereocenters.cpp +++ b/core/indigo-core/molecule/src/molecule_stereocenters.cpp @@ -48,10 +48,14 @@ void MoleculeStereocenters::buildFromBonds(BaseMolecule& baseMolecule, const Ste const Array& bonds_ignore = haworth_finder.getBondsMask(); const Array& atoms_ignore = haworth_finder.getAtomsMask(); + bool check_atropisomery = false; for (int i = baseMolecule.edgeBegin(); i != baseMolecule.edgeEnd(); i = baseMolecule.edgeNext(i)) { - if (bonds_ignore[i] && baseMolecule.getBondDirection(i)) + auto bdir = baseMolecule.getBondDirection(i); + if (bonds_ignore[i] && bdir) sensible_bonds_out[i] = 1; + if (!check_atropisomery && bdir && baseMolecule.getBondTopology(i) == TOPOLOGY_RING) + check_atropisomery = true; } for (int i = baseMolecule.vertexBegin(); i != baseMolecule.vertexEnd(); i = baseMolecule.vertexNext(i)) @@ -63,7 +67,7 @@ void MoleculeStereocenters::buildFromBonds(BaseMolecule& baseMolecule, const Ste bool found = false; try { - found = _buildOneCenter(baseMolecule, i, sensible_bonds_out, false, options.bidirectional_mode, bonds_ignore); + found = _buildOneCenter(baseMolecule, i, sensible_bonds_out, false, options.bidirectional_mode, bonds_ignore, check_atropisomery); } catch (Error&) { @@ -193,6 +197,87 @@ void MoleculeStereocenters::_buildOneFrom3dCoordinates(BaseMolecule& baseMolecul add(baseMolecule, idx, ATOM_ABS, 0, false); } +bool MoleculeStereocenters::isPossibleAtropocenter(BaseMolecule& baseMolecule, int atom_idx, int& possible_atropo_bond) +{ + if (baseMolecule.vertexInRing(atom_idx)) // check if the atom belongs to ring + { + bool has_stereo = false; + const Vertex& v = baseMolecule.getVertex(atom_idx); + // check if the atom has at least one stereo-bond + for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) + { + if (baseMolecule.getBondDirection(v.neiEdge(i))) + { + for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) + { + auto bond_idx = v.neiEdge(i); + if (baseMolecule.getEdgeTopology(bond_idx) == TOPOLOGY_CHAIN) + { + std::unordered_set visited; + RedBlackMap dir_map; + visited.insert(bond_idx); + if (findAtropoStereobonds(baseMolecule, dir_map, atom_idx, visited, true)) + { + visited.clear(); + dir_map.clear(); + visited.insert(bond_idx); + if (hasRing(baseMolecule, v.neiVertex(i), visited)) + { + possible_atropo_bond = bond_idx; + return true; + } + } + } + } + break; + } + } + } + return false; +} + +// recursive search of for stereobonds withing connected rings +bool MoleculeStereocenters::findAtropoStereobonds(BaseMolecule& baseMolecule, RedBlackMap& directions_map, int atom_idx, + std::unordered_set& visited_bonds, bool first_only) +{ + const Vertex& v = baseMolecule.getVertex(atom_idx); + for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) + { + auto bond_idx = v.neiEdge(i); + if (visited_bonds.find(bond_idx) == visited_bonds.end()) + { + visited_bonds.insert(bond_idx); + auto bdir = baseMolecule.getBondDirection(bond_idx); + if (baseMolecule.getBondTopology(bond_idx) == TOPOLOGY_RING) + { + if (bdir && !directions_map.find(bond_idx)) + { + directions_map.insert(bond_idx, bdir); + if (first_only) + return true; + } + findAtropoStereobonds(baseMolecule, directions_map, v.neiVertex(i), visited_bonds); + } + } + } + return directions_map.size(); +} + +bool MoleculeStereocenters::hasRing(BaseMolecule& baseMolecule, int atom_idx, std::unordered_set& visited_bonds) +{ + const Vertex& v = baseMolecule.getVertex(atom_idx); + for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) + { + auto bond_idx = v.neiEdge(i); + if (visited_bonds.find(bond_idx) == visited_bonds.end()) + { + visited_bonds.insert(bond_idx); + return baseMolecule.getBondTopology(bond_idx) == TOPOLOGY_RING ? true : hasRing(baseMolecule, v.neiVertex(i), visited_bonds); + } + } + return false; +} + bool MoleculeStereocenters::isPossibleStereocenter(BaseMolecule& baseMolecule, int atom_idx, bool* possible_implicit_h, bool* possible_lone_pair) { const Vertex& vertex = baseMolecule.getVertex(atom_idx); @@ -264,7 +349,7 @@ bool MoleculeStereocenters::isPossibleStereocenter(BaseMolecule& baseMolecule, i // can be determined by normal direction then do not check if opposite directions // contradicts original ones. bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom_idx, int* sensible_bonds_out, bool bidirectional_mode, - bool bidirectional_either_mode, const Array& bond_ignore) + bool bidirectional_either_mode, const Array& bond_ignore, bool check_atropocenter) { const Vertex& vertex = baseMolecule.getVertex(atom_idx); @@ -336,11 +421,21 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom bool possible_implicit_h = false; bool possible_lone_pair = false; + int possible_atropobond = -1; + int i; - if (!isPossibleStereocenter(baseMolecule, atom_idx, &possible_implicit_h, &possible_lone_pair)) + bool is_center = isPossibleStereocenter(baseMolecule, atom_idx, &possible_implicit_h, &possible_lone_pair); + bool is_atropo_center = false; + if (check_atropocenter && !is_center) + is_atropo_center = isPossibleAtropocenter(baseMolecule, atom_idx, possible_atropobond); + + if (!is_center && !is_atropo_center) return false; + if (possible_atropobond > -1) + stereocenter.is_atropisomeric = true; + // Local synonym to get bond direction auto getDir = [&](int from, int to) { int idx = baseMolecule.findEdgeIndex(from, to); @@ -362,232 +457,249 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom return true; } - if (degree == 4) + if (possible_atropobond > -1) + { + if (!_stereocenters.find(atom_idx)) + _stereocenters.insert(atom_idx, stereocenter); + else + _stereocenters.at(atom_idx).is_atropisomeric = true; + _AtropoCenter& ac = _atropocenters.findOrInsert(atom_idx); + ac.atropo_bond = possible_atropobond; + std::unordered_set visited_bonds; + findAtropoStereobonds(baseMolecule, ac.bond_directions, atom_idx, visited_bonds); + auto bdir = baseMolecule.getBondDirection(possible_atropobond); + if (bdir) + ac.bond_directions.insert(possible_atropobond, bdir); + for (auto i = ac.bond_directions.begin(); i != ac.bond_directions.end(); i = ac.bond_directions.next(i)) + sensible_bonds_out[ac.bond_directions.key(i)] = 1; + } + else if (!_stereocenters.find(atom_idx)) { - // sort by neighbor atom index (ascending) - if (edge_ids[0].rank > edge_ids[1].rank) - std::swap(edge_ids[0], edge_ids[1]); - if (edge_ids[1].rank > edge_ids[2].rank) - std::swap(edge_ids[1], edge_ids[2]); - if (edge_ids[2].rank > edge_ids[3].rank) - std::swap(edge_ids[2], edge_ids[3]); - if (edge_ids[1].rank > edge_ids[2].rank) - std::swap(edge_ids[1], edge_ids[2]); - if (edge_ids[0].rank > edge_ids[1].rank) - std::swap(edge_ids[0], edge_ids[1]); - if (edge_ids[1].rank > edge_ids[2].rank) - std::swap(edge_ids[1], edge_ids[2]); - - int main1 = -1, main2 = -1, side1 = -1, side2 = -1; - int main_dir = 0; - - for (nei_idx = 0; nei_idx < 4; nei_idx++) + if (degree == 4) { - int stereo = getDir(atom_idx, edge_ids[nei_idx].nei_idx); - - if (stereo == BOND_UP || stereo == BOND_DOWN) + // sort by neighbor atom index (ascending) + if (edge_ids[0].rank > edge_ids[1].rank) + std::swap(edge_ids[0], edge_ids[1]); + if (edge_ids[1].rank > edge_ids[2].rank) + std::swap(edge_ids[1], edge_ids[2]); + if (edge_ids[2].rank > edge_ids[3].rank) + std::swap(edge_ids[2], edge_ids[3]); + if (edge_ids[1].rank > edge_ids[2].rank) + std::swap(edge_ids[1], edge_ids[2]); + if (edge_ids[0].rank > edge_ids[1].rank) + std::swap(edge_ids[0], edge_ids[1]); + if (edge_ids[1].rank > edge_ids[2].rank) + std::swap(edge_ids[1], edge_ids[2]); + + int main1 = -1, main2 = -1, side1 = -1, side2 = -1; + int main_dir = 0; + + for (nei_idx = 0; nei_idx < 4; nei_idx++) { - main1 = nei_idx; - main_dir = stereo; - break; - } - } + int stereo = getDir(atom_idx, edge_ids[nei_idx].nei_idx); - if (main1 == -1) - return false; + if (stereo == BOND_UP || stereo == BOND_DOWN) + { + main1 = nei_idx; + main_dir = stereo; + break; + } + } - if (zero_bond_length) - throw Error("zero bond length near atom %d", atom_idx); + if (main1 == -1) + return false; - if (n_pure_hydrogens > 1) - throw Error("%d hydrogens near stereocenter %d", n_pure_hydrogens, atom_idx); + if (zero_bond_length) + throw Error("zero bond length near atom %d", atom_idx); - int xyz1, xyz2; + if (n_pure_hydrogens > 1) + throw Error("%d hydrogens near stereocenter %d", n_pure_hydrogens, atom_idx); - // find main2 as opposite to main1 - if (main2 == -1) - { - xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 1) % 4].vec, edge_ids[(main1 + 2) % 4].vec); - xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 1) % 4].vec, edge_ids[(main1 + 3) % 4].vec); + int xyz1, xyz2; - if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) + // find main2 as opposite to main1 + if (main2 == -1) { - main2 = (main1 + 1) % 4; - side1 = (main1 + 2) % 4; - side2 = (main1 + 3) % 4; - } - } - if (main2 == -1) - { - xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 2) % 4].vec, edge_ids[(main1 + 1) % 4].vec); - xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 2) % 4].vec, edge_ids[(main1 + 3) % 4].vec); + xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 1) % 4].vec, edge_ids[(main1 + 2) % 4].vec); + xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 1) % 4].vec, edge_ids[(main1 + 3) % 4].vec); - if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) - { - main2 = (main1 + 2) % 4; - side1 = (main1 + 1) % 4; - side2 = (main1 + 3) % 4; + if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) + { + main2 = (main1 + 1) % 4; + side1 = (main1 + 2) % 4; + side2 = (main1 + 3) % 4; + } } - } - if (main2 == -1) - { - xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 3) % 4].vec, edge_ids[(main1 + 1) % 4].vec); - xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 3) % 4].vec, edge_ids[(main1 + 2) % 4].vec); + if (main2 == -1) + { + xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 2) % 4].vec, edge_ids[(main1 + 1) % 4].vec); + xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 2) % 4].vec, edge_ids[(main1 + 3) % 4].vec); - if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) + if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) + { + main2 = (main1 + 2) % 4; + side1 = (main1 + 1) % 4; + side2 = (main1 + 3) % 4; + } + } + if (main2 == -1) { - main2 = (main1 + 3) % 4; - side1 = (main1 + 2) % 4; - side2 = (main1 + 1) % 4; + xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 3) % 4].vec, edge_ids[(main1 + 1) % 4].vec); + xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 3) % 4].vec, edge_ids[(main1 + 2) % 4].vec); + + if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) + { + main2 = (main1 + 3) % 4; + side1 = (main1 + 2) % 4; + side2 = (main1 + 1) % 4; + } } - } - if (main2 == -1) - throw Error("internal error: can not find opposite bond near atom %d", atom_idx); + if (main2 == -1) + throw Error("internal error: can not find opposite bond near atom %d", atom_idx); - if (main_dir == BOND_UP && getDir(atom_idx, edge_ids[main2].nei_idx) == BOND_DOWN) - throw Error("stereo types of the opposite bonds mismatch near atom %d", atom_idx); - if (main_dir == BOND_DOWN && getDir(atom_idx, edge_ids[main2].nei_idx) == BOND_UP) - throw Error("stereo types of the opposite bonds mismatch near atom %d", atom_idx); + if (main_dir == BOND_UP && getDir(atom_idx, edge_ids[main2].nei_idx) == BOND_DOWN) + throw Error("stereo types of the opposite bonds mismatch near atom %d", atom_idx); + if (main_dir == BOND_DOWN && getDir(atom_idx, edge_ids[main2].nei_idx) == BOND_UP) + throw Error("stereo types of the opposite bonds mismatch near atom %d", atom_idx); - if (main_dir == getDir(atom_idx, edge_ids[side1].nei_idx)) - throw Error("stereo types of non-opposite bonds match near atom %d", atom_idx); - if (main_dir == getDir(atom_idx, edge_ids[side2].nei_idx)) - throw Error("stereo types of non-opposite bonds match near atom %d", atom_idx); + if (main_dir == getDir(atom_idx, edge_ids[side1].nei_idx)) + throw Error("stereo types of non-opposite bonds match near atom %d", atom_idx); + if (main_dir == getDir(atom_idx, edge_ids[side2].nei_idx)) + throw Error("stereo types of non-opposite bonds match near atom %d", atom_idx); - if (main1 == 3 || main2 == 3) - last_atom_dir = main_dir; - else - last_atom_dir = (main_dir == BOND_UP ? BOND_DOWN : BOND_UP); + if (main1 == 3 || main2 == 3) + last_atom_dir = main_dir; + else + last_atom_dir = (main_dir == BOND_UP ? BOND_DOWN : BOND_UP); - int sign = _sign(edge_ids[0].vec, edge_ids[1].vec, edge_ids[2].vec); + int sign = _sign(edge_ids[0].vec, edge_ids[1].vec, edge_ids[2].vec); - if ((last_atom_dir == BOND_UP && sign > 0) || (last_atom_dir == BOND_DOWN && sign < 0)) - { - pyramid[0] = edge_ids[0].nei_idx; - pyramid[1] = edge_ids[1].nei_idx; - pyramid[2] = edge_ids[2].nei_idx; - } - else - { - pyramid[0] = edge_ids[0].nei_idx; - pyramid[1] = edge_ids[2].nei_idx; - pyramid[2] = edge_ids[1].nei_idx; - } + if ((last_atom_dir == BOND_UP && sign > 0) || (last_atom_dir == BOND_DOWN && sign < 0)) + { + pyramid[0] = edge_ids[0].nei_idx; + pyramid[1] = edge_ids[1].nei_idx; + pyramid[2] = edge_ids[2].nei_idx; + } + else + { + pyramid[0] = edge_ids[0].nei_idx; + pyramid[1] = edge_ids[2].nei_idx; + pyramid[2] = edge_ids[1].nei_idx; + } - pyramid[3] = edge_ids[3].nei_idx; - } - else if (degree == 3) - { - // sort by neighbor atom index (ascending) - if (edge_ids[0].rank > edge_ids[1].rank) - std::swap(edge_ids[0], edge_ids[1]); - if (edge_ids[1].rank > edge_ids[2].rank) - std::swap(edge_ids[1], edge_ids[2]); - if (edge_ids[0].rank > edge_ids[1].rank) - std::swap(edge_ids[0], edge_ids[1]); - - bool degenerate = true; - int dirs[3] = {0, 0, 0}; - int main_nei = -1; // will be assigned if all three neighors belong to the same half-plane - int n_up = 0, n_down = 0; - - for (nei_idx = 0; nei_idx < 3; nei_idx++) - { - dirs[nei_idx] = getDir(atom_idx, edge_ids[nei_idx].nei_idx); - if (dirs[nei_idx] == BOND_UP) - n_up++; - else if (dirs[nei_idx] == BOND_DOWN) - n_down++; + pyramid[3] = edge_ids[3].nei_idx; } - - if (n_down == 0 && n_up == 0) - return false; - - for (nei_idx = 0; nei_idx < 3; nei_idx++) + else if (degree == 3) { - int xyzzy = _xyzzy(edge_ids[(nei_idx + 1) % 3].vec, edge_ids[(nei_idx + 2) % 3].vec, edge_ids[nei_idx].vec); - - if (xyzzy == 1) - main_nei = nei_idx; - if (xyzzy == 2) - degenerate = false; - } + // sort by neighbor atom index (ascending) + if (edge_ids[0].rank > edge_ids[1].rank) + std::swap(edge_ids[0], edge_ids[1]); + if (edge_ids[1].rank > edge_ids[2].rank) + std::swap(edge_ids[1], edge_ids[2]); + if (edge_ids[0].rank > edge_ids[1].rank) + std::swap(edge_ids[0], edge_ids[1]); + + bool degenerate = true; + int dirs[3] = {0, 0, 0}; + int main_nei = -1; // will be assigned if all three neighors belong to the same half-plane + int n_up = 0, n_down = 0; + + for (nei_idx = 0; nei_idx < 3; nei_idx++) + { + dirs[nei_idx] = getDir(atom_idx, edge_ids[nei_idx].nei_idx); + if (dirs[nei_idx] == BOND_UP) + n_up++; + else if (dirs[nei_idx] == BOND_DOWN) + n_down++; + } - int dir = 1; + if (n_down == 0 && n_up == 0) + return false; - if (main_nei != -1) - { - if (dirs[main_nei] != 0) + for (nei_idx = 0; nei_idx < 3; nei_idx++) { - if (dirs[(main_nei + 1) % 3] == dirs[main_nei] || dirs[(main_nei + 2) % 3] == dirs[main_nei]) - throw Error("directions of neighbor stereo bonds match near atom %d", atom_idx); - if (dirs[main_nei] == BOND_UP) - dir = -1; + int xyzzy = _xyzzy(edge_ids[(nei_idx + 1) % 3].vec, edge_ids[(nei_idx + 2) % 3].vec, edge_ids[nei_idx].vec); + + if (xyzzy == 1) + main_nei = nei_idx; + if (xyzzy == 2) + degenerate = false; } - else + + int dir = 1; + + if (main_nei != -1) { - int d1 = dirs[(main_nei + 1) % 3]; - int d2 = dirs[(main_nei + 2) % 3]; + if (dirs[main_nei] != 0) + { + if (dirs[(main_nei + 1) % 3] == dirs[main_nei] || dirs[(main_nei + 2) % 3] == dirs[main_nei]) + throw Error("directions of neighbor stereo bonds match near atom %d", atom_idx); + if (dirs[main_nei] == BOND_UP) + dir = -1; + } + else + { + int d1 = dirs[(main_nei + 1) % 3]; + int d2 = dirs[(main_nei + 2) % 3]; - if (d1 == 0) - d1 = d2; - else if (d2 != 0 && d1 != d2) - throw Error("directions of opposite stereo bonds do not match near atom %d", atom_idx); + if (d1 == 0) + d1 = d2; + else if (d2 != 0 && d1 != d2) + throw Error("directions of opposite stereo bonds do not match near atom %d", atom_idx); - if (d1 == 0) - return false; + if (d1 == 0) + return false; - if (d1 == BOND_DOWN) - dir = -1; + if (d1 == BOND_DOWN) + dir = -1; + } } - } - else if (!degenerate) - { - if (n_down > 0 && n_up > 0) - throw Error("one bond up, one bond down -- indefinite case near atom %d", atom_idx); - - if (!possible_lone_pair) + else if (!degenerate) { - if (n_up == 3) - throw Error("all 3 bonds up near stereoatom %d", atom_idx); - if (n_down == 3) - throw Error("all 3 bonds down near stereoatom %d", atom_idx); + if (n_down > 0 && n_up > 0) + throw Error("one bond up, one bond down -- indefinite case near atom %d", atom_idx); + + if (!possible_lone_pair) + { + if (n_up == 3) + throw Error("all 3 bonds up near stereoatom %d", atom_idx); + if (n_down == 3) + throw Error("all 3 bonds down near stereoatom %d", atom_idx); + } + if (n_down > 0) + dir = -1; } - if (n_down > 0) - dir = -1; - } - else - throw Error("degenerate case for 3 bonds near stereoatom %d", atom_idx); + else + throw Error("degenerate case for 3 bonds near stereoatom %d", atom_idx); - if (zero_bond_length) - throw Error("zero bond length near atom %d", atom_idx); + if (zero_bond_length) + throw Error("zero bond length near atom %d", atom_idx); - if (n_pure_hydrogens > 0 && !possible_lone_pair) - throw Error("have hydrogen(s) besides implicit hydrogen near stereocenter %d", atom_idx); + if (n_pure_hydrogens > 0 && !possible_lone_pair) + throw Error("have hydrogen(s) besides implicit hydrogen near stereocenter %d", atom_idx); - int sign = _sign(edge_ids[0].vec, edge_ids[1].vec, edge_ids[2].vec); + int sign = _sign(edge_ids[0].vec, edge_ids[1].vec, edge_ids[2].vec); - if (sign == dir) - { - pyramid[0] = edge_ids[0].nei_idx; - pyramid[1] = edge_ids[2].nei_idx; - pyramid[2] = edge_ids[1].nei_idx; - } - else - { - pyramid[0] = edge_ids[0].nei_idx; - pyramid[1] = edge_ids[1].nei_idx; - pyramid[2] = edge_ids[2].nei_idx; + if (sign == dir) + { + pyramid[0] = edge_ids[0].nei_idx; + pyramid[1] = edge_ids[2].nei_idx; + pyramid[2] = edge_ids[1].nei_idx; + } + else + { + pyramid[0] = edge_ids[0].nei_idx; + pyramid[1] = edge_ids[1].nei_idx; + pyramid[2] = edge_ids[2].nei_idx; + } + pyramid[3] = -1; } - pyramid[3] = -1; + for (i = 0; i < degree; i++) + if (getDir(atom_idx, edge_ids[i].nei_idx) > 0) + sensible_bonds_out[edge_ids[i].edge_idx] = 1; + _stereocenters.insert(atom_idx, stereocenter); } - - for (i = 0; i < degree; i++) - if (getDir(atom_idx, edge_ids[i].nei_idx) > 0) - sensible_bonds_out[edge_ids[i].edge_idx] = 1; - - _stereocenters.insert(atom_idx, stereocenter); return true; } @@ -713,7 +825,7 @@ void MoleculeStereocenters::setAtropisomeric(int idx, bool val) _stereocenters.at(idx).is_atropisomeric = val; } -bool MoleculeStereocenters::isAtropisomeric(int idx) +bool MoleculeStereocenters::isAtropisomeric(int idx) const { return _stereocenters.at(idx).is_atropisomeric; } @@ -1546,6 +1658,19 @@ void MoleculeStereocenters::markBond(BaseMolecule& baseMolecule, int atom_idx) return; const _Atom& atom = *atom_ptr; + + if (atom.is_atropisomeric) + { + const auto& ac = _atropocenters.at(atom_idx); + for (int i = ac.bond_directions.begin(); i != ac.bond_directions.end(); i = ac.bond_directions.next(i)) + { + int bond_idx = ac.bond_directions.key(i); + int bdir = ac.bond_directions.value(i); + baseMolecule.setBondDirection(bond_idx, bdir); + } + return; + } + int pyramid[4]; int mult = 1; int size = 0; @@ -1639,48 +1764,48 @@ void MoleculeStereocenters::markBond(BaseMolecule& baseMolecule, int atom_idx) if (baseMolecule.getEdge(edge_idx).beg != atom_idx) baseMolecule.swapEdgeEnds(edge_idx); - if (atom.type > ATOM_ANY) + if (BaseMolecule::hasCoord(baseMolecule)) { - std::array dirs; - dirs.fill({0.0, 0.0, 0.0}); - for (j = 0; j < size; j++) + if (atom.type > ATOM_ANY) { - dirs[j] = baseMolecule.getAtomXyz(pyramid[j]); - dirs[j].sub(baseMolecule.getAtomXyz(atom_idx)); - if (!dirs[j].normalize()) - throw Error("zero bond length"); - } + std::array dirs; + dirs.fill({0.0, 0.0, 0.0}); + for (j = 0; j < size; j++) + { + dirs[j] = baseMolecule.getAtomXyz(pyramid[j]); + dirs[j].sub(baseMolecule.getAtomXyz(atom_idx)); + if (!dirs[j].normalize()) + throw Error("zero bond length"); + } - int sign = _sign(dirs[0], dirs[1], dirs[2]); + int sign = _sign(dirs[0], dirs[1], dirs[2]); - if (size == 3) - { - // Check if all the three bonds belong to the same half-plane. - // This is equal to that one of the bonds lies in the smaller - // angle formed by the other two. - if (_xyzzy(dirs[1], dirs[0], dirs[2]) == 1 || _xyzzy(dirs[2], dirs[1], dirs[0]) == 1 || _xyzzy(dirs[0], dirs[2], dirs[1]) == 1) + if (size == 3) { - if (_xyzzy(dirs[1], dirs[0], dirs[2]) == 1) - mult = -1; - baseMolecule.setBondDirection(edge_idx, (sign * mult == 1) ? BOND_DOWN : BOND_UP); + // Check if all the three bonds belong to the same half-plane. + // This is equal to that one of the bonds lies in the smaller + // angle formed by the other two. + if (_xyzzy(dirs[1], dirs[0], dirs[2]) == 1 || _xyzzy(dirs[2], dirs[1], dirs[0]) == 1 || _xyzzy(dirs[0], dirs[2], dirs[1]) == 1) + { + if (_xyzzy(dirs[1], dirs[0], dirs[2]) == 1) + mult = -1; + baseMolecule.setBondDirection(edge_idx, (sign * mult == 1) ? BOND_DOWN : BOND_UP); + } + else + baseMolecule.setBondDirection(edge_idx, (sign == 1) ? BOND_DOWN : BOND_UP); } else - baseMolecule.setBondDirection(edge_idx, (sign == 1) ? BOND_DOWN : BOND_UP); + baseMolecule.setBondDirection(edge_idx, (sign * mult == 1) ? BOND_UP : BOND_DOWN); } else - baseMolecule.setBondDirection(edge_idx, (sign * mult == 1) ? BOND_UP : BOND_DOWN); + baseMolecule.setBondDirection(edge_idx, BOND_EITHER); } - else - baseMolecule.setBondDirection(edge_idx, BOND_EITHER); } void MoleculeStereocenters::markBonds(BaseMolecule& baseMolecule) { for (int i = _stereocenters.begin(); i != _stereocenters.end(); i = _stereocenters.next(i)) - { - if (!_stereocenters.value(i).is_atropisomeric) - markBond(baseMolecule, _stereocenters.key(i)); - } + markBond(baseMolecule, _stereocenters.key(i)); } bool MoleculeStereocenters::isAutomorphism(BaseMolecule& mol, const Array& mapping, const Filter* filter) diff --git a/core/indigo-core/molecule/src/molfile_loader.cpp b/core/indigo-core/molecule/src/molfile_loader.cpp index f1a2e73e0a..6384e76abf 100644 --- a/core/indigo-core/molecule/src/molfile_loader.cpp +++ b/core/indigo-core/molecule/src/molfile_loader.cpp @@ -57,9 +57,7 @@ void MolfileLoader::loadMolecule(Molecule& mol) _mol = &mol; _qmol = 0; _loadMolecule(); - mol.setIgnoreBadValenceFlag(ignore_bad_valence); - if (mol.stereocenters.size() == 0 && !skip_3d_chirality) mol.buildFrom3dCoordinatesStereocenters(stereochemistry_options); } @@ -2063,12 +2061,7 @@ void MolfileLoader::_postLoad() { if (_bmol->stereocenters.getType(i) == 0) { - if (_bmol->isAtropisomerismReferenceAtom(i)) - { - _bmol->stereocenters.add_ignore(*_bmol, i, _stereocenter_types[i], _stereocenter_groups[i], false); - _bmol->stereocenters.setAtropisomeric(i, true); - } - else if (!stereochemistry_options.ignore_errors) + if (!stereochemistry_options.ignore_errors) throw Error("stereo type specified for atom #%d, but the bond " "directions does not say that it is a stereocenter", i); @@ -2081,11 +2074,9 @@ void MolfileLoader::_postLoad() for (i = 0; i < _bonds_num; i++) { - if (_bmol->getBondDirection(i) && (!_sensible_bond_directions[i] || _bmol->getBondTopology(i) == TOPOLOGY_RING)) + if (_bmol->getBondDirection(i) && !_sensible_bond_directions[i]) { - auto& e = _bmol->getEdge(i); - _bmol->setForcedBondDirection(i, _bmol->getBondDirection(i)); - if (!stereochemistry_options.ignore_errors && !_sensible_bond_directions[i]) + if (!stereochemistry_options.ignore_errors) throw Error("direction of bond #%d makes no sense", i); } } diff --git a/core/indigo-core/molecule/src/molfile_saver.cpp b/core/indigo-core/molecule/src/molfile_saver.cpp index c39f250ff1..fe2938d87a 100644 --- a/core/indigo-core/molecule/src/molfile_saver.cpp +++ b/core/indigo-core/molecule/src/molfile_saver.cpp @@ -1910,7 +1910,7 @@ void MolfileSaver::_checkSGroupIndices(BaseMolecule& mol, Array& sgs_list) int MolfileSaver::_getStereocenterParity(BaseMolecule& mol, int idx) { int type = mol.stereocenters.getType(idx); - if (type == 0) + if (type == 0 /* || mol.stereocenters.isAtropisomeric(idx)*/) return 0; if (type == MoleculeStereocenters::ATOM_ANY) return 3; diff --git a/core/indigo-core/molecule/src/smiles_loader.cpp b/core/indigo-core/molecule/src/smiles_loader.cpp index a91babdc1d..aff0c189b9 100644 --- a/core/indigo-core/molecule/src/smiles_loader.cpp +++ b/core/indigo-core/molecule/src/smiles_loader.cpp @@ -355,6 +355,8 @@ void SmilesLoader::_readOtherStuff() { _scanner.skip(1); auto bond_idx = _scanner.readUnsigned(); + if (!_has_directions_on_rings) + _has_directions_on_rings = _bmol->getBondTopology(bond_idx) == TOPOLOGY_RING; if (wmode) { if (bond_idx < _bmol->edgeCount() && atom_idx < _bmol->vertexCount()) @@ -365,7 +367,7 @@ void SmilesLoader::_readOtherStuff() if (v.beg == atom_idx) { - _bmol->setForcedBondDirection(bond_idx, wmode == 'U' ? BOND_UP : BOND_DOWN); + _bmol->setBondDirection(bond_idx, wmode == 'U' ? BOND_UP : BOND_DOWN); } } } @@ -1338,20 +1340,6 @@ void SmilesLoader::_readOtherStuff() _bmol->removeAtoms(to_remove); } -void SmilesLoader::_handleForcedStereo() -{ - auto& fbonds = _bmol->forcedStereoBonds(); - for (int i = fbonds.begin(); i != fbonds.end(); i = fbonds.next(i)) - _bmol->setBondDirection(fbonds.key(i), fbonds.value(i)); - - for (int i = fbonds.begin(); i != fbonds.end(); i = fbonds.next(i)) - { - auto& e = _bmol->getEdge(fbonds.key(i)); - if (_bmol->stereocenters.exists(e.beg) && _bmol->isAtropisomerismReferenceAtom(e.beg)) - _bmol->stereocenters.setAtropisomeric(e.beg, true); - } -} - void SmilesLoader::_validateStereoCenters() { for (int i = _bmol->stereocenters.begin(); i < _bmol->stereocenters.end(); i = _bmol->stereocenters.next(i)) @@ -1938,14 +1926,14 @@ void SmilesLoader::_loadParsedMolecule() { _scanner.skip(1); _readOtherStuff(); - if (_has_atom_coordinates) + if (_has_atom_coordinates || _has_directions_on_rings) { + std::vector sensible_bond_directions; + sensible_bond_directions.resize(_bmol->edgeCount()); + _bmol->buildFromBondsStereocenters(stereochemistry_options, sensible_bond_directions.data()); _bmol->markBondsStereocenters(); _bmol->markBondsAlleneStereo(); } - - if (_bmol->forcedStereoBonds().size()) - _handleForcedStereo(); } // Update attachment orders for rsites diff --git a/core/indigo-core/molecule/src/smiles_saver.cpp b/core/indigo-core/molecule/src/smiles_saver.cpp index a8e6952a53..4b548d09e3 100644 --- a/core/indigo-core/molecule/src/smiles_saver.cpp +++ b/core/indigo-core/molecule/src/smiles_saver.cpp @@ -385,7 +385,7 @@ void SmilesSaver::_saveMolecule() int idx = _written_atoms[i]; - if (_atoms[idx].chirality == 0) + if (_atoms[idx].chirality == 0 || stereocenters.isAtropisomeric(idx)) continue; int type = stereocenters.getType(idx); @@ -1502,7 +1502,6 @@ void SmilesSaver::_writeStereogroups() { int atom, type, group; stereocenters.get(i, atom, type, group, 0); - if (type != MoleculeStereocenters::ATOM_ABS) break; } @@ -1850,7 +1849,7 @@ void SmilesSaver::_writeWedges() auto bond_idx = _written_bonds[i]; auto& e = _bmol->getEdge(bond_idx); auto bdir = _bmol->getBondDirection(bond_idx); - if (bdir && bdir < BOND_EITHER && _bmol->isForcedStereoBond(bond_idx)) + if (bdir && bdir < BOND_EITHER) { const auto& edge = _bmol->getEdge(bond_idx); auto wa_idx = _written_atoms.find(edge.beg); @@ -1892,7 +1891,7 @@ void SmilesSaver::_writeWedges() _output.printf("%d.%d", kvp.first, kvp.second); } } - if (down_dirs.size() || up_dirs.size()) + if ((down_dirs.size() || up_dirs.size()) && BaseMolecule::hasCoord(*_mol)) { _output.writeString(",("); for (int i = 0; i < _written_atoms.size(); ++i) diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index c97759bcf9..cc03a1f1bb 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -396,6 +396,7 @@ int parseParams(Params* p, int argc, char* argv[]) indigoSetOptionBool("treat-x-as-pseudoatom", 1); indigoSetOptionBool("render-coloring", 1); indigoSetOptionBool("render-highlight-color-enabled", 1); + for (; i < argc; i++) { if (strcmp(argv[i], "-w") == 0) From b43585e5ada34e47789232c1c20875c2abfac76d Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 27 Sep 2023 07:45:40 +0200 Subject: [PATCH 10/36] clang fix --- core/indigo-core/molecule/molecule_stereocenter_options.h | 1 - 1 file changed, 1 deletion(-) diff --git a/core/indigo-core/molecule/molecule_stereocenter_options.h b/core/indigo-core/molecule/molecule_stereocenter_options.h index 87196b6a3f..946954017c 100644 --- a/core/indigo-core/molecule/molecule_stereocenter_options.h +++ b/core/indigo-core/molecule/molecule_stereocenter_options.h @@ -45,7 +45,6 @@ namespace indigo // Detect Haworth projection. Default is false. bool detect_haworth_projection; - }; } // namespace indigo From e04f16a852d2842946d3d46d3f335aa5203665db Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 27 Sep 2023 07:56:02 +0200 Subject: [PATCH 11/36] test fix --- .../integration/ref/formats/mol_to_ket.py.out | 17 +---------------- .../tests/formats/ref/atropisomer.ket | 3 +-- 2 files changed, 2 insertions(+), 18 deletions(-) diff --git a/api/tests/integration/ref/formats/mol_to_ket.py.out b/api/tests/integration/ref/formats/mol_to_ket.py.out index 7ffb4d63e1..69f4d6eb4a 100644 --- a/api/tests/integration/ref/formats/mol_to_ket.py.out +++ b/api/tests/integration/ref/formats/mol_to_ket.py.out @@ -2,21 +2,6 @@ 1032-quadra.ket:SUCCEED 1046-imp_hydrogen.ket:SUCCEED SgroupDifferent.ket:SUCCEED -atropisomer.ket:FAILED ---- - -+++ - -@@ -55,8 +55,7 @@ - - 26.818199157714845, - -12.862500190734864, - 0.0 -- ], -- "stereoLabel": "or1" -+ ] - }, - { - "label": "C", +atropisomer.ket:SUCCEED non_atrop.ket:SUCCEED suplabel.ket:SUCCEED diff --git a/api/tests/integration/tests/formats/ref/atropisomer.ket b/api/tests/integration/tests/formats/ref/atropisomer.ket index 7cd4aa00c3..421c41f86a 100644 --- a/api/tests/integration/tests/formats/ref/atropisomer.ket +++ b/api/tests/integration/tests/formats/ref/atropisomer.ket @@ -55,8 +55,7 @@ 26.818199157714845, -12.862500190734864, 0.0 - ], - "stereoLabel": "or1" + ] }, { "label": "C", From 926835651c965d75b672a23817b5d2c3b72902a4 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 27 Sep 2023 08:01:55 +0200 Subject: [PATCH 12/36] test fix --- utils/indigo-depict/main.c | 1 - 1 file changed, 1 deletion(-) diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index cc03a1f1bb..c97759bcf9 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -396,7 +396,6 @@ int parseParams(Params* p, int argc, char* argv[]) indigoSetOptionBool("treat-x-as-pseudoatom", 1); indigoSetOptionBool("render-coloring", 1); indigoSetOptionBool("render-highlight-color-enabled", 1); - for (; i < argc; i++) { if (strcmp(argv[i], "-w") == 0) From 3f759a4d300970f7b3f580b1b0a5db03bc390e67 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 27 Sep 2023 11:45:42 +0200 Subject: [PATCH 13/36] test fix --- .../integration/ref/bingo/molecules.py.out | 14 ++--- .../integration/ref/formats/mol_to_ket.py.out | 17 +++++- .../molecule/molecule_stereocenters.h | 4 ++ .../molecule/src/molecule_json_saver.cpp | 1 + .../molecule/src/molecule_stereocenters.cpp | 57 +++++++++++-------- utils/indigo-depict/main.c | 4 +- 6 files changed, 64 insertions(+), 33 deletions(-) diff --git a/api/tests/integration/ref/bingo/molecules.py.out b/api/tests/integration/ref/bingo/molecules.py.out index cf08ed063b..8eac7d65ec 100644 --- a/api/tests/integration/ref/bingo/molecules.py.out +++ b/api/tests/integration/ref/bingo/molecules.py.out @@ -898,7 +898,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 227 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 233 [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| 237 C1(C2(C(OC(OC3(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC6(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC7(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC8(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC9(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(O2)([H])OC9(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC8(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC7(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC6(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC5(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC4(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC3(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])C1(OS(O[H])(=O)=O)[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H] C1(C2(C(OC(OC3(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC6(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC7(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC8(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC9(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(O2)([H])OC9(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC8(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC7(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC6(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC5(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC4(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC3(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])C1(OS(O[H])(=O)=O)[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H] - 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| + 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| 252 C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| 262 C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] 265 [CH]1C=C1C1=C[CH]1 |^1:0,5| [CH]1C=C1C1=C[CH]1 |^1:0,5| @@ -978,7 +978,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 918 [C@H]12C[C@H]3[C@H]4[C@]56[C@H]([C@H]7[C@]89[C@@H]%10[C@@H]%11C[C@@H](C[C@H]5[C@@H]5C[C@@H](C[C@H]%12[C@@H]%13C[C@@H](C%10)C[C@H]([C@]3%12[C@]86[C@]5%13%11)[C@@H]9C1)C4)C7)C2 [C@H]12C[C@H]3[C@H]4[C@]56[C@H]([C@H]7[C@]89[C@@H]%10[C@@H]%11C[C@@H](C[C@H]5[C@@H]5C[C@@H](C[C@H]%12[C@@H]%13C[C@@H](C%10)C[C@H]([C@]3%12[C@]86[C@]5%13%11)[C@@H]9C1)C4)C7)C2 919 [C@@H]12[C@@]34[12CH]([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C.[12C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[12C@H]12[C@]34C([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,17,18,20,22,23,26,32,34,35,37,39,40,43,49,51,52,54,56,57,60,66,r| [C@@H]12[C@@]34[12CH]([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C.[12C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[12C@H]12[C@]34C([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,17,18,20,22,23,26,32,34,35,37,39,40,43,49,51,52,54,56,57,60,66,r| 920 C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP(O[H])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:85,114,143| C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP(O[H])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:85,114,143| - 941 C[C@]1(C/C(=C2/C[C@]([H])(Cl)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H].C[C@]1(C/C(=C2/C[C@]([H])(Br)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,45,50,55,65,68,73,76,84,r| C[C@]1(C/C(=C2/C[C@]([H])(Cl)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H].C[C@]1(C/C(=C2/C[C@]([H])(Br)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,45,50,55,65,68,73,76,84,r| + 941 C[C@]1(C/C(=C2/C[C@]([H])(Cl)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H].C[C@]1(C/C(=C2/C[C@]([H])(Br)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,45,50,53,54,55,65,68,73,76,84,r| C[C@]1(C/C(=C2/C[C@]([H])(Cl)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H].C[C@]1(C/C(=C2/C[C@]([H])(Br)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,45,50,53,54,55,65,68,73,76,84,r| 947 O1[C@@H]([C@H](C)CO)[C@@H](O)[C@@H]([C@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1 |&1:1,2,6,8,9,16,17,21,23,24,31,32,36,38,39,r| O1[C@@H]([C@H](C)CO)[C@@H](O)[C@@H]([C@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1 |&1:1,2,6,8,9,16,17,21,23,24,31,32,36,38,39,r| 950 [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC |&1:0,2,9,r| [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC |&1:0,2,9,r| 968 [C@@H](C[C@@H](C[C@@H](C)C[C@@H](C)N)C)(N)C |&1:0,2,4,7,r| [C@@H](C[C@@H](C[C@@H](C)C[C@@H](C)N)C)(N)C |&1:0,2,4,7,r| @@ -1059,7 +1059,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1500 [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] 1510 C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| 1511 c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O - 1514 C[C@]1(C/C(=C2/C[C@]([H])(Cl)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,r| C[C@]1(C/C(=C2/C[C@]([H])(Cl)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,r| + 1514 C[C@]1(C/C(=C2/C[C@]([H])(Cl)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,r| C[C@]1(C/C(=C2/C[C@]([H])(Cl)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,r| 1523 [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| 1525 [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| 1527 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| @@ -1098,7 +1098,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] 1814 [C@@H](C[C@@H](C[C@H](C)C[C@H](C)N)C)(N)C |&1:0,2,4,7,r| [C@@H](C[C@@H](C[C@H](C)C[C@H](C)N)C)(N)C |&1:0,2,4,7,r| 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| - 1846 C[C@]1(C/C(=C2/C[C@]([H])(Br)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,r| C[C@]1(C/C(=C2/C[C@]([H])(Br)C(=C3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,11,21,24,29,32,40,r| + 1846 C[C@]1(C/C(=C2/C[C@]([H])(Br)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,r| C[C@]1(C/C(=C2/C[C@]([H])(Br)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,r| 1856 [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| 1861 C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C 1862 c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-].c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][nH][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2C([N-]C)=O c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-].c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][nH][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2C([N-]C)=O @@ -1923,7 +1923,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 118 N[C@]1(C)C[C@]2([C@@]3(C[C@@](N)(C)C3)[C@]32C[C@@](N)(C)C3)C1 |&1:1,4,5,7,11,13,r| N[C@]1(C)C[C@]2([C@@]3(C[C@@](N)(C)C3)[C@]32C[C@@](N)(C)C3)C1 |&1:1,4,5,7,11,13,r| 179 [C@H]1(C[C@H](C)C1)C.[C@H]1(C[C@@H](C)C1)C |&1:0,2,6,8,r| [C@H]1(C[C@H](C)C1)C.[C@H]1(C[C@@H](C)C1)C |&1:0,2,6,8,r| 212 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 - 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| + 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| 305 C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,10,r| C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,10,r| 351 [C@@]12([H])[C@@]3([H])[C@]1([H])C1([H])C2([H])[C@]2([C@]3([H])[C@@]12[H])[H].[C@@]12([H])[C@@]3([H])[C@]4(C5([H])[C@@]1([C@@]2(C5([C@@]34[H])[H])[H])[H])[H].C12([H])[C@]3([C@]4([C@]5([H])[C@]([H])(C1([H])[C@@]34[H])[C@]25[H])[H])[H] |&1:0,2,4,10,11,13,16,18,20,23,24,26,34,35,36,38,42,44,r| [C@@]12([H])[C@@]3([H])[C@]1([H])C1([H])C2([H])[C@]2([C@]3([H])[C@@]12[H])[H].[C@@]12([H])[C@@]3([H])[C@]4(C5([H])[C@@]1([C@@]2(C5([C@@]34[H])[H])[H])[H])[H].C12([H])[C@]3([C@]4([C@]5([H])[C@]([H])(C1([H])[C@@]34[H])[C@]25[H])[H])[H] |&1:0,2,4,10,11,13,16,18,20,23,24,26,34,35,36,38,42,44,r| 387 [C@@]12(C[C@@](N)(C)C1)C[C@@](N)(C)C2 |&1:0,2,7,r| [C@@]12(C[C@@](N)(C)C1)C[C@@](N)(C)C2 |&1:0,2,7,r| @@ -2922,7 +2922,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 212 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 227 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 233 [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| - 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| + 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| 252 C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| 262 C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] 266 C1([H])=C([H])C21C([H])=C([H])C12C([H])=C1[H] C1([H])=C([H])C21C([H])=C([H])C12C([H])=C1[H] @@ -4671,7 +4671,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1839 O([H])[H] O([H])[H] 1954 [O][2H][2H] [O][2H][2H] ** searchSub([Sn](CCC)(C)CC, '') ** - 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:40,41,42,43,r| + 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| 1024 [Sn]([C@@H](/C=C/CO[Si](C(C)(C)C)(C)C)OCOC)(CCCC)(CCCC)CCCC |&1:1,r| [Sn]([C@@H](/C=C/CO[Si](C(C)(C)C)(C)C)OCOC)(CCCC)(CCCC)CCCC |&1:1,r| 1025 [Sn]1(CCCC)(C=CCCC=C1)CCCC [Sn]1(CCCC)(C=CCCC=C1)CCCC ** searchSim([SnH](CCC)(C)CC, 0.9, 1, tanimoto) ** diff --git a/api/tests/integration/ref/formats/mol_to_ket.py.out b/api/tests/integration/ref/formats/mol_to_ket.py.out index 69f4d6eb4a..1ed735bb47 100644 --- a/api/tests/integration/ref/formats/mol_to_ket.py.out +++ b/api/tests/integration/ref/formats/mol_to_ket.py.out @@ -2,6 +2,21 @@ 1032-quadra.ket:SUCCEED 1046-imp_hydrogen.ket:SUCCEED SgroupDifferent.ket:SUCCEED -atropisomer.ket:SUCCEED +atropisomer.ket:FAILED +--- + ++++ + +@@ -55,7 +55,8 @@ + + 26.818199157714845, + -12.862500190734864, + 0.0 +- ] ++ ], ++ "stereoLabel": "or1" + }, + { + "label": "C", non_atrop.ket:SUCCEED suplabel.ket:SUCCEED diff --git a/core/indigo-core/molecule/molecule_stereocenters.h b/core/indigo-core/molecule/molecule_stereocenters.h index 7ae46e81af..aa7b20f7e7 100644 --- a/core/indigo-core/molecule/molecule_stereocenters.h +++ b/core/indigo-core/molecule/molecule_stereocenters.h @@ -86,6 +86,9 @@ namespace indigo void setType(int idx, int type); void setAtropisomeric(int idx, bool val); bool isAtropisomeric(int idx) const; + void setTetrahydral(int idx, bool val); + bool isTetrahydral(int idx) const; + void invertPyramid(int idx); bool sameGroup(int idx1, int idx2); @@ -146,6 +149,7 @@ namespace indigo // (X, Y, Z) go counterclockwise when looking from W. // if there are pure (implicit) hydrogen, it is W bool is_atropisomeric = false; + bool is_tetrahydral = false; int pyramid[4]; }; diff --git a/core/indigo-core/molecule/src/molecule_json_saver.cpp b/core/indigo-core/molecule/src/molecule_json_saver.cpp index 6acfd0d8c9..68fc6bd382 100644 --- a/core/indigo-core/molecule/src/molecule_json_saver.cpp +++ b/core/indigo-core/molecule/src/molecule_json_saver.cpp @@ -1006,6 +1006,7 @@ void MoleculeJsonSaver::saveMolecule(BaseMolecule& bmol, JsonWriter& writer) std::unique_ptr mol(bmol.neu()); mol->clone_KeepIndices(bmol); + if (!BaseMolecule::hasCoord(*mol)) { MoleculeLayout ml(*mol, false); diff --git a/core/indigo-core/molecule/src/molecule_stereocenters.cpp b/core/indigo-core/molecule/src/molecule_stereocenters.cpp index 433a84902d..a6628c6c96 100644 --- a/core/indigo-core/molecule/src/molecule_stereocenters.cpp +++ b/core/indigo-core/molecule/src/molecule_stereocenters.cpp @@ -425,17 +425,13 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom int i; - bool is_center = isPossibleStereocenter(baseMolecule, atom_idx, &possible_implicit_h, &possible_lone_pair); - bool is_atropo_center = false; - if (check_atropocenter && !is_center) - is_atropo_center = isPossibleAtropocenter(baseMolecule, atom_idx, possible_atropobond); + stereocenter.is_tetrahydral = isPossibleStereocenter(baseMolecule, atom_idx, &possible_implicit_h, &possible_lone_pair); + if (check_atropocenter && !stereocenter.is_tetrahydral) + stereocenter.is_atropisomeric = isPossibleAtropocenter(baseMolecule, atom_idx, possible_atropobond); - if (!is_center && !is_atropo_center) + if (!stereocenter.is_tetrahydral && !stereocenter.is_atropisomeric) return false; - if (possible_atropobond > -1) - stereocenter.is_atropisomeric = true; - // Local synonym to get bond direction auto getDir = [&](int from, int to) { int idx = baseMolecule.findEdgeIndex(from, to); @@ -830,6 +826,16 @@ bool MoleculeStereocenters::isAtropisomeric(int idx) const return _stereocenters.at(idx).is_atropisomeric; } +void MoleculeStereocenters::setTetrahydral(int idx, bool val) +{ + _stereocenters.at(idx).is_tetrahydral = val; +} + +bool MoleculeStereocenters::isTetrahydral(int idx) const +{ + return _stereocenters.at(idx).is_tetrahydral; +} + const int* MoleculeStereocenters::getPyramid(int idx) const { return _stereocenters.at(idx).pyramid; @@ -1341,26 +1347,31 @@ void MoleculeStereocenters::buildOnSubmolecule(BaseMolecule& baseMolecule, const new_stereocenter.group = super_stereocenter.group; new_stereocenter.type = super_stereocenter.type; + new_stereocenter.is_atropisomeric = super_stereocenter.is_atropisomeric; + new_stereocenter.is_tetrahydral = super_stereocenter.is_tetrahydral; - for (j = 0; j < 4; j++) + if (!new_stereocenter.is_atropisomeric) { - int idx = super_stereocenter.pyramid[j]; - - if (idx == -1) - new_stereocenter.pyramid[j] = -1; - else + for (j = 0; j < 4; j++) { - int val = mapping[idx]; - if (val != -1 && baseMolecule.findEdgeIndex(sub_idx, val) == -1) - val = -1; - new_stereocenter.pyramid[j] = val; + int idx = super_stereocenter.pyramid[j]; + + if (idx == -1) + new_stereocenter.pyramid[j] = -1; + else + { + int val = mapping[idx]; + if (val != -1 && baseMolecule.findEdgeIndex(sub_idx, val) == -1) + val = -1; + new_stereocenter.pyramid[j] = val; + } } - } - moveMinimalToEnd(new_stereocenter.pyramid); - if (new_stereocenter.pyramid[0] == -1 || new_stereocenter.pyramid[1] == -1 || new_stereocenter.pyramid[2] == -1) - // pyramid is not mapped completely - continue; + moveMinimalToEnd(new_stereocenter.pyramid); + if (new_stereocenter.pyramid[0] == -1 || new_stereocenter.pyramid[1] == -1 || new_stereocenter.pyramid[2] == -1) + // pyramid is not mapped completely + continue; + } _stereocenters.insert(sub_idx, new_stereocenter); diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index c97759bcf9..3b3bc47ded 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -917,7 +917,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - indigoLayout(obj); + //indigoLayout(obj); if (p.out_ext == OEXT_MOL) indigoSaveMolfileToFile(obj, p.outfile); else if (p.out_ext == OEXT_KET) @@ -1016,7 +1016,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - indigoLayout(obj); + //indigoLayout(obj); if (p.out_ext == OEXT_CML) indigoSaveCmlToFile(obj, p.outfile); else if (p.out_ext == OEXT_RXN) From ee18d00ea5cf5dbfe88e69898718ddf85f58f8b6 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 27 Sep 2023 11:48:40 +0200 Subject: [PATCH 14/36] test fix --- utils/indigo-depict/main.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index 3b3bc47ded..c97759bcf9 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -917,7 +917,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - //indigoLayout(obj); + indigoLayout(obj); if (p.out_ext == OEXT_MOL) indigoSaveMolfileToFile(obj, p.outfile); else if (p.out_ext == OEXT_KET) @@ -1016,7 +1016,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - //indigoLayout(obj); + indigoLayout(obj); if (p.out_ext == OEXT_CML) indigoSaveCmlToFile(obj, p.outfile); else if (p.out_ext == OEXT_RXN) From 64f4ac905f25157152221565667c7159e04fdf70 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Fri, 29 Sep 2023 12:59:33 +0200 Subject: [PATCH 15/36] point 1 --- api/c/indigo/src/indigo_layout.cpp | 2 +- .../tests/formats/ref/acd2d_err.ket | 12 +- core/indigo-core/molecule/base_molecule.h | 2 +- .../molecule/molecule_stereocenters.h | 5 +- .../molecule/src/base_molecule.cpp | 4 +- .../src/molecule_automorphism_search.cpp | 2 +- .../molecule/src/molecule_stereocenters.cpp | 701 +++++++++--------- .../molecule/src/molfile_saver.cpp | 2 +- .../molecule/src/smiles_loader.cpp | 2 + .../indigo-core/molecule/src/smiles_saver.cpp | 6 +- 10 files changed, 393 insertions(+), 345 deletions(-) diff --git a/api/c/indigo/src/indigo_layout.cpp b/api/c/indigo/src/indigo_layout.cpp index 4514dbd4da..d1d3ad72cd 100644 --- a/api/c/indigo/src/indigo_layout.cpp +++ b/api/c/indigo/src/indigo_layout.cpp @@ -58,7 +58,7 @@ CEXPORT int indigoLayout(int object) ml.max_iterations = self.layout_max_iterations; ml.bond_length = 1.6f; ml.layout_orientation = (layout_orientation_value)self.layout_orientation; - if (mol->hasAtropisomericCenter()) + if (mol->hasAtropoStereoBonds()) ml.respect_existing_layout = true; TimeoutCancellationHandler cancellation(self.cancellation_timeout); diff --git a/api/tests/integration/tests/formats/ref/acd2d_err.ket b/api/tests/integration/tests/formats/ref/acd2d_err.ket index 8a132ba64f..03ddf7791d 100644 --- a/api/tests/integration/tests/formats/ref/acd2d_err.ket +++ b/api/tests/integration/tests/formats/ref/acd2d_err.ket @@ -14781,7 +14781,8 @@ 7.0, 2.6600000858306886, 0.0 - ] + ], + "stereoLabel": "abs" }, { "label": "N", @@ -14789,7 +14790,8 @@ 7.130000114440918, 1.090000033378601, 0.0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", @@ -14821,7 +14823,8 @@ 6.019999980926514, 0.0, 0.0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", @@ -117803,7 +117806,8 @@ 0.7069000005722046, 1.2137999534606934, 0.0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", diff --git a/core/indigo-core/molecule/base_molecule.h b/core/indigo-core/molecule/base_molecule.h index 73f6c348a9..51f33c6266 100644 --- a/core/indigo-core/molecule/base_molecule.h +++ b/core/indigo-core/molecule/base_molecule.h @@ -418,7 +418,7 @@ namespace indigo const int* getPyramidStereocenters(int idx) const; void markBondsStereocenters(); void markBondStereocenters(int atom_idx); - bool hasAtropisomericCenter(); + bool hasAtropoStereoBonds(); void addStereocenters(int atom_idx, int type, int group, const int pyramid[4]); void addStereocenters(int atom_idx, int type, int group, bool inverse_pyramid); diff --git a/core/indigo-core/molecule/molecule_stereocenters.h b/core/indigo-core/molecule/molecule_stereocenters.h index aa7b20f7e7..62879c8d04 100644 --- a/core/indigo-core/molecule/molecule_stereocenters.h +++ b/core/indigo-core/molecule/molecule_stereocenters.h @@ -117,8 +117,9 @@ namespace indigo bool isPossibleStereocenter(BaseMolecule& baseMolecule, int atom_idx, bool* possible_implicit_h = 0, bool* possible_lone_pair = 0); bool isPossibleAtropocenter(BaseMolecule& baseMolecule, int atom_idx, int& possible_atropo_bond); + bool hasAtropoStereoBonds(BaseMolecule& baseMolecule, int atom_idx); bool findAtropoStereobonds(BaseMolecule& baseMolecule, RedBlackMap& directions_map, int atom_idx, std::unordered_set& visited_bonds, - bool first_only = false); + bool first_only = false, int* sensible_bonds_out = nullptr); bool hasRing(BaseMolecule& baseMolecule, int atom_idx, std::unordered_set& visited_bonds); public: @@ -149,7 +150,7 @@ namespace indigo // (X, Y, Z) go counterclockwise when looking from W. // if there are pure (implicit) hydrogen, it is W bool is_atropisomeric = false; - bool is_tetrahydral = false; + bool is_tetrahydral = true; int pyramid[4]; }; diff --git a/core/indigo-core/molecule/src/base_molecule.cpp b/core/indigo-core/molecule/src/base_molecule.cpp index ff8a5c83ac..805391d563 100644 --- a/core/indigo-core/molecule/src/base_molecule.cpp +++ b/core/indigo-core/molecule/src/base_molecule.cpp @@ -4196,12 +4196,12 @@ void BaseMolecule::markBondsStereocenters() stereocenters.markBonds(*this); } -bool BaseMolecule::hasAtropisomericCenter() +bool BaseMolecule::hasAtropoStereoBonds() { for (int i = stereocenters.begin(); i != stereocenters.end(); i = stereocenters.next(i)) { auto atom_idx = stereocenters.getAtomIndex(i); - if (stereocenters.isAtropisomeric(atom_idx)) + if (stereocenters.hasAtropoStereoBonds(*this, atom_idx)) return true; } return false; diff --git a/core/indigo-core/molecule/src/molecule_automorphism_search.cpp b/core/indigo-core/molecule/src/molecule_automorphism_search.cpp index b52db0f4c1..247ae82766 100644 --- a/core/indigo-core/molecule/src/molecule_automorphism_search.cpp +++ b/core/indigo-core/molecule/src/molecule_automorphism_search.cpp @@ -733,7 +733,7 @@ int MoleculeAutomorphismSearch::_validStereocenterByAtom(int atom_index, Array visited_bonds; + findAtropoStereobonds(baseMolecule, ac.bond_directions, atom_idx, visited_bonds, false, sensible_bonds_out); + auto bdir = baseMolecule.getBondDirection(ac.atropo_bond); + // include possible atropobond itself if its direction is not sensible, but direction is set + if (bdir && !sensible_bonds_out[ac.atropo_bond]) + { + ac.bond_directions.insert(ac.atropo_bond, bdir); + sensible_bonds_out[ac.atropo_bond] = 1; + } + } + } } void MoleculeStereocenters::buildFrom3dCoordinates(BaseMolecule& baseMolecule, const StereocentersOptions& options) @@ -197,6 +216,11 @@ void MoleculeStereocenters::_buildOneFrom3dCoordinates(BaseMolecule& baseMolecul add(baseMolecule, idx, ATOM_ABS, 0, false); } +bool MoleculeStereocenters::hasAtropoStereoBonds(BaseMolecule& baseMolecule, int atom_idx) +{ + return _atropocenters.find(atom_idx) && _atropocenters.at(atom_idx).bond_directions.size(); +} + bool MoleculeStereocenters::isPossibleAtropocenter(BaseMolecule& baseMolecule, int atom_idx, int& possible_atropo_bond) { if (baseMolecule.vertexInRing(atom_idx)) // check if the atom belongs to ring @@ -238,7 +262,7 @@ bool MoleculeStereocenters::isPossibleAtropocenter(BaseMolecule& baseMolecule, i // recursive search of for stereobonds withing connected rings bool MoleculeStereocenters::findAtropoStereobonds(BaseMolecule& baseMolecule, RedBlackMap& directions_map, int atom_idx, - std::unordered_set& visited_bonds, bool first_only) + std::unordered_set& visited_bonds, bool first_only, int* sensible_bonds_out) { const Vertex& v = baseMolecule.getVertex(atom_idx); for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) @@ -252,6 +276,13 @@ bool MoleculeStereocenters::findAtropoStereobonds(BaseMolecule& baseMolecule, Re { if (bdir && !directions_map.find(bond_idx)) { + if (sensible_bonds_out) + { + if (sensible_bonds_out[bond_idx]) + continue; + else + sensible_bonds_out[bond_idx] = 1; + } directions_map.insert(bond_idx, bdir); if (first_only) return true; @@ -351,12 +382,30 @@ bool MoleculeStereocenters::isPossibleStereocenter(BaseMolecule& baseMolecule, i bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom_idx, int* sensible_bonds_out, bool bidirectional_mode, bool bidirectional_either_mode, const Array& bond_ignore, bool check_atropocenter) { - const Vertex& vertex = baseMolecule.getVertex(atom_idx); - - int degree = vertex.degree(); - + int possible_atropobond = -1; _Atom stereocenter; + if (check_atropocenter) + stereocenter.is_atropisomeric = isPossibleAtropocenter(baseMolecule, atom_idx, possible_atropobond); + + // add atropocenter if required + if (possible_atropobond > -1) + { + _AtropoCenter& ac = _atropocenters.findOrInsert(atom_idx); + ac.atropo_bond = possible_atropobond; + if (_stereocenters.find(atom_idx)) + _stereocenters.at(atom_idx).is_atropisomeric = true; + else + { + stereocenter.is_tetrahydral = false; + _stereocenters.insert(atom_idx, stereocenter); + } + } + // check if there is a tetrahydral stereocenter already + if (_stereocenters.find(atom_idx) && _stereocenters.at(atom_idx).is_tetrahydral) + return true; + const Vertex& vertex = baseMolecule.getVertex(atom_idx); + int degree = vertex.degree(); stereocenter.group = 1; stereocenter.type = ATOM_ABS; @@ -403,9 +452,7 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom if (!edge_ids[nei_idx].vec.normalize()) zero_bond_length = true; - if (baseMolecule.getBondOrder(e_idx) == BOND_TRIPLE) - return false; - if (baseMolecule.getBondOrder(e_idx) == BOND_AROMATIC) + if (baseMolecule.getBondOrder(e_idx) == BOND_TRIPLE || baseMolecule.getBondOrder(e_idx) == BOND_AROMATIC) return false; if (baseMolecule.getBondOrder(e_idx) == BOND_DOUBLE) @@ -421,13 +468,8 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom bool possible_implicit_h = false; bool possible_lone_pair = false; - int possible_atropobond = -1; - - int i; stereocenter.is_tetrahydral = isPossibleStereocenter(baseMolecule, atom_idx, &possible_implicit_h, &possible_lone_pair); - if (check_atropocenter && !stereocenter.is_tetrahydral) - stereocenter.is_atropisomeric = isPossibleAtropocenter(baseMolecule, atom_idx, possible_atropobond); if (!stereocenter.is_tetrahydral && !stereocenter.is_atropisomeric) return false; @@ -443,264 +485,261 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom if (is_either) { stereocenter.type = ATOM_ANY; - for (i = 0; i < degree; i++) + for (int i = 0; i < degree; i++) { stereocenter.pyramid[i] = edge_ids[i].nei_idx; if (getDir(atom_idx, edge_ids[i].nei_idx) > 0) sensible_bonds_out[edge_ids[i].edge_idx] = 1; } - _stereocenters.insert(atom_idx, stereocenter); - return true; - } - - if (possible_atropobond > -1) - { - if (!_stereocenters.find(atom_idx)) - _stereocenters.insert(atom_idx, stereocenter); - else - _stereocenters.at(atom_idx).is_atropisomeric = true; - _AtropoCenter& ac = _atropocenters.findOrInsert(atom_idx); - ac.atropo_bond = possible_atropobond; - std::unordered_set visited_bonds; - findAtropoStereobonds(baseMolecule, ac.bond_directions, atom_idx, visited_bonds); - auto bdir = baseMolecule.getBondDirection(possible_atropobond); - if (bdir) - ac.bond_directions.insert(possible_atropobond, bdir); - for (auto i = ac.bond_directions.begin(); i != ac.bond_directions.end(); i = ac.bond_directions.next(i)) - sensible_bonds_out[ac.bond_directions.key(i)] = 1; } - else if (!_stereocenters.find(atom_idx)) + else { - if (degree == 4) + if (stereocenter.is_tetrahydral) { - // sort by neighbor atom index (ascending) - if (edge_ids[0].rank > edge_ids[1].rank) - std::swap(edge_ids[0], edge_ids[1]); - if (edge_ids[1].rank > edge_ids[2].rank) - std::swap(edge_ids[1], edge_ids[2]); - if (edge_ids[2].rank > edge_ids[3].rank) - std::swap(edge_ids[2], edge_ids[3]); - if (edge_ids[1].rank > edge_ids[2].rank) - std::swap(edge_ids[1], edge_ids[2]); - if (edge_ids[0].rank > edge_ids[1].rank) - std::swap(edge_ids[0], edge_ids[1]); - if (edge_ids[1].rank > edge_ids[2].rank) - std::swap(edge_ids[1], edge_ids[2]); - - int main1 = -1, main2 = -1, side1 = -1, side2 = -1; - int main_dir = 0; - - for (nei_idx = 0; nei_idx < 4; nei_idx++) + if (degree == 4) { - int stereo = getDir(atom_idx, edge_ids[nei_idx].nei_idx); - - if (stereo == BOND_UP || stereo == BOND_DOWN) + // sort by neighbor atom index (ascending) + if (edge_ids[0].rank > edge_ids[1].rank) + std::swap(edge_ids[0], edge_ids[1]); + if (edge_ids[1].rank > edge_ids[2].rank) + std::swap(edge_ids[1], edge_ids[2]); + if (edge_ids[2].rank > edge_ids[3].rank) + std::swap(edge_ids[2], edge_ids[3]); + if (edge_ids[1].rank > edge_ids[2].rank) + std::swap(edge_ids[1], edge_ids[2]); + if (edge_ids[0].rank > edge_ids[1].rank) + std::swap(edge_ids[0], edge_ids[1]); + if (edge_ids[1].rank > edge_ids[2].rank) + std::swap(edge_ids[1], edge_ids[2]); + + int main1 = -1, main2 = -1, side1 = -1, side2 = -1; + int main_dir = 0; + + for (nei_idx = 0; nei_idx < 4; nei_idx++) { - main1 = nei_idx; - main_dir = stereo; - break; - } - } - - if (main1 == -1) - return false; - - if (zero_bond_length) - throw Error("zero bond length near atom %d", atom_idx); + int stereo = getDir(atom_idx, edge_ids[nei_idx].nei_idx); - if (n_pure_hydrogens > 1) - throw Error("%d hydrogens near stereocenter %d", n_pure_hydrogens, atom_idx); - - int xyz1, xyz2; - - // find main2 as opposite to main1 - if (main2 == -1) - { - xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 1) % 4].vec, edge_ids[(main1 + 2) % 4].vec); - xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 1) % 4].vec, edge_ids[(main1 + 3) % 4].vec); - - if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) - { - main2 = (main1 + 1) % 4; - side1 = (main1 + 2) % 4; - side2 = (main1 + 3) % 4; + if (stereo == BOND_UP || stereo == BOND_DOWN) + { + main1 = nei_idx; + main_dir = stereo; + break; + } } - } - if (main2 == -1) - { - xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 2) % 4].vec, edge_ids[(main1 + 1) % 4].vec); - xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 2) % 4].vec, edge_ids[(main1 + 3) % 4].vec); - if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) + if (main1 != -1) { - main2 = (main1 + 2) % 4; - side1 = (main1 + 1) % 4; - side2 = (main1 + 3) % 4; - } - } - if (main2 == -1) - { - xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 3) % 4].vec, edge_ids[(main1 + 1) % 4].vec); - xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 3) % 4].vec, edge_ids[(main1 + 2) % 4].vec); + if (zero_bond_length) + throw Error("zero bond length near atom %d", atom_idx); - if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) - { - main2 = (main1 + 3) % 4; - side1 = (main1 + 2) % 4; - side2 = (main1 + 1) % 4; - } - } + if (n_pure_hydrogens > 1) + throw Error("%d hydrogens near stereocenter %d", n_pure_hydrogens, atom_idx); - if (main2 == -1) - throw Error("internal error: can not find opposite bond near atom %d", atom_idx); + int xyz1, xyz2; - if (main_dir == BOND_UP && getDir(atom_idx, edge_ids[main2].nei_idx) == BOND_DOWN) - throw Error("stereo types of the opposite bonds mismatch near atom %d", atom_idx); - if (main_dir == BOND_DOWN && getDir(atom_idx, edge_ids[main2].nei_idx) == BOND_UP) - throw Error("stereo types of the opposite bonds mismatch near atom %d", atom_idx); + // find main2 as opposite to main1 + if (main2 == -1) + { + xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 1) % 4].vec, edge_ids[(main1 + 2) % 4].vec); + xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 1) % 4].vec, edge_ids[(main1 + 3) % 4].vec); - if (main_dir == getDir(atom_idx, edge_ids[side1].nei_idx)) - throw Error("stereo types of non-opposite bonds match near atom %d", atom_idx); - if (main_dir == getDir(atom_idx, edge_ids[side2].nei_idx)) - throw Error("stereo types of non-opposite bonds match near atom %d", atom_idx); + if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) + { + main2 = (main1 + 1) % 4; + side1 = (main1 + 2) % 4; + side2 = (main1 + 3) % 4; + } + } + if (main2 == -1) + { + xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 2) % 4].vec, edge_ids[(main1 + 1) % 4].vec); + xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 2) % 4].vec, edge_ids[(main1 + 3) % 4].vec); - if (main1 == 3 || main2 == 3) - last_atom_dir = main_dir; - else - last_atom_dir = (main_dir == BOND_UP ? BOND_DOWN : BOND_UP); + if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) + { + main2 = (main1 + 2) % 4; + side1 = (main1 + 1) % 4; + side2 = (main1 + 3) % 4; + } + } + if (main2 == -1) + { + xyz1 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 3) % 4].vec, edge_ids[(main1 + 1) % 4].vec); + xyz2 = _xyzzy(edge_ids[main1].vec, edge_ids[(main1 + 3) % 4].vec, edge_ids[(main1 + 2) % 4].vec); - int sign = _sign(edge_ids[0].vec, edge_ids[1].vec, edge_ids[2].vec); + if (xyz1 + xyz2 == 3 || xyz1 + xyz2 == 12) + { + main2 = (main1 + 3) % 4; + side1 = (main1 + 2) % 4; + side2 = (main1 + 1) % 4; + } + } - if ((last_atom_dir == BOND_UP && sign > 0) || (last_atom_dir == BOND_DOWN && sign < 0)) - { - pyramid[0] = edge_ids[0].nei_idx; - pyramid[1] = edge_ids[1].nei_idx; - pyramid[2] = edge_ids[2].nei_idx; - } - else - { - pyramid[0] = edge_ids[0].nei_idx; - pyramid[1] = edge_ids[2].nei_idx; - pyramid[2] = edge_ids[1].nei_idx; - } + if (main2 == -1) + throw Error("internal error: can not find opposite bond near atom %d", atom_idx); - pyramid[3] = edge_ids[3].nei_idx; - } - else if (degree == 3) - { - // sort by neighbor atom index (ascending) - if (edge_ids[0].rank > edge_ids[1].rank) - std::swap(edge_ids[0], edge_ids[1]); - if (edge_ids[1].rank > edge_ids[2].rank) - std::swap(edge_ids[1], edge_ids[2]); - if (edge_ids[0].rank > edge_ids[1].rank) - std::swap(edge_ids[0], edge_ids[1]); - - bool degenerate = true; - int dirs[3] = {0, 0, 0}; - int main_nei = -1; // will be assigned if all three neighors belong to the same half-plane - int n_up = 0, n_down = 0; - - for (nei_idx = 0; nei_idx < 3; nei_idx++) - { - dirs[nei_idx] = getDir(atom_idx, edge_ids[nei_idx].nei_idx); - if (dirs[nei_idx] == BOND_UP) - n_up++; - else if (dirs[nei_idx] == BOND_DOWN) - n_down++; - } + if (main_dir == BOND_UP && getDir(atom_idx, edge_ids[main2].nei_idx) == BOND_DOWN) + throw Error("stereo types of the opposite bonds mismatch near atom %d", atom_idx); + if (main_dir == BOND_DOWN && getDir(atom_idx, edge_ids[main2].nei_idx) == BOND_UP) + throw Error("stereo types of the opposite bonds mismatch near atom %d", atom_idx); - if (n_down == 0 && n_up == 0) - return false; + if (main_dir == getDir(atom_idx, edge_ids[side1].nei_idx)) + throw Error("stereo types of non-opposite bonds match near atom %d", atom_idx); + if (main_dir == getDir(atom_idx, edge_ids[side2].nei_idx)) + throw Error("stereo types of non-opposite bonds match near atom %d", atom_idx); - for (nei_idx = 0; nei_idx < 3; nei_idx++) - { - int xyzzy = _xyzzy(edge_ids[(nei_idx + 1) % 3].vec, edge_ids[(nei_idx + 2) % 3].vec, edge_ids[nei_idx].vec); + if (main1 == 3 || main2 == 3) + last_atom_dir = main_dir; + else + last_atom_dir = (main_dir == BOND_UP ? BOND_DOWN : BOND_UP); - if (xyzzy == 1) - main_nei = nei_idx; - if (xyzzy == 2) - degenerate = false; - } + int sign = _sign(edge_ids[0].vec, edge_ids[1].vec, edge_ids[2].vec); - int dir = 1; + if ((last_atom_dir == BOND_UP && sign > 0) || (last_atom_dir == BOND_DOWN && sign < 0)) + { + pyramid[0] = edge_ids[0].nei_idx; + pyramid[1] = edge_ids[1].nei_idx; + pyramid[2] = edge_ids[2].nei_idx; + } + else + { + pyramid[0] = edge_ids[0].nei_idx; + pyramid[1] = edge_ids[2].nei_idx; + pyramid[2] = edge_ids[1].nei_idx; + } - if (main_nei != -1) + pyramid[3] = edge_ids[3].nei_idx; + } + else + stereocenter.is_tetrahydral = false; + } + else if (degree == 3) { - if (dirs[main_nei] != 0) + // sort by neighbor atom index (ascending) + if (edge_ids[0].rank > edge_ids[1].rank) + std::swap(edge_ids[0], edge_ids[1]); + if (edge_ids[1].rank > edge_ids[2].rank) + std::swap(edge_ids[1], edge_ids[2]); + if (edge_ids[0].rank > edge_ids[1].rank) + std::swap(edge_ids[0], edge_ids[1]); + + bool degenerate = true; + int dirs[3] = {0, 0, 0}; + int main_nei = -1; // will be assigned if all three neighors belong to the same half-plane + int n_up = 0, n_down = 0; + + for (nei_idx = 0; nei_idx < 3; nei_idx++) { - if (dirs[(main_nei + 1) % 3] == dirs[main_nei] || dirs[(main_nei + 2) % 3] == dirs[main_nei]) - throw Error("directions of neighbor stereo bonds match near atom %d", atom_idx); - if (dirs[main_nei] == BOND_UP) - dir = -1; + dirs[nei_idx] = getDir(atom_idx, edge_ids[nei_idx].nei_idx); + if (dirs[nei_idx] == BOND_UP) + n_up++; + else if (dirs[nei_idx] == BOND_DOWN) + n_down++; } - else + + if (n_down || n_up) { - int d1 = dirs[(main_nei + 1) % 3]; - int d2 = dirs[(main_nei + 2) % 3]; + for (nei_idx = 0; nei_idx < 3; nei_idx++) + { + int xyzzy = _xyzzy(edge_ids[(nei_idx + 1) % 3].vec, edge_ids[(nei_idx + 2) % 3].vec, edge_ids[nei_idx].vec); - if (d1 == 0) - d1 = d2; - else if (d2 != 0 && d1 != d2) - throw Error("directions of opposite stereo bonds do not match near atom %d", atom_idx); + if (xyzzy == 1) + main_nei = nei_idx; + if (xyzzy == 2) + degenerate = false; + } - if (d1 == 0) - return false; + int dir = 1; - if (d1 == BOND_DOWN) - dir = -1; - } - } - else if (!degenerate) - { - if (n_down > 0 && n_up > 0) - throw Error("one bond up, one bond down -- indefinite case near atom %d", atom_idx); + if (main_nei != -1) + { + if (dirs[main_nei] != 0) + { + if (dirs[(main_nei + 1) % 3] == dirs[main_nei] || dirs[(main_nei + 2) % 3] == dirs[main_nei]) + throw Error("directions of neighbor stereo bonds match near atom %d", atom_idx); + if (dirs[main_nei] == BOND_UP) + dir = -1; + } + else + { + int d1 = dirs[(main_nei + 1) % 3]; + int d2 = dirs[(main_nei + 2) % 3]; - if (!possible_lone_pair) - { - if (n_up == 3) - throw Error("all 3 bonds up near stereoatom %d", atom_idx); - if (n_down == 3) - throw Error("all 3 bonds down near stereoatom %d", atom_idx); - } - if (n_down > 0) - dir = -1; - } - else - throw Error("degenerate case for 3 bonds near stereoatom %d", atom_idx); + if (d1 == 0) + d1 = d2; + else if (d2 != 0 && d1 != d2) + throw Error("directions of opposite stereo bonds do not match near atom %d", atom_idx); - if (zero_bond_length) - throw Error("zero bond length near atom %d", atom_idx); + if (d1 == 0) + return false; - if (n_pure_hydrogens > 0 && !possible_lone_pair) - throw Error("have hydrogen(s) besides implicit hydrogen near stereocenter %d", atom_idx); + if (d1 == BOND_DOWN) + dir = -1; + } + } + else if (!degenerate) + { + if (n_down > 0 && n_up > 0) + throw Error("one bond up, one bond down -- indefinite case near atom %d", atom_idx); - int sign = _sign(edge_ids[0].vec, edge_ids[1].vec, edge_ids[2].vec); + if (!possible_lone_pair) + { + if (n_up == 3) + throw Error("all 3 bonds up near stereoatom %d", atom_idx); + if (n_down == 3) + throw Error("all 3 bonds down near stereoatom %d", atom_idx); + } + if (n_down > 0) + dir = -1; + } + else + throw Error("degenerate case for 3 bonds near stereoatom %d", atom_idx); - if (sign == dir) - { - pyramid[0] = edge_ids[0].nei_idx; - pyramid[1] = edge_ids[2].nei_idx; - pyramid[2] = edge_ids[1].nei_idx; - } - else - { - pyramid[0] = edge_ids[0].nei_idx; - pyramid[1] = edge_ids[1].nei_idx; - pyramid[2] = edge_ids[2].nei_idx; + if (zero_bond_length) + throw Error("zero bond length near atom %d", atom_idx); + + if (n_pure_hydrogens > 0 && !possible_lone_pair) + throw Error("have hydrogen(s) besides implicit hydrogen near stereocenter %d", atom_idx); + + int sign = _sign(edge_ids[0].vec, edge_ids[1].vec, edge_ids[2].vec); + + if (sign == dir) + { + pyramid[0] = edge_ids[0].nei_idx; + pyramid[1] = edge_ids[2].nei_idx; + pyramid[2] = edge_ids[1].nei_idx; + } + else + { + pyramid[0] = edge_ids[0].nei_idx; + pyramid[1] = edge_ids[1].nei_idx; + pyramid[2] = edge_ids[2].nei_idx; + } + pyramid[3] = -1; + } + else + stereocenter.is_tetrahydral = false; } - pyramid[3] = -1; + + if (stereocenter.is_tetrahydral) + for (int i = 0; i < degree; i++) + if (getDir(atom_idx, edge_ids[i].nei_idx) > 0) + sensible_bonds_out[edge_ids[i].edge_idx] = 1; } - for (i = 0; i < degree; i++) - if (getDir(atom_idx, edge_ids[i].nei_idx) > 0) - sensible_bonds_out[edge_ids[i].edge_idx] = 1; - _stereocenters.insert(atom_idx, stereocenter); } - return true; + if (stereocenter.is_tetrahydral) + { + if (_stereocenters.find(atom_idx)) + _stereocenters.at(atom_idx).is_tetrahydral = true; + else + _stereocenters.insert(atom_idx, stereocenter); + return true; + } + return false; } // 1 -- in the smaller angle, 2 -- in the bigger angle, -// 4 -- in the 'positive' straight angle, 8 -- in the 'negative' straight angle +// 4 -- in t5he 'positive' straight angle, 8 -- in the 'negative' straight angle int MoleculeStereocenters::_xyzzy(const Vec3f& v1, const Vec3f& v2, const Vec3f& u) { const float eps = 1e-3f; @@ -1350,7 +1389,7 @@ void MoleculeStereocenters::buildOnSubmolecule(BaseMolecule& baseMolecule, const new_stereocenter.is_atropisomeric = super_stereocenter.is_atropisomeric; new_stereocenter.is_tetrahydral = super_stereocenter.is_tetrahydral; - if (!new_stereocenter.is_atropisomeric) + if (new_stereocenter.is_tetrahydral) { for (j = 0; j < 4; j++) { @@ -1670,146 +1709,148 @@ void MoleculeStereocenters::markBond(BaseMolecule& baseMolecule, int atom_idx) const _Atom& atom = *atom_ptr; - if (atom.is_atropisomeric) + if (atom.is_tetrahydral) { - const auto& ac = _atropocenters.at(atom_idx); - for (int i = ac.bond_directions.begin(); i != ac.bond_directions.end(); i = ac.bond_directions.next(i)) - { - int bond_idx = ac.bond_directions.key(i); - int bdir = ac.bond_directions.value(i); - baseMolecule.setBondDirection(bond_idx, bdir); - } - return; - } - - int pyramid[4]; - int mult = 1; - int size = 0; - int j; - - memcpy(pyramid, atom.pyramid, 4 * sizeof(int)); + int pyramid[4]; + int mult = 1; + int size = 0; + int j; - const Vertex& vertex = baseMolecule.getVertex(atom_idx); - if (atom.type <= ATOM_ANY) - { - // fill the pyramid - for (j = vertex.neiBegin(); j != vertex.neiEnd() && size < 4; j = vertex.neiNext(j)) - pyramid[size++] = vertex.neiVertex(j); - } - else - size = (pyramid[3] == -1 ? 3 : 4); + memcpy(pyramid, atom.pyramid, 4 * sizeof(int)); - // clear bond directions that goes to this atom, and not from this atom because they can - // be marked by other sterecenter - for (j = vertex.neiBegin(); j != vertex.neiEnd(); j = vertex.neiNext(j)) - if (baseMolecule.getBondDirection2(atom_idx, vertex.neiVertex(j)) != 0) - baseMolecule.setBondDirection(vertex.neiEdge(j), 0); + const Vertex& vertex = baseMolecule.getVertex(atom_idx); + if (atom.type <= ATOM_ANY) + { + // fill the pyramid + for (j = vertex.neiBegin(); j != vertex.neiEnd() && size < 4; j = vertex.neiNext(j)) + pyramid[size++] = vertex.neiVertex(j); + } + else + size = (pyramid[3] == -1 ? 3 : 4); - int edge_idx = -1; + // clear bond directions that goes to this atom, and not from this atom because they can + // be marked by other sterecenter + for (j = vertex.neiBegin(); j != vertex.neiEnd(); j = vertex.neiNext(j)) + if (baseMolecule.getBondDirection2(atom_idx, vertex.neiVertex(j)) != 0) + baseMolecule.setBondDirection(vertex.neiEdge(j), 0); - for (j = 0; j < size; j++) - { - edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]); - if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getVertex(pyramid[size - 1]).degree() == 1) - break; - rotatePyramid(pyramid); - if (size == 4) - mult = -mult; - } + int edge_idx = -1; - if (j == size) - { for (j = 0; j < size; j++) { edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]); - if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getBondTopology(edge_idx) == TOPOLOGY_CHAIN && getType(pyramid[size - 1]) == 0) + if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getVertex(pyramid[size - 1]).degree() == 1) break; rotatePyramid(pyramid); if (size == 4) mult = -mult; } - } - if (j == size) - { - for (j = 0; j < size; j++) + if (j == size) { - edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]); - if (baseMolecule.getBondDirection(edge_idx) == 0 && getType(pyramid[size - 1]) == 0) - break; - rotatePyramid(pyramid); - if (size == 4) - mult = -mult; + for (j = 0; j < size; j++) + { + edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]); + if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getBondTopology(edge_idx) == TOPOLOGY_CHAIN && getType(pyramid[size - 1]) == 0) + break; + rotatePyramid(pyramid); + if (size == 4) + mult = -mult; + } } - } - if (j == size) - { - for (j = 0; j < size; j++) + if (j == size) { - edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]); - if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getBondTopology(edge_idx) == TOPOLOGY_CHAIN) - break; - rotatePyramid(pyramid); - if (size == 4) - mult = -mult; + for (j = 0; j < size; j++) + { + edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]); + if (baseMolecule.getBondDirection(edge_idx) == 0 && getType(pyramid[size - 1]) == 0) + break; + rotatePyramid(pyramid); + if (size == 4) + mult = -mult; + } } - } - if (j == size) - { - for (j = 0; j < size; j++) + if (j == size) { - edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]); - if (baseMolecule.getBondDirection(edge_idx) == 0) - break; - rotatePyramid(pyramid); - if (size == 4) - mult = -mult; + for (j = 0; j < size; j++) + { + edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]); + if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getBondTopology(edge_idx) == TOPOLOGY_CHAIN) + break; + rotatePyramid(pyramid); + if (size == 4) + mult = -mult; + } } - } - - if (j == size) - throw Error("no bond can be marked"); - if (baseMolecule.getEdge(edge_idx).beg != atom_idx) - baseMolecule.swapEdgeEnds(edge_idx); - - if (BaseMolecule::hasCoord(baseMolecule)) - { - if (atom.type > ATOM_ANY) + if (j == size) { - std::array dirs; - dirs.fill({0.0, 0.0, 0.0}); for (j = 0; j < size; j++) { - dirs[j] = baseMolecule.getAtomXyz(pyramid[j]); - dirs[j].sub(baseMolecule.getAtomXyz(atom_idx)); - if (!dirs[j].normalize()) - throw Error("zero bond length"); + edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]); + if (baseMolecule.getBondDirection(edge_idx) == 0) + break; + rotatePyramid(pyramid); + if (size == 4) + mult = -mult; } + } - int sign = _sign(dirs[0], dirs[1], dirs[2]); + if (j == size) + throw Error("no bond can be marked"); - if (size == 3) + if (baseMolecule.getEdge(edge_idx).beg != atom_idx) + baseMolecule.swapEdgeEnds(edge_idx); + + if (BaseMolecule::hasCoord(baseMolecule)) + { + if (atom.type > ATOM_ANY) { - // Check if all the three bonds belong to the same half-plane. - // This is equal to that one of the bonds lies in the smaller - // angle formed by the other two. - if (_xyzzy(dirs[1], dirs[0], dirs[2]) == 1 || _xyzzy(dirs[2], dirs[1], dirs[0]) == 1 || _xyzzy(dirs[0], dirs[2], dirs[1]) == 1) + std::array dirs; + dirs.fill({0.0, 0.0, 0.0}); + for (j = 0; j < size; j++) + { + dirs[j] = baseMolecule.getAtomXyz(pyramid[j]); + dirs[j].sub(baseMolecule.getAtomXyz(atom_idx)); + if (!dirs[j].normalize()) + throw Error("zero bond length"); + } + + int sign = _sign(dirs[0], dirs[1], dirs[2]); + + if (size == 3) { - if (_xyzzy(dirs[1], dirs[0], dirs[2]) == 1) - mult = -1; - baseMolecule.setBondDirection(edge_idx, (sign * mult == 1) ? BOND_DOWN : BOND_UP); + // Check if all the three bonds belong to the same half-plane. + // This is equal to that one of the bonds lies in the smaller + // angle formed by the other two. + if (_xyzzy(dirs[1], dirs[0], dirs[2]) == 1 || _xyzzy(dirs[2], dirs[1], dirs[0]) == 1 || _xyzzy(dirs[0], dirs[2], dirs[1]) == 1) + { + if (_xyzzy(dirs[1], dirs[0], dirs[2]) == 1) + mult = -1; + baseMolecule.setBondDirection(edge_idx, (sign * mult == 1) ? BOND_DOWN : BOND_UP); + } + else + baseMolecule.setBondDirection(edge_idx, (sign == 1) ? BOND_DOWN : BOND_UP); } else - baseMolecule.setBondDirection(edge_idx, (sign == 1) ? BOND_DOWN : BOND_UP); + baseMolecule.setBondDirection(edge_idx, (sign * mult == 1) ? BOND_UP : BOND_DOWN); } else - baseMolecule.setBondDirection(edge_idx, (sign * mult == 1) ? BOND_UP : BOND_DOWN); + baseMolecule.setBondDirection(edge_idx, BOND_EITHER); + } + } + + if (atom.is_atropisomeric) + { + const auto& ac = _atropocenters.at(atom_idx); + for (int i = ac.bond_directions.begin(); i != ac.bond_directions.end(); i = ac.bond_directions.next(i)) + { + int bond_idx = ac.bond_directions.key(i); + int bdir = ac.bond_directions.value(i); + baseMolecule.setBondDirection(bond_idx, bdir); } - else - baseMolecule.setBondDirection(edge_idx, BOND_EITHER); } } diff --git a/core/indigo-core/molecule/src/molfile_saver.cpp b/core/indigo-core/molecule/src/molfile_saver.cpp index fe2938d87a..36e632edf5 100644 --- a/core/indigo-core/molecule/src/molfile_saver.cpp +++ b/core/indigo-core/molecule/src/molfile_saver.cpp @@ -1910,7 +1910,7 @@ void MolfileSaver::_checkSGroupIndices(BaseMolecule& mol, Array& sgs_list) int MolfileSaver::_getStereocenterParity(BaseMolecule& mol, int idx) { int type = mol.stereocenters.getType(idx); - if (type == 0 /* || mol.stereocenters.isAtropisomeric(idx)*/) + if (type == 0 || !mol.stereocenters.isTetrahydral(idx)) return 0; if (type == MoleculeStereocenters::ATOM_ANY) return 3; diff --git a/core/indigo-core/molecule/src/smiles_loader.cpp b/core/indigo-core/molecule/src/smiles_loader.cpp index aff0c189b9..eb0b7d56aa 100644 --- a/core/indigo-core/molecule/src/smiles_loader.cpp +++ b/core/indigo-core/molecule/src/smiles_loader.cpp @@ -412,7 +412,9 @@ void SmilesLoader::_readOtherStuff() if (_bmol->stereocenters.exists(idx)) _bmol->stereocenters.setType(idx, MoleculeStereocenters::ATOM_OR, groupno); else + { _bmol->addStereocenters(idx, MoleculeStereocenters::ATOM_OR, groupno, false); + } if (_scanner.lookNext() == ',') _scanner.skip(1); diff --git a/core/indigo-core/molecule/src/smiles_saver.cpp b/core/indigo-core/molecule/src/smiles_saver.cpp index 4b548d09e3..52970fda21 100644 --- a/core/indigo-core/molecule/src/smiles_saver.cpp +++ b/core/indigo-core/molecule/src/smiles_saver.cpp @@ -263,7 +263,7 @@ void SmilesSaver::_saveMolecule() stereocenters.get(i, atom_idx, type, group, pyramid); - if (type < MoleculeStereocenters::ATOM_AND || stereocenters.isAtropisomeric(atom_idx)) + if (type < MoleculeStereocenters::ATOM_AND || !stereocenters.isTetrahydral(atom_idx)) continue; int implicit_h_idx = -1; @@ -385,7 +385,7 @@ void SmilesSaver::_saveMolecule() int idx = _written_atoms[i]; - if (_atoms[idx].chirality == 0 || stereocenters.isAtropisomeric(idx)) + if (_atoms[idx].chirality == 0 || !stereocenters.isTetrahydral(idx)) continue; int type = stereocenters.getType(idx); @@ -626,7 +626,7 @@ void SmilesSaver::_saveMolecule() _writeRingBonds(); _writeUnsaturated(); _writeSubstitutionCounts(); - if (_bmol->hasAtropisomericCenter()) + if (_bmol->hasAtropoStereoBonds()) _writeWedges(); if (_comma) From 6f383ef3ac2d6b2f42569c2078a314a68c55c0f7 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Tue, 3 Oct 2023 10:16:13 +0200 Subject: [PATCH 16/36] stereocenters fixed --- .../basic/buffer_string_load_iterate.py.out | 12 +- .../integration/ref/basic/fold_unfold.py.out | 276 +++++++++--------- .../ref/basic/ketfile_stereo_desc.py.out | 17 +- .../ref/basic/molfile_stereo_desc.py.out | 4 +- .../ref/basic/stereocenters.py.out | 93 +++--- .../integration/ref/bingo/molecules.py.out | 50 ++-- api/tests/integration/ref/formats/cdx.py.out | 4 +- .../integration/ref/formats/ket_to_sdf.py.out | 24 +- .../integration/ref/formats/sdf_to_ket.py.out | 94 +++++- .../ref/formats/serialize_badmols.py.out | 16 +- .../ref/formats/serialize_badrxns.py.out | 24 +- .../integration/ref/rsmiles/rsmiles2.py.out | 4 +- .../ref/stereo/bidirectional.py.out | 18 +- .../molecule/molecule_stereocenters.h | 9 +- .../molecule/src/molecule_stereocenters.cpp | 35 ++- .../molecule/src/smiles_loader.cpp | 8 +- 16 files changed, 421 insertions(+), 267 deletions(-) diff --git a/api/tests/integration/ref/basic/buffer_string_load_iterate.py.out b/api/tests/integration/ref/basic/buffer_string_load_iterate.py.out index 3c241d861f..dcd6e78794 100644 --- a/api/tests/integration/ref/basic/buffer_string_load_iterate.py.out +++ b/api/tests/integration/ref/basic/buffer_string_load_iterate.py.out @@ -10230,10 +10230,10 @@ O=C(N)[C@H]1[C@@H](C(N[2H])=O)C1C([NH-])=O [C@@H]1(C)[C@H](C)[C@H]1C [C@@H]1(C)[C@H](C)[C@@H]1C O1[C@H]([C@@H]1[2H])CCCC -[C@@H]12OC(O[C@@H]1C([C@@H]([C@@H]1OC(OC1)(C)C)O2)=O)(C)C +[C@@H]12OC(O[C@@H]1C([C@@H]([C@@H]1OC(OC1)(C)C)O2)=O)(C)C |wU:6.15,wD:0.0,4.3,7.8,(2.26,0.59,;3.82,0.58,;4.30,-0.91,;3.02,-1.82,;1.76,-0.89,;0.27,-0.89,;-0.20,0.58,;-1.67,1.05,;-2.91,0.15,;-4.17,1.08,;-3.70,2.51,;-2.15,2.50,;-5.68,1.41,;-5.22,-0.05,;1.02,1.49,;-0.64,-2.14,;5.32,-2.07,;5.81,-0.60,)| [P@@](C(C)(C)C)(C1C=CC=CC=1)C1=CC=CC=C1OC [P@](C(C)(C)C)(C1C=CC=CC=1)C1=CC=CC=C1OC -[C@H]12OC(O[C@H]1O[C@H](C1COC(C)(C)O1)C2=O)(C)C +[C@H]12OC(O[C@H]1O[C@H](C1COC(C)(C)O1)C2=O)(C)C |wU:6.7,wD:0.0,4.3,(5.93,-3.99,;6.58,-4.47,;7.24,-4.00,;6.99,-3.22,;6.18,-3.22,;5.49,-2.73,;4.82,-3.22,;4.04,-2.97,;3.57,-2.30,;2.78,-2.54,;2.77,-3.37,;1.95,-3.44,;2.43,-4.12,;3.55,-3.63,;5.09,-3.99,;4.61,-4.67,;8.04,-3.83,;7.79,-4.62,)| C[C@H]([C@H](Cl)CC)Cl CC([C@H](Cl)CC)Cl C1[C@H](C)[C@](O)(CO)C(OCC2[C@]3([H])[C@@H](CCN3CC=2)OC(/C/1=C\C)=O)=O @@ -10468,10 +10468,10 @@ O=C(N)[C@H]1[C@@H](C(N[2H])=O)C1C([NH-])=O [C@@H]1(C)[C@H](C)[C@H]1C [C@@H]1(C)[C@H](C)[C@@H]1C O1[C@H]([C@@H]1[2H])CCCC -[C@@H]12OC(O[C@@H]1C([C@@H]([C@@H]1OC(OC1)(C)C)O2)=O)(C)C +[C@@H]12OC(O[C@@H]1C([C@@H]([C@@H]1OC(OC1)(C)C)O2)=O)(C)C |wU:6.15,wD:0.0,4.3,7.8,(2.26,0.59,;3.82,0.58,;4.30,-0.91,;3.02,-1.82,;1.76,-0.89,;0.27,-0.89,;-0.20,0.58,;-1.67,1.05,;-2.91,0.15,;-4.17,1.08,;-3.70,2.51,;-2.15,2.50,;-5.68,1.41,;-5.22,-0.05,;1.02,1.49,;-0.64,-2.14,;5.32,-2.07,;5.81,-0.60,)| [P@@](C(C)(C)C)(C1C=CC=CC=1)C1=CC=CC=C1OC [P@](C(C)(C)C)(C1C=CC=CC=1)C1=CC=CC=C1OC -[C@H]12OC(O[C@H]1O[C@H](C1COC(C)(C)O1)C2=O)(C)C +[C@H]12OC(O[C@H]1O[C@H](C1COC(C)(C)O1)C2=O)(C)C |wU:6.7,wD:0.0,4.3,(5.93,-3.99,;6.58,-4.47,;7.24,-4.00,;6.99,-3.22,;6.18,-3.22,;5.49,-2.73,;4.82,-3.22,;4.04,-2.97,;3.57,-2.30,;2.78,-2.54,;2.77,-3.37,;1.95,-3.44,;2.43,-4.12,;3.55,-3.63,;5.09,-3.99,;4.61,-4.67,;8.04,-3.83,;7.79,-4.62,)| C[C@H]([C@H](Cl)CC)Cl CC([C@H](Cl)CC)Cl C1[C@H](C)[C@](O)(CO)C(OCC2[C@]3([H])[C@@H](CCN3CC=2)OC(/C/1=C\C)=O)=O @@ -35741,7 +35741,7 @@ C(O)(C)C=C>>C(=O)(C)CC [C:1]1([F:33])([O:4][C:10]2[C:15]([F:20])=[C:19]([C:21]([F:24])=[C:17]([F:22])[C:14]=2[F:18])[F:23])[C:3]([F:9])=[C:8]([C:11](=O)[C:6]([F:12])=[C:2]1[F:7])[F:13].[C:25]1([NH:28][NH2:31])=[CH:27][CH:30]=[CH:32][CH:29]=[CH:26]1>>[C:1]1(=[C:3]([F:9])[C:8](=[C:11]([N:31]=[N:28][C:25]2[CH:26]=[CH:29][CH:32]=[CH:30][CH:27]=2)[C:6]([F:12])=[C:2]1[F:7])[F:13])[O:4][C:10]1[C:15]([F:20])=[C:19]([C:21]([F:24])=[C:17]([F:22])[C:14]=1[F:18])[F:23].[C:11]1([N:31]=[N:28][C:25]2[CH:26]=[CH:29][CH:32]=[CH:30][CH:27]=2)[C:8]([F:13])=[C:3]([C:1]([F:33])=[C:2]([F:7])[C:6]=1[F:12])[F:9] [C@:1]1([H])([C:4]#[C:8][CH3:13])[CH2:3][O:7]C(C)(C)[N:2]1[C:6](=[O:12])OC(C)(C)C.C(C)(C)(C)OC(=O)OC(=O)[O:19][C:18]([CH3:22])([CH3:21])[CH3:20]>>[C@H:1]([C:3](=O)[OH:7])([C:4]#[C:8][CH3:13])[NH:2][C:6](=[O:12])[O:19][C:18]([CH3:22])([CH3:21])[CH3:20].[NH:2]([C:1](=O)[C:4]#[C:8][CH3:13])[C:6](=[O:12])[O:19][C:18]([CH3:22])([CH3:21])[CH3:20] [C:1]1([Si](C)(C)C)([O:21][CH2:3]1)[CH:2](OS(=O)(=O)C)[C:6]1([CH2:13][CH2:15][CH2:19][CH3:20])[O:22][CH2:11]1>>[C:6]1([CH2:13][CH2:15][CH2:19][CH3:20])=[CH:11][O:22][C:1]([CH2:3]F)=[CH:2]1.[C:6]1([CH2:13][CH2:15][CH2:19][CH3:20])=[CH:11][O:22][C:1]([CH2:3][OH:21])=[CH:2]1 -[C:1]1([O:48][CH2:4]1)([C@@:3]1([H])[CH2:9][CH2:17][C@@:14]2([H])[C@:24]3([H])[CH2:27][CH:29]=[C:30]4[CH2:33][C@H:35]([CH2:34][CH2:31][C@:28]4([CH3:32])[C@@:26]3([H])[CH2:25][CH2:15][C@:8]12[CH3:16])[O:36][Si](C)(C)C(C)(C)C)[CH:2](OS(=O)(=O)C)[C:6]1([Si](C)(C)C)[O:49][CH2:10]1>>[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10]F)=[CH:2]1.[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10][OH:49])=[CH:2]1 |w:0,34,40,a:3,7,9,15,18,20,24,47,51,53,57,63,65,69,78,82,84,88,94,96,100| +[C@:1]1([O:48][CH2:4]1)([C@@:3]1([H])[CH2:9][CH2:17][C@@:14]2([H])[C@:24]3([H])[CH2:27][CH:29]=[C:30]4[CH2:33][C@H:35]([CH2:34][CH2:31][C@:28]4([CH3:32])[C@@:26]3([H])[CH2:25][CH2:15][C@:8]12[CH3:16])[O:36][Si](C)(C)C(C)(C)C)[CH:2](OS(=O)(=O)C)[C:6]1([Si](C)(C)C)[O:49][CH2:10]1>>[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10]F)=[CH:2]1.[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10][OH:49])=[CH:2]1 |a:0,3,7,9,15,18,20,24,47,51,53,57,63,65,69,78,82,84,88,94,96,100,w:34,40| [C@H:1]1([CH2:4][C:9](=[O:13])[O:12][CH3:14])[C:3](=[O:8])[CH2:7][C@@:10]2([H])[CH:11]=[CH:6][C@:2]1([H])[O:29]2.S(=O)(=O)(C(F)(F)F)O[Si:22]([CH3:28])([CH3:27])[CH3:26]>>[CH:10]1([O:29][Si:22]([CH3:28])([CH3:27])[CH3:26])[CH2:11][CH2:6][CH:2]=[C:1]([CH2:4][C:9](=[O:13])[O:12][CH3:14])[C:3](=[O:8])[CH2:7]1.[C@@H:2]1([CH2:6][CH2:11][CH:10]=[CH:7][C:3](=[O:8])[C@@H:1]1[CH2:4][C:9](=[O:13])[O:12][CH3:14])[O:29][Si:22]([CH3:28])([CH3:27])[CH3:26].[C@@:3]12([CH:7]=[CH:10][CH2:11][CH2:6][C@H:2]([O:29][Si:22]([CH3:28])([CH3:27])[CH3:26])[C@@:1]1([H])[C@@H:4]2[C:9](=[O:13])[O:12][CH3:14])[O:8][Si:22]([CH3:28])([CH3:27])[CH3:26] |&1:0,9,13,46,53,64,69,75,77| [C:1]1([O:4][Si:8]([CH3:14])([CH3:13])[C:12]([CH3:21])([CH3:20])[CH3:19])=[CH:3][C:7](=[CH:9][CH:5]=[C:2]1[O:6][Si:10]([CH3:17])([CH3:16])[C:15]([CH3:24])([CH3:23])[CH3:22])[CH2:11][N:18]([C:26](=[O:29])[C:28]([F:33])([F:32])[F:31])[CH2:25][CH2:27][C:30]1[CH:35]=[CH:37][C:38]([OH:39])=[CH:36][CH:34]=1>>[C:30]12([CH:34]=[CH:36][C:38](=[O:39])[CH:37]=[CH:35]1)[CH2:27][CH2:25][N:18]([CH2:11][C:7]1[CH:3]=[C:1]([C:2]([O:6][Si:10]([CH3:16])([CH3:17])[C:15]([CH3:24])([CH3:22])[CH3:23])=[CH:5][C:9]2=1)[O:4][Si:8]([CH3:13])([CH3:14])[C:12]([CH3:21])([CH3:19])[CH3:20])[C:26](=[O:29])[C:28]([F:33])([F:31])[F:32].[C:9]12[CH:5]=[C:2]([C:1]([O:4][Si:8]([CH3:13])([CH3:14])[C:12]([CH3:21])([CH3:19])[CH3:20])=[CH:3][C:7]=1[CH2:11][N:18]([C:26](=[O:29])[C:28]([F:33])([F:31])[F:32])[CH2:25][CH2:27][C:30]1[CH:34]=[CH:36][C:38]([OH:39])=[CH:37][C:35]2=1)[O:6][Si:10]([CH3:16])([CH3:17])[C:15]([CH3:24])([CH3:22])[CH3:23] [C:12]1([N+:11]([O-:4])=[O:5])=[CH:7][C:9](=[C:8]([F:1])[CH:6]=[C:10]1[F:3])[F:2].[C:23]([CH3:15])([CH3:14])([CH3:13])[O:25][C:24](=[O:17])[N:26]1[CH2:21][CH2:19][CH:22]([OH:16])[CH2:18][CH2:20]1>>[C:8]1([CH:6]=[C:10]([C:12]([N+:11]([O-:4])=[O:5])=[CH:7][C:9]=1[F:2])[F:3])[O:16][CH:22]1[CH2:19][CH2:21][N:26]([C:24](=[O:17])[O:25][C:23]([CH3:15])([CH3:13])[CH3:14])[CH2:20][CH2:18]1.[C:10]1(=[CH:6][C:8](=[C:9]([F:2])[CH:7]=[C:12]1[N+:11]([O-:4])=[O:5])[F:1])[O:16][CH:22]1[CH2:19][CH2:21][N:26]([C:24](=[O:17])[O:25][C:23]([CH3:15])([CH3:13])[CH3:14])[CH2:20][CH2:18]1 @@ -36072,7 +36072,7 @@ C(O)(C)C=C>>C(=O)(C)CC [C:1]1([F:33])([O:4][C:10]2[C:15]([F:20])=[C:19]([C:21]([F:24])=[C:17]([F:22])[C:14]=2[F:18])[F:23])[C:3]([F:9])=[C:8]([C:11](=O)[C:6]([F:12])=[C:2]1[F:7])[F:13].[C:25]1([NH:28][NH2:31])=[CH:27][CH:30]=[CH:32][CH:29]=[CH:26]1>>[C:1]1(=[C:3]([F:9])[C:8](=[C:11]([N:31]=[N:28][C:25]2[CH:26]=[CH:29][CH:32]=[CH:30][CH:27]=2)[C:6]([F:12])=[C:2]1[F:7])[F:13])[O:4][C:10]1[C:15]([F:20])=[C:19]([C:21]([F:24])=[C:17]([F:22])[C:14]=1[F:18])[F:23].[C:11]1([N:31]=[N:28][C:25]2[CH:26]=[CH:29][CH:32]=[CH:30][CH:27]=2)[C:8]([F:13])=[C:3]([C:1]([F:33])=[C:2]([F:7])[C:6]=1[F:12])[F:9] [C@:1]1([H])([C:4]#[C:8][CH3:13])[CH2:3][O:7]C(C)(C)[N:2]1[C:6](=[O:12])OC(C)(C)C.C(C)(C)(C)OC(=O)OC(=O)[O:19][C:18]([CH3:22])([CH3:21])[CH3:20]>>[C@H:1]([C:3](=O)[OH:7])([C:4]#[C:8][CH3:13])[NH:2][C:6](=[O:12])[O:19][C:18]([CH3:22])([CH3:21])[CH3:20].[NH:2]([C:1](=O)[C:4]#[C:8][CH3:13])[C:6](=[O:12])[O:19][C:18]([CH3:22])([CH3:21])[CH3:20] [C:1]1([Si](C)(C)C)([O:21][CH2:3]1)[CH:2](OS(=O)(=O)C)[C:6]1([CH2:13][CH2:15][CH2:19][CH3:20])[O:22][CH2:11]1>>[C:6]1([CH2:13][CH2:15][CH2:19][CH3:20])=[CH:11][O:22][C:1]([CH2:3]F)=[CH:2]1.[C:6]1([CH2:13][CH2:15][CH2:19][CH3:20])=[CH:11][O:22][C:1]([CH2:3][OH:21])=[CH:2]1 -[C:1]1([O:48][CH2:4]1)([C@@:3]1([H])[CH2:9][CH2:17][C@@:14]2([H])[C@:24]3([H])[CH2:27][CH:29]=[C:30]4[CH2:33][C@H:35]([CH2:34][CH2:31][C@:28]4([CH3:32])[C@@:26]3([H])[CH2:25][CH2:15][C@:8]12[CH3:16])[O:36][Si](C)(C)C(C)(C)C)[CH:2](OS(=O)(=O)C)[C:6]1([Si](C)(C)C)[O:49][CH2:10]1>>[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10]F)=[CH:2]1.[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10][OH:49])=[CH:2]1 |w:0,34,40,a:3,7,9,15,18,20,24,47,51,53,57,63,65,69,78,82,84,88,94,96,100| +[C@:1]1([O:48][CH2:4]1)([C@@:3]1([H])[CH2:9][CH2:17][C@@:14]2([H])[C@:24]3([H])[CH2:27][CH:29]=[C:30]4[CH2:33][C@H:35]([CH2:34][CH2:31][C@:28]4([CH3:32])[C@@:26]3([H])[CH2:25][CH2:15][C@:8]12[CH3:16])[O:36][Si](C)(C)C(C)(C)C)[CH:2](OS(=O)(=O)C)[C:6]1([Si](C)(C)C)[O:49][CH2:10]1>>[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10]F)=[CH:2]1.[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10][OH:49])=[CH:2]1 |a:0,3,7,9,15,18,20,24,47,51,53,57,63,65,69,78,82,84,88,94,96,100,w:34,40| [C@H:1]1([CH2:4][C:9](=[O:13])[O:12][CH3:14])[C:3](=[O:8])[CH2:7][C@@:10]2([H])[CH:11]=[CH:6][C@:2]1([H])[O:29]2.S(=O)(=O)(C(F)(F)F)O[Si:22]([CH3:28])([CH3:27])[CH3:26]>>[CH:10]1([O:29][Si:22]([CH3:28])([CH3:27])[CH3:26])[CH2:11][CH2:6][CH:2]=[C:1]([CH2:4][C:9](=[O:13])[O:12][CH3:14])[C:3](=[O:8])[CH2:7]1.[C@@H:2]1([CH2:6][CH2:11][CH:10]=[CH:7][C:3](=[O:8])[C@@H:1]1[CH2:4][C:9](=[O:13])[O:12][CH3:14])[O:29][Si:22]([CH3:28])([CH3:27])[CH3:26].[C@@:3]12([CH:7]=[CH:10][CH2:11][CH2:6][C@H:2]([O:29][Si:22]([CH3:28])([CH3:27])[CH3:26])[C@@:1]1([H])[C@@H:4]2[C:9](=[O:13])[O:12][CH3:14])[O:8][Si:22]([CH3:28])([CH3:27])[CH3:26] |&1:0,9,13,46,53,64,69,75,77| [C:1]1([O:4][Si:8]([CH3:14])([CH3:13])[C:12]([CH3:21])([CH3:20])[CH3:19])=[CH:3][C:7](=[CH:9][CH:5]=[C:2]1[O:6][Si:10]([CH3:17])([CH3:16])[C:15]([CH3:24])([CH3:23])[CH3:22])[CH2:11][N:18]([C:26](=[O:29])[C:28]([F:33])([F:32])[F:31])[CH2:25][CH2:27][C:30]1[CH:35]=[CH:37][C:38]([OH:39])=[CH:36][CH:34]=1>>[C:30]12([CH:34]=[CH:36][C:38](=[O:39])[CH:37]=[CH:35]1)[CH2:27][CH2:25][N:18]([CH2:11][C:7]1[CH:3]=[C:1]([C:2]([O:6][Si:10]([CH3:16])([CH3:17])[C:15]([CH3:24])([CH3:22])[CH3:23])=[CH:5][C:9]2=1)[O:4][Si:8]([CH3:13])([CH3:14])[C:12]([CH3:21])([CH3:19])[CH3:20])[C:26](=[O:29])[C:28]([F:33])([F:31])[F:32].[C:9]12[CH:5]=[C:2]([C:1]([O:4][Si:8]([CH3:13])([CH3:14])[C:12]([CH3:21])([CH3:19])[CH3:20])=[CH:3][C:7]=1[CH2:11][N:18]([C:26](=[O:29])[C:28]([F:33])([F:31])[F:32])[CH2:25][CH2:27][C:30]1[CH:34]=[CH:36][C:38]([OH:39])=[CH:37][C:35]2=1)[O:6][Si:10]([CH3:16])([CH3:17])[C:15]([CH3:24])([CH3:22])[CH3:23] [C:12]1([N+:11]([O-:4])=[O:5])=[CH:7][C:9](=[C:8]([F:1])[CH:6]=[C:10]1[F:3])[F:2].[C:23]([CH3:15])([CH3:14])([CH3:13])[O:25][C:24](=[O:17])[N:26]1[CH2:21][CH2:19][CH:22]([OH:16])[CH2:18][CH2:20]1>>[C:8]1([CH:6]=[C:10]([C:12]([N+:11]([O-:4])=[O:5])=[CH:7][C:9]=1[F:2])[F:3])[O:16][CH:22]1[CH2:19][CH2:21][N:26]([C:24](=[O:17])[O:25][C:23]([CH3:15])([CH3:13])[CH3:14])[CH2:20][CH2:18]1.[C:10]1(=[CH:6][C:8](=[C:9]([F:2])[CH:7]=[C:12]1[N+:11]([O-:4])=[O:5])[F:1])[O:16][CH:22]1[CH2:19][CH2:21][N:26]([C:24](=[O:17])[O:25][C:23]([CH3:15])([CH3:13])[CH3:14])[CH2:20][CH2:18]1 diff --git a/api/tests/integration/ref/basic/fold_unfold.py.out b/api/tests/integration/ref/basic/fold_unfold.py.out index dbdafd51dc..575f9ad8a2 100644 --- a/api/tests/integration/ref/basic/fold_unfold.py.out +++ b/api/tests/integration/ref/basic/fold_unfold.py.out @@ -11,9 +11,9 @@ testing ../../../../../data/molecules/basic/sugars.sdf [C@]1([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])OC1(O[H])C([H])([H])O[H])O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] [C@@H]1([C@H](O)[C@@H](COC1(O)CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O -[C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C -[C@@]1(C([H])([H])OC(=O)C([H])([H])[H])(O[C@@]([H])([C@@]([H])(OC(=O)C([H])([H])[H])[C@]1([H])OC(=O)C([H])([H])[H])C([H])([H])OC(=O)C([H])([H])[H])O[C@@]1([H])O[C@@]([H])([C@@]([H])(OC(=O)C([H])([H])[H])[C@]([H])(OC(=O)C([H])([H])[H])[C@@]1([H])OC(=O)C([H])([H])[H])C([H])([H])OC(=O)C([H])([H])[H] -[C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C +[C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C |wU:13.14,7.18,0.23,32.33,26.43,wD:0.0,8.8,24.25,27.28,37.39,(-0.84,0.15,;-0.86,-0.61,;-0.20,-1.00,;-0.23,-1.77,;0.40,-2.18,;-0.86,-2.14,;-0.79,0.87,;-1.48,1.16,;-1.97,0.59,;-2.72,0.64,;-3.04,1.33,;-3.79,1.41,;-2.62,1.96,;-1.58,-0.02,;-1.87,-0.72,;-2.63,-0.83,;-2.93,-1.52,;-3.08,-0.24,;-1.64,1.91,;-1.01,2.33,;-1.07,3.09,;-0.49,3.50,;-1.67,3.41,;-0.10,0.15,;0.54,-0.23,;0.54,-0.97,;1.19,-1.34,;1.86,-0.96,;2.51,-1.34,;3.17,-0.96,;3.83,-1.34,;3.16,-0.22,;1.86,-0.22,;2.51,0.15,;2.50,0.91,;3.16,1.29,;1.84,1.29,;1.19,0.15,;1.19,0.91,;0.54,1.28,;0.53,2.04,;-0.10,0.90,;1.20,-2.11,;1.92,-2.34,;1.94,-3.10,;2.60,-3.46,;1.29,-3.50,)| +[C@@]1(C([H])([H])OC(=O)C([H])([H])[H])(O[C@@]([H])([C@@]([H])(OC(=O)C([H])([H])[H])[C@]1([H])OC(=O)C([H])([H])[H])C([H])([H])OC(=O)C([H])([H])[H])O[C@@]1([H])O[C@@]([H])([C@@]([H])(OC(=O)C([H])([H])[H])[C@]([H])(OC(=O)C([H])([H])[H])[C@@]1([H])OC(=O)C([H])([H])[H])C([H])([H])OC(=O)C([H])([H])[H] |wU:23.25,12.32,0.42,57.59,46.76,wD:0.0,14.15,43.45,48.50,66.69,(-0.84,0.15,;-0.86,-0.61,;0.00,0.00,;0.00,0.00,;-0.20,-1.00,;-0.23,-1.77,;0.40,-2.18,;-0.86,-2.14,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-0.79,0.87,;-1.48,1.16,;0.00,0.00,;-1.97,0.59,;0.00,0.00,;-2.72,0.64,;-3.04,1.33,;-3.79,1.41,;-2.62,1.96,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-1.58,-0.02,;0.00,0.00,;-1.87,-0.72,;-2.63,-0.83,;-2.93,-1.52,;-3.08,-0.24,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-1.64,1.91,;0.00,0.00,;0.00,0.00,;-1.01,2.33,;-1.07,3.09,;-0.49,3.50,;-1.67,3.41,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-0.10,0.15,;0.54,-0.23,;0.00,0.00,;0.54,-0.97,;1.19,-1.34,;0.00,0.00,;1.86,-0.96,;0.00,0.00,;2.51,-1.34,;3.17,-0.96,;3.83,-1.34,;3.16,-0.22,;0.00,0.00,;0.00,0.00,;0.00,0.00,;1.86,-0.22,;0.00,0.00,;2.51,0.15,;2.50,0.91,;3.16,1.29,;1.84,1.29,;0.00,0.00,;0.00,0.00,;0.00,0.00,;1.19,0.15,;0.00,0.00,;1.19,0.91,;0.54,1.28,;0.53,2.04,;-0.10,0.90,;0.00,0.00,;0.00,0.00,;0.00,0.00,;1.20,-2.11,;0.00,0.00,;0.00,0.00,;1.92,-2.34,;1.94,-3.10,;2.60,-3.46,;1.29,-3.50,;0.00,0.00,;0.00,0.00,;0.00,0.00,)| +[C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C |wU:13.14,7.18,0.23,32.33,26.43,wD:0.0,8.8,24.25,27.28,37.39,(-0.84,0.15,;-0.86,-0.61,;-0.20,-1.00,;-0.23,-1.77,;0.40,-2.18,;-0.86,-2.14,;-0.79,0.87,;-1.48,1.16,;-1.97,0.59,;-2.72,0.64,;-3.04,1.33,;-3.79,1.41,;-2.62,1.96,;-1.58,-0.02,;-1.87,-0.72,;-2.63,-0.83,;-2.93,-1.52,;-3.08,-0.24,;-1.64,1.91,;-1.01,2.33,;-1.07,3.09,;-0.49,3.50,;-1.67,3.41,;-0.10,0.15,;0.54,-0.23,;0.54,-0.97,;1.19,-1.34,;1.86,-0.96,;2.51,-1.34,;3.17,-0.96,;3.83,-1.34,;3.16,-0.22,;1.86,-0.22,;2.51,0.15,;2.50,0.91,;3.16,1.29,;1.84,1.29,;1.19,0.15,;1.19,0.91,;0.54,1.28,;0.53,2.04,;-0.10,0.90,;1.20,-2.11,;1.92,-2.34,;1.94,-3.10,;2.60,-3.46,;1.29,-3.50,)| [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O [C@]1(C([H])([H])O[H])([C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] @@ -27,17 +27,17 @@ testing ../../../../../data/molecules/basic/sugars.sdf [C@@]1([H])([C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] [C@H]1([C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O -[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O -[C@]1([H])([C@]([H])(O[H])[C@]([H])([C@@]([H])(O[C@@]2([H])[C@]([H])(O[H])[C@]([H])(C([H])(O[H])O[C@]2([H])C([H])([H])O[H])O[H])O[C@]1([H])C([H])([H])O[H])O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] -[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O +[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |wU:1.1,7.7,13.14,18.20,29.31,26.35,wD:6.5,9.16,4.17,3.22,0.23,24.26,27.29,23.34,(0.82,0.83,;0.36,1.57,;0.76,2.31,;-0.48,1.53,;-0.88,0.78,;-1.72,0.75,;-2.13,-0.01,;-2.99,-0.02,;-3.43,0.68,;-3.39,-0.78,;-2.93,-1.50,;-3.33,-2.26,;-2.07,-1.47,;-1.67,-0.72,;-0.82,-0.69,;-0.37,-1.41,;-4.23,-0.81,;-0.42,0.05,;0.42,0.08,;0.87,-0.63,;0.47,-1.38,;-0.93,2.26,;1.67,0.87,;2.13,0.14,;2.98,0.18,;3.38,0.93,;3.44,-0.53,;3.03,-1.29,;3.49,-2.00,;2.18,-1.32,;1.78,-2.07,;0.92,-2.10,;1.73,-0.60,;4.28,-0.50,)| +[C@]1([H])([C@]([H])(O[H])[C@]([H])([C@@]([H])(O[C@@]2([H])[C@]([H])(O[H])[C@]([H])(C([H])(O[H])O[C@]2([H])C([H])([H])O[H])O[H])O[C@]1([H])C([H])([H])O[H])O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] |wU:2.3,13.14,24.26,34.37,56.59,50.66,wD:11.10,17.31,8.33,6.42,0.44,46.49,52.55,44.65,(0.82,0.83,;0.00,0.00,;0.36,1.57,;0.00,0.00,;0.76,2.31,;0.00,0.00,;-0.48,1.53,;0.00,0.00,;-0.88,0.78,;0.00,0.00,;-1.72,0.75,;-2.13,-0.01,;0.00,0.00,;-2.99,-0.02,;0.00,0.00,;-3.43,0.68,;0.00,0.00,;-3.39,-0.78,;0.00,0.00,;-2.93,-1.50,;0.00,0.00,;-3.33,-2.26,;0.00,0.00,;-2.07,-1.47,;-1.67,-0.72,;0.00,0.00,;-0.82,-0.69,;0.00,0.00,;0.00,0.00,;-0.37,-1.41,;0.00,0.00,;-4.23,-0.81,;0.00,0.00,;-0.42,0.05,;0.42,0.08,;0.00,0.00,;0.87,-0.63,;0.00,0.00,;0.00,0.00,;0.47,-1.38,;0.00,0.00,;-0.93,2.26,;0.00,0.00,;1.67,0.87,;2.13,0.14,;0.00,0.00,;2.98,0.18,;0.00,0.00,;3.38,0.93,;0.00,0.00,;3.44,-0.53,;0.00,0.00,;3.03,-1.29,;0.00,0.00,;3.49,-2.00,;0.00,0.00,;2.18,-1.32,;0.00,0.00,;1.78,-2.07,;0.00,0.00,;0.00,0.00,;0.92,-2.10,;0.00,0.00,;1.73,-0.60,;4.28,-0.50,;0.00,0.00,)| +[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O 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|wU:6.7,12.13,0.22,35.37,49.51,53.55,47.62,29.66,wD:0.0,10.20,25.27,31.33,41.41,43.45,23.65,(-2.18,-0.79,;-1.50,-1.14,;0.00,0.00,;0.00,0.00,;-0.88,-0.70,;0.00,0.00,;-2.43,-1.51,;0.00,0.00,;-1.99,-2.13,;0.00,0.00,;-3.18,-1.50,;0.00,0.00,;-3.39,-0.76,;0.00,0.00,;-4.13,-0.49,;0.00,0.00,;0.00,0.00,;-4.25,0.24,;0.00,0.00,;-2.79,-0.33,;-3.64,-2.09,;0.00,0.00,;-1.63,0.09,;-0.95,0.45,;0.00,0.00,;-0.94,1.21,;0.00,0.00,;-1.59,1.60,;0.00,0.00,;-0.27,1.57,;0.00,0.00,;0.38,1.18,;0.00,0.00,;1.03,1.54,;0.00,0.00,;0.36,0.42,;0.00,0.00,;0.99,0.02,;0.00,0.00,;0.00,0.00,;1.66,0.39,;2.31,-0.01,;0.00,0.00,;2.98,0.34,;0.00,0.00,;3.00,1.11,;0.00,0.00,;3.63,-0.04,;0.00,0.00,;3.61,-0.80,;0.00,0.00,;4.26,-1.19,;0.00,0.00,;2.93,-1.16,;0.00,0.00,;2.92,-1.91,;0.00,0.00,;0.00,0.00,;2.24,-2.28,;0.00,0.00,;2.29,-0.76,;4.29,0.31,;0.00,0.00,;-0.31,0.06,;-0.25,2.33,;0.00,0.00,)| +[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,25.26,27.28,24.32,15.35,wD:0.0,5.10,13.14,16.17,21.21,22.23,12.34,(-2.18,-0.79,;-1.50,-1.14,;-0.88,-0.70,;-2.43,-1.51,;-1.99,-2.13,;-3.18,-1.50,;-3.39,-0.76,;-4.13,-0.49,;-4.25,0.24,;-2.79,-0.33,;-3.64,-2.09,;-1.63,0.09,;-0.95,0.45,;-0.94,1.21,;-1.59,1.60,;-0.27,1.57,;0.38,1.18,;1.03,1.54,;0.36,0.42,;0.99,0.02,;1.66,0.39,;2.31,-0.01,;2.98,0.34,;3.00,1.11,;3.63,-0.04,;3.61,-0.80,;4.26,-1.19,;2.93,-1.16,;2.92,-1.91,;2.24,-2.28,;2.29,-0.76,;4.29,0.31,;-0.31,0.06,;-0.25,2.33,)| -[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O3)O)O2)O)O1)O 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|wU:3.3,6.6,0.11,18.19,25.26,27.28,34.35,36.37,33.41,24.44,15.47,wD:0.0,5.10,13.14,16.17,21.21,22.23,30.30,31.32,12.46,(-2.54,-1.21,;-2.00,-1.50,;-1.48,-1.14,;-2.76,-1.79,;-2.40,-2.31,;-3.39,-1.79,;-3.56,-1.17,;-4.14,-0.97,;-4.27,-0.35,;-3.05,-0.84,;-3.77,-2.27,;-2.22,-0.69,;-1.97,-0.13,;-2.33,0.38,;-2.94,0.31,;-2.07,0.94,;-1.45,0.99,;-1.20,1.56,;-1.08,0.49,;-0.47,0.55,;-0.22,1.11,;0.40,1.17,;0.64,1.73,;0.30,2.24,;1.25,1.80,;1.62,1.30,;2.24,1.35,;1.37,0.72,;1.72,0.22,;2.34,0.29,;2.70,-0.21,;3.32,-0.15,;3.58,0.40,;3.68,-0.66,;3.42,-1.22,;3.78,-1.73,;2.80,-1.28,;2.54,-1.84,;1.93,-1.91,;2.44,-0.78,;4.30,-0.59,;0.74,0.66,;1.52,2.36,;-1.35,-0.07,;-2.43,1.43,)| +[C@]1(C([H])([H])O[H])([C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]2([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]3([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O3)O[H])O2)O[H])O1)O[H] |wU:6.7,12.13,0.22,35.37,49.51,53.55,67.69,71.73,65.80,47.84,29.88,wD:0.0,10.20,25.27,31.33,41.41,43.45,59.59,61.63,23.87,(-2.54,-1.21,;-2.00,-1.50,;0.00,0.00,;0.00,0.00,;-1.48,-1.14,;0.00,0.00,;-2.76,-1.79,;0.00,0.00,;-2.40,-2.31,;0.00,0.00,;-3.39,-1.79,;0.00,0.00,;-3.56,-1.17,;0.00,0.00,;-4.14,-0.97,;0.00,0.00,;0.00,0.00,;-4.27,-0.35,;0.00,0.00,;-3.05,-0.84,;-3.77,-2.27,;0.00,0.00,;-2.22,-0.69,;-1.97,-0.13,;0.00,0.00,;-2.33,0.38,;0.00,0.00,;-2.94,0.31,;0.00,0.00,;-2.07,0.94,;0.00,0.00,;-1.45,0.99,;0.00,0.00,;-1.20,1.56,;0.00,0.00,;-1.08,0.49,;0.00,0.00,;-0.47,0.55,;0.00,0.00,;0.00,0.00,;-0.22,1.11,;0.40,1.17,;0.00,0.00,;0.64,1.73,;0.00,0.00,;0.30,2.24,;0.00,0.00,;1.25,1.80,;0.00,0.00,;1.62,1.30,;0.00,0.00,;2.24,1.35,;0.00,0.00,;1.37,0.72,;0.00,0.00,;1.72,0.22,;0.00,0.00,;0.00,0.00,;2.34,0.29,;2.70,-0.21,;0.00,0.00,;3.32,-0.15,;0.00,0.00,;3.58,0.40,;0.00,0.00,;3.68,-0.66,;0.00,0.00,;3.42,-1.22,;0.00,0.00,;3.78,-1.73,;0.00,0.00,;2.80,-1.28,;0.00,0.00,;2.54,-1.84,;0.00,0.00,;0.00,0.00,;1.93,-1.91,;0.00,0.00,;2.44,-0.78,;4.30,-0.59,;0.00,0.00,;0.74,0.66,;1.52,2.36,;0.00,0.00,;-1.35,-0.07,;-2.43,1.43,;0.00,0.00,)| +[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O3)O)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,25.26,27.28,34.35,36.37,33.41,24.44,15.47,wD:0.0,5.10,13.14,16.17,21.21,22.23,30.30,31.32,12.46,(-2.54,-1.21,;-2.00,-1.50,;-1.48,-1.14,;-2.76,-1.79,;-2.40,-2.31,;-3.39,-1.79,;-3.56,-1.17,;-4.14,-0.97,;-4.27,-0.35,;-3.05,-0.84,;-3.77,-2.27,;-2.22,-0.69,;-1.97,-0.13,;-2.33,0.38,;-2.94,0.31,;-2.07,0.94,;-1.45,0.99,;-1.20,1.56,;-1.08,0.49,;-0.47,0.55,;-0.22,1.11,;0.40,1.17,;0.64,1.73,;0.30,2.24,;1.25,1.80,;1.62,1.30,;2.24,1.35,;1.37,0.72,;1.72,0.22,;2.34,0.29,;2.70,-0.21,;3.32,-0.15,;3.58,0.40,;3.68,-0.66,;3.42,-1.22,;3.78,-1.73,;2.80,-1.28,;2.54,-1.84,;1.93,-1.91,;2.44,-0.78,;4.30,-0.59,;0.74,0.66,;1.52,2.36,;-1.35,-0.07,;-2.43,1.43,)| [C@H]12[C@H](O)[C@H]([C@@H](OC)O[C@@H]1COC(C1C=CC=CC=1)O2)O [C@]12([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(OC([H])([H])[H])O[C@]1([H])C([H])([H])OC([H])(C1C([H])=C([H])C([H])=C([H])C=1[H])O2)O[H] @@ -51,13 +51,13 @@ testing ../../../../../data/molecules/basic/sugars.sdf [C@]12([H])O[C@@]3([H])O[C@@]([H])([C@@]([H])(O[C@@]4([H])O[C@@]([H])([C@@]([H])(O[C@@]5([H])O[C@@]([H])([C@@]([H])(O[C@@]6([H])O[C@@]([H])([C@]([H])([C@]([H])(O[H])[C@@]6([H])O[H])O[C@]6([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O6)O[C@]6([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O6)O[C@]6([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O6)O[C@]([H])([C@]([H])(O[H])[C@@]1([H])O[H])O[C@]2([H])C([H])([H])O[H])C([H])([H])O[H])[C@]([H])(O[H])[C@@]5([H])O[H])C([H])([H])O[H])[C@]([H])(O[H])[C@@]4([H])O[H])C([H])([H])O[H])[C@]([H])(O[H])[C@@]3([H])O[H])C([H])([H])O[H] [C@H]12O[C@H]3O[C@@H]([C@@H](O[C@H]4O[C@@H]([C@@H](O[C@H]5O[C@@H]([C@@H](O[C@H]6O[C@@H]([C@H]([C@H](O)[C@H]6O)O[C@@H]6[C@H](O)[C@@H](O)[C@@H]([C@@H](CO)O6)O[C@@H]6[C@H](O)[C@@H](O)[C@@H]([C@@H](CO)O6)O[C@@H]6[C@H](O)[C@@H](O)[C@@H]([C@@H](CO)O6)O[C@H]([C@H](O)[C@H]1O)O[C@@H]2CO)CO)[C@H](O)[C@H]5O)CO)[C@H](O)[C@H]4O)CO)[C@H](O)[C@H]3O)CO -[C@@H]1(O[C@@H]2O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)COC(=O)C)[C@@H](COC(=O)C)O[C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C -[C@]1([H])(O[C@]2([H])O[C@@]([H])([C@@]([H])(OC(=O)C([H])([H])[H])[C@]([H])(OC(=O)C([H])([H])[H])[C@@]2([H])OC(=O)C([H])([H])[H])C([H])([H])OC(=O)C([H])([H])[H])[C@@]([H])(C([H])([H])OC(=O)C([H])([H])[H])O[C@]([H])(OC(=O)C([H])([H])[H])[C@]([H])(OC(=O)C([H])([H])[H])[C@@]1([H])OC(=O)C([H])([H])[H] -[C@@H]1(O[C@@H]2O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)COC(=O)C)[C@@H](COC(=O)C)O[C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C 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|wU:3.4,17.18,6.35,45.47,76.79,wD:0.1,8.9,26.28,58.60,67.69,(1.18,-0.62,;0.00,0.00,;0.39,-1.08,;-0.33,-0.61,;0.00,0.00,;-0.33,0.23,;-1.12,0.67,;0.00,0.00,;-1.89,0.23,;0.00,0.00,;-2.68,0.67,;-2.68,1.57,;-3.44,2.03,;-1.89,2.02,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-1.89,-0.63,;0.00,0.00,;-2.68,-1.08,;-3.43,-0.62,;-4.23,-1.07,;-3.43,0.24,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-1.12,-1.07,;0.00,0.00,;-1.11,-1.97,;-1.89,-2.43,;-1.89,-3.32,;-2.68,-1.97,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-1.12,1.57,;0.00,0.00,;0.00,0.00,;-0.33,2.03,;-0.34,2.93,;0.39,3.38,;-1.12,3.38,;0.00,0.00,;0.00,0.00,;0.00,0.00,;1.18,0.22,;0.00,0.00,;0.40,0.66,;0.00,0.00,;0.00,0.00,;0.40,1.56,;1.19,2.02,;1.19,2.93,;2.03,1.63,;0.00,0.00,;0.00,0.00,;0.00,0.00,;1.95,0.70,;2.74,0.24,;0.00,0.00,;3.49,0.70,;3.49,1.59,;4.28,2.04,;2.74,2.05,;0.00,0.00,;0.00,0.00,;0.00,0.00,;2.74,-0.60,;0.00,0.00,;3.50,-1.07,;3.50,-1.97,;4.28,-2.42,;2.73,-2.41,;0.00,0.00,;0.00,0.00,;0.00,0.00,;1.95,-1.06,;0.00,0.00,;1.95,-1.96,;1.18,-2.42,;1.19,-3.30,;0.39,-1.98,;0.00,0.00,;0.00,0.00,;0.00,0.00,)| +[C@@H]1(O[C@@H]2O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)COC(=O)C)[C@@H](COC(=O)C)O[C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C |wU:2.2,10.10,4.20,25.26,42.44,wD:0.0,5.5,15.16,32.33,37.38,(1.18,-0.62,;0.39,-1.08,;-0.33,-0.61,;-0.33,0.23,;-1.12,0.67,;-1.89,0.23,;-2.68,0.67,;-2.68,1.57,;-3.44,2.03,;-1.89,2.02,;-1.89,-0.63,;-2.68,-1.08,;-3.43,-0.62,;-4.23,-1.07,;-3.43,0.24,;-1.12,-1.07,;-1.11,-1.97,;-1.89,-2.43,;-1.89,-3.32,;-2.68,-1.97,;-1.12,1.57,;-0.33,2.03,;-0.34,2.93,;0.39,3.38,;-1.12,3.38,;1.18,0.22,;0.40,0.66,;0.40,1.56,;1.19,2.02,;1.19,2.93,;2.03,1.63,;1.95,0.70,;2.74,0.24,;3.49,0.70,;3.49,1.59,;4.28,2.04,;2.74,2.05,;2.74,-0.60,;3.50,-1.07,;3.50,-1.97,;4.28,-2.42,;2.73,-2.41,;1.95,-1.06,;1.95,-1.96,;1.18,-2.42,;1.19,-3.30,;0.39,-1.98,)| -[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@@H](O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O -[C@]1([H])([C@]([H])(O[H])[C@]([H])([C@@]([H])(O[C@@]2([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])O[C@]2([H])C([H])([H])O[H])O[H])O[C@]1([H])C([H])([H])O[H])O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[C@]2([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O2)O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] -[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@@H](O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O +[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@@H](O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O |wU:1.1,7.7,13.14,18.20,35.37,32.41,40.43,26.47,wD:6.5,10.10,9.16,4.17,3.22,0.23,24.26,27.29,30.32,33.35,29.40,23.46,(0.63,-0.13,;0.87,-0.52,;0.58,-0.96,;1.36,-0.52,;1.60,-0.11,;2.17,-0.11,;2.70,-0.15,;2.97,-0.62,;2.72,-1.08,;3.48,-0.60,;3.75,-0.15,;4.31,-0.15,;3.48,0.29,;2.96,0.29,;2.68,0.77,;2.93,1.23,;3.73,-1.08,;1.36,0.31,;0.87,0.31,;0.59,0.77,;0.83,1.22,;1.63,-0.99,;0.11,-0.17,;-0.51,-0.23,;-0.76,-0.70,;-0.47,-1.18,;-1.30,-0.70,;-1.57,-0.24,;-2.12,-0.24,;-2.66,-0.21,;-2.91,-0.67,;-2.62,-1.15,;-3.44,-0.68,;-3.70,-0.22,;-4.28,-0.22,;-3.46,0.23,;-3.76,0.71,;-3.50,1.18,;-2.93,0.23,;-3.70,-1.18,;-1.31,0.20,;-1.60,0.68,;-1.34,1.15,;-0.80,0.21,;-1.56,-1.20,)| +[C@]1([H])([C@]([H])(O[H])[C@]([H])([C@@]([H])(O[C@@]2([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])O[C@]2([H])C([H])([H])O[H])O[H])O[C@]1([H])C([H])([H])O[H])O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[C@]2([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O2)O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] |wU:2.3,13.14,24.26,34.37,67.70,61.77,77.81,50.88,wD:11.10,19.20,17.31,8.33,6.42,0.44,46.49,52.55,57.60,63.66,55.76,44.87,(0.63,-0.13,;0.00,0.00,;0.87,-0.52,;0.00,0.00,;0.58,-0.96,;0.00,0.00,;1.36,-0.52,;0.00,0.00,;1.60,-0.11,;0.00,0.00,;2.17,-0.11,;2.70,-0.15,;0.00,0.00,;2.97,-0.62,;0.00,0.00,;2.72,-1.08,;0.00,0.00,;3.48,-0.60,;0.00,0.00,;3.75,-0.15,;0.00,0.00,;4.31,-0.15,;0.00,0.00,;3.48,0.29,;2.96,0.29,;0.00,0.00,;2.68,0.77,;0.00,0.00,;0.00,0.00,;2.93,1.23,;0.00,0.00,;3.73,-1.08,;0.00,0.00,;1.36,0.31,;0.87,0.31,;0.00,0.00,;0.59,0.77,;0.00,0.00,;0.00,0.00,;0.83,1.22,;0.00,0.00,;1.63,-0.99,;0.00,0.00,;0.11,-0.17,;-0.51,-0.23,;0.00,0.00,;-0.76,-0.70,;0.00,0.00,;-0.47,-1.18,;0.00,0.00,;-1.30,-0.70,;0.00,0.00,;-1.57,-0.24,;0.00,0.00,;-2.12,-0.24,;-2.66,-0.21,;0.00,0.00,;-2.91,-0.67,;0.00,0.00,;-2.62,-1.15,;0.00,0.00,;-3.44,-0.68,;0.00,0.00,;-3.70,-0.22,;0.00,0.00,;-4.28,-0.22,;0.00,0.00,;-3.46,0.23,;0.00,0.00,;-3.76,0.71,;0.00,0.00,;0.00,0.00,;-3.50,1.18,;0.00,0.00,;-2.93,0.23,;-3.70,-1.18,;0.00,0.00,;-1.31,0.20,;0.00,0.00,;-1.60,0.68,;0.00,0.00,;0.00,0.00,;-1.34,1.15,;0.00,0.00,;-0.80,0.21,;-1.56,-1.20,;0.00,0.00,)| 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[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@H]1[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]4[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O4)O)O3)O)O2)O)O1)O [C@]1(C([H])([H])O[H])([C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@@]1([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]2([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]3([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]4([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O4)O[H])O3)O[H])O2)O[H])O1)O[H] diff --git a/api/tests/integration/ref/basic/ketfile_stereo_desc.py.out b/api/tests/integration/ref/basic/ketfile_stereo_desc.py.out index 118bfdad0b..c3d52f61b4 100644 --- a/api/tests/integration/ref/basic/ketfile_stereo_desc.py.out +++ b/api/tests/integration/ref/basic/ketfile_stereo_desc.py.out @@ -37,5 +37,20 @@ t4_S.mol:SUCCEED t4_S_iso.mol:SUCCEED trans.mol:SUCCEED without_stereo_label.mol:SUCCEED -crazystereo.rxn:SUCCEED +crazystereo.rxn:FAILED +--- + ++++ + +@@ -216,7 +216,8 @@ + + 9.062226295471192, + 0.7499902248382568, + 0.0 +- ] ++ ], ++ "stereoLabel": "&1" + }, + { + "label": "C", diff --git a/api/tests/integration/ref/basic/molfile_stereo_desc.py.out b/api/tests/integration/ref/basic/molfile_stereo_desc.py.out index 7a1990e0b6..63cfe19281 100644 --- a/api/tests/integration/ref/basic/molfile_stereo_desc.py.out +++ b/api/tests/integration/ref/basic/molfile_stereo_desc.py.out @@ -2360,7 +2360,7 @@ M V30 COUNTS 15 16 1 0 0 M V30 BEGIN ATOM M V30 1 C 0.0884 2.7107 0.0 0 M V30 2 C -0.6261 2.2982 0.0 0 -M V30 3 C -0.6261 1.4732 0.0 0 CFG=3 +M V30 3 C -0.6261 1.4732 0.0 0 CFG=1 M V30 4 C 0.0884 1.0607 0.0 0 M V30 5 C 0.8029 1.4732 0.0 0 M V30 6 C 0.8029 2.2982 0.0 0 @@ -2393,7 +2393,7 @@ M V30 15 2 13 14 M V30 16 1 13 15 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 7) +M V30 MDLV30/STERAC1 ATOMS=(2 3 7) M V30 END COLLECTION M V30 BEGIN SGROUP M V30 1 DAT 1 ATOMS=(1 7) FIELDNAME=INDIGO_CIP_DESC FIELDDISP=" 0.0000 - diff --git a/api/tests/integration/ref/basic/stereocenters.py.out b/api/tests/integration/ref/basic/stereocenters.py.out index 4db078722d..5fe0fc8258 100644 --- a/api/tests/integration/ref/basic/stereocenters.py.out +++ b/api/tests/integration/ref/basic/stereocenters.py.out @@ -30,7 +30,7 @@ C(P)(O)N 12,18,19,-1 13,20,18,-1 15,21,16,-1 -3: [C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C +3: [C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C 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|wU:1.1,7.7,13.14,18.20,29.31,26.35,wD:6.5,9.16,4.17,3.22,0.23,24.26,27.29,23.34,(0.82,0.83,;0.36,1.57,;0.76,2.31,;-0.48,1.53,;-0.88,0.78,;-1.72,0.75,;-2.13,-0.01,;-2.99,-0.02,;-3.43,0.68,;-3.39,-0.78,;-2.93,-1.50,;-3.33,-2.26,;-2.07,-1.47,;-1.67,-0.72,;-0.82,-0.69,;-0.37,-1.41,;-4.23,-0.81,;-0.42,0.05,;0.42,0.08,;0.87,-0.63,;0.47,-1.38,;-0.93,2.26,;1.67,0.87,;2.13,0.14,;2.98,0.18,;3.38,0.93,;3.44,-0.53,;3.03,-1.29,;3.49,-2.00,;2.18,-1.32,;1.78,-2.07,;0.92,-2.10,;1.73,-0.60,;4.28,-0.50,)| 1,2,3,-1 0,5,4,-1 0,7,8,-1 @@ -91,7 +91,7 @@ C(P)(O)N 18,27,26,-1 18,28,29,-1 23,32,30,-1 -8: [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O2)O)O1)O +8: [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,25.26,27.28,24.32,15.35,wD:0.0,5.10,13.14,16.17,21.21,22.23,12.34,(-2.18,-0.79,;-1.50,-1.14,;-0.88,-0.70,;-2.43,-1.51,;-1.99,-2.13,;-3.18,-1.50,;-3.39,-0.76,;-4.13,-0.49,;-4.25,0.24,;-2.79,-0.33,;-3.64,-2.09,;-1.63,0.09,;-0.95,0.45,;-0.94,1.21,;-1.59,1.60,;-0.27,1.57,;0.38,1.18,;1.03,1.54,;0.36,0.42,;0.99,0.02,;1.66,0.39,;2.31,-0.01,;2.98,0.34,;3.00,1.11,;3.63,-0.04,;3.61,-0.80,;4.26,-1.19,;2.93,-1.16,;2.92,-1.91,;2.24,-2.28,;2.29,-0.76,;4.29,0.31,;-0.31,0.06,;-0.25,2.33,)| 1,3,2,4 0,8,7,-1 1,10,11,-1 @@ -106,7 +106,7 @@ C(P)(O)N 24,29,30,-1 25,31,29,-1 26,27,32,-1 -9: [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O3)O)O2)O)O1)O +9: [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O3)O)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,25.26,27.28,34.35,36.37,33.41,24.44,15.47,wD:0.0,5.10,13.14,16.17,21.21,22.23,30.30,31.32,12.46,(-2.54,-1.21,;-2.00,-1.50,;-1.48,-1.14,;-2.76,-1.79,;-2.40,-2.31,;-3.39,-1.79,;-3.56,-1.17,;-4.14,-0.97,;-4.27,-0.35,;-3.05,-0.84,;-3.77,-2.27,;-2.22,-0.69,;-1.97,-0.13,;-2.33,0.38,;-2.94,0.31,;-2.07,0.94,;-1.45,0.99,;-1.20,1.56,;-1.08,0.49,;-0.47,0.55,;-0.22,1.11,;0.40,1.17,;0.64,1.73,;0.30,2.24,;1.25,1.80,;1.62,1.30,;2.24,1.35,;1.37,0.72,;1.72,0.22,;2.34,0.29,;2.70,-0.21,;3.32,-0.15,;3.58,0.40,;3.68,-0.66,;3.42,-1.22,;3.78,-1.73,;2.80,-1.28,;2.54,-1.84,;1.93,-1.91,;2.44,-0.78,;4.30,-0.59,;0.74,0.66,;1.52,2.36,;-1.35,-0.07,;-2.43,1.43,)| 1,3,2,4 0,8,7,-1 1,10,11,-1 @@ -179,7 +179,7 @@ C(P)(O)N 78,85,84,-1 79,84,86,-1 80,81,83,-1 -13: [C@@H]1(O[C@@H]2O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)COC(=O)C)[C@@H](COC(=O)C)O[C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C +13: [C@@H]1(O[C@@H]2O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)COC(=O)C)[C@@H](COC(=O)C)O[C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C |wU:2.2,10.10,4.20,25.26,42.44,wD:0.0,5.5,15.16,32.33,37.38,(1.18,-0.62,;0.39,-1.08,;-0.33,-0.61,;-0.33,0.23,;-1.12,0.67,;-1.89,0.23,;-2.68,0.67,;-2.68,1.57,;-3.44,2.03,;-1.89,2.02,;-1.89,-0.63,;-2.68,-1.08,;-3.43,-0.62,;-4.23,-1.07,;-3.43,0.24,;-1.12,-1.07,;-1.11,-1.97,;-1.89,-2.43,;-1.89,-3.32,;-2.68,-1.97,;-1.12,1.57,;-0.33,2.03,;-0.34,2.93,;0.39,3.38,;-1.12,3.38,;1.18,0.22,;0.40,0.66,;0.40,1.56,;1.19,2.02,;1.19,2.93,;2.03,1.63,;1.95,0.70,;2.74,0.24,;3.49,0.70,;3.49,1.59,;4.28,2.04,;2.74,2.05,;2.74,-0.60,;3.50,-1.07,;3.50,-1.97,;4.28,-2.42,;2.73,-2.41,;1.95,-1.06,;1.95,-1.96,;1.18,-2.42,;1.19,-3.30,;0.39,-1.98,)| 1,2,3,-1 0,4,5,-1 0,7,6,-1 @@ -190,7 +190,7 @@ C(P)(O)N 13,29,28,-1 14,28,31,-1 20,22,34,-1 -14: [C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@@H](O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O +14: [C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@@H](O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O |wU:1.1,7.7,13.14,18.20,35.37,32.41,40.43,26.47,wD:6.5,10.10,9.16,4.17,3.22,0.23,24.26,27.29,30.32,33.35,29.40,23.46,(0.63,-0.13,;0.87,-0.52,;0.58,-0.96,;1.36,-0.52,;1.60,-0.11,;2.17,-0.11,;2.70,-0.15,;2.97,-0.62,;2.72,-1.08,;3.48,-0.60,;3.75,-0.15,;4.31,-0.15,;3.48,0.29,;2.96,0.29,;2.68,0.77,;2.93,1.23,;3.73,-1.08,;1.36,0.31,;0.87,0.31,;0.59,0.77,;0.83,1.22,;1.63,-0.99,;0.11,-0.17,;-0.51,-0.23,;-0.76,-0.70,;-0.47,-1.18,;-1.30,-0.70,;-1.57,-0.24,;-2.12,-0.24,;-2.66,-0.21,;-2.91,-0.67,;-2.62,-1.15,;-3.44,-0.68,;-3.70,-0.22,;-4.28,-0.22,;-3.46,0.23,;-3.76,0.71,;-3.50,1.18,;-2.93,0.23,;-3.70,-1.18,;-1.31,0.20,;-1.60,0.68,;-1.34,1.15,;-0.80,0.21,;-1.56,-1.20,)| 1,2,3,-1 0,5,4,-1 0,7,8,-1 @@ -326,7 +326,7 @@ C(P)(O)N 26,31,32,-1 27,33,31,-1 28,34,29,-1 -22: [C@@]1(COC(=O)C(C)C)(O[C@@H]([C@@H](OC(=O)C(C)C)[C@@H]1OC(=O)C(C)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C(C)C)[C@H](OC(=O)C(C)C)[C@H]1OC(=O)C(C)C)COC(=O)C +22: [C@@]1(COC(=O)C(C)C)(O[C@@H]([C@@H](OC(=O)C(C)C)[C@@H]1OC(=O)C(C)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C(C)C)[C@H](OC(=O)C(C)C)[C@H]1OC(=O)C(C)C)COC(=O)C |wU:17.18,9.24,0.29,40.41,32.55,wD:0.0,10.10,30.31,33.34,47.49,(-0.96,-0.08,;-1.03,-0.81,;-0.47,-1.28,;-0.57,-2.03,;0.03,-2.50,;-1.21,-2.32,;-1.31,-3.08,;-1.81,-1.87,;-0.84,0.64,;-1.52,0.97,;-2.02,0.42,;-2.79,0.54,;-3.07,1.25,;-2.58,1.85,;-3.82,1.36,;-4.28,0.75,;-4.10,2.06,;-1.70,-0.22,;-2.02,-0.87,;-2.76,-0.93,;-3.21,-0.31,;-3.12,-1.61,;-3.87,-1.64,;-2.69,-2.23,;-1.64,1.72,;-1.06,2.21,;-1.43,2.86,;-1.06,3.51,;-1.95,2.88,;-0.22,-0.01,;0.40,-0.38,;0.40,-1.11,;1.04,-1.48,;1.69,-1.11,;2.34,-1.48,;2.99,-1.11,;2.99,-0.37,;3.63,-1.48,;3.63,-2.22,;4.28,-1.11,;1.69,-0.37,;2.33,-0.01,;2.34,0.73,;1.69,1.10,;2.99,1.10,;3.63,0.73,;2.99,1.86,;1.04,-0.01,;1.04,0.73,;0.47,1.22,;-0.21,0.95,;0.61,1.94,;0.04,2.43,;1.31,2.21,;1.04,-2.22,;1.76,-2.41,;1.83,-3.16,;2.51,-3.46,;1.23,-3.59,)| 1,3,2,4 0,6,5,-1 1,8,10,-1 @@ -365,7 +365,7 @@ C(P)(O)N 1,9,10,-1 2,9,11,-1 4,13,6,-1 -26: [C@@]1(COC(=O)C2=CC=CC=C2)(O[C@@H]([C@@H](OC(=O)C2C=CC=CC=2)[C@@H]1OC(=O)C1=CC=CC=C1)COC(=O)C1C=CC=CC=1)O[C@H]1O[C@@H]([C@@H](OC(=O)C2C=CC=CC=2)[C@H](OC(=O)C2C=CC=CC=2)[C@H]1OC(=O)C1=CC=CC=C1)COC(=O)C1C=CC=CC=1 +26: [C@@]1(COC(=O)C2=CC=CC=C2)(O[C@@H]([C@@H](OC(=O)C2C=CC=CC=2)[C@@H]1OC(=O)C1=CC=CC=C1)COC(=O)C1C=CC=CC=1)O[C@H]1O[C@@H]([C@@H](OC(=O)C2C=CC=CC=2)[C@H](OC(=O)C2C=CC=CC=2)[C@H]1OC(=O)C1=CC=CC=C1)COC(=O)C1C=CC=CC=1 |wU:23.26,12.36,0.47,57.63,46.85,wD:0.0,13.14,44.49,47.52,67.75,(-0.58,0.14,;-0.60,-0.40,;-0.12,-0.67,;-0.12,-1.21,;0.31,-1.51,;-0.61,-1.49,;-0.63,-2.01,;-1.08,-2.29,;-1.56,-2.01,;-1.53,-1.47,;-1.07,-1.20,;-0.46,0.65,;-0.92,0.95,;-1.32,0.60,;-1.85,0.71,;-2.02,1.23,;-1.64,1.64,;-2.56,1.36,;-2.70,1.88,;-3.25,2.00,;-3.63,1.58,;-3.47,1.08,;-2.92,0.95,;-1.11,0.09,;-1.39,-0.36,;-1.94,-0.33,;-2.20,0.09,;-2.22,-0.80,;-1.96,-1.29,;-2.22,-1.76,;-2.78,-1.75,;-3.05,-1.27,;-2.76,-0.80,;-0.96,1.49,;-0.52,1.82,;-0.58,2.35,;-0.28,2.54,;-0.98,2.70,;-1.50,2.51,;-1.92,2.85,;-1.82,3.40,;-1.32,3.59,;-0.92,3.23,;-0.04,0.09,;0.40,-0.21,;0.36,-0.74,;0.80,-1.04,;1.30,-0.80,;1.74,-1.11,;2.23,-0.87,;2.28,-0.34,;2.69,-1.16,;3.18,-0.93,;3.63,-1.23,;3.59,-1.78,;3.10,-2.02,;2.64,-1.72,;1.33,-0.27,;1.82,-0.04,;1.85,0.50,;1.40,0.80,;2.35,0.74,;2.38,1.29,;2.88,1.53,;3.32,1.22,;3.29,0.68,;2.80,0.44,;0.88,0.03,;0.91,0.57,;0.47,0.87,;0.00,0.63,;0.50,1.40,;0.99,1.64,;1.02,2.19,;0.59,2.49,;0.10,2.26,;0.06,1.71,;0.77,-1.58,;1.20,-1.88,;1.16,-2.43,;0.68,-2.66,;1.61,-2.74,;1.57,-3.28,;2.02,-3.59,;2.52,-3.37,;2.56,-2.82,;2.11,-2.51,)| 1,3,2,4 0,6,5,-1 1,8,10,-1 @@ -375,7 +375,7 @@ C(P)(O)N 12,30,29,-1 13,29,32,-1 19,21,40,-1 -27: [C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)CO[C@H]1O[C@@H]([C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C +27: [C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)CO[C@H]1O[C@@H]([C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C |wU:0.0,8.8,32.33,26.43,47.49,52.54,46.64,wD:13.14,7.18,0.23,24.25,27.28,37.39,44.45,57.60,(-2.28,-0.50,;-2.97,-0.42,;-3.23,0.21,;-3.92,0.29,;-4.19,0.94,;-4.34,-0.23,;-1.59,-0.46,;-1.32,-1.10,;-1.85,-1.55,;-1.80,-2.23,;-1.17,-2.53,;-1.12,-3.22,;-0.60,-2.14,;-2.44,-1.18,;-3.08,-1.44,;-3.18,-2.14,;-3.82,-2.40,;-2.62,-2.55,;-0.64,-1.26,;-0.17,-0.75,;0.48,-0.92,;0.97,-0.41,;0.67,-1.58,;-2.27,0.17,;-1.65,0.50,;-1.06,0.14,;-0.46,0.47,;-0.43,1.16,;0.16,1.49,;0.18,2.19,;0.79,2.50,;-0.40,2.54,;-1.03,1.52,;-1.01,2.21,;-1.60,2.57,;-1.58,3.27,;-2.20,2.25,;-1.64,1.19,;-2.23,1.54,;-2.84,1.22,;-3.42,1.59,;-2.86,0.53,;0.12,0.11,;0.73,0.43,;1.32,0.07,;1.30,-0.60,;1.89,-0.97,;2.51,-0.64,;3.10,-1.00,;3.71,-0.67,;4.30,-1.03,;3.72,0.01,;2.53,0.04,;3.13,0.37,;3.16,1.06,;3.76,1.39,;2.56,1.42,;1.93,0.40,;1.95,1.09,;1.36,1.46,;1.38,2.14,;0.75,1.12,;1.88,-1.65,;1.26,-1.99,;1.24,-2.68,;0.64,-3.01,;1.84,-3.04,)| 1,3,2,4 0,6,5,-1 1,8,10,-1 @@ -390,7 +390,7 @@ C(P)(O)N 45,51,50,-1 46,50,53,-1 47,54,49,-1 -28: [C@@H]1(OS(=O)(=O)C2=CC=C(C)C=C2)[C@@H](OS(=O)(=O)C2C=CC(C)=CC=2)[C@H](O[C@@H]2COC(C3C=CC=CC=3)O[C@@H]12)OC +28: [C@@H]1(OS(=O)(=O)C2=CC=C(C)C=C2)[C@@H](OS(=O)(=O)C2C=CC(C)=CC=2)[C@H](O[C@@H]2COC(C3C=CC=CC=3)O[C@@H]12)OC |wU:0.0,26.28,wD:12.13,37.39,24.42,(-0.58,0.96,;-0.95,0.29,;-0.57,-0.35,;-1.21,-0.72,;0.08,0.02,;-0.20,-1.00,;-0.59,-1.64,;-0.20,-2.32,;0.53,-2.32,;0.86,-2.98,;0.92,-1.66,;0.55,-1.00,;0.19,0.96,;0.61,0.34,;1.34,0.34,;1.34,1.09,;1.35,-0.40,;2.09,0.35,;2.46,1.00,;3.20,1.01,;3.60,0.36,;4.34,0.35,;3.24,-0.28,;2.47,-0.30,;0.54,1.61,;0.17,2.26,;-0.58,2.26,;-0.97,2.90,;-1.73,2.89,;-2.09,2.26,;-2.84,2.26,;-3.21,1.61,;-3.97,1.61,;-4.34,2.26,;-3.99,2.89,;-3.22,2.90,;-1.71,1.61,;-0.96,1.61,;1.30,1.61,;1.67,2.26,)| 1,2,3,-1 0,4,5,-1 0,7,6,-1 @@ -406,7 +406,7 @@ C(P)(O)N 12,26,25,-1 13,25,28,-1 18,20,33,-1 -30: [C@@]1(COCC(O)C)(O[C@@H]([C@@H](OCC(O)C)[C@@H]1OCC(O)C)COCC(O)C)O[C@H]1O[C@@H]([C@@H](OCC(O)C)[C@H](OCC(O)C)[C@H]1OCC(O)C)COCC(O)C +30: [C@@]1(COCC(O)C)(O[C@@H]([C@@H](OCC(O)C)[C@@H]1OCC(O)C)COCC(O)C)O[C@H]1O[C@@H]([C@@H](OCC(O)C)[C@H](OCC(O)C)[C@H]1OCC(O)C)COCC(O)C |wU:0.0,9.9,37.38,30.50,wD:15.16,8.21,0.27,28.29,31.32,43.45,(-0.91,0.71,;-1.20,1.39,;-0.77,1.98,;-1.07,2.67,;-1.80,2.62,;-2.22,3.24,;-2.13,1.95,;-0.48,0.11,;-0.91,-0.47,;-1.62,-0.23,;-2.22,-0.68,;-2.14,-1.41,;-2.75,-1.85,;-2.67,-2.59,;-3.42,-1.55,;-1.62,0.47,;-2.22,0.92,;-2.89,0.61,;-3.49,1.05,;-4.17,0.75,;-3.42,1.80,;-0.69,-1.18,;0.05,-1.29,;0.26,-2.00,;-0.23,-2.54,;-0.02,-3.26,;-0.95,-2.38,;-0.28,1.07,;0.35,0.70,;0.35,-0.01,;0.99,-0.39,;1.64,-0.01,;2.28,-0.39,;2.92,-0.01,;3.57,-0.39,;4.21,-0.02,;3.57,-1.13,;1.64,0.70,;2.28,1.07,;2.29,1.82,;2.93,2.19,;2.93,2.93,;3.58,1.82,;1.00,1.07,;1.00,1.81,;0.43,2.29,;0.56,3.03,;-0.00,3.51,;1.25,3.28,;0.98,-1.13,;1.62,-1.51,;1.48,-2.23,;2.05,-2.72,;1.93,-3.46,;2.74,-2.47,)| 1,3,2,4 0,6,5,-1 1,8,10,-1 @@ -443,7 +443,7 @@ C(P)(O)N 8,18,19,-1 9,20,18,-1 13,22,14,-1 -34: C1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)O1)O +34: C1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)O1)O |wU:1.1,7.7,13.14,18.20,29.31,38.40,35.44,26.47,wD:6.5,9.16,4.17,3.22,24.26,27.29,32.33,33.35,36.38,23.46,(-0.41,-2.19,;0.07,-2.75,;-0.13,-3.46,;0.80,-2.58,;1.03,-1.88,;1.76,-1.73,;1.98,-1.02,;2.69,-0.89,;3.22,-1.41,;2.91,-0.18,;2.42,0.37,;2.65,1.08,;1.68,0.21,;1.45,-0.49,;0.76,-0.64,;0.25,-0.10,;3.63,-0.01,;0.54,-1.34,;-0.20,-1.48,;-0.70,-0.96,;-0.48,-0.25,;1.30,-3.14,;-1.14,-2.35,;-1.63,-1.80,;-2.35,-1.97,;-2.59,-2.68,;-2.87,-1.41,;-2.63,-0.70,;-3.13,-0.18,;-1.90,-0.57,;-1.70,0.13,;-2.21,0.68,;-1.98,1.39,;-2.48,1.93,;-3.20,1.78,;-2.25,2.64,;-1.52,2.80,;-1.31,3.51,;-1.01,2.25,;-0.29,2.41,;0.19,1.86,;-1.24,1.54,;-2.76,3.19,;-1.41,-1.11,;-3.59,-1.58,)| 0,5,4,-1 0,7,8,-1 2,11,12,-1 @@ -462,7 +462,7 @@ C(P)(O)N 34,40,41,-1 35,42,40,-1 37,43,38,-1 -35: [C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@H](OCCSCCC(=O)OC)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)O1)O +35: [C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@H](OCCSCCC(=O)OC)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)O1)O |wU:1.1,7.7,10.10,22.23,27.29,38.40,47.49,44.53,35.56,wD:6.5,9.25,4.26,3.31,0.32,33.35,36.38,41.42,42.44,45.47,32.55,(-0.78,-2.38,;-0.52,-2.92,;-0.83,-3.41,;0.08,-2.95,;0.40,-2.46,;1.00,-2.50,;1.33,-1.98,;1.93,-2.03,;2.19,-2.56,;2.24,-1.53,;1.98,-0.99,;2.31,-0.50,;2.03,0.03,;2.37,0.51,;2.11,1.04,;2.44,1.53,;2.18,2.06,;2.51,2.55,;3.10,2.52,;2.25,3.10,;2.57,3.59,;1.39,-0.96,;1.06,-1.46,;0.47,-1.42,;0.20,-0.90,;2.84,-1.56,;0.13,-1.92,;-0.46,-1.89,;-0.71,-1.36,;-0.37,-0.86,;0.34,-3.48,;-1.37,-2.34,;-1.63,-1.80,;-2.24,-1.77,;-2.57,-2.26,;-2.48,-1.24,;-2.14,-0.76,;-2.42,-0.22,;-1.57,-0.79,;-1.23,-0.31,;-1.50,0.22,;-1.17,0.73,;-1.44,1.26,;-2.02,1.30,;-1.10,1.74,;-0.51,1.71,;-0.19,2.21,;-0.26,1.17,;0.34,1.14,;0.60,0.61,;-0.57,0.68,;-1.38,2.28,;-1.29,-1.33,;-3.07,-1.22,)| 1,2,3,-1 0,5,4,-1 0,7,8,-1 @@ -483,7 +483,7 @@ C(P)(O)N 34,41,42,-1 35,43,41,-1 37,45,38,-1 -36: [C@@]1(CO[Si](C)(C)C)(O[C@@H]([C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C)CO[Si](C)(C)C)O[C@H]1O[C@@H]([C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)CO[Si](C)(C)C +36: [C@@]1(CO[Si](C)(C)C)(O[C@@H]([C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C)CO[Si](C)(C)C)O[C@H]1O[C@@H]([C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)CO[Si](C)(C)C |wU:15.16,8.21,0.27,37.38,30.50,wD:0.0,9.9,28.29,31.32,43.45,(0.83,-0.49,;0.52,-1.32,;1.10,-1.97,;0.79,-2.78,;0.51,-3.54,;1.60,-3.03,;-0.02,-2.46,;1.54,-1.01,;2.26,-0.52,;2.00,0.27,;2.52,0.97,;2.18,1.76,;1.82,2.54,;2.94,2.09,;1.37,1.44,;1.12,0.28,;0.62,1.00,;-0.06,1.44,;-0.74,1.97,;0.51,2.25,;-0.45,0.81,;3.08,-0.76,;3.71,-0.18,;3.52,0.65,;4.34,0.83,;2.68,0.46,;3.33,1.47,;0.12,-0.18,;-0.60,-0.17,;-1.04,0.57,;-1.92,0.57,;-2.35,-0.16,;-3.22,-0.16,;-3.64,0.57,;-4.34,0.13,;-2.91,1.01,;-4.07,1.26,;-1.92,-0.93,;-2.36,-1.69,;-3.20,-1.69,;-3.19,-2.51,;-3.22,-0.83,;-4.03,-1.70,;-1.04,-0.93,;-0.60,-1.71,;-1.05,-2.42,;-0.33,-2.85,;-1.78,-2.00,;-1.47,-3.16,;-2.36,1.33,;-1.93,2.09,;-2.35,2.83,;-1.62,3.22,;-3.09,2.41,;-2.74,3.54,)| 1,3,2,4 0,6,5,-1 1,8,10,-1 @@ -527,7 +527,7 @@ C(P)(O)N 0,7,6,-1 1,10,9,-1 2,11,9,-1 -41: [C@@H]1(O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C +41: [C@@H]1(O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C |wU:8.8,2.18,32.33,26.43,wD:3.3,13.14,0.23,24.25,27.28,37.39,(-0.53,0.87,;-1.16,1.40,;-1.93,1.07,;-2.05,0.25,;-2.80,-0.07,;-3.49,0.43,;-4.24,0.11,;-3.37,1.26,;-1.40,-0.27,;-1.50,-1.09,;-2.27,-1.40,;-2.39,-2.23,;-2.93,-0.91,;-0.62,0.07,;0.03,-0.46,;-0.07,-1.28,;0.59,-1.79,;-0.85,-1.61,;-2.59,1.58,;-2.49,2.41,;-3.14,2.90,;-3.93,2.59,;-3.06,3.49,;0.23,1.18,;0.89,0.68,;0.77,-0.14,;1.43,-0.66,;2.20,-0.35,;2.86,-0.87,;3.63,-0.56,;4.29,-1.08,;3.75,0.25,;2.32,0.46,;3.10,0.78,;3.22,1.60,;4.00,1.91,;2.56,2.11,;1.67,0.98,;1.79,1.80,;1.13,2.32,;1.25,3.15,;0.36,2.01,;1.30,-1.48,;1.97,-2.00,;1.84,-2.83,;2.49,-3.34,;1.07,-3.14,)| 1,2,3,-1 0,4,5,-1 1,9,8,-1 @@ -609,7 +609,7 @@ C(P)(O)N 62,71,70,-1 62,72,73,-1 67,76,74,-1 -49: [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)O1)O +49: [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,21.21,27.28,24.32,15.35,wD:0.0,5.10,13.14,16.17,22.23,25.26,12.34,(-2.36,-0.36,;-1.84,-0.95,;-1.09,-0.76,;-2.87,-0.95,;-2.68,-1.71,;-3.58,-0.67,;-3.51,0.10,;-4.11,0.63,;-3.95,1.40,;-2.77,0.29,;-4.24,-1.07,;-1.76,0.09,;-1.07,0.46,;-1.06,1.24,;-1.71,1.64,;-0.37,1.60,;0.30,1.20,;0.97,1.57,;0.28,0.42,;0.92,0.02,;1.61,0.39,;2.27,-0.01,;2.95,0.35,;2.97,1.13,;3.62,-0.04,;3.60,-0.81,;4.26,-1.21,;2.90,-1.18,;2.89,-1.95,;2.20,-2.33,;2.24,-0.77,;4.29,0.32,;-0.40,0.06,;-0.35,2.38,)| 1,3,2,4 0,8,7,-1 1,10,11,-1 @@ -624,7 +624,7 @@ C(P)(O)N 24,29,30,-1 25,31,29,-1 26,32,27,-1 -50: [C@]12([H])C(=O)C=C3[C@]4([H])C[C@@](CC[C@@]4(CC[C@@]3(C)[C@]1(C)CC[C@@]1([H])C(C)(C)[C@H](CC[C@]21C)O[C@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O[C@H]1[C@H](O)[C@H]([C@H](O)[C@@H](C(=O)O)O1)O)C(=O)O)C)(C)C(=O)O +50: 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[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@@H](O[C@H]3[C@H](O)[C@H]([C@@H](OC4C=CC([N+]([O-])=O)=CC=4)O[C@@H]3CO)O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O[C@@H]2[C@H](O)[C@H]([C@H](O[C@@H]3[C@H](O)[C@H]([C@H](O)[C@@H](CO)O3)O)[C@@H](CO)O2)O)[C@@H](CO)O1)O +54: [C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@@H](O[C@H]3[C@H](O)[C@H]([C@@H](OC4C=CC([N+]([O-])=O)=CC=4)O[C@@H]3CO)O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O[C@@H]2[C@H](O)[C@H]([C@H](O[C@@H]3[C@H](O)[C@H]([C@H](O)[C@@H](CO)O3)O)[C@@H](CO)O2)O)[C@@H](CO)O1)O 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1,2,3,-1 0,5,4,-1 0,7,8,-1 @@ -894,7 +894,7 @@ C(P)(O)N 1,8,9,-1 2,10,8,-1 4,12,5,-1 -68: C12=C(C(C)COC(=O)C)C[C@H](O)[C@]1(C)C=C1[C@@H](COC)CC[C@@]1([H])[C@@H](C)[C@@H](O)[C@@H]2O[C@H]1O[C@@H]([C@@H](O)[C@H](OC(=O)C)[C@H]1O)COC(C)(C)C=C |t:15| +68: C12=C(C(C)COC(=O)C)C[C@H](O)[C@]1(C)C=C1[C@@H](COC)CC[C@@]1([H])[C@@H](C)[C@@H](O)[C@@H]2O[C@H]1O[C@@H]([C@@H](O)[C@H](OC(=O)C)[C@H]1O)COC(C)(C)C=C |t:15,wU:12.13,16.17,24.26,26.28,35.38,32.45,wD:10.10,22.24,28.31,30.33,33.36,40.44,(0.99,-1.31,;1.53,-1.09,;1.67,-0.50,;1.23,-0.09,;2.24,-0.33,;2.39,0.25,;1.96,0.67,;1.39,0.49,;2.09,1.26,;1.89,-1.61,;1.53,-2.10,;1.69,-2.67,;0.99,-1.92,;1.05,-2.48,;0.62,-2.25,;-0.02,-2.25,;-0.40,-2.76,;-0.23,-3.34,;0.35,-3.48,;0.78,-3.04,;-0.98,-2.57,;-0.94,-1.99,;-0.38,-1.86,;-0.98,-1.56,;-0.37,-1.26,;-0.88,-0.92,;-0.02,-0.89,;-0.44,-0.44,;0.67,-0.89,;0.37,0.45,;-0.11,0.83,;-0.00,1.49,;-0.54,1.91,;-1.18,1.66,;-1.64,2.02,;-1.26,0.98,;-1.82,0.73,;-1.89,0.13,;-1.41,-0.22,;-2.44,-0.08,;-0.73,0.57,;-0.82,-0.03,;-0.46,2.51,;-0.93,2.87,;-1.48,2.65,;-2.03,2.81,;-1.96,2.31,;-1.56,3.36,;-2.11,3.59,)| 0,4,5,6 0,7,8,-1 1,12,9,-1 @@ -913,7 +913,7 @@ C(P)(O)N 1,8,9,-1 2,10,8,-1 4,14,5,-1 -70: 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[C@@H]12[C@H](O)[C@H]([C@@H](O[C@H]3[C@H](O)[C@H]([C@@H](O[C@H]4[C@H](O)[C@H]([C@@H](O[C@H]5[C@H](O)[C@H]([C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O1)O)O[C@@H]4COC1[C@H](O)[C@H]([C@H](O[C@@H]4[C@H](O)[C@H]([C@H](O)[C@@H](CO)O4)O)[C@@H](CO)O1)O)O)O[C@@H]3COC1[C@H](O)[C@H]([C@H](O[C@@H]3[C@H](O)[C@H]([C@H](O)[C@@H](CO)O3)O)[C@@H](CO)O1)O)O)O[C@@H]2COC1[C@H](O)[C@H](C(O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O)O +267: [C@@H]12[C@H](O)[C@H]([C@@H](O[C@H]3[C@H](O)[C@H]([C@@H](O[C@H]4[C@H](O)[C@H]([C@@H](O[C@H]5[C@H](O)[C@H]([C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O1)O)O[C@@H]4COC1[C@H](O)[C@H]([C@H](O[C@@H]4[C@H](O)[C@H]([C@H](O)[C@@H](CO)O4)O)[C@@H](CO)O1)O)O)O[C@@H]3COC1[C@H](O)[C@H]([C@H](O[C@@H]3[C@H](O)[C@H]([C@H](O)[C@@H](CO)O3)O)[C@@H](CO)O1)O)O)O[C@@H]2COC1[C@H](O)[C@H](C(O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O)O |wU:4.4,7.7,13.13,19.19,24.25,39.40,36.44,44.46,30.50,51.54,57.61,72.76,69.80,77.82,63.86,84.90,90.97,105.112,102.116,110.118,96.122,116.124,119.128,138.148,135.152,143.154,129.158,121.159,0.160,151.165,166.180,163.184,171.186,157.190,178.195,193.210,190.214,198.216,184.220,220.240,217.244,225.246,211.250,3.251,wD:1.1,6.5,10.10,12.11,16.16,18.17,28.29,31.32,33.33,34.35,37.38,22.51,50.52,53.56,61.65,64.68,66.69,67.71,70.74,55.87,83.88,86.92,94.101,97.104,99.105,100.107,103.110,88.123,117.126,123.133,127.137,130.140,132.141,133.143,136.146,21.161,155.169,158.172,160.173,161.175,164.178,15.191,182.199,185.202,187.203,188.205,191.208,9.221,205.225,209.229,214.233,215.235,218.238,(-0.28,-1.50,;-0.45,-1.59,;-0.45,-1.78,;-0.61,-1.50,;-0.62,-1.31,;-0.90,-1.18,;-0.90,-0.99,;-0.73,-0.91,;-0.57,-1.01,;-0.71,-0.72,;-0.87,-0.61,;-0.86,0.05,;-0.65,0.53,;-0.48,0.62,;-0.32,0.52,;-0.48,0.81,;-0.64,0.91,;-0.62,1.20,;-0.37,1.32,;-0.20,1.23,;-0.20,1.04,;-0.03,1.32,;-0.03,1.52,;-0.20,1.61,;-0.37,1.51,;-0.53,1.61,;-0.53,1.82,;-0.72,1.90,;-0.91,1.79,;-0.91,1.59,;-1.11,1.90,;-1.10,2.11,;-1.30,2.22,;-1.50,2.12,;-1.50,1.90,;-1.33,1.80,;-1.69,1.80,;-1.88,1.90,;-2.09,1.81,;-1.88,2.13,;-2.08,2.24,;-2.27,2.14,;-1.68,2.23,;-1.70,1.59,;-0.90,2.20,;-0.89,2.43,;-1.10,2.54,;-0.72,2.10,;-1.29,1.85,;0.19,1.67,;0.47,1.56,;0.47,1.36,;0.31,1.27,;0.64,1.27,;0.64,1.08,;0.81,1.37,;0.81,1.57,;0.63,1.66,;0.63,1.85,;0.44,1.92,;0.43,2.13,;0.23,2.22,;0.07,2.12,;0.23,2.46,;0.42,2.57,;0.41,2.80,;0.21,2.91,;0.01,2.80,;0.01,2.58,;-0.18,2.90,;-0.18,3.12,;-0.38,3.22,;0.01,3.23,;0.01,3.46,;-0.18,3.57,;0.20,3.12,;-0.36,2.80,;0.61,2.47,;0.79,2.58,;0.79,2.79,;0.61,2.23,;0.07,2.53,;1.38,0.85,;1.36,0.29,;1.19,0.20,;1.03,0.30,;1.18,0.01,;1.03,-0.08,;1.35,-0.09,;1.52,-0.00,;1.52,0.19,;1.70,0.29,;1.87,0.19,;2.03,0.31,;2.03,0.56,;1.83,0.64,;2.22,0.67,;2.42,0.57,;2.62,0.70,;2.61,0.94,;2.41,1.05,;2.23,0.94,;2.40,1.27,;2.59,1.39,;2.58,1.62,;2.80,1.29,;2.99,1.40,;2.99,1.62,;2.81,1.05,;2.20,1.38,;2.42,0.35,;2.63,0.24,;2.82,0.37,;2.22,0.22,;2.22,0.84,;1.51,-0.46,;0.76,-1.13,;0.76,-1.33,;0.92,-1.41,;0.59,-1.43,;0.60,-1.62,;0.42,-1.34,;0.41,-1.16,;0.57,-1.04,;0.57,-0.85,;0.76,-0.77,;0.77,-0.56,;0.58,-0.43,;0.38,-0.49,;0.61,-0.18,;0.82,-0.11,;0.87,0.12,;0.68,0.26,;0.47,0.18,;0.44,0.01,;0.31,0.32,;0.34,0.54,;0.17,0.68,;0.54,0.61,;0.59,0.85,;0.42,0.99,;0.72,0.47,;0.10,0.25,;0.99,-0.27,;1.16,-0.18,;1.33,-0.30,;0.96,-0.49,;0.49,-0.10,;0.20,-1.56,;0.13,1.25,;-0.81,0.82,;-0.81,0.62,;-0.98,0.53,;-1.12,0.66,;-1.34,0.58,;-1.39,0.36,;-1.25,0.21,;-1.62,0.30,;-1.78,0.46,;-2.01,0.40,;-2.07,0.18,;-1.91,0.02,;-1.69,0.03,;-1.97,-0.20,;-2.19,-0.26,;-2.25,-0.48,;-2.35,-0.09,;-2.57,-0.14,;-2.64,-0.37,;-2.29,0.12,;-1.81,-0.38,;-1.71,0.67,;-1.86,0.84,;-2.09,0.78,;-1.48,0.73,;-1.66,0.14,;-0.32,0.91,;-1.03,-0.70,;-1.07,-0.89,;-1.23,-0.97,;-1.37,-0.84,;-1.59,-0.90,;-1.66,-1.11,;-1.52,-1.29,;-1.90,-1.16,;-2.04,-0.99,;-2.28,-1.03,;-2.36,-1.26,;-2.21,-1.43,;-1.98,-1.41,;-2.29,-1.65,;-2.51,-1.69,;-2.59,-1.90,;-2.66,-1.51,;-2.90,-1.54,;-2.98,-1.76,;-2.58,-1.30,;-2.14,-1.83,;-1.96,-0.78,;-2.11,-0.60,;-2.33,-0.65,;-1.72,-0.74,;-1.97,-1.31,;-0.55,-0.63,;-0.46,-1.22,;-0.29,-1.31,;-0.12,-1.21,;0.10,-1.35,;0.11,-1.99,;0.30,-2.10,;0.50,-2.01,;0.31,-2.36,;0.10,-2.46,;0.09,-2.70,;0.28,-2.83,;0.49,-2.72,;0.53,-2.56,;0.68,-2.86,;0.68,-3.08,;0.88,-3.20,;0.46,-3.19,;0.45,-3.42,;0.64,-3.55,;0.27,-3.06,;0.91,-2.74,;-0.09,-2.34,;-0.29,-2.44,;-0.31,-2.70,;-0.09,-2.10,;0.47,-2.46,;-0.78,-1.60,)| 1,2,3,-1 0,5,4,-1 0,7,8,-1 diff --git a/api/tests/integration/ref/bingo/molecules.py.out b/api/tests/integration/ref/bingo/molecules.py.out index 8eac7d65ec..dc7aad3ec4 100644 --- a/api/tests/integration/ref/bingo/molecules.py.out +++ b/api/tests/integration/ref/bingo/molecules.py.out @@ -55,7 +55,7 @@ Structure 359 excluded: stereocenters: 4 hydrogens near stereocenter 0 Structure 361 excluded: stereocenters: stereo types of non-opposite bonds match near atom 5 Structure 365 excluded: molfile loader: direction of bond #0 makes no sense Structure 372 excluded: molfile loader: direction of bond #5 makes no sense -Structure 380 excluded: molfile loader: direction of bond #0 makes no sense +Structure 380 excluded: molfile loader: direction of bond #2 makes no sense Structure 390 excluded: element: bad valence on C having 3 drawn bonds, charge 0, and 2 radical electrons Structure 400 excluded: molfile loader: direction of bond #9 makes no sense Structure 405 excluded: molfile loader: direction of bond #1 makes no sense @@ -153,6 +153,7 @@ Structure 916 excluded: stereocenters: stereo types of the opposite bonds mismat Structure 931 excluded: stereocenters: one bond up, one bond down -- indefinite case near atom 1 Structure 936 excluded: molfile loader: direction of bond #2 makes no sense Structure 940 excluded: element: bad valence on Ar having 0 drawn bonds, charge 0, and 2 radical electrons +Structure 941 excluded: molfile loader: direction of bond #4 makes no sense Structure 943 excluded: element: bad valence on H having 2 drawn bonds, charge -2, and 0 radical electrons Structure 948 excluded: molfile loader: direction of bond #15 makes no sense Structure 955 excluded: element: bad valence on H having 0 drawn bonds, charge -3, and 0 radical electrons @@ -224,11 +225,12 @@ Structure 1440 excluded: molfile loader: direction of bond #0 makes no sense Structure 1464 excluded: molfile loader: direction of bond #5 makes no sense Structure 1466 excluded: molfile loader: direction of bond #5 makes no sense Structure 1468 excluded: molfile loader: direction of bond #7 makes no sense -Structure 1490 excluded: molfile loader: direction of bond #31 makes no sense +Structure 1490 excluded: molfile loader: direction of bond #32 makes no sense Structure 1492 excluded: stereocenters: directions of neighbor stereo bonds match near atom 0 Structure 1498 excluded: molfile loader: direction of bond #3 makes no sense Structure 1501 excluded: stereocenters: directions of neighbor stereo bonds match near atom 0 Structure 1505 excluded: element: bad valence on C having 4 drawn bonds, charge -1, and 1 radical electrons +Structure 1514 excluded: molfile loader: direction of bond #4 makes no sense Structure 1552 excluded: element: bad valence on H having 1 drawn bonds, charge 1, and 0 radical electrons Structure 1564 excluded: stereocenters: all 3 bonds up near stereoatom 97 Structure 1567 excluded: molfile loader: direction of bond #5 makes no sense @@ -249,7 +251,7 @@ Structure 1692 excluded: stereocenters: all 3 bonds up near stereoatom 6 Structure 1696 excluded: element: bad valence on C having 5 drawn bonds, charge 0, and 0 radical electrons Structure 1718 excluded: molfile loader: direction of bond #0 makes no sense Structure 1733 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 1 -Structure 1739 excluded: molfile loader: direction of bond #2 makes no sense +Structure 1739 excluded: molfile loader: direction of bond #4 makes no sense Structure 1742 excluded: element: bad valence on C having 4 drawn bonds, charge 1, and 1 radical electrons Structure 1753 excluded: element: bad valence on N having 4 drawn bonds, charge 0, and 0 radical electrons Structure 1761 excluded: molfile loader: direction of bond #4 makes no sense @@ -267,6 +269,7 @@ Structure 1831 excluded: molfile loader: direction of bond #9 makes no sense Structure 1842 excluded: element: bad valence on I having 2 drawn bonds, charge 0, and 0 radical electrons Structure 1843 excluded: molfile loader: direction of bond #8 makes no sense Structure 1844 excluded: molfile loader: direction of bond #13 makes no sense +Structure 1846 excluded: molfile loader: direction of bond #4 makes no sense Structure 1848 excluded: molfile loader: direction of bond #9 makes no sense Structure 1851 excluded: stereocenters: 2 hydrogens near stereocenter 8 Structure 1857 excluded: molfile loader: direction of bond #1 makes no sense @@ -300,7 +303,7 @@ Structure 2013 excluded: molfile loader: direction of bond #5 makes no sense Structure 2014 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 0 Structure 2017 excluded: molfile loader: direction of bond #7 makes no sense Structure 2018 excluded: element: bad valence on N having 5 drawn bonds, charge 1, and 0 radical electrons -Finished indexing 2026 structures. 300 wrong structures excluded +Finished indexing 2026 structures. 303 wrong structures excluded ** searchSub(C(CN)C(F)F, '') ** 1986 C(C(C(C(N1CO[Si](C)(C)OC1)=O)(F)F)(F)F)(C(C(C(F)(F)F)(F)F)(F)F)(F)F C(C(C(C(N1CO[Si](C)(C)OC1)=O)(F)F)(F)F)(C(C(C(F)(F)F)(F)F)(F)F)(F)F ** searchSim(C(CN)C(F)F, 0.9, 1, tanimoto) ** @@ -978,7 +981,6 @@ Finished indexing 2026 structures. 300 wrong structures excluded 918 [C@H]12C[C@H]3[C@H]4[C@]56[C@H]([C@H]7[C@]89[C@@H]%10[C@@H]%11C[C@@H](C[C@H]5[C@@H]5C[C@@H](C[C@H]%12[C@@H]%13C[C@@H](C%10)C[C@H]([C@]3%12[C@]86[C@]5%13%11)[C@@H]9C1)C4)C7)C2 [C@H]12C[C@H]3[C@H]4[C@]56[C@H]([C@H]7[C@]89[C@@H]%10[C@@H]%11C[C@@H](C[C@H]5[C@@H]5C[C@@H](C[C@H]%12[C@@H]%13C[C@@H](C%10)C[C@H]([C@]3%12[C@]86[C@]5%13%11)[C@@H]9C1)C4)C7)C2 919 [C@@H]12[C@@]34[12CH]([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C.[12C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[12C@H]12[C@]34C([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,17,18,20,22,23,26,32,34,35,37,39,40,43,49,51,52,54,56,57,60,66,r| [C@@H]12[C@@]34[12CH]([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C.[12C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C.[12C@H]12[C@]34C([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,17,18,20,22,23,26,32,34,35,37,39,40,43,49,51,52,54,56,57,60,66,r| 920 C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP(O[H])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:85,114,143| C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP(O[H])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:85,114,143| - 941 C[C@]1(C/C(=C2/C[C@]([H])(Cl)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H].C[C@]1(C/C(=C2/C[C@]([H])(Br)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,45,50,53,54,55,65,68,73,76,84,r| C[C@]1(C/C(=C2/C[C@]([H])(Cl)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H].C[C@]1(C/C(=C2/C[C@]([H])(Br)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,45,50,53,54,55,65,68,73,76,84,r| 947 O1[C@@H]([C@H](C)CO)[C@@H](O)[C@@H]([C@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1 |&1:1,2,6,8,9,16,17,21,23,24,31,32,36,38,39,r| O1[C@@H]([C@H](C)CO)[C@@H](O)[C@@H]([C@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1.O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1 |&1:1,2,6,8,9,16,17,21,23,24,31,32,36,38,39,r| 950 [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC |&1:0,2,9,r| [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC |&1:0,2,9,r| 968 [C@@H](C[C@@H](C[C@@H](C)C[C@@H](C)N)C)(N)C |&1:0,2,4,7,r| [C@@H](C[C@@H](C[C@@H](C)C[C@@H](C)N)C)(N)C |&1:0,2,4,7,r| @@ -1055,11 +1057,10 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1470 C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] 1477 c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-] c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-] 1481 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] - 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| + 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| 1500 [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] 1510 C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| 1511 c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O - 1514 C[C@]1(C/C(=C2/C[C@]([H])(Cl)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,r| C[C@]1(C/C(=C2/C[C@]([H])(Cl)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Br)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,r| 1523 [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| 1525 [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| 1527 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| @@ -1097,8 +1098,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1803 [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] 1814 [C@@H](C[C@@H](C[C@H](C)C[C@H](C)N)C)(N)C |&1:0,2,4,7,r| [C@@H](C[C@@H](C[C@H](C)C[C@H](C)N)C)(N)C |&1:0,2,4,7,r| - 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| - 1846 C[C@]1(C/C(=C2/C[C@]([H])(Br)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,r| C[C@]1(C/C(=C2/C[C@]([H])(Br)[C@@](=[C@@]3[C@]([H])(C)C/C(=C4/CC([H])(C)[C@@]([H])(C)[C@@](C)([H])C/4)/C[C@@]3([H])C)[C@@]([H])(Cl)C/2)/CC([H])(C)[C@]1([H])C)[H] |&1:1,6,9,10,11,21,24,29,32,40,r| + 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| 1856 [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| 1861 C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C 1862 c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-].c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][nH][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2C([N-]C)=O c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-].c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][nH][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2C([N-]C)=O @@ -1479,7 +1479,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1366 c1(N2C[C@H](CNC(C)=O)OC2=O)cc(F)c([C@]2([C@@]3([H])[C@@]2(C[S@@](C3)=O)[H])[H])cc1 c1(N2C[C@H](CNC(C)=O)OC2=O)cc(F)c([C@]2([C@@]3([H])[C@@]2(C[S@@](C3)=O)[H])[H])cc1 1541 C(C(C([H])([H])[H])(C([H])([H])[H])N(C([C@@]1(C([H])([H])N(C(c2c([H])c([H])c([H])[n]c2[H])([H])[H])C([H])([H])C([H])([H])N1C([C@](C([C@](C(c1c([H])c([H])c([H])c([H])c1[H])([H])[H])(C(N([C@]1(c2c(c(c(c([H])c2C([H])([H])[C@]1(OC(C(C(C(=O)OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])=O)[H])[H])[H])[H])[H])[H])=O)[H])([H])[H])(O[H])[H])([H])[H])[H])=O)[H])([H])([H])[H] C(C(C([H])([H])[H])(C([H])([H])[H])N(C([C@@]1(C([H])([H])N(C(c2c([H])c([H])c([H])[n]c2[H])([H])[H])C([H])([H])C([H])([H])N1C([C@](C([C@](C(c1c([H])c([H])c([H])c([H])c1[H])([H])[H])(C(N([C@]1(c2c(c(c(c([H])c2C([H])([H])[C@]1(OC(C(C(C(=O)OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])=O)[H])[H])[H])[H])[H])[H])=O)[H])([H])[H])(O[H])[H])([H])[H])[H])=O)[H])([H])([H])[H] 1670 N1(CC(=O)OCC=CC1)CP(O)(O)=O N1(CC(=O)OCC=CC1)CP(O)(O)=O - 1766 C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| + 1766 C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] 1962 CN1CCCOCC1 CN1CCCOCC1 1971 [C@]1(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[C@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[H])([H])C2([H])[H])C(=O)O[H])([H])C1([H])[H])(OC1([C@@](O[C@@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](OP(OP(=O)(OC(C(N([H])[H])([H])[H])([H])[H])O[H])(=O)O[H])([H])C(O[C@]3(OC(C(C(O[C@@]4([C@@](O[H])([H])C(O[H])([H])[C@](C(O[H])(C(O[H])([H])[H])[H])(O[H])C([H])([H])O4)[H])([H])[H])(O[H])[H])([H])[C@](OP(=O)(O[H])O[H])([H])C(O[C@]4(C(O[H])([H])C(O[C@]5(C(O[C@]6(C(O[C@@]7([C@](N(C(=O)C([H])([H])[H])[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(O[H])([H])[C@@](O[C@]7(C(O[H])([H])C(OC8([C@](O[H])([H])C(O[H])([H])C(O[C@]9(C(O[C@]%10(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O%10)[H])([H])C(O[C@@]%10(OC(C([H])([H])[H])([H])[C@](O[H])([H])C([H])([H])C%10(O[H])[H])[H])([H])[C@@](O[H])([H])C(C(O[H])([H])[H])([H])O9)[H])([H])[C@@](C([H])([H])[H])([H])O8)[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(C(O[H])([H])[H])([H])O6)[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[C@@](O[H])([H])C(C(O[C@]5(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[H])([H])O4)[H])([H])[C@]3(O[H])[H])[H])([H])[C@]2(O[H])[H])[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O[C@](C(=O)O[H])(OC(C2([C@@](OP(=O)(O[H])O[H])([H])C(OC(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@@](N(C(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)[H])([H])[C@@](OC(C3(O[C@](C(P(=O)(O[H])O[H])([H])[H])([H])C(C(C(C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[C@](OC(C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@]3(O[H])[H])[H])([H])[H])([H])O2)[H])([H])[H])C1([H])[H])[H])C(=O)O[H] [C@]1(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[C@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[H])([H])C2([H])[H])C(=O)O[H])([H])C1([H])[H])(OC1([C@@](O[C@@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](OP(OP(=O)(OC(C(N([H])[H])([H])[H])([H])[H])O[H])(=O)O[H])([H])C(O[C@]3(OC(C(C(O[C@@]4([C@@](O[H])([H])C(O[H])([H])[C@](C(O[H])(C(O[H])([H])[H])[H])(O[H])C([H])([H])O4)[H])([H])[H])(O[H])[H])([H])[C@](OP(=O)(O[H])O[H])([H])C(O[C@]4(C(O[H])([H])C(O[C@]5(C(O[C@]6(C(O[C@@]7([C@](N(C(=O)C([H])([H])[H])[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(O[H])([H])[C@@](O[C@]7(C(O[H])([H])C(OC8([C@](O[H])([H])C(O[H])([H])C(O[C@]9(C(O[C@]%10(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O%10)[H])([H])C(O[C@@]%10(OC(C([H])([H])[H])([H])[C@](O[H])([H])C([H])([H])C%10(O[H])[H])[H])([H])[C@@](O[H])([H])C(C(O[H])([H])[H])([H])O9)[H])([H])[C@@](C([H])([H])[H])([H])O8)[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(C(O[H])([H])[H])([H])O6)[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[C@@](O[H])([H])C(C(O[C@]5(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[H])([H])O4)[H])([H])[C@]3(O[H])[H])[H])([H])[C@]2(O[H])[H])[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O[C@](C(=O)O[H])(OC(C2([C@@](OP(=O)(O[H])O[H])([H])C(OC(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@@](N(C(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)[H])([H])[C@@](OC(C3(O[C@](C(P(=O)(O[H])O[H])([H])[H])([H])C(C(C(C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[C@](OC(C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@]3(O[H])[H])[H])([H])[H])([H])O2)[H])([H])[H])C1([H])[H])[H])C(=O)O[H] @@ -1835,7 +1835,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1408 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] 1470 C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] 1481 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] - 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| + 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| 1500 [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] 1527 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| 1620 C1(COC(C)(C)OC1)(CO)N C1(COC(C)(C)OC1)(CO)N @@ -1846,7 +1846,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1744 C(C1(C([H])([H])C2(C(OC(O2)(C(C(C(C(C(C(C(C(C(C2(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C([H])([H])[H])(/C(=C(/C(C(C(C(C(C3(C([H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C(C4(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(/C(=C(/C(=C(/C(C(C(C(C(/C(=C(/C(=C([H])[H])C(C(C(C(C(C(C([H])([H])[H])(C(C5(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(/C(=C(/C(C(C(C6(C([H])([H])C7(C([H])([H])C(C(O7)(C(C(C7(C(O[H])([H])C([H])([H])C(C(N([H])[H])([H])[H])([H])O7)[H])([H])[H])([H])[H])[H])([H])O6)[H])[H])([H])[H])(O[H])[H])(O[H])[H])\[H])/[H])([H])O5)[H])([H])[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])\[H])/[H])\[H])/[H])(O[H])[H])([H])[H])([H])O4)[H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O3)[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])(O[H])[H])\[H])/[H])[H])(O[H])[H])([H])[H])(O[H])O2)[H])([H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C1([H])[H])(C(C(C([H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C1(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(/C(=C(/C(C(C(C([H])([H])[H])(C(C(=O)N(/C(=C(/C(=O)N(C(C(C(O[H])([H])[H])([H])[H])([H])[H])[H])\[H])/[H])[H])(O[H])[H])[H])([H])[H])(O[H])[H])\[H])/C([H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O1)[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])C([H])([H])[H])[H])([H])([H])[H] C(C1(C([H])([H])C2(C(OC(O2)(C(C(C(C(C(C(C(C(C(C2(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C([H])([H])[H])(/C(=C(/C(C(C(C(C(C3(C([H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C(C4(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(/C(=C(/C(=C(/C(C(C(C(C(/C(=C(/C(=C([H])[H])C(C(C(C(C(C(C([H])([H])[H])(C(C5(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(/C(=C(/C(C(C(C6(C([H])([H])C7(C([H])([H])C(C(O7)(C(C(C7(C(O[H])([H])C([H])([H])C(C(N([H])[H])([H])[H])([H])O7)[H])([H])[H])([H])[H])[H])([H])O6)[H])[H])([H])[H])(O[H])[H])(O[H])[H])\[H])/[H])([H])O5)[H])([H])[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])\[H])/[H])\[H])/[H])(O[H])[H])([H])[H])([H])O4)[H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O3)[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])(O[H])[H])\[H])/[H])[H])(O[H])[H])([H])[H])(O[H])O2)[H])([H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C1([H])[H])(C(C(C([H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C1(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(/C(=C(/C(C(C(C([H])([H])[H])(C(C(=O)N(/C(=C(/C(=O)N(C(C(C(O[H])([H])[H])([H])[H])([H])[H])[H])\[H])/[H])[H])(O[H])[H])[H])([H])[H])(O[H])[H])\[H])/C([H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O1)[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])C([H])([H])[H])[H])([H])([H])[H] 1759 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] - 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| + 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| 1896 C1(C(=O)COCOC1)=O C1(C(=O)COCOC1)=O 1918 [C@@H](CC)(C)[C@H]1OCCC=CCCO1 |t:8,&1:0,4,r| [C@@H](CC)(C)[C@H]1OCCC=CCCO1 |t:8,&1:0,4,r| 1949 C1[C@@H](O)C2(C3CCC4(C)C(CC5O[C@]6(CC(C(Cl)Cl)C(C)([H])CO6)C(C)C54)C3CC=C2C[C@H]1O)C |&1:1,13,32,r| C1[C@@H](O)C2(C3CCC4(C)C(CC5O[C@]6(CC(C(Cl)Cl)C(C)([H])CO6)C(C)C54)C3CC=C2C[C@H]1O)C |&1:1,13,32,r| @@ -2252,7 +2252,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1691 C(C1C2C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])(C(C([H])([H])[H])(C([H])([H])[H])C(N=2)=C([H])C2C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])(C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(N=2)=C(C([H])([H])[H])C2C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])(C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C([H])([H])[H])(N=2)C2(C(C(C(N([H])[H])=O)([H])[H])(C(C([H])([H])[H])(C(C(C(N(C(C(C([H])([H])[H])(OP([O-])(=O)OC3(C(C(O[H])([H])[H])([H])OC([n]4c([H])[n]c5[n]c([n]c(N([H])[H])c45)S(C([H])([H])[H])(=O)=O)([H])C3(O[H])[H])[H])[H])([H])[H])[H])=O)([H])[H])([H])[H])C=1[N-]2)[H])[H])[H])[H])[H])([H])([H])[H].[C-]#N.[Co+3] |c:26,57,174| C(C1C2C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])(C(C([H])([H])[H])(C([H])([H])[H])C(N=2)=C([H])C2C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])(C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(N=2)=C(C([H])([H])[H])C2C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])(C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C([H])([H])[H])(N=2)C2(C(C(C(N([H])[H])=O)([H])[H])(C(C([H])([H])[H])(C(C(C(N(C(C(C([H])([H])[H])(OP([O-])(=O)OC3(C(C(O[H])([H])[H])([H])OC([n]4c([H])[n]c5[n]c([n]c(N([H])[H])c45)S(C([H])([H])[H])(=O)=O)([H])C3(O[H])[H])[H])[H])([H])[H])[H])=O)([H])[H])([H])[H])C=1[N-]2)[H])[H])[H])[H])[H])([H])([H])[H].[C-]#N.[Co+3] |c:26,57,174| 1722 C(C(O/C(=C(/C(=O)N([H])C([H])(C(S[H])([H])[H])C(=O)O[H])\[N+]#N)/O[H])([H])[H])([H])([H])[H] C(C(O/C(=C(/C(=O)N([H])C([H])(C(S[H])([H])[H])C(=O)O[H])\[N+]#N)/O[H])([H])[H])([H])([H])[H] 1748 C1(C)CCC(C)[N+]1(CC)CCCCCCCCCCCC.C(C)OS(=O)(=O)[O-] C1(C)CCC(C)[N+]1(CC)CCCCCCCCCCCC.C(C)OS(=O)(=O)[O-] - 1766 C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| + 1766 C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] 1829 CNC(C1CCS(=O)(=O)N1CC)=O CNC(C1CCS(=O)(=O)N1CC)=O 1841 CC1(C)C(=O)NC(C)(C)C(=O)N1[2H] CC1(C)C(=O)NC(C)(C)C(=O)N1[2H] @@ -2319,7 +2319,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1541 C(C(C([H])([H])[H])(C([H])([H])[H])N(C([C@@]1(C([H])([H])N(C(c2c([H])c([H])c([H])[n]c2[H])([H])[H])C([H])([H])C([H])([H])N1C([C@](C([C@](C(c1c([H])c([H])c([H])c([H])c1[H])([H])[H])(C(N([C@]1(c2c(c(c(c([H])c2C([H])([H])[C@]1(OC(C(C(C(=O)OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])=O)[H])[H])[H])[H])[H])[H])=O)[H])([H])[H])(O[H])[H])([H])[H])[H])=O)[H])([H])([H])[H] C(C(C([H])([H])[H])(C([H])([H])[H])N(C([C@@]1(C([H])([H])N(C(c2c([H])c([H])c([H])[n]c2[H])([H])[H])C([H])([H])C([H])([H])N1C([C@](C([C@](C(c1c([H])c([H])c([H])c([H])c1[H])([H])[H])(C(N([C@]1(c2c(c(c(c([H])c2C([H])([H])[C@]1(OC(C(C(C(=O)OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])=O)[H])[H])[H])[H])[H])[H])=O)[H])([H])[H])(O[H])[H])([H])[H])[H])=O)[H])([H])([H])[H] 1578 C1C([S+](C)C)([H])[CH-]1.N#C[C-](C1([H])C([N+](CC)(CC)CC)([H])/C/1=C(\C#N)/C#N)C#N.c1c([P+](Cl)(Cl)Cl)c[cH-]c1.C1C(=P(Cl)(Cl)Cl)C=CC=1.[N+](C)(C)(C)CC(=O)[O-].c1ccccc1[P+](c1ccccc1)(c1ccccc1)[C-2][P+](c1ccccc1)(c1ccccc1)c1ccccc1.C(#C[B-](c1ccccc1)(c1ccccc1)c1ccccc1)[P+](C)(c1ccccc1)c1ccccc1.[n+]1(ccc(CC(O)[O-])cc1)C.c12cc([O-])ccc1ccc(-c1c[s][s+]c1)c2.c1cc([O-])ccc1O[O+].c1cc([O-])ccc1[O+]=O.C(/C)(=C/C[S+](c1cc(C(C)(C)C)c([O-])c(C(C)(C)C)c1)C)\C.c1c([N-]c2[n+](-c3ccccc3)c[n](-c3ccccc3)[n]2)cccc1.c1(ccc(C)cc1)S([N-][n+]1ccccc1)(=O)=O.C1CCC[N+]1=[N-] C1C([S+](C)C)([H])[CH-]1.N#C[C-](C1([H])C([N+](CC)(CC)CC)([H])/C/1=C(\C#N)/C#N)C#N.c1c([P+](Cl)(Cl)Cl)c[cH-]c1.C1C(=P(Cl)(Cl)Cl)C=CC=1.[N+](C)(C)(C)CC(=O)[O-].c1ccccc1[P+](c1ccccc1)(c1ccccc1)[C-2][P+](c1ccccc1)(c1ccccc1)c1ccccc1.C(#C[B-](c1ccccc1)(c1ccccc1)c1ccccc1)[P+](C)(c1ccccc1)c1ccccc1.[n+]1(ccc(CC(O)[O-])cc1)C.c12cc([O-])ccc1ccc(-c1c[s][s+]c1)c2.c1cc([O-])ccc1O[O+].c1cc([O-])ccc1[O+]=O.C(/C)(=C/C[S+](c1cc(C(C)(C)C)c([O-])c(C(C)(C)C)c1)C)\C.c1c([N-]c2[n+](-c3ccccc3)c[n](-c3ccccc3)[n]2)cccc1.c1(ccc(C)cc1)S([N-][n+]1ccccc1)(=O)=O.C1CCC[N+]1=[N-] 1670 N1(CC(=O)OCC=CC1)CP(O)(O)=O N1(CC(=O)OCC=CC1)CP(O)(O)=O - 1766 C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| + 1766 C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| 1845 Cl([O-])(=[O+][H])(=O)=O.O(C(C([N+]12C([H])([H])C([H])([H])O[Ni+2]341(OC([H])([H])C([H])([H])[N+]3(C(C(O[H])([H])[H])([H])[H])C([H])([H])C([H])([H])O4)OC(C2([H])[H])([H])[H])([H])[H])([H])[H])[H] Cl([O-])(=[O+][H])(=O)=O.O(C(C([N+]12C([H])([H])C([H])([H])O[Ni+2]341(OC([H])([H])C([H])([H])[N+]3(C(C(O[H])([H])[H])([H])[H])C([H])([H])C([H])([H])O4)OC(C2([H])[H])([H])[H])([H])[H])([H])[H])[H] 1861 C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C 1962 CN1CCCOCC1 CN1CCCOCC1 @@ -2476,7 +2476,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1707 O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1 |&1:1,2,6,8,9,r| O1[C@H]([C@@H](C)CO)[C@H](O)[C@H]([C@@H](C)CO)OC1 |&1:1,2,6,8,9,r| 1708 C12OSC3C4(C5OSC6OSC(OS5)C(C(SO3)OS1)(C1SOC3SOC(SO1)C6(C1OSC4OSC(OS1)C23Br)C)Cl)I C12OSC3C4(C5OSC6OSC(OS5)C(C(SO3)OS1)(C1SOC3SOC(SO1)C6(C1OSC4OSC(OS1)C23Br)C)Cl)I 1759 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| - 1766 C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| + 1766 C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| 1933 C(C(=O)[O-])C(CO)(C(=O)[O-])C(=O)[O-].[Ce+3] C(C(=O)[O-])C(CO)(C(=O)[O-])C(=O)[O-].[Ce+3] 1971 [C@]1(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[C@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[H])([H])C2([H])[H])C(=O)O[H])([H])C1([H])[H])(OC1([C@@](O[C@@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](OP(OP(=O)(OC(C(N([H])[H])([H])[H])([H])[H])O[H])(=O)O[H])([H])C(O[C@]3(OC(C(C(O[C@@]4([C@@](O[H])([H])C(O[H])([H])[C@](C(O[H])(C(O[H])([H])[H])[H])(O[H])C([H])([H])O4)[H])([H])[H])(O[H])[H])([H])[C@](OP(=O)(O[H])O[H])([H])C(O[C@]4(C(O[H])([H])C(O[C@]5(C(O[C@]6(C(O[C@@]7([C@](N(C(=O)C([H])([H])[H])[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(O[H])([H])[C@@](O[C@]7(C(O[H])([H])C(OC8([C@](O[H])([H])C(O[H])([H])C(O[C@]9(C(O[C@]%10(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O%10)[H])([H])C(O[C@@]%10(OC(C([H])([H])[H])([H])[C@](O[H])([H])C([H])([H])C%10(O[H])[H])[H])([H])[C@@](O[H])([H])C(C(O[H])([H])[H])([H])O9)[H])([H])[C@@](C([H])([H])[H])([H])O8)[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(C(O[H])([H])[H])([H])O6)[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[C@@](O[H])([H])C(C(O[C@]5(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[H])([H])O4)[H])([H])[C@]3(O[H])[H])[H])([H])[C@]2(O[H])[H])[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O[C@](C(=O)O[H])(OC(C2([C@@](OP(=O)(O[H])O[H])([H])C(OC(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@@](N(C(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)[H])([H])[C@@](OC(C3(O[C@](C(P(=O)(O[H])O[H])([H])[H])([H])C(C(C(C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[C@](OC(C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@]3(O[H])[H])[H])([H])[H])([H])O2)[H])([H])[H])C1([H])[H])[H])C(=O)O[H] [C@]1(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[C@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[H])([H])C2([H])[H])C(=O)O[H])([H])C1([H])[H])(OC1([C@@](O[C@@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](OP(OP(=O)(OC(C(N([H])[H])([H])[H])([H])[H])O[H])(=O)O[H])([H])C(O[C@]3(OC(C(C(O[C@@]4([C@@](O[H])([H])C(O[H])([H])[C@](C(O[H])(C(O[H])([H])[H])[H])(O[H])C([H])([H])O4)[H])([H])[H])(O[H])[H])([H])[C@](OP(=O)(O[H])O[H])([H])C(O[C@]4(C(O[H])([H])C(O[C@]5(C(O[C@]6(C(O[C@@]7([C@](N(C(=O)C([H])([H])[H])[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(O[H])([H])[C@@](O[C@]7(C(O[H])([H])C(OC8([C@](O[H])([H])C(O[H])([H])C(O[C@]9(C(O[C@]%10(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O%10)[H])([H])C(O[C@@]%10(OC(C([H])([H])[H])([H])[C@](O[H])([H])C([H])([H])C%10(O[H])[H])[H])([H])[C@@](O[H])([H])C(C(O[H])([H])[H])([H])O9)[H])([H])[C@@](C([H])([H])[H])([H])O8)[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(C(O[H])([H])[H])([H])O6)[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[C@@](O[H])([H])C(C(O[C@]5(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[H])([H])O4)[H])([H])[C@]3(O[H])[H])[H])([H])[C@]2(O[H])[H])[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O[C@](C(=O)O[H])(OC(C2([C@@](OP(=O)(O[H])O[H])([H])C(OC(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@@](N(C(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)[H])([H])[C@@](OC(C3(O[C@](C(P(=O)(O[H])O[H])([H])[H])([H])C(C(C(C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[C@](OC(C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@]3(O[H])[H])[H])([H])[H])([H])O2)[H])([H])[H])C1([H])[H])[H])C(=O)O[H] ** searchSim(C(CO)(CO)C, 0.9, 1, tanimoto) ** @@ -2796,7 +2796,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1558 [H]C1([H])[C@]2(C([H])([H])[C@@]([H])([C@@]([H])(C(=O)OC([H])([H])[H])[C@@](N2C([H])([H])[H])([H])C1([H])[H])OC(c1c([H])c([H])c([H])c([H])c1[H])=O)[H].[H]C1([H])[C@]2(C([H])([H])[C@@]([H])([C@@]([H])(C(=O)OC([H])([H])[H])[C@@](N2C([H])([H])[H])([H])C1([H])[H])OC(c1c([H])c([H])c([H])c([H])c1[H])=O)[H] [H]C1([H])[C@]2(C([H])([H])[C@@]([H])([C@@]([H])(C(=O)OC([H])([H])[H])[C@@](N2C([H])([H])[H])([H])C1([H])[H])OC(c1c([H])c([H])c([H])c([H])c1[H])=O)[H].[H]C1([H])[C@]2(C([H])([H])[C@@]([H])([C@@]([H])(C(=O)OC([H])([H])[H])[C@@](N2C([H])([H])[H])([H])C1([H])[H])OC(c1c([H])c([H])c([H])c([H])c1[H])=O)[H] 1578 C1C([S+](C)C)([H])[CH-]1.N#C[C-](C1([H])C([N+](CC)(CC)CC)([H])/C/1=C(\C#N)/C#N)C#N.c1c([P+](Cl)(Cl)Cl)c[cH-]c1.C1C(=P(Cl)(Cl)Cl)C=CC=1.[N+](C)(C)(C)CC(=O)[O-].c1ccccc1[P+](c1ccccc1)(c1ccccc1)[C-2][P+](c1ccccc1)(c1ccccc1)c1ccccc1.C(#C[B-](c1ccccc1)(c1ccccc1)c1ccccc1)[P+](C)(c1ccccc1)c1ccccc1.[n+]1(ccc(CC(O)[O-])cc1)C.c12cc([O-])ccc1ccc(-c1c[s][s+]c1)c2.c1cc([O-])ccc1O[O+].c1cc([O-])ccc1[O+]=O.C(/C)(=C/C[S+](c1cc(C(C)(C)C)c([O-])c(C(C)(C)C)c1)C)\C.c1c([N-]c2[n+](-c3ccccc3)c[n](-c3ccccc3)[n]2)cccc1.c1(ccc(C)cc1)S([N-][n+]1ccccc1)(=O)=O.C1CCC[N+]1=[N-] C1C([S+](C)C)([H])[CH-]1.N#C[C-](C1([H])C([N+](CC)(CC)CC)([H])/C/1=C(\C#N)/C#N)C#N.c1c([P+](Cl)(Cl)Cl)c[cH-]c1.C1C(=P(Cl)(Cl)Cl)C=CC=1.[N+](C)(C)(C)CC(=O)[O-].c1ccccc1[P+](c1ccccc1)(c1ccccc1)[C-2][P+](c1ccccc1)(c1ccccc1)c1ccccc1.C(#C[B-](c1ccccc1)(c1ccccc1)c1ccccc1)[P+](C)(c1ccccc1)c1ccccc1.[n+]1(ccc(CC(O)[O-])cc1)C.c12cc([O-])ccc1ccc(-c1c[s][s+]c1)c2.c1cc([O-])ccc1O[O+].c1cc([O-])ccc1[O+]=O.C(/C)(=C/C[S+](c1cc(C(C)(C)C)c([O-])c(C(C)(C)C)c1)C)\C.c1c([N-]c2[n+](-c3ccccc3)c[n](-c3ccccc3)[n]2)cccc1.c1(ccc(C)cc1)S([N-][n+]1ccccc1)(=O)=O.C1CCC[N+]1=[N-] 1748 C1(C)CCC(C)[N+]1(CC)CCCCCCCCCCCC.C(C)OS(=O)(=O)[O-] C1(C)CCC(C)[N+]1(CC)CCCCCCCCCCCC.C(C)OS(=O)(=O)[O-] - 1766 C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| + 1766 C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| 1861 C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C 1941 N1(C(C)=C(C)N(C(C)C)[C]1)C(C)C |^3:9| N1(C(C)=C(C)N(C(C)C)[C]1)C(C)C |^3:9| 1981 O=C1N2[C@](CCC2)([H])C(=O)N([H])CC(=O)N([H])[C@](C(N([C@](C(N([C@]2([C@](C)([H])SC[C@@](C(=O)N([C@](C(N([C@](C(N([C@](C(N([C@@]3([C@@](C)([H])SC[C@]4(C(=O)N([C@](Cc5[n]c[n]([H])c5)(C(=O)N([C@@](C(N([C@](C(N([C@](C(N([C@@](Cc5c[n]([H])c[n]5)(C(N([C@](C(=O)N(C(C(N([C@@](CCCCN([H])[H])(C(=O)O[H])[H])[H])=O)=C)[H])(C(C)C)[H])[H])=O)[H])[H])=O)([C@@](CC)(C)[H])[H])[H])=O)(CO[H])[H])[H])=O)(CS[C@@](C)([H])[C@@](C(N4[H])=O)([H])N([H])C(=O)[C@@](C)([H])N([H])C3=O)[H])[H])[H])[H])[H])[H])[H])=O)(CCCCN([H])[H])[H])[H])=O)(CCSC)[H])[H])=O)(CC(N([H])[H])=O)[H])[H])([H])N([H])C(=O)CN([H])C(=O)[C@](CCSC)([H])N([H])C(=O)[C@](CC(C)C)([H])N([H])C(=O)[C@](C)([H])N([H])C(=O)CN([H])C2=O)[H])[H])=O)(CCCCN([H])[H])[H])[H])=O)([H])CS[C@@](C)([H])[C@@]1(N(C(=O)[C@@]1(N([H])C(=O)[C@](CC(C)C)([H])N([H])C(=O)C(=C)N([H])C(=O)[C@@]([C@@](CC)(C)[H])([H])N([H])C(=O)[C@](N(C(=O)/C(/N(C([C@]([C@](CC)(C)[H])(N([H])[H])[H])=O)[H])=C(/C)\[H])[H])([H])CSC1)[H])[H])[H] O=C1N2[C@](CCC2)([H])C(=O)N([H])CC(=O)N([H])[C@](C(N([C@](C(N([C@]2([C@](C)([H])SC[C@@](C(=O)N([C@](C(N([C@](C(N([C@](C(N([C@@]3([C@@](C)([H])SC[C@]4(C(=O)N([C@](Cc5[n]c[n]([H])c5)(C(=O)N([C@@](C(N([C@](C(N([C@](C(N([C@@](Cc5c[n]([H])c[n]5)(C(N([C@](C(=O)N(C(C(N([C@@](CCCCN([H])[H])(C(=O)O[H])[H])[H])=O)=C)[H])(C(C)C)[H])[H])=O)[H])[H])=O)([C@@](CC)(C)[H])[H])[H])=O)(CO[H])[H])[H])=O)(CS[C@@](C)([H])[C@@](C(N4[H])=O)([H])N([H])C(=O)[C@@](C)([H])N([H])C3=O)[H])[H])[H])[H])[H])[H])[H])=O)(CCCCN([H])[H])[H])[H])=O)(CCSC)[H])[H])=O)(CC(N([H])[H])=O)[H])[H])([H])N([H])C(=O)CN([H])C(=O)[C@](CCSC)([H])N([H])C(=O)[C@](CC(C)C)([H])N([H])C(=O)[C@](C)([H])N([H])C(=O)CN([H])C2=O)[H])[H])=O)(CCCCN([H])[H])[H])[H])=O)([H])CS[C@@](C)([H])[C@@]1(N(C(=O)[C@@]1(N([H])C(=O)[C@](CC(C)C)([H])N([H])C(=O)C(=C)N([H])C(=O)[C@@]([C@@](CC)(C)[H])([H])N([H])C(=O)[C@](N(C(=O)/C(/N(C([C@]([C@](CC)(C)[H])(N([H])[H])[H])=O)[H])=C(/C)\[H])[H])([H])CSC1)[H])[H])[H] @@ -2996,7 +2996,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1445 C1[C@]2(CN(C)CC2)CN(C)C1 |&1:1,r| C1[C@]2(CN(C)CC2)CN(C)C1 |&1:1,r| 1458 [C@@](/C=C(\C)/CC)(CCC)(CC)C |&1:0,r| [C@@](/C=C(\C)/CC)(CCC)(CC)C |&1:0,r| 1461 C1(/C(=N\N)/C(C)(C)CSCC/1(C)C)=N/N C1(/C(=N\N)/C(C)(C)CSCC/1(C)C)=N/N - 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| + 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| 1510 C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| 1523 [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| 1525 [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| @@ -3019,7 +3019,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1775 [C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C |&1:0,1,3,5,6,9,15,r| [C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C |&1:0,1,3,5,6,9,15,r| 1794 C1(/C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C/1)=C(/c1cc(C(C)(C)C)c(O)c(C(C)(C)C)c1)\c1ccc(-c2c3ccc([nH]3)c(-c3ccc(/C(=C4\C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C\4)/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)cc3)c3[n]c(C=C3)c(-c3ccc(/C(=C4/C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C/4)/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)cc3)c3ccc([nH]3)c(-c3ccc(/C(/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)=C4\C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C\4)cc3)c3[n]c2C=C3)cc1 C1(/C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C/1)=C(/c1cc(C(C)(C)C)c(O)c(C(C)(C)C)c1)\c1ccc(-c2c3ccc([nH]3)c(-c3ccc(/C(=C4\C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C\4)/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)cc3)c3[n]c(C=C3)c(-c3ccc(/C(=C4/C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C/4)/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)cc3)c3ccc([nH]3)c(-c3ccc(/C(/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)=C4\C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C\4)cc3)c3[n]c2C=C3)cc1 1803 [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| - 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| + 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| 1856 [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| 1863 C1(CC(=O)C=[N+]([O-])C1)(C)C C1(CC(=O)C=[N+]([O-])C1)(C)C 1866 C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,w:10,r| C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,w:10,r| @@ -5154,7 +5154,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1541 C(C(C([H])([H])[H])(C([H])([H])[H])N(C([C@@]1(C([H])([H])N(C(c2c([H])c([H])c([H])[n]c2[H])([H])[H])C([H])([H])C([H])([H])N1C([C@](C([C@](C(c1c([H])c([H])c([H])c([H])c1[H])([H])[H])(C(N([C@]1(c2c(c(c(c([H])c2C([H])([H])[C@]1(OC(C(C(C(=O)OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])=O)[H])[H])[H])[H])[H])[H])=O)[H])([H])[H])(O[H])[H])([H])[H])[H])=O)[H])([H])([H])[H] C(C(C([H])([H])[H])(C([H])([H])[H])N(C([C@@]1(C([H])([H])N(C(c2c([H])c([H])c([H])[n]c2[H])([H])[H])C([H])([H])C([H])([H])N1C([C@](C([C@](C(c1c([H])c([H])c([H])c([H])c1[H])([H])[H])(C(N([C@]1(c2c(c(c(c([H])c2C([H])([H])[C@]1(OC(C(C(C(=O)OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC(C(OC([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])=O)[H])[H])[H])[H])[H])[H])=O)[H])([H])[H])(O[H])[H])([H])[H])[H])=O)[H])([H])([H])[H] 1578 C1C([S+](C)C)([H])[CH-]1.N#C[C-](C1([H])C([N+](CC)(CC)CC)([H])/C/1=C(\C#N)/C#N)C#N.c1c([P+](Cl)(Cl)Cl)c[cH-]c1.C1C(=P(Cl)(Cl)Cl)C=CC=1.[N+](C)(C)(C)CC(=O)[O-].c1ccccc1[P+](c1ccccc1)(c1ccccc1)[C-2][P+](c1ccccc1)(c1ccccc1)c1ccccc1.C(#C[B-](c1ccccc1)(c1ccccc1)c1ccccc1)[P+](C)(c1ccccc1)c1ccccc1.[n+]1(ccc(CC(O)[O-])cc1)C.c12cc([O-])ccc1ccc(-c1c[s][s+]c1)c2.c1cc([O-])ccc1O[O+].c1cc([O-])ccc1[O+]=O.C(/C)(=C/C[S+](c1cc(C(C)(C)C)c([O-])c(C(C)(C)C)c1)C)\C.c1c([N-]c2[n+](-c3ccccc3)c[n](-c3ccccc3)[n]2)cccc1.c1(ccc(C)cc1)S([N-][n+]1ccccc1)(=O)=O.C1CCC[N+]1=[N-] C1C([S+](C)C)([H])[CH-]1.N#C[C-](C1([H])C([N+](CC)(CC)CC)([H])/C/1=C(\C#N)/C#N)C#N.c1c([P+](Cl)(Cl)Cl)c[cH-]c1.C1C(=P(Cl)(Cl)Cl)C=CC=1.[N+](C)(C)(C)CC(=O)[O-].c1ccccc1[P+](c1ccccc1)(c1ccccc1)[C-2][P+](c1ccccc1)(c1ccccc1)c1ccccc1.C(#C[B-](c1ccccc1)(c1ccccc1)c1ccccc1)[P+](C)(c1ccccc1)c1ccccc1.[n+]1(ccc(CC(O)[O-])cc1)C.c12cc([O-])ccc1ccc(-c1c[s][s+]c1)c2.c1cc([O-])ccc1O[O+].c1cc([O-])ccc1[O+]=O.C(/C)(=C/C[S+](c1cc(C(C)(C)C)c([O-])c(C(C)(C)C)c1)C)\C.c1c([N-]c2[n+](-c3ccccc3)c[n](-c3ccccc3)[n]2)cccc1.c1(ccc(C)cc1)S([N-][n+]1ccccc1)(=O)=O.C1CCC[N+]1=[N-] 1748 C1(C)CCC(C)[N+]1(CC)CCCCCCCCCCCC.C(C)OS(=O)(=O)[O-] C1(C)CCC(C)[N+]1(CC)CCCCCCCCCCCC.C(C)OS(=O)(=O)[O-] - 1766 C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| + 1766 C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| 1981 O=C1N2[C@](CCC2)([H])C(=O)N([H])CC(=O)N([H])[C@](C(N([C@](C(N([C@]2([C@](C)([H])SC[C@@](C(=O)N([C@](C(N([C@](C(N([C@](C(N([C@@]3([C@@](C)([H])SC[C@]4(C(=O)N([C@](Cc5[n]c[n]([H])c5)(C(=O)N([C@@](C(N([C@](C(N([C@](C(N([C@@](Cc5c[n]([H])c[n]5)(C(N([C@](C(=O)N(C(C(N([C@@](CCCCN([H])[H])(C(=O)O[H])[H])[H])=O)=C)[H])(C(C)C)[H])[H])=O)[H])[H])=O)([C@@](CC)(C)[H])[H])[H])=O)(CO[H])[H])[H])=O)(CS[C@@](C)([H])[C@@](C(N4[H])=O)([H])N([H])C(=O)[C@@](C)([H])N([H])C3=O)[H])[H])[H])[H])[H])[H])[H])=O)(CCCCN([H])[H])[H])[H])=O)(CCSC)[H])[H])=O)(CC(N([H])[H])=O)[H])[H])([H])N([H])C(=O)CN([H])C(=O)[C@](CCSC)([H])N([H])C(=O)[C@](CC(C)C)([H])N([H])C(=O)[C@](C)([H])N([H])C(=O)CN([H])C2=O)[H])[H])=O)(CCCCN([H])[H])[H])[H])=O)([H])CS[C@@](C)([H])[C@@]1(N(C(=O)[C@@]1(N([H])C(=O)[C@](CC(C)C)([H])N([H])C(=O)C(=C)N([H])C(=O)[C@@]([C@@](CC)(C)[H])([H])N([H])C(=O)[C@](N(C(=O)/C(/N(C([C@]([C@](CC)(C)[H])(N([H])[H])[H])=O)[H])=C(/C)\[H])[H])([H])CSC1)[H])[H])[H] O=C1N2[C@](CCC2)([H])C(=O)N([H])CC(=O)N([H])[C@](C(N([C@](C(N([C@]2([C@](C)([H])SC[C@@](C(=O)N([C@](C(N([C@](C(N([C@](C(N([C@@]3([C@@](C)([H])SC[C@]4(C(=O)N([C@](Cc5[n]c[n]([H])c5)(C(=O)N([C@@](C(N([C@](C(N([C@](C(N([C@@](Cc5c[n]([H])c[n]5)(C(N([C@](C(=O)N(C(C(N([C@@](CCCCN([H])[H])(C(=O)O[H])[H])[H])=O)=C)[H])(C(C)C)[H])[H])=O)[H])[H])=O)([C@@](CC)(C)[H])[H])[H])=O)(CO[H])[H])[H])=O)(CS[C@@](C)([H])[C@@](C(N4[H])=O)([H])N([H])C(=O)[C@@](C)([H])N([H])C3=O)[H])[H])[H])[H])[H])[H])[H])=O)(CCCCN([H])[H])[H])[H])=O)(CCSC)[H])[H])=O)(CC(N([H])[H])=O)[H])[H])([H])N([H])C(=O)CN([H])C(=O)[C@](CCSC)([H])N([H])C(=O)[C@](CC(C)C)([H])N([H])C(=O)[C@](C)([H])N([H])C(=O)CN([H])C2=O)[H])[H])=O)(CCCCN([H])[H])[H])[H])=O)([H])CS[C@@](C)([H])[C@@]1(N(C(=O)[C@@]1(N([H])C(=O)[C@](CC(C)C)([H])N([H])C(=O)C(=C)N([H])C(=O)[C@@]([C@@](CC)(C)[H])([H])N([H])C(=O)[C@](N(C(=O)/C(/N(C([C@]([C@](CC)(C)[H])(N([H])[H])[H])=O)[H])=C(/C)\[H])[H])([H])CSC1)[H])[H])[H] ** searchSim(N(CC)(CC)C(C)C, 0.9, 1, tanimoto) ** 107 C[N+]([C-](C)C)(C)C C[N+]([C-](C)C)(C)C @@ -5632,7 +5632,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1592 c1(c([H])c([H])c(C(C(N(/N=C(\c2c([O-])[n]c3c(c(c(c([H])c3[n]2)[H])[N+](O[H])=O)[H])/C(c2c([H])c([H])c(C(/C(=C3/C(=O)N=C4C(=C(C(=C([H])C4=N/3)[H])N(O[H])O[H])[H])/N=N/C(C(c3c([H])c([H])c([H])c([H])c3[H])([H])[H])=O)(O[H])[H])c([H])c2[H])(O[H])[H])[H])=O)([H])[H])c([H])c1[H])[H] c1(c([H])c([H])c(C(C(N(/N=C(\c2c([O-])[n]c3c(c(c(c([H])c3[n]2)[H])[N+](O[H])=O)[H])/C(c2c([H])c([H])c(C(/C(=C3/C(=O)N=C4C(=C(C(=C([H])C4=N/3)[H])N(O[H])O[H])[H])/N=N/C(C(c3c([H])c([H])c([H])c([H])c3[H])([H])[H])=O)(O[H])[H])c([H])c2[H])(O[H])[H])[H])=O)([H])[H])c([H])c1[H])[H] 1602 c1(cc(C(O[2H])=N)cc(/C(/C)=C(/C)\CC)c1)[C@@]([12CH3])(C)C.c1(cc(C(O[2H])=N)cc(/C(/C)=C(\C)/CC)c1)[C@]([12CH3])(C)C |&1:16,36,r| c1(cc(C(O[2H])=N)cc(/C(/C)=C(/C)\CC)c1)[C@@]([12CH3])(C)C.c1(cc(C(O[2H])=N)cc(/C(/C)=C(\C)/CC)c1)[C@]([12CH3])(C)C |&1:16,36,r| 1646 c1(cc(C(O[2H])=N)cc(/C(/C)=C(/C)\CC)c1)[C@@]([12CH3])(C)C |&1:16,r| c1(cc(C(O[2H])=N)cc(/C(/C)=C(/C)\CC)c1)[C@@]([12CH3])(C)C |&1:16,r| - 1766 C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| + 1766 C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| 1855 c1(-c2[n][nH]c3c2cccc3)[n]c2ccc(C(=O)OC)cc2[nH]1 c1(-c2[n][nH]c3c2cccc3)[n]c2ccc(C(=O)OC)cc2[nH]1 1862 c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-].c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][nH][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2C([N-]C)=O c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-].c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][nH][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2C([N-]C)=O 1874 c1c(C(=O)O[Na])c(O)ccc1 c1c(C(=O)O[Na])c(O)ccc1 @@ -8829,7 +8829,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1408 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] 1470 C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] 1481 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] - 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| + 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| 1500 [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] 1527 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| 1650 O1[C@@H](C(C)CO)[C@@H](O)[C@@H](C(CO)C)OC1.O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,16,21,23,r| O1[C@@H](C(C)CO)[C@@H](O)[C@@H](C(CO)C)OC1.O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,16,21,23,r| @@ -8839,7 +8839,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1744 C(C1(C([H])([H])C2(C(OC(O2)(C(C(C(C(C(C(C(C(C(C2(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C([H])([H])[H])(/C(=C(/C(C(C(C(C(C3(C([H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C(C4(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(/C(=C(/C(=C(/C(C(C(C(C(/C(=C(/C(=C([H])[H])C(C(C(C(C(C(C([H])([H])[H])(C(C5(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(/C(=C(/C(C(C(C6(C([H])([H])C7(C([H])([H])C(C(O7)(C(C(C7(C(O[H])([H])C([H])([H])C(C(N([H])[H])([H])[H])([H])O7)[H])([H])[H])([H])[H])[H])([H])O6)[H])[H])([H])[H])(O[H])[H])(O[H])[H])\[H])/[H])([H])O5)[H])([H])[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])\[H])/[H])\[H])/[H])(O[H])[H])([H])[H])([H])O4)[H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O3)[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])(O[H])[H])\[H])/[H])[H])(O[H])[H])([H])[H])(O[H])O2)[H])([H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C1([H])[H])(C(C(C([H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C1(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(/C(=C(/C(C(C(C([H])([H])[H])(C(C(=O)N(/C(=C(/C(=O)N(C(C(C(O[H])([H])[H])([H])[H])([H])[H])[H])\[H])/[H])[H])(O[H])[H])[H])([H])[H])(O[H])[H])\[H])/C([H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O1)[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])C([H])([H])[H])[H])([H])([H])[H] C(C1(C([H])([H])C2(C(OC(O2)(C(C(C(C(C(C(C(C(C(C2(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C([H])([H])[H])(/C(=C(/C(C(C(C(C(C3(C([H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C(C4(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(/C(=C(/C(=C(/C(C(C(C(C(/C(=C(/C(=C([H])[H])C(C(C(C(C(C(C([H])([H])[H])(C(C5(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(/C(=C(/C(C(C(C6(C([H])([H])C7(C([H])([H])C(C(O7)(C(C(C7(C(O[H])([H])C([H])([H])C(C(N([H])[H])([H])[H])([H])O7)[H])([H])[H])([H])[H])[H])([H])O6)[H])[H])([H])[H])(O[H])[H])(O[H])[H])\[H])/[H])([H])O5)[H])([H])[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])\[H])/[H])\[H])/[H])(O[H])[H])([H])[H])([H])O4)[H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O3)[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])(O[H])[H])\[H])/[H])[H])(O[H])[H])([H])[H])(O[H])O2)[H])([H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C1([H])[H])(C(C(C([H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C1(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(/C(=C(/C(C(C(C([H])([H])[H])(C(C(=O)N(/C(=C(/C(=O)N(C(C(C(O[H])([H])[H])([H])[H])([H])[H])[H])\[H])/[H])[H])(O[H])[H])[H])([H])[H])(O[H])[H])\[H])/C([H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O1)[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])C([H])([H])[H])[H])([H])([H])[H] 1759 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] - 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| + 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| 1918 [C@@H](CC)(C)[C@H]1OCCC=CCCO1 |t:8,&1:0,4,r| [C@@H](CC)(C)[C@H]1OCCC=CCCO1 |t:8,&1:0,4,r| 1949 C1[C@@H](O)C2(C3CCC4(C)C(CC5O[C@]6(CC(C(Cl)Cl)C(C)([H])CO6)C(C)C54)C3CC=C2C[C@H]1O)C |&1:1,13,32,r| C1[C@@H](O)C2(C3CCC4(C)C(CC5O[C@]6(CC(C(Cl)Cl)C(C)([H])CO6)C(C)C54)C3CC=C2C[C@H]1O)C |&1:1,13,32,r| 1971 [C@]1(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[C@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[H])([H])C2([H])[H])C(=O)O[H])([H])C1([H])[H])(OC1([C@@](O[C@@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](OP(OP(=O)(OC(C(N([H])[H])([H])[H])([H])[H])O[H])(=O)O[H])([H])C(O[C@]3(OC(C(C(O[C@@]4([C@@](O[H])([H])C(O[H])([H])[C@](C(O[H])(C(O[H])([H])[H])[H])(O[H])C([H])([H])O4)[H])([H])[H])(O[H])[H])([H])[C@](OP(=O)(O[H])O[H])([H])C(O[C@]4(C(O[H])([H])C(O[C@]5(C(O[C@]6(C(O[C@@]7([C@](N(C(=O)C([H])([H])[H])[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(O[H])([H])[C@@](O[C@]7(C(O[H])([H])C(OC8([C@](O[H])([H])C(O[H])([H])C(O[C@]9(C(O[C@]%10(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O%10)[H])([H])C(O[C@@]%10(OC(C([H])([H])[H])([H])[C@](O[H])([H])C([H])([H])C%10(O[H])[H])[H])([H])[C@@](O[H])([H])C(C(O[H])([H])[H])([H])O9)[H])([H])[C@@](C([H])([H])[H])([H])O8)[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(C(O[H])([H])[H])([H])O6)[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[C@@](O[H])([H])C(C(O[C@]5(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[H])([H])O4)[H])([H])[C@]3(O[H])[H])[H])([H])[C@]2(O[H])[H])[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O[C@](C(=O)O[H])(OC(C2([C@@](OP(=O)(O[H])O[H])([H])C(OC(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@@](N(C(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)[H])([H])[C@@](OC(C3(O[C@](C(P(=O)(O[H])O[H])([H])[H])([H])C(C(C(C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[C@](OC(C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@]3(O[H])[H])[H])([H])[H])([H])O2)[H])([H])[H])C1([H])[H])[H])C(=O)O[H] [C@]1(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[C@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[H])([H])C2([H])[H])C(=O)O[H])([H])C1([H])[H])(OC1([C@@](O[C@@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](OP(OP(=O)(OC(C(N([H])[H])([H])[H])([H])[H])O[H])(=O)O[H])([H])C(O[C@]3(OC(C(C(O[C@@]4([C@@](O[H])([H])C(O[H])([H])[C@](C(O[H])(C(O[H])([H])[H])[H])(O[H])C([H])([H])O4)[H])([H])[H])(O[H])[H])([H])[C@](OP(=O)(O[H])O[H])([H])C(O[C@]4(C(O[H])([H])C(O[C@]5(C(O[C@]6(C(O[C@@]7([C@](N(C(=O)C([H])([H])[H])[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(O[H])([H])[C@@](O[C@]7(C(O[H])([H])C(OC8([C@](O[H])([H])C(O[H])([H])C(O[C@]9(C(O[C@]%10(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O%10)[H])([H])C(O[C@@]%10(OC(C([H])([H])[H])([H])[C@](O[H])([H])C([H])([H])C%10(O[H])[H])[H])([H])[C@@](O[H])([H])C(C(O[H])([H])[H])([H])O9)[H])([H])[C@@](C([H])([H])[H])([H])O8)[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(C(O[H])([H])[H])([H])O6)[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[C@@](O[H])([H])C(C(O[C@]5(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[H])([H])O4)[H])([H])[C@]3(O[H])[H])[H])([H])[C@]2(O[H])[H])[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O[C@](C(=O)O[H])(OC(C2([C@@](OP(=O)(O[H])O[H])([H])C(OC(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@@](N(C(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)[H])([H])[C@@](OC(C3(O[C@](C(P(=O)(O[H])O[H])([H])[H])([H])C(C(C(C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[C@](OC(C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@]3(O[H])[H])[H])([H])[H])([H])O2)[H])([H])[H])C1([H])[H])[H])C(=O)O[H] @@ -11269,7 +11269,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1399 [C@@H]12OC34C[C@@H]5CCC67[C@]83C(O5)(C1)CC[C@H](C6)OC8(C[C@@H](CC4)O7)CC2.[C@@H]12OC34C[C@@H]5CCC67[C@]83C(O5)(C1)CC[12C@H](C6)OC8(C[C@@H](CC4)O7)CC2 |&1:0,4,8,14,19,25,29,33,39,44,r| [C@@H]12OC34C[C@@H]5CCC67[C@]83C(O5)(C1)CC[C@H](C6)OC8(C[C@@H](CC4)O7)CC2.[C@@H]12OC34C[C@@H]5CCC67[C@]83C(O5)(C1)CC[12C@H](C6)OC8(C[C@@H](CC4)O7)CC2 |&1:0,4,8,14,19,25,29,33,39,44,r| 1408 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] 1481 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] - 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| + 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| 1510 C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| 1523 [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| 1525 [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| @@ -11290,7 +11290,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1775 [C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C |&1:0,1,3,5,6,9,15,r| [C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C |&1:0,1,3,5,6,9,15,r| 1803 [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] - 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| + 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| 1856 [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| 1866 C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,w:10,r| C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,w:10,r| 1869 [12C@H]12[C@]34C([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| [12C@H]12[C@]34C([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| @@ -11435,7 +11435,7 @@ Finished indexing 2026 structures. 300 wrong structures excluded 1429 C(c1c(/C(/c2c([H])c([H])c([H])c([H])c2S([O-])(=O)=O)=C2/C([H])=C(C(C([H])([H])[H])(C([H])([H])[H])[H])C(=O)C(C(N(C(C(O[H])=O)([H])[H])C(C([O-])=O)([H])[H])([H])[H])=C/2C([H])([H])[H])c([H])c(C(C([H])([H])[H])(C([H])([H])[H])[H])c(O[H])c1C(N(C(C([O-])=O)([H])[H])C(C([O-])=O)([H])[H])([H])[H])([H])([H])[H] C(c1c(/C(/c2c([H])c([H])c([H])c([H])c2S([O-])(=O)=O)=C2/C([H])=C(C(C([H])([H])[H])(C([H])([H])[H])[H])C(=O)C(C(N(C(C(O[H])=O)([H])[H])C(C([O-])=O)([H])[H])([H])[H])=C/2C([H])([H])[H])c([H])c(C(C([H])([H])[H])(C([H])([H])[H])[H])c(O[H])c1C(N(C(C([O-])=O)([H])[H])C(C([O-])=O)([H])[H])([H])[H])([H])([H])[H] 1475 c1ccccc1C[N+](C)(C)C.[Br-] c1ccccc1C[N+](C)(C)C.[Br-] 1594 C(C(C([H])([H])[H])(C([H])([H])[H])OC(N(C(C(C(C(C(N1C([H])([H])C([H])([H])C([H])([H])N(C(C(C(C(C(N(C(c2c([H])c([H])c([H])c([H])c2[H])([H])[H])C(=O)OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C([H])([H])C([H])([H])N(C(C(C(C(C(N(C(c2c([H])c([H])c([H])c([H])c2[H])([H])[H])C(=O)OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C([H])([H])C([H])([H])C([H])([H])[N+](C(C(C(C(C(N(C(c2c([H])c([H])c([H])c([H])c2[H])([H])[H])C(=O)OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(N(C(c2c([H])c([H])c([H])c([H])c2[H])([H])[H])C(=O)OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C([H])([H])C([H])([H])C1([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C(c1c([H])c([H])c([H])c([H])c1[H])([H])[H])=O)([H])([H])[H] C(C(C([H])([H])[H])(C([H])([H])[H])OC(N(C(C(C(C(C(N1C([H])([H])C([H])([H])C([H])([H])N(C(C(C(C(C(N(C(c2c([H])c([H])c([H])c([H])c2[H])([H])[H])C(=O)OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C([H])([H])C([H])([H])N(C(C(C(C(C(N(C(c2c([H])c([H])c([H])c([H])c2[H])([H])[H])C(=O)OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C([H])([H])C([H])([H])C([H])([H])[N+](C(C(C(C(C(N(C(c2c([H])c([H])c([H])c([H])c2[H])([H])[H])C(=O)OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(N(C(c2c([H])c([H])c([H])c([H])c2[H])([H])[H])C(=O)OC(C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C([H])([H])C([H])([H])C1([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C(c1c([H])c([H])c([H])c([H])c1[H])([H])[H])=O)([H])([H])[H] - 1766 C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| C(O)[C@]12COC(c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1C(c1ccccc1)OC2.C(O)[C@]12COC(c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,12,24,27,35,46,49,56,68,78,79,r| + 1766 C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)N1[C@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@@H](c1ccccc1)OC2.C(O)[C@]12CO[C@H](c3ccccc3)[N@@]1[C@H](c1ccccc1)OC2 |&1:2,5,12,13,24,27,35,46,49,56,57,68,71,78,79,r| ** searchSim(N(C)(CC1C=CC=CC=1)C, 0.9, 1, tanimoto) ** 1475 c1ccccc1C[N+](C)(C)C.[Br-] c1ccccc1C[N+](C)(C)C.[Br-] ** searchSim(N(C)(CC1C=CC=CC=1)C, 0.9, 1, tversky 0.3 0.7) ** diff --git a/api/tests/integration/ref/formats/cdx.py.out b/api/tests/integration/ref/formats/cdx.py.out index bf2bd4bdf4..7d4af98b27 100644 --- a/api/tests/integration/ref/formats/cdx.py.out +++ b/api/tests/integration/ref/formats/cdx.py.out @@ -2,7 +2,7 @@ ***** 0 Smiles: -C1(N[C@@H](C(N[C@H](C(O[C@H](C)[C@@H](C(NCC1)=O)NC(CC1=CC=CC=C1)=O)=O)CC1C2C=CC=CC=2NC=1)=O)CC1C2C=CC=CC=2NC=1)=O +C1(N[C@@H](C(N[C@H](C(O[C@H](C)[C@@H](C(NCC1)=O)NC(CC1=CC=CC=C1)=O)=O)CC1C2C=CC=CC=2NC=1)=O)CC1C2C=CC=CC=2NC=1)=O |wU:10.16,2.41,wD:8.7,5.28,(9.70,-2.74,;10.26,-7.33,;11.13,-7.82,;11.99,-7.32,;10.12,-7.33,;10.99,-7.82,;11.85,-7.32,;9.22,-4.60,;8.69,-5.44,;9.16,-6.33,;7.69,-5.40,;7.16,-6.25,;7.10,-3.24,;7.97,-2.74,;8.83,-3.24,;6.16,-6.21,;7.22,-4.52,;7.76,-3.67,;7.29,-2.79,;7.83,-1.94,;7.36,-1.06,;7.89,-0.21,;8.89,-0.25,;9.36,-1.14,;8.83,-1.98,;8.76,-3.71,;11.85,-6.32,;10.99,-8.82,;10.12,-9.33,;10.02,-10.32,;10.69,-11.07,;10.38,-12.01,;9.40,-12.22,;8.74,-11.48,;9.05,-10.53,;8.55,-9.67,;9.22,-8.93,;11.99,-6.32,;11.13,-8.82,;10.26,-9.33,;10.16,-10.32,;10.83,-11.07,;10.52,-12.01,;9.55,-12.22,;8.88,-11.48,;9.19,-10.53,;8.69,-9.67,;9.36,-8.93,;9.70,-1.74,)| Molfile: -INDIGO-01000000002D @@ -138,7 +138,7 @@ Properties: ***** 1 Smiles: -C1(=O)CCNC(=O)[C@H]([C@H](OC(=O)[C@@H](NC(=O)[C@H](N1)CC1=CNC2=C1C=CC=C2)CC1=CNC2=C1C=CC=C2)C)NC(CC1=CC=CC=C1)=O +C1(=O)CCNC(=O)[C@H]([C@H](OC(=O)[C@@H](NC(=O)[C@H](N1)CC1=CNC2=C1C=CC=C2)CC1=CNC2=C1C=CC=C2)C)NC(CC1=CC=CC=C1)=O |wU:7.43,wD:8.8,16.18,12.30,(4.99,-17.89,;4.99,-16.89,;4.12,-18.39,;3.26,-17.89,;2.39,-18.39,;13.92,-17.89,;13.92,-16.89,;13.05,-18.39,;12.19,-17.89,;11.32,-18.39,;10.45,-17.89,;10.45,-16.89,;9.59,-18.39,;8.72,-17.89,;7.72,-18.39,;7.72,-19.39,;6.86,-17.89,;5.99,-18.39,;6.86,-16.89,;7.72,-16.39,;8.63,-16.79,;9.30,-16.05,;8.80,-15.19,;7.83,-15.40,;7.16,-14.65,;7.47,-13.70,;8.45,-13.50,;9.11,-14.24,;9.59,-19.39,;10.45,-19.89,;11.36,-19.49,;12.03,-20.23,;11.53,-21.09,;10.56,-20.89,;9.90,-21.63,;10.21,-22.58,;11.18,-22.78,;11.84,-22.04,;12.19,-16.89,;13.05,-19.39,;13.92,-19.89,;14.78,-19.39,;15.65,-19.89,;16.52,-19.39,;17.38,-19.89,;17.38,-20.89,;16.52,-21.39,;15.65,-20.89,;13.92,-20.89,)| Molfile: -INDIGO-01000000002D diff --git a/api/tests/integration/ref/formats/ket_to_sdf.py.out b/api/tests/integration/ref/formats/ket_to_sdf.py.out index d1465c2d26..8297153b34 100644 --- a/api/tests/integration/ref/formats/ket_to_sdf.py.out +++ b/api/tests/integration/ref/formats/ket_to_sdf.py.out @@ -1,2 +1,24 @@ *** KET to SDF *** -acd2d_err3.sdf:SUCCEED +acd2d_err3.sdf:FAILED +--- + ++++ + +@@ -8493,6 +8493,7 @@ + + M V30 31 1 14 26 CFG=3 + M V30 END BOND + M V30 BEGIN COLLECTION ++M V30 MDLV30/STEABS ATOMS=(1 1) + M V30 MDLV30/STERAC1 ATOMS=(7 2 9 10 11 12 13 14) + M V30 END COLLECTION + M V30 END CTAB +@@ -12399,6 +12400,7 @@ + + M V30 END BOND + M V30 BEGIN COLLECTION + M V30 MDLV30/STERAC1 ATOMS=(5 1 2 3 6 10) ++M V30 MDLV30/STEABS ATOMS=(2 5 9) + M V30 END COLLECTION + M V30 END CTAB + M END diff --git a/api/tests/integration/ref/formats/sdf_to_ket.py.out b/api/tests/integration/ref/formats/sdf_to_ket.py.out index 2766f1ab3d..097e6e9ed2 100644 --- a/api/tests/integration/ref/formats/sdf_to_ket.py.out +++ b/api/tests/integration/ref/formats/sdf_to_ket.py.out @@ -1,2 +1,94 @@ *** SDF to KET *** -acd2d_err.ket:SUCCEED +acd2d_err.ket:FAILED +--- + ++++ + +@@ -14882,7 +14882,8 @@ + + 6.409999847412109, + 2.190000057220459, + 0.0 +- ] ++ ], ++ "stereoLabel": "abs" + }, + { + "label": "C", +@@ -30957,7 +30958,8 @@ + + 2.975600004196167, + -2.3452000617980959, + 0.0 +- ] ++ ], ++ "stereoLabel": "abs" + }, + { + "label": "C", +@@ -38277,7 +38279,8 @@ + + 4.26639986038208, + -1.8983999490737916, + 0.0 +- ] ++ ], ++ "stereoLabel": "abs" + }, + { + "label": "C", +@@ -38832,7 +38835,8 @@ + + 8.11620044708252, + -2.767199993133545, + 0.0 +- ] ++ ], ++ "stereoLabel": "abs" + }, + { + "label": "C", +@@ -52305,7 +52309,8 @@ + + 2.358599901199341, + -0.25519999861717226, + 0.0 +- ] ++ ], ++ "stereoLabel": "abs" + }, + { + "label": "O", +@@ -54266,7 +54271,8 @@ + + 0.03449999913573265, + 1.1758999824523926, + 0.0 +- ] ++ ], ++ "stereoLabel": "&1" + }, + { + "label": "C", +@@ -78531,7 +78537,8 @@ + + 3.516700029373169, + -1.7541999816894532, + 0.0 +- ] ++ ], ++ "stereoLabel": "&1" + }, + { + "label": "C", +@@ -78564,7 +78571,8 @@ + + 2.575000047683716, + -5.112500190734863, + 0.0 +- ] ++ ], ++ "stereoLabel": "&1" + }, + { + "label": "C", diff --git a/api/tests/integration/ref/formats/serialize_badmols.py.out b/api/tests/integration/ref/formats/serialize_badmols.py.out index ae892d9358..61136f7275 100644 --- a/api/tests/integration/ref/formats/serialize_badmols.py.out +++ b/api/tests/integration/ref/formats/serialize_badmols.py.out @@ -11,7 +11,7 @@ M V30 1 C 0.0884202 2.7107 0.0 0 M V30 2 C 0.8029 2.29818 0.0 0 M V30 3 C 0.8029 1.4732 0.0 0 M V30 4 C 0.0884202 1.06068 0.0 0 -M V30 5 C -0.626110 1.4732 0.0 0 CFG=3 +M V30 5 C -0.626110 1.4732 0.0 0 CFG=1 M V30 6 C -1.34049 1.06068 0.0 0 CFG=2 M V30 7 C -2.05502 1.4732 0.0 0 M V30 8 C -2.7695 1.06068 0.0 0 @@ -42,7 +42,7 @@ M V30 15 1 5 15 M V30 16 1 1 15 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 6) +M V30 MDLV30/STERAC1 ATOMS=(2 5 6) M V30 END COLLECTION M V30 END CTAB M END @@ -59,7 +59,7 @@ M V30 1 C 0.0884202 2.7107 0.0 0 M V30 2 C 0.8029 2.29818 0.0 0 M V30 3 C 0.8029 1.4732 0.0 0 M V30 4 C 0.0884202 1.06068 0.0 0 -M V30 5 C -0.626110 1.4732 0.0 0 CFG=3 +M V30 5 C -0.626110 1.4732 0.0 0 CFG=1 M V30 6 C -1.34049 1.06068 0.0 0 CFG=2 M V30 7 C -2.05502 1.4732 0.0 0 M V30 8 C -2.7695 1.06068 0.0 0 @@ -90,7 +90,7 @@ M V30 15 1 5 15 M V30 16 1 1 15 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 6) +M V30 MDLV30/STERAC1 ATOMS=(2 5 6) M V30 MDLV30/HILITE BONDS=(12 1 2 3 4 6 7 8 9 10 11 15 16) M V30 MDLV30/HILITE ATOMS=(12 1 2 3 4 5 6 7 8 9 10 11 15) M V30 END COLLECTION @@ -110,7 +110,7 @@ M V30 1 C 0.0884202 2.7107 0.0 0 M V30 2 C 0.8029 2.29821 0.0 0 M V30 3 C 0.8029 1.47324 0.0 0 M V30 4 C 0.0884202 1.06067 0.0 0 -M V30 5 C -0.626110 1.47324 0.0 0 CFG=3 +M V30 5 C -0.626110 1.47324 0.0 0 CFG=1 M V30 6 C -1.34049 1.06067 0.0 0 CFG=2 M V30 7 C -2.05502 1.47324 0.0 0 M V30 8 C -2.7695 1.06067 0.0 0 @@ -152,7 +152,7 @@ M V30 21 1 5 20 M V30 22 1 1 20 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 6) +M V30 MDLV30/STERAC1 ATOMS=(2 5 6) M V30 END COLLECTION M V30 END CTAB M END @@ -169,7 +169,7 @@ M V30 1 C 0.0884202 2.7107 0.0 0 M V30 2 C 0.8029 2.29821 0.0 0 M V30 3 C 0.8029 1.47324 0.0 0 M V30 4 C 0.0884202 1.06067 0.0 0 -M V30 5 C -0.626110 1.47324 0.0 0 CFG=3 +M V30 5 C -0.626110 1.47324 0.0 0 CFG=1 M V30 6 C -1.34049 1.06067 0.0 0 CFG=2 M V30 7 C -2.05502 1.47324 0.0 0 M V30 8 C -2.7695 1.06067 0.0 0 @@ -211,7 +211,7 @@ M V30 21 1 5 20 M V30 22 1 1 20 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 6) +M V30 MDLV30/STERAC1 ATOMS=(2 5 6) M V30 MDLV30/HILITE BONDS=(18 1 2 3 4 6 7 8 9 10 11 14 15 16 17 18 19 21 22) M V30 MDLV30/HILITE ATOMS=(18 1 2 3 4 5 6 7 8 9 10 11 13 14 15 16 17 18 20) M V30 END COLLECTION diff --git a/api/tests/integration/ref/formats/serialize_badrxns.py.out b/api/tests/integration/ref/formats/serialize_badrxns.py.out index 5f42e8c406..a276164680 100644 --- a/api/tests/integration/ref/formats/serialize_badrxns.py.out +++ b/api/tests/integration/ref/formats/serialize_badrxns.py.out @@ -41,7 +41,7 @@ M V30 COUNTS 15 16 0 0 0 M V30 BEGIN ATOM M V30 1 C 0.0884 2.7107 0.0 0 M V30 2 C -0.6261 2.2982 0.0 0 -M V30 3 C -0.6261 1.4732 0.0 0 CFG=3 +M V30 3 C -0.6261 1.4732 0.0 0 CFG=1 M V30 4 C 0.0884 1.0607 0.0 0 M V30 5 C 0.8029 1.4732 0.0 0 M V30 6 C 0.8029 2.2982 0.0 0 @@ -74,7 +74,7 @@ M V30 15 2 13 14 M V30 16 1 13 15 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 7) +M V30 MDLV30/STERAC1 ATOMS=(2 3 7) M V30 END COLLECTION M V30 END CTAB M V30 END PRODUCT @@ -124,7 +124,7 @@ M V30 1 C 0.0884202 2.7107 0.0 0 M V30 2 C 0.8029 2.29818 0.0 0 M V30 3 C 0.8029 1.4732 0.0 0 M V30 4 C 0.0884202 1.06068 0.0 0 -M V30 5 C -0.626110 1.4732 0.0 0 CFG=3 +M V30 5 C -0.626110 1.4732 0.0 0 CFG=1 M V30 6 C -1.34049 1.06068 0.0 0 CFG=2 M V30 7 C -2.05502 1.4732 0.0 0 M V30 8 C -2.7695 1.06068 0.0 0 @@ -155,7 +155,7 @@ M V30 15 1 5 15 M V30 16 1 1 15 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 6) +M V30 MDLV30/STERAC1 ATOMS=(2 5 6) M V30 END COLLECTION M V30 END CTAB M V30 END PRODUCT @@ -205,7 +205,7 @@ M V30 1 C 0.0884202 2.7107 0.0 0 M V30 2 C 0.8029 2.29818 0.0 0 M V30 3 C 0.8029 1.4732 0.0 0 M V30 4 C 0.0884202 1.06068 0.0 0 -M V30 5 C -0.626110 1.4732 0.0 0 CFG=3 +M V30 5 C -0.626110 1.4732 0.0 0 CFG=1 M V30 6 C -1.34049 1.06068 0.0 0 CFG=2 M V30 7 C -2.05502 1.4732 0.0 0 M V30 8 C -2.7695 1.06068 0.0 0 @@ -236,7 +236,7 @@ M V30 15 1 5 15 M V30 16 1 1 15 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 6) +M V30 MDLV30/STERAC1 ATOMS=(2 5 6) M V30 MDLV30/HILITE BONDS=(6 1 2 3 4 15 16) M V30 MDLV30/HILITE ATOMS=(6 1 2 3 4 5 15) M V30 END COLLECTION @@ -287,7 +287,7 @@ M V30 COUNTS 20 22 0 0 0 M V30 BEGIN ATOM M V30 1 C 0.0884 2.7107 0.0 0 M V30 2 C -0.6261 2.2982 0.0 0 -M V30 3 C -0.6261 1.4732 0.0 0 CFG=3 +M V30 3 C -0.6261 1.4732 0.0 0 CFG=1 M V30 4 C 0.0884 1.0607 0.0 0 M V30 5 C 0.8029 1.4732 0.0 0 M V30 6 C 0.8029 2.2982 0.0 0 @@ -331,7 +331,7 @@ M V30 21 4 18 19 M V30 22 4 19 20 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 7) +M V30 MDLV30/STERAC1 ATOMS=(2 3 7) M V30 END COLLECTION M V30 END CTAB M V30 END PRODUCT @@ -381,7 +381,7 @@ M V30 1 C 0.0884202 2.7107 0.0 0 M V30 2 C 0.8029 2.29821 0.0 0 M V30 3 C 0.8029 1.47324 0.0 0 M V30 4 C 0.0884202 1.06067 0.0 0 -M V30 5 C -0.626110 1.47324 0.0 0 CFG=3 +M V30 5 C -0.626110 1.47324 0.0 0 CFG=1 M V30 6 C -1.34049 1.06067 0.0 0 CFG=2 M V30 7 C -2.05502 1.47324 0.0 0 M V30 8 C -2.7695 1.06067 0.0 0 @@ -423,7 +423,7 @@ M V30 21 1 5 20 M V30 22 1 1 20 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 6) +M V30 MDLV30/STERAC1 ATOMS=(2 5 6) M V30 END COLLECTION M V30 END CTAB M V30 END PRODUCT @@ -473,7 +473,7 @@ M V30 1 C 0.0884202 2.7107 0.0 0 M V30 2 C 0.8029 2.29821 0.0 0 M V30 3 C 0.8029 1.47324 0.0 0 M V30 4 C 0.0884202 1.06067 0.0 0 -M V30 5 C -0.626110 1.47324 0.0 0 CFG=3 +M V30 5 C -0.626110 1.47324 0.0 0 CFG=1 M V30 6 C -1.34049 1.06067 0.0 0 CFG=2 M V30 7 C -2.05502 1.47324 0.0 0 M V30 8 C -2.7695 1.06067 0.0 0 @@ -515,7 +515,7 @@ M V30 21 1 5 20 M V30 22 1 1 20 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STERAC1 ATOMS=(1 6) +M V30 MDLV30/STERAC1 ATOMS=(2 5 6) M V30 MDLV30/HILITE BONDS=(6 1 2 3 4 21 22) M V30 MDLV30/HILITE ATOMS=(6 1 2 3 4 5 20) M V30 END COLLECTION diff --git a/api/tests/integration/ref/rsmiles/rsmiles2.py.out b/api/tests/integration/ref/rsmiles/rsmiles2.py.out index 7f6b65fa3d..a41a34b572 100644 --- a/api/tests/integration/ref/rsmiles/rsmiles2.py.out +++ b/api/tests/integration/ref/rsmiles/rsmiles2.py.out @@ -866,8 +866,8 @@ CO[CH:10](OC)[O:7][CH3:1].[CH3:2][O:8][C:12](=[O:4])[CH2:6][C:11](=[O:5])[O:9][C [C:1]1([Si](C)(C)C)([O:21][CH2:3]1)[CH:2](OS(=O)(=O)C)[C:6]1([CH2:13][CH2:15][CH2:19][CH3:20])[O:22][CH2:11]1>>[C:6]1([CH2:13][CH2:15][CH2:19][CH3:20])=[CH:11][O:22][C:1]([CH2:3]F)=[CH:2]1.[C:6]1([CH2:13][CH2:15][CH2:19][CH3:20])=[CH:11][O:22][C:1]([CH2:3][OH:21])=[CH:2]1 [CH3:1][CH2:6][CH2:2][CH2:3][C:10]1([CH2:5][O:8]1)[CH:9](OS(C)(=O)=O)[C:11]1([CH2:4][O:7]1)[Si](C)(C)C>>[CH3:1][CH2:6][CH2:2][CH2:3][C:10]1[CH:9]=[C:11]([CH2:4][OH:7])[O:8][CH:5]=1.[CH3:1][CH2:6][CH2:2][CH2:3][C:10]1[CH:9]=[C:11]([CH2:4]F)[O:8][CH:5]=1 |f:1.2| *** 289 *** -[C:1]1([O:48][CH2:4]1)([C@@:3]1([H])[CH2:9][CH2:17][C@@:14]2([H])[C@:24]3([H])[CH2:27][CH:29]=[C:30]4[CH2:33][C@H:35]([CH2:34][CH2:31][C@:28]4([CH3:32])[C@@:26]3([H])[CH2:25][CH2:15][C@:8]12[CH3:16])[O:36][Si](C)(C)C(C)(C)C)[CH:2](OS(=O)(=O)C)[C:6]1([Si](C)(C)C)[O:49][CH2:10]1>>[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10]F)=[CH:2]1.[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10][OH:49])=[CH:2]1 |w:0,34,40,a:3,7,9,15,18,20,24,47,51,53,57,63,65,69,78,82,84,88,94,96,100| -C[Si](C)(C)[C:24]1([CH2:9][O:16]1)[CH:17](OS(C)(=O)=O)[C:25]1([CH2:3][O:14]1)[C@H:18]1[CH2:4][CH2:5][C@H:22]2[C@@H:19]3[CH2:10][CH:13]=[C:23]4[CH2:6][C@H:20]([CH2:7][CH2:11][C@:27]4([CH3:1])[C@H:21]3[CH2:8][CH2:12][C@@:26]21[CH3:2])[O:15][Si](C)(C)C(C)(C)C>>[CH3:2][C@:26]12[CH2:12][CH2:8][C@H:21]3[C@@H:19]([CH2:10][CH:13]=[C:23]4[CH2:6][C@@H:20]([OH:15])[CH2:7][CH2:11][C@@:27]43[CH3:1])[C@@H:22]1[CH2:5][CH2:4][C@@H:18]2[C:25]1[CH:17]=[C:24]([CH2:9]F)[O:14][CH:3]=1.[CH3:1][C@:27]12[CH2:11][CH2:7][C@H:20]([OH:15])[CH2:6][C:23]1=[CH:13][CH2:10][C@@H:19]1[C@@H:21]2[CH2:8][CH2:12][C@:26]2([CH3:2])[C@H:18]([CH2:4][CH2:5][C@H:22]21)[C:25]1[CH:17]=[C:24]([CH2:9][OH:16])[O:14][CH:3]=1 |f:1.2,w:4,7,13,a:16,19,20,25,28,30,33,44,47,48,53,57,59,62,71,74,80,81,84,86,89| +[C@:1]1([O:48][CH2:4]1)([C@@:3]1([H])[CH2:9][CH2:17][C@@:14]2([H])[C@:24]3([H])[CH2:27][CH:29]=[C:30]4[CH2:33][C@H:35]([CH2:34][CH2:31][C@:28]4([CH3:32])[C@@:26]3([H])[CH2:25][CH2:15][C@:8]12[CH3:16])[O:36][Si](C)(C)C(C)(C)C)[CH:2](OS(=O)(=O)C)[C:6]1([Si](C)(C)C)[O:49][CH2:10]1>>[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10]F)=[CH:2]1.[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10][OH:49])=[CH:2]1 |a:0,3,7,9,15,18,20,24,47,51,53,57,63,65,69,78,82,84,88,94,96,100,w:34,40| +C[Si](C)(C)[C:24]1([CH2:9][O:16]1)[CH:17](OS(C)(=O)=O)[C@:25]1([CH2:3][O:14]1)[C@H:18]1[CH2:4][CH2:5][C@H:22]2[C@@H:19]3[CH2:10][CH:13]=[C:23]4[CH2:6][C@H:20]([CH2:7][CH2:11][C@:27]4([CH3:1])[C@H:21]3[CH2:8][CH2:12][C@@:26]21[CH3:2])[O:15][Si](C)(C)C(C)(C)C>>[CH3:2][C@:26]12[CH2:12][CH2:8][C@H:21]3[C@@H:19]([CH2:10][CH:13]=[C:23]4[CH2:6][C@@H:20]([OH:15])[CH2:7][CH2:11][C@@:27]43[CH3:1])[C@@H:22]1[CH2:5][CH2:4][C@@H:18]2[C:25]1[CH:17]=[C:24]([CH2:9]F)[O:14][CH:3]=1.[CH3:1][C@:27]12[CH2:11][CH2:7][C@H:20]([OH:15])[CH2:6][C:23]1=[CH:13][CH2:10][C@@H:19]1[C@@H:21]2[CH2:8][CH2:12][C@:26]2([CH3:2])[C@H:18]([CH2:4][CH2:5][C@H:22]21)[C:25]1[CH:17]=[C:24]([CH2:9][OH:16])[O:14][CH:3]=1 |f:1.2,w:4,7,a:13,16,19,20,25,28,30,33,44,47,48,53,57,59,62,71,74,80,81,84,86,89| *** 290 *** [C@H:1]1([CH2:4][C:9](=[O:13])[O:12][CH3:14])[C:3](=[O:8])[CH2:7][C@@:10]2([H])[CH:11]=[CH:6][C@:2]1([H])[O:29]2.S(=O)(=O)(C(F)(F)F)O[Si:22]([CH3:28])([CH3:27])[CH3:26]>>[CH:10]1([O:29][Si:22]([CH3:28])([CH3:27])[CH3:26])[CH2:11][CH2:6][CH:2]=[C:1]([CH2:4][C:9](=[O:13])[O:12][CH3:14])[C:3](=[O:8])[CH2:7]1.[C@@H:2]1([CH2:6][CH2:11][CH:10]=[CH:7][C:3](=[O:8])[C@@H:1]1[CH2:4][C:9](=[O:13])[O:12][CH3:14])[O:29][Si:22]([CH3:28])([CH3:27])[CH3:26].[C@@:3]12([CH:7]=[CH:10][CH2:11][CH2:6][C@H:2]([O:29][Si:22]([CH3:28])([CH3:27])[CH3:26])[C@@:1]1([H])[C@@H:4]2[C:9](=[O:13])[O:12][CH3:14])[O:8][Si:22]([CH3:28])([CH3:27])[CH3:26] |&1:0,9,13,46,53,64,69,75,77| [CH3:1][O:12][C:16](=[O:6])[CH2:8][C@@H:13]1[C@@H:14]2[CH:10]=[CH:9][C@H:15]([CH2:7][C:17]1=[O:5])[O:11]2.[CH3:2][Si:18]([CH3:3])([CH3:4])OS(=O)(=O)C(F)(F)F>>[CH3:4][Si:18]([CH3:2])([CH3:3])[O:11][C@@H:14]1[CH2:10][CH2:9][CH:15]=[CH:7][C:17](=[O:5])[C@H:13]1[CH2:8][C:16](=[O:6])[O:12][CH3:1].[CH3:4][Si:18]([CH3:2])([CH3:3])[O:11][CH:15]1[CH2:7][C:17](=[O:5])[C:13]([CH2:8][C:16](=[O:6])[O:12][CH3:1])=[CH:14][CH2:10][CH2:9]1.[CH3:3][Si:18]([CH3:2])([CH3:4])[O:11][C@@H:14]1[CH2:10][CH2:9][CH:15]=[CH:7][C@:17]2([O:5][Si:18]([CH3:3])([CH3:2])[CH3:4])[C@H:13]1[C@H:8]2[C:16](=[O:6])[O:12][CH3:1] |f:0.1,2.3.4,&1:5,6,9,31,38,67,72,78,79| diff --git a/api/tests/integration/ref/stereo/bidirectional.py.out b/api/tests/integration/ref/stereo/bidirectional.py.out index 99901048f5..e1cdb013f8 100644 --- a/api/tests/integration/ref/stereo/bidirectional.py.out +++ b/api/tests/integration/ref/stereo/bidirectional.py.out @@ -3,8 +3,8 @@ 02.mol C1CCC([C@@H]2C=CC(N([H])C2=O)=O)O1 |&1:4,r| 03.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 04.mol C1CCC([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:4,r| -05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| -06.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| +05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r,wU:4.3,wD:3.2,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| +06.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r,wD:3.2,3.3,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| 07.mol stereocenters: one bond up, one bond down -- indefinite case near atom 3 08.mol C1CC[C@@](C)(C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 09.mol C1CC[C@@](C)(C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| @@ -26,9 +26,9 @@ test2.mol stereocenters: one bond up, one bond down -- indefinite case near atom 02.mol C1CCC([C@@H]2C=CC(N([H])C2=O)=O)O1 |&1:4,r| 03.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 04.mol C1CCC([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:4,r| -05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| -06.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| -07.mol C1CCC(C2C=CC(N([H])C2=O)=O)O1 +05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r,wU:4.3,wD:3.2,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| +06.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r,wD:3.2,3.3,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| +07.mol C1CCC(C2C=CC(N([H])C2=O)=O)O1 |&1:3,r,wU:3.2,wD:3.3,(-2.06,-0.81,;-1.79,-1.62,;-0.94,-1.62,;-0.70,-0.78,;0.04,-0.14,;-0.15,0.64,;0.46,1.24,;1.22,1.01,;1.53,0.12,;2.06,-0.05,;0.82,-0.39,;1.04,-1.18,;1.84,1.62,;-1.41,-0.31,)| 08.mol C1CC[C@@](C)(C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 09.mol C1CC[C@@](C)(C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 10.mol C1CCC(C)(C2C=CC(N([H])C2=O)=O)O1 @@ -49,8 +49,8 @@ test2.mol C1(CCCO1)N 02.mol C1CC[C@H]([C@@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| 03.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| 04.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| -05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| -06.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| +05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r,wU:4.3,wD:3.2,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| +06.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r,wD:3.2,3.3,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| 07.mol stereocenters: one bond up, one bond down -- indefinite case near atom 3 08.mol C1CC[C@@](C)([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,5,r| 09.mol C1CC[C@@](C)([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,5,r| @@ -72,8 +72,8 @@ test2.mol stereocenters: one bond up, one bond down -- indefinite case near atom 02.mol C1CC[C@H]([C@@H]2C=CC(N([H])C2=O)=O)O1 03.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 04.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 -05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 -06.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 +05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |wU:4.10,wD:3.13,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| +06.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |wU:4.10,wD:3.13,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| 07.mol stereocenters: one bond up, one bond down -- indefinite case near atom 3 08.mol C1CC[C@@](C)([C@H]2C=CC(N([H])C2=O)=O)O1 09.mol C1CC[C@@](C)([C@H]2C=CC(N([H])C2=O)=O)O1 diff --git a/core/indigo-core/molecule/molecule_stereocenters.h b/core/indigo-core/molecule/molecule_stereocenters.h index 62879c8d04..2bb23b30c2 100644 --- a/core/indigo-core/molecule/molecule_stereocenters.h +++ b/core/indigo-core/molecule/molecule_stereocenters.h @@ -56,6 +56,7 @@ namespace indigo void markBonds(BaseMolecule& baseMolecule); void markBond(BaseMolecule& baseMolecule, int atom_idx); + void markAtropisomericBond(BaseMolecule& baseMolecule, int atom_idx); // takes mapping from supermolecule to submolecule void buildOnSubmolecule(BaseMolecule& baseMolecule, const BaseMolecule& super, int* mapping); @@ -142,15 +143,17 @@ namespace indigo static void rotatePyramid(int* pyramid); private: - struct _Atom + struct _Atom { + _Atom() : type(-1), group(1), is_atropisomeric(false), is_tetrahydral(true), pyramid{-1,-1,-1,-1} + {} int type; // ANY, AND, OR, ABS int group; // stereogroup index // [X, Y, Z, W] -- atom indices or -1 for implicit hydrogen // (X, Y, Z) go counterclockwise when looking from W. // if there are pure (implicit) hydrogen, it is W - bool is_atropisomeric = false; - bool is_tetrahydral = true; + bool is_atropisomeric; + bool is_tetrahydral; int pyramid[4]; }; diff --git a/core/indigo-core/molecule/src/molecule_stereocenters.cpp b/core/indigo-core/molecule/src/molecule_stereocenters.cpp index 6fd594ab69..feac98aa2f 100644 --- a/core/indigo-core/molecule/src/molecule_stereocenters.cpp +++ b/core/indigo-core/molecule/src/molecule_stereocenters.cpp @@ -384,12 +384,12 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom { int possible_atropobond = -1; _Atom stereocenter; - if (check_atropocenter) - stereocenter.is_atropisomeric = isPossibleAtropocenter(baseMolecule, atom_idx, possible_atropobond); + stereocenter.group = 1; + stereocenter.type = ATOM_ABS; - // add atropocenter if required - if (possible_atropobond > -1) + if (check_atropocenter && isPossibleAtropocenter(baseMolecule, atom_idx, possible_atropobond)) { + stereocenter.is_atropisomeric = true; _AtropoCenter& ac = _atropocenters.findOrInsert(atom_idx); ac.atropo_bond = possible_atropobond; if (_stereocenters.find(atom_idx)) @@ -400,15 +400,13 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom _stereocenters.insert(atom_idx, stereocenter); } } + // check if there is a tetrahydral stereocenter already if (_stereocenters.find(atom_idx) && _stereocenters.at(atom_idx).is_tetrahydral) return true; const Vertex& vertex = baseMolecule.getVertex(atom_idx); int degree = vertex.degree(); - stereocenter.group = 1; - stereocenter.type = ATOM_ABS; - int* pyramid = stereocenter.pyramid; int nei_idx = 0; _EdgeIndVec edge_ids[4]; @@ -429,15 +427,19 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom bool is_either = false; bool zero_bond_length = false; + std::unordered_set atropo_bonds_ignore; for (int i = vertex.neiBegin(); i != vertex.neiEnd(); i = vertex.neiNext(i)) { + int e_idx = vertex.neiEdge(i); int v_idx = vertex.neiVertex(i); edge_ids[nei_idx].edge_idx = e_idx; edge_ids[nei_idx].nei_idx = v_idx; + if (stereocenter.is_atropisomeric && baseMolecule.getBondDirection(e_idx) && baseMolecule.getBondTopology(e_idx) == TOPOLOGY_RING) + atropo_bonds_ignore.insert(e_idx); if (baseMolecule.possibleAtomNumberAndIsotope(v_idx, ELEM_H, 0)) { if (baseMolecule.getAtomNumber(v_idx) == ELEM_H && baseMolecule.getAtomIsotope(v_idx) == 0) @@ -477,7 +479,7 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom // Local synonym to get bond direction auto getDir = [&](int from, int to) { int idx = baseMolecule.findEdgeIndex(from, to); - if (bond_ignore[idx]) + if (bond_ignore[idx] /* || atropo_bonds_ignore.find(idx) != atropo_bonds_ignore.end()*/) return 0; return _getDirection(baseMolecule, from, to, bidirectional_mode); }; @@ -730,7 +732,11 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom if (stereocenter.is_tetrahydral) { if (_stereocenters.find(atom_idx)) - _stereocenters.at(atom_idx).is_tetrahydral = true; + { + auto& sc = _stereocenters.at(atom_idx); + sc.is_tetrahydral = true; + std::copy(std::begin(stereocenter.pyramid), std::end(stereocenter.pyramid), std::begin(sc.pyramid)); + } else _stereocenters.insert(atom_idx, stereocenter); return true; @@ -1069,7 +1075,7 @@ bool MoleculeStereocenters::checkSub(BaseMolecule& query, BaseMolecule& target, if (stereocenters_vertex_filter != 0 && !stereocenters_vertex_filter->valid(iq)) continue; - if (cq.type < ATOM_AND) + if (cq.type < ATOM_AND || !cq.is_tetrahydral) continue; int stereo_group_and = -1; @@ -1841,7 +1847,14 @@ void MoleculeStereocenters::markBond(BaseMolecule& baseMolecule, int atom_idx) baseMolecule.setBondDirection(edge_idx, BOND_EITHER); } } +} +void MoleculeStereocenters::markAtropisomericBond(BaseMolecule& baseMolecule, int atom_idx) +{ + const _Atom* atom_ptr = _stereocenters.at2(atom_idx); + if (atom_ptr == NULL) + return; + const _Atom& atom = *atom_ptr; if (atom.is_atropisomeric) { const auto& ac = _atropocenters.at(atom_idx); @@ -1858,6 +1871,8 @@ void MoleculeStereocenters::markBonds(BaseMolecule& baseMolecule) { for (int i = _stereocenters.begin(); i != _stereocenters.end(); i = _stereocenters.next(i)) markBond(baseMolecule, _stereocenters.key(i)); + for (int i = _stereocenters.begin(); i != _stereocenters.end(); i = _stereocenters.next(i)) + markAtropisomericBond(baseMolecule, _stereocenters.key(i)); } bool MoleculeStereocenters::isAutomorphism(BaseMolecule& mol, const Array& mapping, const Filter* filter) diff --git a/core/indigo-core/molecule/src/smiles_loader.cpp b/core/indigo-core/molecule/src/smiles_loader.cpp index eb0b7d56aa..019a27a9e3 100644 --- a/core/indigo-core/molecule/src/smiles_loader.cpp +++ b/core/indigo-core/molecule/src/smiles_loader.cpp @@ -392,7 +392,10 @@ void SmilesLoader::_readOtherStuff() _overtly_defined_abs.insert(idx); } else + { _bmol->addStereocenters(idx, MoleculeStereocenters::ATOM_ABS, 0, false); + _bmol->stereocenters.setTetrahydral(idx, false); + } if (_scanner.lookNext() == ',') _scanner.skip(1); @@ -414,6 +417,7 @@ void SmilesLoader::_readOtherStuff() else { _bmol->addStereocenters(idx, MoleculeStereocenters::ATOM_OR, groupno, false); + _bmol->stereocenters.setTetrahydral(idx, false); } if (_scanner.lookNext() == ',') @@ -433,8 +437,10 @@ void SmilesLoader::_readOtherStuff() if (_bmol->stereocenters.exists(idx)) _bmol->stereocenters.setType(idx, MoleculeStereocenters::ATOM_AND, groupno); else + { _bmol->addStereocenters(idx, MoleculeStereocenters::ATOM_AND, groupno, false); - + _bmol->stereocenters.setTetrahydral(idx, false); + } if (_scanner.lookNext() == ',') _scanner.skip(1); } From 97f7c23779e925a9873ca7e9472ed397d53ec0d6 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Tue, 3 Oct 2023 10:23:37 +0200 Subject: [PATCH 17/36] stereocenters fixed --- core/indigo-core/molecule/molecule_stereocenters.h | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/core/indigo-core/molecule/molecule_stereocenters.h b/core/indigo-core/molecule/molecule_stereocenters.h index 2bb23b30c2..1852980de6 100644 --- a/core/indigo-core/molecule/molecule_stereocenters.h +++ b/core/indigo-core/molecule/molecule_stereocenters.h @@ -143,10 +143,11 @@ namespace indigo static void rotatePyramid(int* pyramid); private: - struct _Atom + struct _Atom { - _Atom() : type(-1), group(1), is_atropisomeric(false), is_tetrahydral(true), pyramid{-1,-1,-1,-1} - {} + _Atom() : type(-1), group(1), is_atropisomeric(false), is_tetrahydral(true), pyramid{-1, -1, -1, -1} + { + } int type; // ANY, AND, OR, ABS int group; // stereogroup index // [X, Y, Z, W] -- atom indices or -1 for implicit hydrogen From dad9634fcb5e4419e7136b5eda0d23b2222a10fa Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Tue, 3 Oct 2023 13:16:22 +0200 Subject: [PATCH 18/36] tests fixed --- .../integration/ref/formats/ket_to_sdf.py.out | 24 +------------------ .../tests/basic/ref/crazystereo.ket | 3 ++- .../tests/formats/ref/acd2d_err.ket | 24 ++++++++++++------- .../tests/formats/ref/acd2d_err3.sdf | 2 ++ .../tests/formats/ref/atropisomer.ket | 3 ++- 5 files changed, 23 insertions(+), 33 deletions(-) diff --git a/api/tests/integration/ref/formats/ket_to_sdf.py.out b/api/tests/integration/ref/formats/ket_to_sdf.py.out index 8297153b34..d1465c2d26 100644 --- a/api/tests/integration/ref/formats/ket_to_sdf.py.out +++ b/api/tests/integration/ref/formats/ket_to_sdf.py.out @@ -1,24 +1,2 @@ *** KET to SDF *** -acd2d_err3.sdf:FAILED ---- - -+++ - -@@ -8493,6 +8493,7 @@ - - M V30 31 1 14 26 CFG=3 - M V30 END BOND - M V30 BEGIN COLLECTION -+M V30 MDLV30/STEABS ATOMS=(1 1) - M V30 MDLV30/STERAC1 ATOMS=(7 2 9 10 11 12 13 14) - M V30 END COLLECTION - M V30 END CTAB -@@ -12399,6 +12400,7 @@ - - M V30 END BOND - M V30 BEGIN COLLECTION - M V30 MDLV30/STERAC1 ATOMS=(5 1 2 3 6 10) -+M V30 MDLV30/STEABS ATOMS=(2 5 9) - M V30 END COLLECTION - M V30 END CTAB - M END +acd2d_err3.sdf:SUCCEED diff --git a/api/tests/integration/tests/basic/ref/crazystereo.ket b/api/tests/integration/tests/basic/ref/crazystereo.ket index fe4a79bc83..e381f2a6b5 100644 --- a/api/tests/integration/tests/basic/ref/crazystereo.ket +++ b/api/tests/integration/tests/basic/ref/crazystereo.ket @@ -216,7 +216,8 @@ 9.062226295471192, 0.7499902248382568, 0.0 - ] + ], + "stereoLabel": "&1" }, { "label": "C", diff --git a/api/tests/integration/tests/formats/ref/acd2d_err.ket b/api/tests/integration/tests/formats/ref/acd2d_err.ket index 03ddf7791d..5e6c9f6c4b 100644 --- a/api/tests/integration/tests/formats/ref/acd2d_err.ket +++ b/api/tests/integration/tests/formats/ref/acd2d_err.ket @@ -14882,7 +14882,8 @@ 6.409999847412109, 2.190000057220459, 0.0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", @@ -30957,7 +30958,8 @@ 2.975600004196167, -2.3452000617980959, 0.0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", @@ -38277,7 +38279,8 @@ 4.26639986038208, -1.8983999490737916, 0.0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", @@ -38832,7 +38835,8 @@ 8.11620044708252, -2.767199993133545, 0.0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", @@ -52305,7 +52309,8 @@ 2.358599901199341, -0.25519999861717226, 0.0 - ] + ], + "stereoLabel": "abs" }, { "label": "O", @@ -54266,7 +54271,8 @@ 0.03449999913573265, 1.1758999824523926, 0.0 - ] + ], + "stereoLabel": "&1" }, { "label": "C", @@ -78531,7 +78537,8 @@ 3.516700029373169, -1.7541999816894532, 0.0 - ] + ], + "stereoLabel": "&1" }, { "label": "C", @@ -78564,7 +78571,8 @@ 2.575000047683716, -5.112500190734863, 0.0 - ] + ], + "stereoLabel": "&1" }, { "label": "C", diff --git a/api/tests/integration/tests/formats/ref/acd2d_err3.sdf b/api/tests/integration/tests/formats/ref/acd2d_err3.sdf index 7f61be9c7b..05cea7c00f 100644 --- a/api/tests/integration/tests/formats/ref/acd2d_err3.sdf +++ b/api/tests/integration/tests/formats/ref/acd2d_err3.sdf @@ -8493,6 +8493,7 @@ M V30 30 1 13 25 CFG=3 M V30 31 1 14 26 CFG=3 M V30 END BOND M V30 BEGIN COLLECTION +M V30 MDLV30/STEABS ATOMS=(1 1) M V30 MDLV30/STERAC1 ATOMS=(7 2 9 10 11 12 13 14) M V30 END COLLECTION M V30 END CTAB @@ -12399,6 +12400,7 @@ M V30 35 2 16 18 M V30 END BOND M V30 BEGIN COLLECTION M V30 MDLV30/STERAC1 ATOMS=(5 1 2 3 6 10) +M V30 MDLV30/STEABS ATOMS=(2 5 9) M V30 END COLLECTION M V30 END CTAB M END diff --git a/api/tests/integration/tests/formats/ref/atropisomer.ket b/api/tests/integration/tests/formats/ref/atropisomer.ket index 421c41f86a..7cd4aa00c3 100644 --- a/api/tests/integration/tests/formats/ref/atropisomer.ket +++ b/api/tests/integration/tests/formats/ref/atropisomer.ket @@ -55,7 +55,8 @@ 26.818199157714845, -12.862500190734864, 0.0 - ] + ], + "stereoLabel": "or1" }, { "label": "C", From 1d83dc980ce49b916474d2bae737f23714ecf5bb Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Tue, 3 Oct 2023 13:20:55 +0200 Subject: [PATCH 19/36] tests fixed --- .../ref/basic/ketfile_stereo_desc.py.out | 17 +---------------- 1 file changed, 1 insertion(+), 16 deletions(-) diff --git a/api/tests/integration/ref/basic/ketfile_stereo_desc.py.out b/api/tests/integration/ref/basic/ketfile_stereo_desc.py.out index c3d52f61b4..118bfdad0b 100644 --- a/api/tests/integration/ref/basic/ketfile_stereo_desc.py.out +++ b/api/tests/integration/ref/basic/ketfile_stereo_desc.py.out @@ -37,20 +37,5 @@ t4_S.mol:SUCCEED t4_S_iso.mol:SUCCEED trans.mol:SUCCEED without_stereo_label.mol:SUCCEED -crazystereo.rxn:FAILED ---- - -+++ - -@@ -216,7 +216,8 @@ - - 9.062226295471192, - 0.7499902248382568, - 0.0 -- ] -+ ], -+ "stereoLabel": "&1" - }, - { - "label": "C", +crazystereo.rxn:SUCCEED From 8f9a83048564613d9e432014c453c4e4de46cba1 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Tue, 3 Oct 2023 14:01:41 +0200 Subject: [PATCH 20/36] tests fixed --- .../integration/ref/formats/mol_to_ket.py.out | 17 +--- .../integration/ref/formats/sdf_to_ket.py.out | 94 +------------------ 2 files changed, 2 insertions(+), 109 deletions(-) diff --git a/api/tests/integration/ref/formats/mol_to_ket.py.out b/api/tests/integration/ref/formats/mol_to_ket.py.out index 1ed735bb47..69f4d6eb4a 100644 --- a/api/tests/integration/ref/formats/mol_to_ket.py.out +++ b/api/tests/integration/ref/formats/mol_to_ket.py.out @@ -2,21 +2,6 @@ 1032-quadra.ket:SUCCEED 1046-imp_hydrogen.ket:SUCCEED SgroupDifferent.ket:SUCCEED -atropisomer.ket:FAILED ---- - -+++ - -@@ -55,7 +55,8 @@ - - 26.818199157714845, - -12.862500190734864, - 0.0 -- ] -+ ], -+ "stereoLabel": "or1" - }, - { - "label": "C", +atropisomer.ket:SUCCEED non_atrop.ket:SUCCEED suplabel.ket:SUCCEED diff --git a/api/tests/integration/ref/formats/sdf_to_ket.py.out b/api/tests/integration/ref/formats/sdf_to_ket.py.out index 097e6e9ed2..2766f1ab3d 100644 --- a/api/tests/integration/ref/formats/sdf_to_ket.py.out +++ b/api/tests/integration/ref/formats/sdf_to_ket.py.out @@ -1,94 +1,2 @@ *** SDF to KET *** -acd2d_err.ket:FAILED ---- - -+++ - -@@ -14882,7 +14882,8 @@ - - 6.409999847412109, - 2.190000057220459, - 0.0 -- ] -+ ], -+ "stereoLabel": "abs" - }, - { - "label": "C", -@@ -30957,7 +30958,8 @@ - - 2.975600004196167, - -2.3452000617980959, - 0.0 -- ] -+ ], -+ "stereoLabel": "abs" - }, - { - "label": "C", -@@ -38277,7 +38279,8 @@ - - 4.26639986038208, - -1.8983999490737916, - 0.0 -- ] -+ ], -+ "stereoLabel": "abs" - }, - { - "label": "C", -@@ -38832,7 +38835,8 @@ - - 8.11620044708252, - -2.767199993133545, - 0.0 -- ] -+ ], -+ "stereoLabel": "abs" - }, - { - "label": "C", -@@ -52305,7 +52309,8 @@ - - 2.358599901199341, - -0.25519999861717226, - 0.0 -- ] -+ ], -+ "stereoLabel": "abs" - }, - { - "label": "O", -@@ -54266,7 +54271,8 @@ - - 0.03449999913573265, - 1.1758999824523926, - 0.0 -- ] -+ ], -+ "stereoLabel": "&1" - }, - { - "label": "C", -@@ -78531,7 +78537,8 @@ - - 3.516700029373169, - -1.7541999816894532, - 0.0 -- ] -+ ], -+ "stereoLabel": "&1" - }, - { - "label": "C", -@@ -78564,7 +78571,8 @@ - - 2.575000047683716, - -5.112500190734863, - 0.0 -- ] -+ ], -+ "stereoLabel": "&1" - }, - { - "label": "C", +acd2d_err.ket:SUCCEED From b68f89f12642874ee2fd1e03dee1cd40e2efeb68 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Tue, 3 Oct 2023 16:06:20 +0200 Subject: [PATCH 21/36] fix atropisomers detecytion algorythm --- .../integration/ref/basic/fold_unfold.py.out | 276 +++++++++--------- .../ref/basic/stereocenters.py.out | 93 +++--- .../integration/ref/bingo/molecules.py.out | 33 +-- api/tests/integration/ref/formats/cdx.py.out | 4 +- .../tests/formats/ref/acd2d_err.ket | 33 +-- .../tests/formats/ref/acd2d_err3.sdf | 1 - .../molecule/src/molecule_stereocenters.cpp | 21 +- 7 files changed, 224 insertions(+), 237 deletions(-) diff --git a/api/tests/integration/ref/basic/fold_unfold.py.out b/api/tests/integration/ref/basic/fold_unfold.py.out index 575f9ad8a2..dbdafd51dc 100644 --- a/api/tests/integration/ref/basic/fold_unfold.py.out +++ b/api/tests/integration/ref/basic/fold_unfold.py.out @@ -11,9 +11,9 @@ testing ../../../../../data/molecules/basic/sugars.sdf [C@]1([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])OC1(O[H])C([H])([H])O[H])O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] [C@@H]1([C@H](O)[C@@H](COC1(O)CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O -[C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C |wU:13.14,7.18,0.23,32.33,26.43,wD:0.0,8.8,24.25,27.28,37.39,(-0.84,0.15,;-0.86,-0.61,;-0.20,-1.00,;-0.23,-1.77,;0.40,-2.18,;-0.86,-2.14,;-0.79,0.87,;-1.48,1.16,;-1.97,0.59,;-2.72,0.64,;-3.04,1.33,;-3.79,1.41,;-2.62,1.96,;-1.58,-0.02,;-1.87,-0.72,;-2.63,-0.83,;-2.93,-1.52,;-3.08,-0.24,;-1.64,1.91,;-1.01,2.33,;-1.07,3.09,;-0.49,3.50,;-1.67,3.41,;-0.10,0.15,;0.54,-0.23,;0.54,-0.97,;1.19,-1.34,;1.86,-0.96,;2.51,-1.34,;3.17,-0.96,;3.83,-1.34,;3.16,-0.22,;1.86,-0.22,;2.51,0.15,;2.50,0.91,;3.16,1.29,;1.84,1.29,;1.19,0.15,;1.19,0.91,;0.54,1.28,;0.53,2.04,;-0.10,0.90,;1.20,-2.11,;1.92,-2.34,;1.94,-3.10,;2.60,-3.46,;1.29,-3.50,)| -[C@@]1(C([H])([H])OC(=O)C([H])([H])[H])(O[C@@]([H])([C@@]([H])(OC(=O)C([H])([H])[H])[C@]1([H])OC(=O)C([H])([H])[H])C([H])([H])OC(=O)C([H])([H])[H])O[C@@]1([H])O[C@@]([H])([C@@]([H])(OC(=O)C([H])([H])[H])[C@]([H])(OC(=O)C([H])([H])[H])[C@@]1([H])OC(=O)C([H])([H])[H])C([H])([H])OC(=O)C([H])([H])[H] |wU:23.25,12.32,0.42,57.59,46.76,wD:0.0,14.15,43.45,48.50,66.69,(-0.84,0.15,;-0.86,-0.61,;0.00,0.00,;0.00,0.00,;-0.20,-1.00,;-0.23,-1.77,;0.40,-2.18,;-0.86,-2.14,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-0.79,0.87,;-1.48,1.16,;0.00,0.00,;-1.97,0.59,;0.00,0.00,;-2.72,0.64,;-3.04,1.33,;-3.79,1.41,;-2.62,1.96,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-1.58,-0.02,;0.00,0.00,;-1.87,-0.72,;-2.63,-0.83,;-2.93,-1.52,;-3.08,-0.24,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-1.64,1.91,;0.00,0.00,;0.00,0.00,;-1.01,2.33,;-1.07,3.09,;-0.49,3.50,;-1.67,3.41,;0.00,0.00,;0.00,0.00,;0.00,0.00,;-0.10,0.15,;0.54,-0.23,;0.00,0.00,;0.54,-0.97,;1.19,-1.34,;0.00,0.00,;1.86,-0.96,;0.00,0.00,;2.51,-1.34,;3.17,-0.96,;3.83,-1.34,;3.16,-0.22,;0.00,0.00,;0.00,0.00,;0.00,0.00,;1.86,-0.22,;0.00,0.00,;2.51,0.15,;2.50,0.91,;3.16,1.29,;1.84,1.29,;0.00,0.00,;0.00,0.00,;0.00,0.00,;1.19,0.15,;0.00,0.00,;1.19,0.91,;0.54,1.28,;0.53,2.04,;-0.10,0.90,;0.00,0.00,;0.00,0.00,;0.00,0.00,;1.20,-2.11,;0.00,0.00,;0.00,0.00,;1.92,-2.34,;1.94,-3.10,;2.60,-3.46,;1.29,-3.50,;0.00,0.00,;0.00,0.00,;0.00,0.00,)| -[C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C |wU:13.14,7.18,0.23,32.33,26.43,wD:0.0,8.8,24.25,27.28,37.39,(-0.84,0.15,;-0.86,-0.61,;-0.20,-1.00,;-0.23,-1.77,;0.40,-2.18,;-0.86,-2.14,;-0.79,0.87,;-1.48,1.16,;-1.97,0.59,;-2.72,0.64,;-3.04,1.33,;-3.79,1.41,;-2.62,1.96,;-1.58,-0.02,;-1.87,-0.72,;-2.63,-0.83,;-2.93,-1.52,;-3.08,-0.24,;-1.64,1.91,;-1.01,2.33,;-1.07,3.09,;-0.49,3.50,;-1.67,3.41,;-0.10,0.15,;0.54,-0.23,;0.54,-0.97,;1.19,-1.34,;1.86,-0.96,;2.51,-1.34,;3.17,-0.96,;3.83,-1.34,;3.16,-0.22,;1.86,-0.22,;2.51,0.15,;2.50,0.91,;3.16,1.29,;1.84,1.29,;1.19,0.15,;1.19,0.91,;0.54,1.28,;0.53,2.04,;-0.10,0.90,;1.20,-2.11,;1.92,-2.34,;1.94,-3.10,;2.60,-3.46,;1.29,-3.50,)| +[C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C +[C@@]1(C([H])([H])OC(=O)C([H])([H])[H])(O[C@@]([H])([C@@]([H])(OC(=O)C([H])([H])[H])[C@]1([H])OC(=O)C([H])([H])[H])C([H])([H])OC(=O)C([H])([H])[H])O[C@@]1([H])O[C@@]([H])([C@@]([H])(OC(=O)C([H])([H])[H])[C@]([H])(OC(=O)C([H])([H])[H])[C@@]1([H])OC(=O)C([H])([H])[H])C([H])([H])OC(=O)C([H])([H])[H] +[C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O [C@]1(C([H])([H])O[H])([C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] @@ -27,17 +27,17 @@ testing ../../../../../data/molecules/basic/sugars.sdf [C@@]1([H])([C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] [C@H]1([C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O -[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |wU:1.1,7.7,13.14,18.20,29.31,26.35,wD:6.5,9.16,4.17,3.22,0.23,24.26,27.29,23.34,(0.82,0.83,;0.36,1.57,;0.76,2.31,;-0.48,1.53,;-0.88,0.78,;-1.72,0.75,;-2.13,-0.01,;-2.99,-0.02,;-3.43,0.68,;-3.39,-0.78,;-2.93,-1.50,;-3.33,-2.26,;-2.07,-1.47,;-1.67,-0.72,;-0.82,-0.69,;-0.37,-1.41,;-4.23,-0.81,;-0.42,0.05,;0.42,0.08,;0.87,-0.63,;0.47,-1.38,;-0.93,2.26,;1.67,0.87,;2.13,0.14,;2.98,0.18,;3.38,0.93,;3.44,-0.53,;3.03,-1.29,;3.49,-2.00,;2.18,-1.32,;1.78,-2.07,;0.92,-2.10,;1.73,-0.60,;4.28,-0.50,)| -[C@]1([H])([C@]([H])(O[H])[C@]([H])([C@@]([H])(O[C@@]2([H])[C@]([H])(O[H])[C@]([H])(C([H])(O[H])O[C@]2([H])C([H])([H])O[H])O[H])O[C@]1([H])C([H])([H])O[H])O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] |wU:2.3,13.14,24.26,34.37,56.59,50.66,wD:11.10,17.31,8.33,6.42,0.44,46.49,52.55,44.65,(0.82,0.83,;0.00,0.00,;0.36,1.57,;0.00,0.00,;0.76,2.31,;0.00,0.00,;-0.48,1.53,;0.00,0.00,;-0.88,0.78,;0.00,0.00,;-1.72,0.75,;-2.13,-0.01,;0.00,0.00,;-2.99,-0.02,;0.00,0.00,;-3.43,0.68,;0.00,0.00,;-3.39,-0.78,;0.00,0.00,;-2.93,-1.50,;0.00,0.00,;-3.33,-2.26,;0.00,0.00,;-2.07,-1.47,;-1.67,-0.72,;0.00,0.00,;-0.82,-0.69,;0.00,0.00,;0.00,0.00,;-0.37,-1.41,;0.00,0.00,;-4.23,-0.81,;0.00,0.00,;-0.42,0.05,;0.42,0.08,;0.00,0.00,;0.87,-0.63,;0.00,0.00,;0.00,0.00,;0.47,-1.38,;0.00,0.00,;-0.93,2.26,;0.00,0.00,;1.67,0.87,;2.13,0.14,;0.00,0.00,;2.98,0.18,;0.00,0.00,;3.38,0.93,;0.00,0.00,;3.44,-0.53,;0.00,0.00,;3.03,-1.29,;0.00,0.00,;3.49,-2.00,;0.00,0.00,;2.18,-1.32,;0.00,0.00,;1.78,-2.07,;0.00,0.00,;0.00,0.00,;0.92,-2.10,;0.00,0.00,;1.73,-0.60,;4.28,-0.50,;0.00,0.00,)| -[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |wU:1.1,7.7,13.14,18.20,29.31,26.35,wD:6.5,9.16,4.17,3.22,0.23,24.26,27.29,23.34,(0.82,0.83,;0.36,1.57,;0.76,2.31,;-0.48,1.53,;-0.88,0.78,;-1.72,0.75,;-2.13,-0.01,;-2.99,-0.02,;-3.43,0.68,;-3.39,-0.78,;-2.93,-1.50,;-3.33,-2.26,;-2.07,-1.47,;-1.67,-0.72,;-0.82,-0.69,;-0.37,-1.41,;-4.23,-0.81,;-0.42,0.05,;0.42,0.08,;0.87,-0.63,;0.47,-1.38,;-0.93,2.26,;1.67,0.87,;2.13,0.14,;2.98,0.18,;3.38,0.93,;3.44,-0.53,;3.03,-1.29,;3.49,-2.00,;2.18,-1.32,;1.78,-2.07,;0.92,-2.10,;1.73,-0.60,;4.28,-0.50,)| +[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O +[C@]1([H])([C@]([H])(O[H])[C@]([H])([C@@]([H])(O[C@@]2([H])[C@]([H])(O[H])[C@]([H])(C([H])(O[H])O[C@]2([H])C([H])([H])O[H])O[H])O[C@]1([H])C([H])([H])O[H])O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O1)O[H] +[C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O -[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,25.26,27.28,24.32,15.35,wD:0.0,5.10,13.14,16.17,21.21,22.23,12.34,(-2.18,-0.79,;-1.50,-1.14,;-0.88,-0.70,;-2.43,-1.51,;-1.99,-2.13,;-3.18,-1.50,;-3.39,-0.76,;-4.13,-0.49,;-4.25,0.24,;-2.79,-0.33,;-3.64,-2.09,;-1.63,0.09,;-0.95,0.45,;-0.94,1.21,;-1.59,1.60,;-0.27,1.57,;0.38,1.18,;1.03,1.54,;0.36,0.42,;0.99,0.02,;1.66,0.39,;2.31,-0.01,;2.98,0.34,;3.00,1.11,;3.63,-0.04,;3.61,-0.80,;4.26,-1.19,;2.93,-1.16,;2.92,-1.91,;2.24,-2.28,;2.29,-0.76,;4.29,0.31,;-0.31,0.06,;-0.25,2.33,)| -[C@]1(C([H])([H])O[H])([C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]2([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O2)O[H])O1)O[H] |wU:6.7,12.13,0.22,35.37,49.51,53.55,47.62,29.66,wD:0.0,10.20,25.27,31.33,41.41,43.45,23.65,(-2.18,-0.79,;-1.50,-1.14,;0.00,0.00,;0.00,0.00,;-0.88,-0.70,;0.00,0.00,;-2.43,-1.51,;0.00,0.00,;-1.99,-2.13,;0.00,0.00,;-3.18,-1.50,;0.00,0.00,;-3.39,-0.76,;0.00,0.00,;-4.13,-0.49,;0.00,0.00,;0.00,0.00,;-4.25,0.24,;0.00,0.00,;-2.79,-0.33,;-3.64,-2.09,;0.00,0.00,;-1.63,0.09,;-0.95,0.45,;0.00,0.00,;-0.94,1.21,;0.00,0.00,;-1.59,1.60,;0.00,0.00,;-0.27,1.57,;0.00,0.00,;0.38,1.18,;0.00,0.00,;1.03,1.54,;0.00,0.00,;0.36,0.42,;0.00,0.00,;0.99,0.02,;0.00,0.00,;0.00,0.00,;1.66,0.39,;2.31,-0.01,;0.00,0.00,;2.98,0.34,;0.00,0.00,;3.00,1.11,;0.00,0.00,;3.63,-0.04,;0.00,0.00,;3.61,-0.80,;0.00,0.00,;4.26,-1.19,;0.00,0.00,;2.93,-1.16,;0.00,0.00,;2.92,-1.91,;0.00,0.00,;0.00,0.00,;2.24,-2.28,;0.00,0.00,;2.29,-0.76,;4.29,0.31,;0.00,0.00,;-0.31,0.06,;-0.25,2.33,;0.00,0.00,)| -[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,25.26,27.28,24.32,15.35,wD:0.0,5.10,13.14,16.17,21.21,22.23,12.34,(-2.18,-0.79,;-1.50,-1.14,;-0.88,-0.70,;-2.43,-1.51,;-1.99,-2.13,;-3.18,-1.50,;-3.39,-0.76,;-4.13,-0.49,;-4.25,0.24,;-2.79,-0.33,;-3.64,-2.09,;-1.63,0.09,;-0.95,0.45,;-0.94,1.21,;-1.59,1.60,;-0.27,1.57,;0.38,1.18,;1.03,1.54,;0.36,0.42,;0.99,0.02,;1.66,0.39,;2.31,-0.01,;2.98,0.34,;3.00,1.11,;3.63,-0.04,;3.61,-0.80,;4.26,-1.19,;2.93,-1.16,;2.92,-1.91,;2.24,-2.28,;2.29,-0.76,;4.29,0.31,;-0.31,0.06,;-0.25,2.33,)| +[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O2)O)O1)O +[C@]1(C([H])([H])O[H])([C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]2([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O2)O[H])O1)O[H] +[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O2)O)O1)O -[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O3)O)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,25.26,27.28,34.35,36.37,33.41,24.44,15.47,wD:0.0,5.10,13.14,16.17,21.21,22.23,30.30,31.32,12.46,(-2.54,-1.21,;-2.00,-1.50,;-1.48,-1.14,;-2.76,-1.79,;-2.40,-2.31,;-3.39,-1.79,;-3.56,-1.17,;-4.14,-0.97,;-4.27,-0.35,;-3.05,-0.84,;-3.77,-2.27,;-2.22,-0.69,;-1.97,-0.13,;-2.33,0.38,;-2.94,0.31,;-2.07,0.94,;-1.45,0.99,;-1.20,1.56,;-1.08,0.49,;-0.47,0.55,;-0.22,1.11,;0.40,1.17,;0.64,1.73,;0.30,2.24,;1.25,1.80,;1.62,1.30,;2.24,1.35,;1.37,0.72,;1.72,0.22,;2.34,0.29,;2.70,-0.21,;3.32,-0.15,;3.58,0.40,;3.68,-0.66,;3.42,-1.22,;3.78,-1.73,;2.80,-1.28,;2.54,-1.84,;1.93,-1.91,;2.44,-0.78,;4.30,-0.59,;0.74,0.66,;1.52,2.36,;-1.35,-0.07,;-2.43,1.43,)| -[C@]1(C([H])([H])O[H])([C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]2([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]3([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O3)O[H])O2)O[H])O1)O[H] |wU:6.7,12.13,0.22,35.37,49.51,53.55,67.69,71.73,65.80,47.84,29.88,wD:0.0,10.20,25.27,31.33,41.41,43.45,59.59,61.63,23.87,(-2.54,-1.21,;-2.00,-1.50,;0.00,0.00,;0.00,0.00,;-1.48,-1.14,;0.00,0.00,;-2.76,-1.79,;0.00,0.00,;-2.40,-2.31,;0.00,0.00,;-3.39,-1.79,;0.00,0.00,;-3.56,-1.17,;0.00,0.00,;-4.14,-0.97,;0.00,0.00,;0.00,0.00,;-4.27,-0.35,;0.00,0.00,;-3.05,-0.84,;-3.77,-2.27,;0.00,0.00,;-2.22,-0.69,;-1.97,-0.13,;0.00,0.00,;-2.33,0.38,;0.00,0.00,;-2.94,0.31,;0.00,0.00,;-2.07,0.94,;0.00,0.00,;-1.45,0.99,;0.00,0.00,;-1.20,1.56,;0.00,0.00,;-1.08,0.49,;0.00,0.00,;-0.47,0.55,;0.00,0.00,;0.00,0.00,;-0.22,1.11,;0.40,1.17,;0.00,0.00,;0.64,1.73,;0.00,0.00,;0.30,2.24,;0.00,0.00,;1.25,1.80,;0.00,0.00,;1.62,1.30,;0.00,0.00,;2.24,1.35,;0.00,0.00,;1.37,0.72,;0.00,0.00,;1.72,0.22,;0.00,0.00,;0.00,0.00,;2.34,0.29,;2.70,-0.21,;0.00,0.00,;3.32,-0.15,;0.00,0.00,;3.58,0.40,;0.00,0.00,;3.68,-0.66,;0.00,0.00,;3.42,-1.22,;0.00,0.00,;3.78,-1.73,;0.00,0.00,;2.80,-1.28,;0.00,0.00,;2.54,-1.84,;0.00,0.00,;0.00,0.00,;1.93,-1.91,;0.00,0.00,;2.44,-0.78,;4.30,-0.59,;0.00,0.00,;0.74,0.66,;1.52,2.36,;0.00,0.00,;-1.35,-0.07,;-2.43,1.43,;0.00,0.00,)| -[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O3)O)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,25.26,27.28,34.35,36.37,33.41,24.44,15.47,wD:0.0,5.10,13.14,16.17,21.21,22.23,30.30,31.32,12.46,(-2.54,-1.21,;-2.00,-1.50,;-1.48,-1.14,;-2.76,-1.79,;-2.40,-2.31,;-3.39,-1.79,;-3.56,-1.17,;-4.14,-0.97,;-4.27,-0.35,;-3.05,-0.84,;-3.77,-2.27,;-2.22,-0.69,;-1.97,-0.13,;-2.33,0.38,;-2.94,0.31,;-2.07,0.94,;-1.45,0.99,;-1.20,1.56,;-1.08,0.49,;-0.47,0.55,;-0.22,1.11,;0.40,1.17,;0.64,1.73,;0.30,2.24,;1.25,1.80,;1.62,1.30,;2.24,1.35,;1.37,0.72,;1.72,0.22,;2.34,0.29,;2.70,-0.21,;3.32,-0.15,;3.58,0.40,;3.68,-0.66,;3.42,-1.22,;3.78,-1.73,;2.80,-1.28,;2.54,-1.84,;1.93,-1.91,;2.44,-0.78,;4.30,-0.59,;0.74,0.66,;1.52,2.36,;-1.35,-0.07,;-2.43,1.43,)| +[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O3)O)O2)O)O1)O +[C@]1(C([H])([H])O[H])([C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]2([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]3([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O3)O[H])O2)O[H])O1)O[H] +[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O3)O)O2)O)O1)O [C@H]12[C@H](O)[C@H]([C@@H](OC)O[C@@H]1COC(C1C=CC=CC=1)O2)O [C@]12([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(OC([H])([H])[H])O[C@]1([H])C([H])([H])OC([H])(C1C([H])=C([H])C([H])=C([H])C=1[H])O2)O[H] @@ -51,13 +51,13 @@ testing ../../../../../data/molecules/basic/sugars.sdf [C@]12([H])O[C@@]3([H])O[C@@]([H])([C@@]([H])(O[C@@]4([H])O[C@@]([H])([C@@]([H])(O[C@@]5([H])O[C@@]([H])([C@@]([H])(O[C@@]6([H])O[C@@]([H])([C@]([H])([C@]([H])(O[H])[C@@]6([H])O[H])O[C@]6([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O6)O[C@]6([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O6)O[C@]6([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O6)O[C@]([H])([C@]([H])(O[H])[C@@]1([H])O[H])O[C@]2([H])C([H])([H])O[H])C([H])([H])O[H])[C@]([H])(O[H])[C@@]5([H])O[H])C([H])([H])O[H])[C@]([H])(O[H])[C@@]4([H])O[H])C([H])([H])O[H])[C@]([H])(O[H])[C@@]3([H])O[H])C([H])([H])O[H] [C@H]12O[C@H]3O[C@@H]([C@@H](O[C@H]4O[C@@H]([C@@H](O[C@H]5O[C@@H]([C@@H](O[C@H]6O[C@@H]([C@H]([C@H](O)[C@H]6O)O[C@@H]6[C@H](O)[C@@H](O)[C@@H]([C@@H](CO)O6)O[C@@H]6[C@H](O)[C@@H](O)[C@@H]([C@@H](CO)O6)O[C@@H]6[C@H](O)[C@@H](O)[C@@H]([C@@H](CO)O6)O[C@H]([C@H](O)[C@H]1O)O[C@@H]2CO)CO)[C@H](O)[C@H]5O)CO)[C@H](O)[C@H]4O)CO)[C@H](O)[C@H]3O)CO 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[C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@H]1[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]4[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O4)O)O3)O)O2)O)O1)O [C@]1(C([H])([H])O[H])([C@@]([H])(O[H])[C@@]([H])([C@@]([H])(C([H])([H])O[H])O1)O[H])O[C@@]1([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]2([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]3([H])[C@]([H])(O[H])[C@]([H])([C@]([H])(O[H])[C@@]([H])(C([H])([H])O[C@]4([H])[C@]([H])(O[H])[C@]([H])([C@@]([H])(O[H])[C@@]([H])(C([H])([H])O[H])O4)O[H])O3)O[H])O2)O[H])O1)O[H] diff --git a/api/tests/integration/ref/basic/stereocenters.py.out b/api/tests/integration/ref/basic/stereocenters.py.out index 5fe0fc8258..4db078722d 100644 --- a/api/tests/integration/ref/basic/stereocenters.py.out +++ b/api/tests/integration/ref/basic/stereocenters.py.out @@ -30,7 +30,7 @@ C(P)(O)N 12,18,19,-1 13,20,18,-1 15,21,16,-1 -3: [C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C |wU:13.14,7.18,0.23,32.33,26.43,wD:0.0,8.8,24.25,27.28,37.39,(-0.84,0.15,;-0.86,-0.61,;-0.20,-1.00,;-0.23,-1.77,;0.40,-2.18,;-0.86,-2.14,;-0.79,0.87,;-1.48,1.16,;-1.97,0.59,;-2.72,0.64,;-3.04,1.33,;-3.79,1.41,;-2.62,1.96,;-1.58,-0.02,;-1.87,-0.72,;-2.63,-0.83,;-2.93,-1.52,;-3.08,-0.24,;-1.64,1.91,;-1.01,2.33,;-1.07,3.09,;-0.49,3.50,;-1.67,3.41,;-0.10,0.15,;0.54,-0.23,;0.54,-0.97,;1.19,-1.34,;1.86,-0.96,;2.51,-1.34,;3.17,-0.96,;3.83,-1.34,;3.16,-0.22,;1.86,-0.22,;2.51,0.15,;2.50,0.91,;3.16,1.29,;1.84,1.29,;1.19,0.15,;1.19,0.91,;0.54,1.28,;0.53,2.04,;-0.10,0.90,;1.20,-2.11,;1.92,-2.34,;1.94,-3.10,;2.60,-3.46,;1.29,-3.50,)| +3: [C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C 1,3,2,4 0,6,5,-1 1,8,10,-1 @@ -76,7 +76,7 @@ C(P)(O)N 8,18,19,-1 9,20,18,-1 13,21,14,-1 -7: [C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |wU:1.1,7.7,13.14,18.20,29.31,26.35,wD:6.5,9.16,4.17,3.22,0.23,24.26,27.29,23.34,(0.82,0.83,;0.36,1.57,;0.76,2.31,;-0.48,1.53,;-0.88,0.78,;-1.72,0.75,;-2.13,-0.01,;-2.99,-0.02,;-3.43,0.68,;-3.39,-0.78,;-2.93,-1.50,;-3.33,-2.26,;-2.07,-1.47,;-1.67,-0.72,;-0.82,-0.69,;-0.37,-1.41,;-4.23,-0.81,;-0.42,0.05,;0.42,0.08,;0.87,-0.63,;0.47,-1.38,;-0.93,2.26,;1.67,0.87,;2.13,0.14,;2.98,0.18,;3.38,0.93,;3.44,-0.53,;3.03,-1.29,;3.49,-2.00,;2.18,-1.32,;1.78,-2.07,;0.92,-2.10,;1.73,-0.60,;4.28,-0.50,)| +7: [C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O 1,2,3,-1 0,5,4,-1 0,7,8,-1 @@ -91,7 +91,7 @@ C(P)(O)N 18,27,26,-1 18,28,29,-1 23,32,30,-1 -8: [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,25.26,27.28,24.32,15.35,wD:0.0,5.10,13.14,16.17,21.21,22.23,12.34,(-2.18,-0.79,;-1.50,-1.14,;-0.88,-0.70,;-2.43,-1.51,;-1.99,-2.13,;-3.18,-1.50,;-3.39,-0.76,;-4.13,-0.49,;-4.25,0.24,;-2.79,-0.33,;-3.64,-2.09,;-1.63,0.09,;-0.95,0.45,;-0.94,1.21,;-1.59,1.60,;-0.27,1.57,;0.38,1.18,;1.03,1.54,;0.36,0.42,;0.99,0.02,;1.66,0.39,;2.31,-0.01,;2.98,0.34,;3.00,1.11,;3.63,-0.04,;3.61,-0.80,;4.26,-1.19,;2.93,-1.16,;2.92,-1.91,;2.24,-2.28,;2.29,-0.76,;4.29,0.31,;-0.31,0.06,;-0.25,2.33,)| +8: [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O2)O)O1)O 1,3,2,4 0,8,7,-1 1,10,11,-1 @@ -106,7 +106,7 @@ C(P)(O)N 24,29,30,-1 25,31,29,-1 26,27,32,-1 -9: [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O3)O)O2)O)O1)O |wU:3.3,6.6,0.11,18.19,25.26,27.28,34.35,36.37,33.41,24.44,15.47,wD:0.0,5.10,13.14,16.17,21.21,22.23,30.30,31.32,12.46,(-2.54,-1.21,;-2.00,-1.50,;-1.48,-1.14,;-2.76,-1.79,;-2.40,-2.31,;-3.39,-1.79,;-3.56,-1.17,;-4.14,-0.97,;-4.27,-0.35,;-3.05,-0.84,;-3.77,-2.27,;-2.22,-0.69,;-1.97,-0.13,;-2.33,0.38,;-2.94,0.31,;-2.07,0.94,;-1.45,0.99,;-1.20,1.56,;-1.08,0.49,;-0.47,0.55,;-0.22,1.11,;0.40,1.17,;0.64,1.73,;0.30,2.24,;1.25,1.80,;1.62,1.30,;2.24,1.35,;1.37,0.72,;1.72,0.22,;2.34,0.29,;2.70,-0.21,;3.32,-0.15,;3.58,0.40,;3.68,-0.66,;3.42,-1.22,;3.78,-1.73,;2.80,-1.28,;2.54,-1.84,;1.93,-1.91,;2.44,-0.78,;4.30,-0.59,;0.74,0.66,;1.52,2.36,;-1.35,-0.07,;-2.43,1.43,)| +9: [C@]1(CO)([C@@H](O)[C@@H]([C@@H](CO)O1)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@@H](O)[C@@H](CO[C@@H]3[C@H](O)[C@H]([C@@H](O)[C@@H](CO)O3)O)O2)O)O1)O 1,3,2,4 0,8,7,-1 1,10,11,-1 @@ -179,7 +179,7 @@ C(P)(O)N 78,85,84,-1 79,84,86,-1 80,81,83,-1 -13: [C@@H]1(O[C@@H]2O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)COC(=O)C)[C@@H](COC(=O)C)O[C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C |wU:2.2,10.10,4.20,25.26,42.44,wD:0.0,5.5,15.16,32.33,37.38,(1.18,-0.62,;0.39,-1.08,;-0.33,-0.61,;-0.33,0.23,;-1.12,0.67,;-1.89,0.23,;-2.68,0.67,;-2.68,1.57,;-3.44,2.03,;-1.89,2.02,;-1.89,-0.63,;-2.68,-1.08,;-3.43,-0.62,;-4.23,-1.07,;-3.43,0.24,;-1.12,-1.07,;-1.11,-1.97,;-1.89,-2.43,;-1.89,-3.32,;-2.68,-1.97,;-1.12,1.57,;-0.33,2.03,;-0.34,2.93,;0.39,3.38,;-1.12,3.38,;1.18,0.22,;0.40,0.66,;0.40,1.56,;1.19,2.02,;1.19,2.93,;2.03,1.63,;1.95,0.70,;2.74,0.24,;3.49,0.70,;3.49,1.59,;4.28,2.04,;2.74,2.05,;2.74,-0.60,;3.50,-1.07,;3.50,-1.97,;4.28,-2.42,;2.73,-2.41,;1.95,-1.06,;1.95,-1.96,;1.18,-2.42,;1.19,-3.30,;0.39,-1.98,)| +13: [C@@H]1(O[C@@H]2O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]2OC(=O)C)COC(=O)C)[C@@H](COC(=O)C)O[C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C 1,2,3,-1 0,4,5,-1 0,7,6,-1 @@ -190,7 +190,7 @@ C(P)(O)N 13,29,28,-1 14,28,31,-1 20,22,34,-1 -14: [C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@@H](O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O |wU:1.1,7.7,13.14,18.20,35.37,32.41,40.43,26.47,wD:6.5,10.10,9.16,4.17,3.22,0.23,24.26,27.29,30.32,33.35,29.40,23.46,(0.63,-0.13,;0.87,-0.52,;0.58,-0.96,;1.36,-0.52,;1.60,-0.11,;2.17,-0.11,;2.70,-0.15,;2.97,-0.62,;2.72,-1.08,;3.48,-0.60,;3.75,-0.15,;4.31,-0.15,;3.48,0.29,;2.96,0.29,;2.68,0.77,;2.93,1.23,;3.73,-1.08,;1.36,0.31,;0.87,0.31,;0.59,0.77,;0.83,1.22,;1.63,-0.99,;0.11,-0.17,;-0.51,-0.23,;-0.76,-0.70,;-0.47,-1.18,;-1.30,-0.70,;-1.57,-0.24,;-2.12,-0.24,;-2.66,-0.21,;-2.91,-0.67,;-2.62,-1.15,;-3.44,-0.68,;-3.70,-0.22,;-4.28,-0.22,;-3.46,0.23,;-3.76,0.71,;-3.50,1.18,;-2.93,0.23,;-3.70,-1.18,;-1.31,0.20,;-1.60,0.68,;-1.34,1.15,;-0.80,0.21,;-1.56,-1.20,)| +14: [C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@@H](O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O 1,2,3,-1 0,5,4,-1 0,7,8,-1 @@ -326,7 +326,7 @@ C(P)(O)N 26,31,32,-1 27,33,31,-1 28,34,29,-1 -22: [C@@]1(COC(=O)C(C)C)(O[C@@H]([C@@H](OC(=O)C(C)C)[C@@H]1OC(=O)C(C)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C(C)C)[C@H](OC(=O)C(C)C)[C@H]1OC(=O)C(C)C)COC(=O)C |wU:17.18,9.24,0.29,40.41,32.55,wD:0.0,10.10,30.31,33.34,47.49,(-0.96,-0.08,;-1.03,-0.81,;-0.47,-1.28,;-0.57,-2.03,;0.03,-2.50,;-1.21,-2.32,;-1.31,-3.08,;-1.81,-1.87,;-0.84,0.64,;-1.52,0.97,;-2.02,0.42,;-2.79,0.54,;-3.07,1.25,;-2.58,1.85,;-3.82,1.36,;-4.28,0.75,;-4.10,2.06,;-1.70,-0.22,;-2.02,-0.87,;-2.76,-0.93,;-3.21,-0.31,;-3.12,-1.61,;-3.87,-1.64,;-2.69,-2.23,;-1.64,1.72,;-1.06,2.21,;-1.43,2.86,;-1.06,3.51,;-1.95,2.88,;-0.22,-0.01,;0.40,-0.38,;0.40,-1.11,;1.04,-1.48,;1.69,-1.11,;2.34,-1.48,;2.99,-1.11,;2.99,-0.37,;3.63,-1.48,;3.63,-2.22,;4.28,-1.11,;1.69,-0.37,;2.33,-0.01,;2.34,0.73,;1.69,1.10,;2.99,1.10,;3.63,0.73,;2.99,1.86,;1.04,-0.01,;1.04,0.73,;0.47,1.22,;-0.21,0.95,;0.61,1.94,;0.04,2.43,;1.31,2.21,;1.04,-2.22,;1.76,-2.41,;1.83,-3.16,;2.51,-3.46,;1.23,-3.59,)| +22: [C@@]1(COC(=O)C(C)C)(O[C@@H]([C@@H](OC(=O)C(C)C)[C@@H]1OC(=O)C(C)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C(C)C)[C@H](OC(=O)C(C)C)[C@H]1OC(=O)C(C)C)COC(=O)C 1,3,2,4 0,6,5,-1 1,8,10,-1 @@ -365,7 +365,7 @@ C(P)(O)N 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+26: [C@@]1(COC(=O)C2=CC=CC=C2)(O[C@@H]([C@@H](OC(=O)C2C=CC=CC=2)[C@@H]1OC(=O)C1=CC=CC=C1)COC(=O)C1C=CC=CC=1)O[C@H]1O[C@@H]([C@@H](OC(=O)C2C=CC=CC=2)[C@H](OC(=O)C2C=CC=CC=2)[C@H]1OC(=O)C1=CC=CC=C1)COC(=O)C1C=CC=CC=1 1,3,2,4 0,6,5,-1 1,8,10,-1 @@ -375,7 +375,7 @@ C(P)(O)N 12,30,29,-1 13,29,32,-1 19,21,40,-1 -27: [C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)CO[C@H]1O[C@@H]([C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C 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[C@@]1(COC(=O)C)(O[C@@H]([C@@H](OC(=O)C)[C@@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)CO[C@H]1O[C@@H]([C@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C 1,3,2,4 0,6,5,-1 1,8,10,-1 @@ -390,7 +390,7 @@ C(P)(O)N 45,51,50,-1 46,50,53,-1 47,54,49,-1 -28: [C@@H]1(OS(=O)(=O)C2=CC=C(C)C=C2)[C@@H](OS(=O)(=O)C2C=CC(C)=CC=2)[C@H](O[C@@H]2COC(C3C=CC=CC=3)O[C@@H]12)OC |wU:0.0,26.28,wD:12.13,37.39,24.42,(-0.58,0.96,;-0.95,0.29,;-0.57,-0.35,;-1.21,-0.72,;0.08,0.02,;-0.20,-1.00,;-0.59,-1.64,;-0.20,-2.32,;0.53,-2.32,;0.86,-2.98,;0.92,-1.66,;0.55,-1.00,;0.19,0.96,;0.61,0.34,;1.34,0.34,;1.34,1.09,;1.35,-0.40,;2.09,0.35,;2.46,1.00,;3.20,1.01,;3.60,0.36,;4.34,0.35,;3.24,-0.28,;2.47,-0.30,;0.54,1.61,;0.17,2.26,;-0.58,2.26,;-0.97,2.90,;-1.73,2.89,;-2.09,2.26,;-2.84,2.26,;-3.21,1.61,;-3.97,1.61,;-4.34,2.26,;-3.99,2.89,;-3.22,2.90,;-1.71,1.61,;-0.96,1.61,;1.30,1.61,;1.67,2.26,)| +28: [C@@H]1(OS(=O)(=O)C2=CC=C(C)C=C2)[C@@H](OS(=O)(=O)C2C=CC(C)=CC=2)[C@H](O[C@@H]2COC(C3C=CC=CC=3)O[C@@H]12)OC 1,2,3,-1 0,4,5,-1 0,7,6,-1 @@ -406,7 +406,7 @@ C(P)(O)N 12,26,25,-1 13,25,28,-1 18,20,33,-1 -30: [C@@]1(COCC(O)C)(O[C@@H]([C@@H](OCC(O)C)[C@@H]1OCC(O)C)COCC(O)C)O[C@H]1O[C@@H]([C@@H](OCC(O)C)[C@H](OCC(O)C)[C@H]1OCC(O)C)COCC(O)C 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C1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)O1)O |wU:1.1,7.7,13.14,18.20,29.31,38.40,35.44,26.47,wD:6.5,9.16,4.17,3.22,24.26,27.29,32.33,33.35,36.38,23.46,(-0.41,-2.19,;0.07,-2.75,;-0.13,-3.46,;0.80,-2.58,;1.03,-1.88,;1.76,-1.73,;1.98,-1.02,;2.69,-0.89,;3.22,-1.41,;2.91,-0.18,;2.42,0.37,;2.65,1.08,;1.68,0.21,;1.45,-0.49,;0.76,-0.64,;0.25,-0.10,;3.63,-0.01,;0.54,-1.34,;-0.20,-1.48,;-0.70,-0.96,;-0.48,-0.25,;1.30,-3.14,;-1.14,-2.35,;-1.63,-1.80,;-2.35,-1.97,;-2.59,-2.68,;-2.87,-1.41,;-2.63,-0.70,;-3.13,-0.18,;-1.90,-0.57,;-1.70,0.13,;-2.21,0.68,;-1.98,1.39,;-2.48,1.93,;-3.20,1.78,;-2.25,2.64,;-1.52,2.80,;-1.31,3.51,;-1.01,2.25,;-0.29,2.41,;0.19,1.86,;-1.24,1.54,;-2.76,3.19,;-1.41,-1.11,;-3.59,-1.58,)| +34: C1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H](C(O)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)O1)O 0,5,4,-1 0,7,8,-1 2,11,12,-1 @@ -462,7 +462,7 @@ C(P)(O)N 34,40,41,-1 35,42,40,-1 37,43,38,-1 -35: [C@@H]1([C@H](O)[C@H]([C@@H](O[C@H]2[C@H](O)[C@H]([C@H](OCCSCCC(=O)OC)O[C@@H]2CO)O)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)O1)O 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+483,7 @@ C(P)(O)N 34,41,42,-1 35,43,41,-1 37,45,38,-1 -36: [C@@]1(CO[Si](C)(C)C)(O[C@@H]([C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C)CO[Si](C)(C)C)O[C@H]1O[C@@H]([C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)CO[Si](C)(C)C |wU:15.16,8.21,0.27,37.38,30.50,wD:0.0,9.9,28.29,31.32,43.45,(0.83,-0.49,;0.52,-1.32,;1.10,-1.97,;0.79,-2.78,;0.51,-3.54,;1.60,-3.03,;-0.02,-2.46,;1.54,-1.01,;2.26,-0.52,;2.00,0.27,;2.52,0.97,;2.18,1.76,;1.82,2.54,;2.94,2.09,;1.37,1.44,;1.12,0.28,;0.62,1.00,;-0.06,1.44,;-0.74,1.97,;0.51,2.25,;-0.45,0.81,;3.08,-0.76,;3.71,-0.18,;3.52,0.65,;4.34,0.83,;2.68,0.46,;3.33,1.47,;0.12,-0.18,;-0.60,-0.17,;-1.04,0.57,;-1.92,0.57,;-2.35,-0.16,;-3.22,-0.16,;-3.64,0.57,;-4.34,0.13,;-2.91,1.01,;-4.07,1.26,;-1.92,-0.93,;-2.36,-1.69,;-3.20,-1.69,;-3.19,-2.51,;-3.22,-0.83,;-4.03,-1.70,;-1.04,-0.93,;-0.60,-1.71,;-1.05,-2.42,;-0.33,-2.85,;-1.78,-2.00,;-1.47,-3.16,;-2.36,1.33,;-1.93,2.09,;-2.35,2.83,;-1.62,3.22,;-3.09,2.41,;-2.74,3.54,)| +36: [C@@]1(CO[Si](C)(C)C)(O[C@@H]([C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C)CO[Si](C)(C)C)O[C@H]1O[C@@H]([C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C)CO[Si](C)(C)C 1,3,2,4 0,6,5,-1 1,8,10,-1 @@ -527,7 +527,7 @@ C(P)(O)N 0,7,6,-1 1,10,9,-1 2,11,9,-1 -41: [C@@H]1(O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C)O[C@H]1O[C@@H]([C@@H](OC(=O)C)[C@H](OC(=O)C)[C@H]1OC(=O)C)COC(=O)C 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+216: [C@@H]12[C@H](O)[C@H]([C@@H](O[C@H]3[C@H](O)[C@H]([C@@H](O[C@H]4[C@H](O)[C@H]([C@@H](O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5CO)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5CO)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5CO)O1)O[C@@H]4CO)O)O[C@@H]3CO)O)O[C@@H]2CO[C@@H]1[C@H](O)[C@H]([C@H](O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O)O 1,2,3,-1 0,5,4,-1 0,7,8,-1 @@ -3814,7 +3814,7 @@ C(P)(O)N 35,40,41,-1 36,42,40,-1 37,43,38,-1 -260: [C@@]1(CO)(O[C@@H]([C@@H](O)[C@@H]1O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O)CO)OC1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O.O 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|&1:0,1,3,4,16,21,22,24,25,27,r,wU:0.0,1.1,1.2,4.3,4.4,16.18,21.22,21.23,22.24,22.25,25.26,25.27,wD:3.20,0.21,27.29,24.33,(-0.83,0.76,;-0.39,0.04,;-0.80,-0.70,;0.45,0.05,;0.87,0.78,;1.71,0.79,;2.14,0.07,;2.98,0.08,;3.42,-0.65,;3.00,-1.39,;3.43,-2.12,;3.02,-2.86,;4.28,-2.11,;2.15,-1.40,;1.72,-0.67,;0.44,1.52,;-0.41,1.50,;-0.84,2.23,;-0.43,2.97,;0.88,-0.68,;-1.67,0.75,;-2.11,0.02,;-2.95,0.04,;-3.36,0.78,;-3.39,-0.69,;-2.98,-1.42,;-3.42,-2.15,;-2.13,-1.45,;-1.72,-2.19,;-2.16,-2.91,;-1.70,-0.72,;-4.24,-0.67,)| - -1,-1,-1,-1 +261: C1([C@H](O)[C@H]([C@H](OC2C=CC([N+]([O-])=O)=CC=2)O[C@@H]1CO)O)O[C@@H]1[C@H](O)[C@H]([C@H](O)[C@@H](CO)O1)O |&1:1,3,4,16,21,22,24,25,27,r| 0,5,4,-1 0,7,8,-1 2,11,12,-1 @@ -3989,7 +3988,7 @@ C(P)(O)N 99,109,113,-1 100,114,109,-1 104,107,106,-1 -267: [C@@H]12[C@H](O)[C@H]([C@@H](O[C@H]3[C@H](O)[C@H]([C@@H](O[C@H]4[C@H](O)[C@H]([C@@H](O[C@H]5[C@H](O)[C@H]([C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O1)O)O[C@@H]4COC1[C@H](O)[C@H]([C@H](O[C@@H]4[C@H](O)[C@H]([C@H](O)[C@@H](CO)O4)O)[C@@H](CO)O1)O)O)O[C@@H]3COC1[C@H](O)[C@H]([C@H](O[C@@H]3[C@H](O)[C@H]([C@H](O)[C@@H](CO)O3)O)[C@@H](CO)O1)O)O)O[C@@H]2COC1[C@H](O)[C@H](C(O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O)O |wU:4.4,7.7,13.13,19.19,24.25,39.40,36.44,44.46,30.50,51.54,57.61,72.76,69.80,77.82,63.86,84.90,90.97,105.112,102.116,110.118,96.122,116.124,119.128,138.148,135.152,143.154,129.158,121.159,0.160,151.165,166.180,163.184,171.186,157.190,178.195,193.210,190.214,198.216,184.220,220.240,217.244,225.246,211.250,3.251,wD:1.1,6.5,10.10,12.11,16.16,18.17,28.29,31.32,33.33,34.35,37.38,22.51,50.52,53.56,61.65,64.68,66.69,67.71,70.74,55.87,83.88,86.92,94.101,97.104,99.105,100.107,103.110,88.123,117.126,123.133,127.137,130.140,132.141,133.143,136.146,21.161,155.169,158.172,160.173,161.175,164.178,15.191,182.199,185.202,187.203,188.205,191.208,9.221,205.225,209.229,214.233,215.235,218.238,(-0.28,-1.50,;-0.45,-1.59,;-0.45,-1.78,;-0.61,-1.50,;-0.62,-1.31,;-0.90,-1.18,;-0.90,-0.99,;-0.73,-0.91,;-0.57,-1.01,;-0.71,-0.72,;-0.87,-0.61,;-0.86,0.05,;-0.65,0.53,;-0.48,0.62,;-0.32,0.52,;-0.48,0.81,;-0.64,0.91,;-0.62,1.20,;-0.37,1.32,;-0.20,1.23,;-0.20,1.04,;-0.03,1.32,;-0.03,1.52,;-0.20,1.61,;-0.37,1.51,;-0.53,1.61,;-0.53,1.82,;-0.72,1.90,;-0.91,1.79,;-0.91,1.59,;-1.11,1.90,;-1.10,2.11,;-1.30,2.22,;-1.50,2.12,;-1.50,1.90,;-1.33,1.80,;-1.69,1.80,;-1.88,1.90,;-2.09,1.81,;-1.88,2.13,;-2.08,2.24,;-2.27,2.14,;-1.68,2.23,;-1.70,1.59,;-0.90,2.20,;-0.89,2.43,;-1.10,2.54,;-0.72,2.10,;-1.29,1.85,;0.19,1.67,;0.47,1.56,;0.47,1.36,;0.31,1.27,;0.64,1.27,;0.64,1.08,;0.81,1.37,;0.81,1.57,;0.63,1.66,;0.63,1.85,;0.44,1.92,;0.43,2.13,;0.23,2.22,;0.07,2.12,;0.23,2.46,;0.42,2.57,;0.41,2.80,;0.21,2.91,;0.01,2.80,;0.01,2.58,;-0.18,2.90,;-0.18,3.12,;-0.38,3.22,;0.01,3.23,;0.01,3.46,;-0.18,3.57,;0.20,3.12,;-0.36,2.80,;0.61,2.47,;0.79,2.58,;0.79,2.79,;0.61,2.23,;0.07,2.53,;1.38,0.85,;1.36,0.29,;1.19,0.20,;1.03,0.30,;1.18,0.01,;1.03,-0.08,;1.35,-0.09,;1.52,-0.00,;1.52,0.19,;1.70,0.29,;1.87,0.19,;2.03,0.31,;2.03,0.56,;1.83,0.64,;2.22,0.67,;2.42,0.57,;2.62,0.70,;2.61,0.94,;2.41,1.05,;2.23,0.94,;2.40,1.27,;2.59,1.39,;2.58,1.62,;2.80,1.29,;2.99,1.40,;2.99,1.62,;2.81,1.05,;2.20,1.38,;2.42,0.35,;2.63,0.24,;2.82,0.37,;2.22,0.22,;2.22,0.84,;1.51,-0.46,;0.76,-1.13,;0.76,-1.33,;0.92,-1.41,;0.59,-1.43,;0.60,-1.62,;0.42,-1.34,;0.41,-1.16,;0.57,-1.04,;0.57,-0.85,;0.76,-0.77,;0.77,-0.56,;0.58,-0.43,;0.38,-0.49,;0.61,-0.18,;0.82,-0.11,;0.87,0.12,;0.68,0.26,;0.47,0.18,;0.44,0.01,;0.31,0.32,;0.34,0.54,;0.17,0.68,;0.54,0.61,;0.59,0.85,;0.42,0.99,;0.72,0.47,;0.10,0.25,;0.99,-0.27,;1.16,-0.18,;1.33,-0.30,;0.96,-0.49,;0.49,-0.10,;0.20,-1.56,;0.13,1.25,;-0.81,0.82,;-0.81,0.62,;-0.98,0.53,;-1.12,0.66,;-1.34,0.58,;-1.39,0.36,;-1.25,0.21,;-1.62,0.30,;-1.78,0.46,;-2.01,0.40,;-2.07,0.18,;-1.91,0.02,;-1.69,0.03,;-1.97,-0.20,;-2.19,-0.26,;-2.25,-0.48,;-2.35,-0.09,;-2.57,-0.14,;-2.64,-0.37,;-2.29,0.12,;-1.81,-0.38,;-1.71,0.67,;-1.86,0.84,;-2.09,0.78,;-1.48,0.73,;-1.66,0.14,;-0.32,0.91,;-1.03,-0.70,;-1.07,-0.89,;-1.23,-0.97,;-1.37,-0.84,;-1.59,-0.90,;-1.66,-1.11,;-1.52,-1.29,;-1.90,-1.16,;-2.04,-0.99,;-2.28,-1.03,;-2.36,-1.26,;-2.21,-1.43,;-1.98,-1.41,;-2.29,-1.65,;-2.51,-1.69,;-2.59,-1.90,;-2.66,-1.51,;-2.90,-1.54,;-2.98,-1.76,;-2.58,-1.30,;-2.14,-1.83,;-1.96,-0.78,;-2.11,-0.60,;-2.33,-0.65,;-1.72,-0.74,;-1.97,-1.31,;-0.55,-0.63,;-0.46,-1.22,;-0.29,-1.31,;-0.12,-1.21,;0.10,-1.35,;0.11,-1.99,;0.30,-2.10,;0.50,-2.01,;0.31,-2.36,;0.10,-2.46,;0.09,-2.70,;0.28,-2.83,;0.49,-2.72,;0.53,-2.56,;0.68,-2.86,;0.68,-3.08,;0.88,-3.20,;0.46,-3.19,;0.45,-3.42,;0.64,-3.55,;0.27,-3.06,;0.91,-2.74,;-0.09,-2.34,;-0.29,-2.44,;-0.31,-2.70,;-0.09,-2.10,;0.47,-2.46,;-0.78,-1.60,)| +267: [C@@H]12[C@H](O)[C@H]([C@@H](O[C@H]3[C@H](O)[C@H]([C@@H](O[C@H]4[C@H](O)[C@H]([C@@H](O[C@H]5[C@H](O)[C@H]([C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O[C@H]5[C@H](O)[C@@H](O)[C@H](O[C@@H]5COC5[C@H](O)[C@H]([C@H](O[C@@H]6[C@H](O)[C@H]([C@H](O)[C@@H](CO)O6)O)[C@@H](CO)O5)O)O1)O)O[C@@H]4COC1[C@H](O)[C@H]([C@H](O[C@@H]4[C@H](O)[C@H]([C@H](O)[C@@H](CO)O4)O)[C@@H](CO)O1)O)O)O[C@@H]3COC1[C@H](O)[C@H]([C@H](O[C@@H]3[C@H](O)[C@H]([C@H](O)[C@@H](CO)O3)O)[C@@H](CO)O1)O)O)O[C@@H]2COC1[C@H](O)[C@H](C(O[C@@H]2[C@H](O)[C@H]([C@H](O)[C@@H](CO)O2)O)[C@@H](CO)O1)O)O 1,2,3,-1 0,5,4,-1 0,7,8,-1 diff --git a/api/tests/integration/ref/bingo/molecules.py.out b/api/tests/integration/ref/bingo/molecules.py.out index dc7aad3ec4..d42b33ee08 100644 --- a/api/tests/integration/ref/bingo/molecules.py.out +++ b/api/tests/integration/ref/bingo/molecules.py.out @@ -27,6 +27,7 @@ Structure 207 excluded: stereocenters: stereo types of the opposite bonds mismat Structure 241 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 0 Structure 242 excluded: molfile loader: direction of bond #2 makes no sense Structure 245 excluded: element: bad valence on H having 0 drawn bonds, charge 3, and 0 radical electrons +Structure 251 excluded: molfile loader: direction of bond #54 makes no sense Structure 253 excluded: molfile loader: direction of bond #5 makes no sense Structure 255 excluded: molfile loader: direction of bond #5 makes no sense Structure 256 excluded: element: bad valence on H having 1 drawn bonds, charge 2, and 0 radical electrons @@ -55,7 +56,7 @@ Structure 359 excluded: stereocenters: 4 hydrogens near stereocenter 0 Structure 361 excluded: stereocenters: stereo types of non-opposite bonds match near atom 5 Structure 365 excluded: molfile loader: direction of bond #0 makes no sense Structure 372 excluded: molfile loader: direction of bond #5 makes no sense -Structure 380 excluded: molfile loader: direction of bond #2 makes no sense +Structure 380 excluded: molfile loader: direction of bond #0 makes no sense Structure 390 excluded: element: bad valence on C having 3 drawn bonds, charge 0, and 2 radical electrons Structure 400 excluded: molfile loader: direction of bond #9 makes no sense Structure 405 excluded: molfile loader: direction of bond #1 makes no sense @@ -225,7 +226,7 @@ Structure 1440 excluded: molfile loader: direction of bond #0 makes no sense Structure 1464 excluded: molfile loader: direction of bond #5 makes no sense Structure 1466 excluded: molfile loader: direction of bond #5 makes no sense Structure 1468 excluded: molfile loader: direction of bond #7 makes no sense -Structure 1490 excluded: molfile loader: direction of bond #32 makes no sense +Structure 1490 excluded: molfile loader: direction of bond #31 makes no sense Structure 1492 excluded: stereocenters: directions of neighbor stereo bonds match near atom 0 Structure 1498 excluded: molfile loader: direction of bond #3 makes no sense Structure 1501 excluded: stereocenters: directions of neighbor stereo bonds match near atom 0 @@ -251,7 +252,7 @@ Structure 1692 excluded: stereocenters: all 3 bonds up near stereoatom 6 Structure 1696 excluded: element: bad valence on C having 5 drawn bonds, charge 0, and 0 radical electrons Structure 1718 excluded: molfile loader: direction of bond #0 makes no sense Structure 1733 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 1 -Structure 1739 excluded: molfile loader: direction of bond #4 makes no sense +Structure 1739 excluded: molfile loader: direction of bond #2 makes no sense Structure 1742 excluded: element: bad valence on C having 4 drawn bonds, charge 1, and 1 radical electrons Structure 1753 excluded: element: bad valence on N having 4 drawn bonds, charge 0, and 0 radical electrons Structure 1761 excluded: molfile loader: direction of bond #4 makes no sense @@ -303,7 +304,7 @@ Structure 2013 excluded: molfile loader: direction of bond #5 makes no sense Structure 2014 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 0 Structure 2017 excluded: molfile loader: direction of bond #7 makes no sense Structure 2018 excluded: element: bad valence on N having 5 drawn bonds, charge 1, and 0 radical electrons -Finished indexing 2026 structures. 303 wrong structures excluded +Finished indexing 2026 structures. 304 wrong structures excluded ** searchSub(C(CN)C(F)F, '') ** 1986 C(C(C(C(N1CO[Si](C)(C)OC1)=O)(F)F)(F)F)(C(C(C(F)(F)F)(F)F)(F)F)(F)F C(C(C(C(N1CO[Si](C)(C)OC1)=O)(F)F)(F)F)(C(C(C(F)(F)F)(F)F)(F)F)(F)F ** searchSim(C(CN)C(F)F, 0.9, 1, tanimoto) ** @@ -901,7 +902,6 @@ Finished indexing 2026 structures. 303 wrong structures excluded 227 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 233 [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| 237 C1(C2(C(OC(OC3(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC6(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC7(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC8(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC9(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(O2)([H])OC9(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC8(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC7(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC6(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC5(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC4(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC3(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])C1(OS(O[H])(=O)=O)[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H] C1(C2(C(OC(OC3(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC6(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC7(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC8(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OC9(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(O2)([H])OC9(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC8(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC7(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC6(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC5(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC4(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])OC3(C(OS(O[H])(=O)=O)([H])[H])[H])[H])([H])C1(OS(O[H])(=O)=O)[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H] - 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| 252 C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| 262 C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] 265 [CH]1C=C1C1=C[CH]1 |^1:0,5| [CH]1C=C1C1=C[CH]1 |^1:0,5| @@ -1057,7 +1057,7 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1470 C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] 1477 c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-] c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-] 1481 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] - 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| + 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| 1500 [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] 1510 C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| 1511 c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O @@ -1098,7 +1098,7 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1803 [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] 1814 [C@@H](C[C@@H](C[C@H](C)C[C@H](C)N)C)(N)C |&1:0,2,4,7,r| [C@@H](C[C@@H](C[C@H](C)C[C@H](C)N)C)(N)C |&1:0,2,4,7,r| - 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| + 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| 1856 [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| 1861 C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C C/C=C/N1[C-](C2CCCCC2)C(=O)[O+]=C1C 1862 c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-].c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][nH][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2C([N-]C)=O c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2C(NC)=O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/[O-].c12[n](CCCCCc3c(-c4[n][n][n][n-]4)cc(C)[n]3C)c(OCC)[n]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][nH][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2/C(=N/C)/O.c12[n+](CCCCCc3c(-c4[n][n-][n][n]4)cc(C)[n]3C)c(OCC)[nH]c1cccc2C([N-]C)=O @@ -1835,7 +1835,7 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1408 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] 1470 C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] 1481 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] - 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| + 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| 1500 [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] 1527 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| 1620 C1(COC(C)(C)OC1)(CO)N C1(COC(C)(C)OC1)(CO)N @@ -1846,7 +1846,7 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1744 C(C1(C([H])([H])C2(C(OC(O2)(C(C(C(C(C(C(C(C(C(C2(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C([H])([H])[H])(/C(=C(/C(C(C(C(C(C3(C([H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C(C4(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(/C(=C(/C(=C(/C(C(C(C(C(/C(=C(/C(=C([H])[H])C(C(C(C(C(C(C([H])([H])[H])(C(C5(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(/C(=C(/C(C(C(C6(C([H])([H])C7(C([H])([H])C(C(O7)(C(C(C7(C(O[H])([H])C([H])([H])C(C(N([H])[H])([H])[H])([H])O7)[H])([H])[H])([H])[H])[H])([H])O6)[H])[H])([H])[H])(O[H])[H])(O[H])[H])\[H])/[H])([H])O5)[H])([H])[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])\[H])/[H])\[H])/[H])(O[H])[H])([H])[H])([H])O4)[H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O3)[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])(O[H])[H])\[H])/[H])[H])(O[H])[H])([H])[H])(O[H])O2)[H])([H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C1([H])[H])(C(C(C([H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C1(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(/C(=C(/C(C(C(C([H])([H])[H])(C(C(=O)N(/C(=C(/C(=O)N(C(C(C(O[H])([H])[H])([H])[H])([H])[H])[H])\[H])/[H])[H])(O[H])[H])[H])([H])[H])(O[H])[H])\[H])/C([H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O1)[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])C([H])([H])[H])[H])([H])([H])[H] C(C1(C([H])([H])C2(C(OC(O2)(C(C(C(C(C(C(C(C(C(C2(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C([H])([H])[H])(/C(=C(/C(C(C(C(C(C3(C([H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C(C4(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(/C(=C(/C(=C(/C(C(C(C(C(/C(=C(/C(=C([H])[H])C(C(C(C(C(C(C([H])([H])[H])(C(C5(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(/C(=C(/C(C(C(C6(C([H])([H])C7(C([H])([H])C(C(O7)(C(C(C7(C(O[H])([H])C([H])([H])C(C(N([H])[H])([H])[H])([H])O7)[H])([H])[H])([H])[H])[H])([H])O6)[H])[H])([H])[H])(O[H])[H])(O[H])[H])\[H])/[H])([H])O5)[H])([H])[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])\[H])/[H])\[H])/[H])(O[H])[H])([H])[H])([H])O4)[H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O3)[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])(O[H])[H])\[H])/[H])[H])(O[H])[H])([H])[H])(O[H])O2)[H])([H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C1([H])[H])(C(C(C([H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C1(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(/C(=C(/C(C(C(C([H])([H])[H])(C(C(=O)N(/C(=C(/C(=O)N(C(C(C(O[H])([H])[H])([H])[H])([H])[H])[H])\[H])/[H])[H])(O[H])[H])[H])([H])[H])(O[H])[H])\[H])/C([H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O1)[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])C([H])([H])[H])[H])([H])([H])[H] 1759 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] - 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| + 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| 1896 C1(C(=O)COCOC1)=O C1(C(=O)COCOC1)=O 1918 [C@@H](CC)(C)[C@H]1OCCC=CCCO1 |t:8,&1:0,4,r| [C@@H](CC)(C)[C@H]1OCCC=CCCO1 |t:8,&1:0,4,r| 1949 C1[C@@H](O)C2(C3CCC4(C)C(CC5O[C@]6(CC(C(Cl)Cl)C(C)([H])CO6)C(C)C54)C3CC=C2C[C@H]1O)C |&1:1,13,32,r| C1[C@@H](O)C2(C3CCC4(C)C(CC5O[C@]6(CC(C(Cl)Cl)C(C)([H])CO6)C(C)C54)C3CC=C2C[C@H]1O)C |&1:1,13,32,r| @@ -1923,7 +1923,6 @@ Finished indexing 2026 structures. 303 wrong structures excluded 118 N[C@]1(C)C[C@]2([C@@]3(C[C@@](N)(C)C3)[C@]32C[C@@](N)(C)C3)C1 |&1:1,4,5,7,11,13,r| N[C@]1(C)C[C@]2([C@@]3(C[C@@](N)(C)C3)[C@]32C[C@@](N)(C)C3)C1 |&1:1,4,5,7,11,13,r| 179 [C@H]1(C[C@H](C)C1)C.[C@H]1(C[C@@H](C)C1)C |&1:0,2,6,8,r| [C@H]1(C[C@H](C)C1)C.[C@H]1(C[C@@H](C)C1)C |&1:0,2,6,8,r| 212 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 - 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| 305 C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,10,r| C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,10,r| 351 [C@@]12([H])[C@@]3([H])[C@]1([H])C1([H])C2([H])[C@]2([C@]3([H])[C@@]12[H])[H].[C@@]12([H])[C@@]3([H])[C@]4(C5([H])[C@@]1([C@@]2(C5([C@@]34[H])[H])[H])[H])[H].C12([H])[C@]3([C@]4([C@]5([H])[C@]([H])(C1([H])[C@@]34[H])[C@]25[H])[H])[H] |&1:0,2,4,10,11,13,16,18,20,23,24,26,34,35,36,38,42,44,r| [C@@]12([H])[C@@]3([H])[C@]1([H])C1([H])C2([H])[C@]2([C@]3([H])[C@@]12[H])[H].[C@@]12([H])[C@@]3([H])[C@]4(C5([H])[C@@]1([C@@]2(C5([C@@]34[H])[H])[H])[H])[H].C12([H])[C@]3([C@]4([C@]5([H])[C@]([H])(C1([H])[C@@]34[H])[C@]25[H])[H])[H] |&1:0,2,4,10,11,13,16,18,20,23,24,26,34,35,36,38,42,44,r| 387 [C@@]12(C[C@@](N)(C)C1)C[C@@](N)(C)C2 |&1:0,2,7,r| [C@@]12(C[C@@](N)(C)C1)C[C@@](N)(C)C2 |&1:0,2,7,r| @@ -2922,7 +2921,6 @@ Finished indexing 2026 structures. 303 wrong structures excluded 212 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 N(C12[Rh]345678(C9(N(CC)CC)[Rh]%10%11%12%1313(C1C%10=C%11C%12=C%131)[Rh]13%10%11249C2=C1C3=C%10C%112)C1C5C6=C7C8=1)(CC)CC.C12(C)CC(C1)(C)C2 227 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 C1[C@@H]2[C@@]34[C@@H]5[C@H]6[C@H]7[C@@]89[C@H]%10CC[C@@H]([C@H]2[C@@H]8CC5)[C@@]25[C@@]39[C@@]38[C@H]([C@@H]%10[C@@H]2CC[C@H]3[C@H]([C@@H]4CC[C@H]86)[C@@H]5C1)CC7 233 [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| [C@H]12[C@]34[12CH]([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| - 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| 252 C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| C(c1c([H])c2c([n](c([n]2)[H])C2(C(O[H])([H])C(OP([O-])(=O)OC(C([H])([H])[H])(C(N(C(C(C(C3(C([H])([H])[H])C(C(C(N([H])[H])=O)([H])[H])([H])C4(C5(C([H])([H])[H])C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C6C(C([H])([H])[H])(C(C(N([H])[H])=O)([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(=C7C(C([H])([H])[H])(C([H])([H])[H])C(C(C(C(N([H])[H])=O)([H])[H])([H])[H])([H])C(C(C([H])([H])[H])=C3[N-]4)=N7)[H])=N6)=N5)[H])([H])[H])([H])[H])=O)[H])([H])[H])[H])([H])C(C(O[H])([H])[H])([H])O2)[H])c([H])c1C([H])([H])[H])([H])([H])[H].[Co+3] |t:84,113,142| 262 C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] C1(C([H])([H])C2(C([H])([H])C2([H])[H])C21C([H])([H])C2([H])[H])([H])[H] 266 C1([H])=C([H])C21C([H])=C([H])C12C([H])=C1[H] C1([H])=C([H])C21C([H])=C([H])C12C([H])=C1[H] @@ -2996,7 +2994,7 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1445 C1[C@]2(CN(C)CC2)CN(C)C1 |&1:1,r| C1[C@]2(CN(C)CC2)CN(C)C1 |&1:1,r| 1458 [C@@](/C=C(\C)/CC)(CCC)(CC)C |&1:0,r| [C@@](/C=C(\C)/CC)(CCC)(CC)C |&1:0,r| 1461 C1(/C(=N\N)/C(C)(C)CSCC/1(C)C)=N/N C1(/C(=N\N)/C(C)(C)CSCC/1(C)C)=N/N - 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| + 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| 1510 C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| 1523 [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| 1525 [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| @@ -3019,7 +3017,7 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1775 [C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C |&1:0,1,3,5,6,9,15,r| [C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C |&1:0,1,3,5,6,9,15,r| 1794 C1(/C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C/1)=C(/c1cc(C(C)(C)C)c(O)c(C(C)(C)C)c1)\c1ccc(-c2c3ccc([nH]3)c(-c3ccc(/C(=C4\C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C\4)/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)cc3)c3[n]c(C=C3)c(-c3ccc(/C(=C4/C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C/4)/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)cc3)c3ccc([nH]3)c(-c3ccc(/C(/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)=C4\C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C\4)cc3)c3[n]c2C=C3)cc1 C1(/C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C/1)=C(/c1cc(C(C)(C)C)c(O)c(C(C)(C)C)c1)\c1ccc(-c2c3ccc([nH]3)c(-c3ccc(/C(=C4\C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C\4)/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)cc3)c3[n]c(C=C3)c(-c3ccc(/C(=C4/C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C/4)/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)cc3)c3ccc([nH]3)c(-c3ccc(/C(/c4cc(C(C)(C)C)c(O)c(C(C)(C)C)c4)=C4\C=C(C(C)(C)C)C(=O)C(C(C)(C)C)=C\4)cc3)c3[n]c2C=C3)cc1 1803 [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| - 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| + 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| 1856 [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| 1863 C1(CC(=O)C=[N+]([O-])C1)(C)C C1(CC(=O)C=[N+]([O-])C1)(C)C 1866 C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,w:10,r| C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,w:10,r| @@ -4671,7 +4669,6 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1839 O([H])[H] O([H])[H] 1954 [O][2H][2H] [O][2H][2H] ** searchSub([Sn](CCC)(C)CC, '') ** - 251 N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| N(C12[Rh]345678(C9C3=C4C5=C69)C3(N(CC)CC)[Rh]456917(C1C4=C5C6=C91)[Rh]1456238C2C1C4=C5C6=2)(CC)CC.C12(C)CC(C1)(C)C2.C12=C3[Sn@]1([C@@H]23)[C@@H]([C@@]12[C@H]3C1=C23)C |&1:39,40,41,42,43,r| 1024 [Sn]([C@@H](/C=C/CO[Si](C(C)(C)C)(C)C)OCOC)(CCCC)(CCCC)CCCC |&1:1,r| [Sn]([C@@H](/C=C/CO[Si](C(C)(C)C)(C)C)OCOC)(CCCC)(CCCC)CCCC |&1:1,r| 1025 [Sn]1(CCCC)(C=CCCC=C1)CCCC [Sn]1(CCCC)(C=CCCC=C1)CCCC ** searchSim([SnH](CCC)(C)CC, 0.9, 1, tanimoto) ** @@ -8829,7 +8826,7 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1408 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] 1470 C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] C1(C(OS(=O)(=O)O[H])([H])C2(OC3(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC4(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC5(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC6(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC7(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC8(C(OS(=O)(=O)O[H])([H])C(OS(=O)(=O)O[H])([H])C(OC1(C(O2)(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC8(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC7(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC6(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC5(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC4(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])([H])OC3(C(N(S(=O)(=O)O[H])[H])([H])[H])[H])[H])[H])(OS(=O)(=O)O[H])[H] 1481 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] - 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| + 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| 1500 [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] [C@]([C@@]([C@](C(N(C(C(C(C(C(C(N(C([C@@]([C@]([C@](O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H])(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])=O)[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])=O)(OS(O[H])(=O)=O)[H])(OS(O[H])(=O)=O)[H])(O[C@]1([C@@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](OS(O[H])(=O)=O)([H])[C@](C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])([C@](OS(=O)(=O)O[H])(C(OS(O[H])(=O)=O)([H])[H])[H])[H] 1527 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| 1650 O1[C@@H](C(C)CO)[C@@H](O)[C@@H](C(CO)C)OC1.O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,16,21,23,r| O1[C@@H](C(C)CO)[C@@H](O)[C@@H](C(CO)C)OC1.O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,16,21,23,r| @@ -8839,7 +8836,7 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1744 C(C1(C([H])([H])C2(C(OC(O2)(C(C(C(C(C(C(C(C(C(C2(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C([H])([H])[H])(/C(=C(/C(C(C(C(C(C3(C([H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C(C4(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(/C(=C(/C(=C(/C(C(C(C(C(/C(=C(/C(=C([H])[H])C(C(C(C(C(C(C([H])([H])[H])(C(C5(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(/C(=C(/C(C(C(C6(C([H])([H])C7(C([H])([H])C(C(O7)(C(C(C7(C(O[H])([H])C([H])([H])C(C(N([H])[H])([H])[H])([H])O7)[H])([H])[H])([H])[H])[H])([H])O6)[H])[H])([H])[H])(O[H])[H])(O[H])[H])\[H])/[H])([H])O5)[H])([H])[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])\[H])/[H])\[H])/[H])(O[H])[H])([H])[H])([H])O4)[H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O3)[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])(O[H])[H])\[H])/[H])[H])(O[H])[H])([H])[H])(O[H])O2)[H])([H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C1([H])[H])(C(C(C([H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C1(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(/C(=C(/C(C(C(C([H])([H])[H])(C(C(=O)N(/C(=C(/C(=O)N(C(C(C(O[H])([H])[H])([H])[H])([H])[H])[H])\[H])/[H])[H])(O[H])[H])[H])([H])[H])(O[H])[H])\[H])/C([H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O1)[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])C([H])([H])[H])[H])([H])([H])[H] C(C1(C([H])([H])C2(C(OC(O2)(C(C(C(C(C(C(C(C(C(C2(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C([H])([H])[H])(/C(=C(/C(C(C(C(C(C3(C([H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(C(C4(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(/C(=C(/C(=C(/C(C(C(C(C(/C(=C(/C(=C([H])[H])C(C(C(C(C(C(C([H])([H])[H])(C(C5(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(/C(=C(/C(C(C(C6(C([H])([H])C7(C([H])([H])C(C(O7)(C(C(C7(C(O[H])([H])C([H])([H])C(C(N([H])[H])([H])[H])([H])O7)[H])([H])[H])([H])[H])[H])([H])O6)[H])[H])([H])[H])(O[H])[H])(O[H])[H])\[H])/[H])([H])O5)[H])([H])[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])\[H])/[H])\[H])/[H])(O[H])[H])([H])[H])([H])O4)[H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O3)[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])(O[H])[H])\[H])/[H])[H])(O[H])[H])([H])[H])(O[H])O2)[H])([H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])C1([H])[H])(C(C(C([H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C1(C(O[H])([H])C(O[H])([H])C(O[H])([H])C(C(C(C(/C(=C(/C(C(C(C([H])([H])[H])(C(C(=O)N(/C(=C(/C(=O)N(C(C(C(O[H])([H])[H])([H])[H])([H])[H])[H])\[H])/[H])[H])(O[H])[H])[H])([H])[H])(O[H])[H])\[H])/C([H])([H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])O1)[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])(O[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])C([H])([H])[H])[H])([H])([H])[H] 1759 O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| O1[C@H](C(C)CO)[C@H](O)[C@H](C(C)CO)OC1 |&1:1,6,8,r| 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] - 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| + 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| 1918 [C@@H](CC)(C)[C@H]1OCCC=CCCO1 |t:8,&1:0,4,r| [C@@H](CC)(C)[C@H]1OCCC=CCCO1 |t:8,&1:0,4,r| 1949 C1[C@@H](O)C2(C3CCC4(C)C(CC5O[C@]6(CC(C(Cl)Cl)C(C)([H])CO6)C(C)C54)C3CC=C2C[C@H]1O)C |&1:1,13,32,r| C1[C@@H](O)C2(C3CCC4(C)C(CC5O[C@]6(CC(C(Cl)Cl)C(C)([H])CO6)C(C)C54)C3CC=C2C[C@H]1O)C |&1:1,13,32,r| 1971 [C@]1(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[C@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[H])([H])C2([H])[H])C(=O)O[H])([H])C1([H])[H])(OC1([C@@](O[C@@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](OP(OP(=O)(OC(C(N([H])[H])([H])[H])([H])[H])O[H])(=O)O[H])([H])C(O[C@]3(OC(C(C(O[C@@]4([C@@](O[H])([H])C(O[H])([H])[C@](C(O[H])(C(O[H])([H])[H])[H])(O[H])C([H])([H])O4)[H])([H])[H])(O[H])[H])([H])[C@](OP(=O)(O[H])O[H])([H])C(O[C@]4(C(O[H])([H])C(O[C@]5(C(O[C@]6(C(O[C@@]7([C@](N(C(=O)C([H])([H])[H])[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(O[H])([H])[C@@](O[C@]7(C(O[H])([H])C(OC8([C@](O[H])([H])C(O[H])([H])C(O[C@]9(C(O[C@]%10(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O%10)[H])([H])C(O[C@@]%10(OC(C([H])([H])[H])([H])[C@](O[H])([H])C([H])([H])C%10(O[H])[H])[H])([H])[C@@](O[H])([H])C(C(O[H])([H])[H])([H])O9)[H])([H])[C@@](C([H])([H])[H])([H])O8)[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(C(O[H])([H])[H])([H])O6)[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[C@@](O[H])([H])C(C(O[C@]5(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[H])([H])O4)[H])([H])[C@]3(O[H])[H])[H])([H])[C@]2(O[H])[H])[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O[C@](C(=O)O[H])(OC(C2([C@@](OP(=O)(O[H])O[H])([H])C(OC(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@@](N(C(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)[H])([H])[C@@](OC(C3(O[C@](C(P(=O)(O[H])O[H])([H])[H])([H])C(C(C(C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[C@](OC(C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@]3(O[H])[H])[H])([H])[H])([H])O2)[H])([H])[H])C1([H])[H])[H])C(=O)O[H] [C@]1(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[C@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](O[H])([H])C(O[H])([H])C2([H])[H])C(=O)O[H])([H])C1([H])[H])(OC1([C@@](O[C@@]2(OC(C(O[H])(C(O[H])([H])[H])[H])([H])[C@](OP(OP(=O)(OC(C(N([H])[H])([H])[H])([H])[H])O[H])(=O)O[H])([H])C(O[C@]3(OC(C(C(O[C@@]4([C@@](O[H])([H])C(O[H])([H])[C@](C(O[H])(C(O[H])([H])[H])[H])(O[H])C([H])([H])O4)[H])([H])[H])(O[H])[H])([H])[C@](OP(=O)(O[H])O[H])([H])C(O[C@]4(C(O[H])([H])C(O[C@]5(C(O[C@]6(C(O[C@@]7([C@](N(C(=O)C([H])([H])[H])[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(O[H])([H])[C@@](O[C@]7(C(O[H])([H])C(OC8([C@](O[H])([H])C(O[H])([H])C(O[C@]9(C(O[C@]%10(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O%10)[H])([H])C(O[C@@]%10(OC(C([H])([H])[H])([H])[C@](O[H])([H])C([H])([H])C%10(O[H])[H])[H])([H])[C@@](O[H])([H])C(C(O[H])([H])[H])([H])O9)[H])([H])[C@@](C([H])([H])[H])([H])O8)[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O7)[H])([H])C(C(O[H])([H])[H])([H])O6)[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[C@@](O[H])([H])C(C(O[C@]5(C(O[H])([H])C(O[H])([H])[C@](O[H])([H])C(C(O[H])([H])[H])([H])O5)[H])([H])[H])([H])O4)[H])([H])[C@]3(O[H])[H])[H])([H])[C@]2(O[H])[H])[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O[C@](C(=O)O[H])(OC(C2([C@@](OP(=O)(O[H])O[H])([H])C(OC(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@@](N(C(C(C(OC(=O)C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)[H])([H])[C@@](OC(C3(O[C@](C(P(=O)(O[H])O[H])([H])[H])([H])C(C(C(C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[C@](OC(C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])=O)([H])[C@]3(O[H])[H])[H])([H])[H])([H])O2)[H])([H])[H])C1([H])[H])[H])C(=O)O[H] @@ -11269,7 +11266,7 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1399 [C@@H]12OC34C[C@@H]5CCC67[C@]83C(O5)(C1)CC[C@H](C6)OC8(C[C@@H](CC4)O7)CC2.[C@@H]12OC34C[C@@H]5CCC67[C@]83C(O5)(C1)CC[12C@H](C6)OC8(C[C@@H](CC4)O7)CC2 |&1:0,4,8,14,19,25,29,33,39,44,r| [C@@H]12OC34C[C@@H]5CCC67[C@]83C(O5)(C1)CC[C@H](C6)OC8(C[C@@H](CC4)O7)CC2.[C@@H]12OC34C[C@@H]5CCC67[C@]83C(O5)(C1)CC[12C@H](C6)OC8(C[C@@H](CC4)O7)CC2 |&1:0,4,8,14,19,25,29,33,39,44,r| 1408 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] 1481 C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] C1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OC5(C(OS(O[H])(=O)=O)([H])C(OC(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C5(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C4(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C3(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C2(OS(O[H])(=O)=O)[H])[H])([H])OC(C(OS(O[H])(=O)=O)([H])[H])([H])C1(OS(O[H])(=O)=O)[H])(OC1(C(OS(O[H])(=O)=O)([H])C(OC2(C(OS(O[H])(=O)=O)([H])C(OC3(C(OS(O[H])(=O)=O)([H])C(OC4(C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O4)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O3)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O2)[H])([H])C(OS(O[H])(=O)=O)([H])C(C(OS(O[H])(=O)=O)([H])[H])([H])O1)[H])[H] - 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| + 1482 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H].C1CCCC1 |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| 1510 C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| C12=[C@@]=C(C[C@@](C1)(C)Br)[C@@H](C)C[C@@]1(C[C@H](C)C3C[C@@](CC(=[C@@]=3)[C@@H](C)C1)(Br)C)C[C@@H]2C |&1:4,8,11,13,17,21,27,r| 1523 [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| [C@]1(Br)(C)CCC2[C@H](C[C@@]3(C[C@@H](C)C4=[C@]=C(CC[C@](Br)(C)CC4)[C@H](C)C3)C[C@H](C)C(=[C@@]=2)CC1)C.[C@]1(Br)(C)CCC2=[C@@]=C([C@H](C[C@]3(C[C@H](C)C4=[C@]=C(CC[C@](C)(Br)CC4)[C@@H](C)C3)C[C@@H]2C)C)CC1 |&1:0,6,8,10,17,22,26,33,41,43,45,52,57,61,r| 1525 [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| [C@]([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12C3[C@H]1[C@H]23)[C@]12[C@@H]3C1[C@H]23)([C@]([C@]12[C@@H]3C1[C@H]23)([C@]12[C@@H]3C1[C@H]23)[C@]12[C@@H]3C1[C@H]23)C |&1:0,1,2,3,5,6,7,9,10,11,13,14,15,16,18,19,21,22,23,24,26,27,28,29,31,32,33,35,36,37,39,r| @@ -11290,7 +11287,7 @@ Finished indexing 2026 structures. 303 wrong structures excluded 1775 [C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C |&1:0,1,3,5,6,9,15,r| [C@@H]12[C@@]34C([C@@H](C[C@@H]3[C@H](CC4[C@@H](C1)C)C)C)C[C@@H]2C |&1:0,1,3,5,6,9,15,r| 1803 [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| [C@@](C)([C@](CCC)(CC)C)([C@](CCC)(CC)C)CC.[C@](CC)(C)([C@](CCC)(CC)C)[C@@](C)(CCC)CC.[C@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.[C@@](CC)(C)(C(CCC)(CC)C)C(CCC)(CC)C.C(C)[C@@]1(C[C@@](CC)(C)C1)C.C([C@]1(C)CC(CC)(C)C1)C.C([C@]1(C)C[C@]2(C[C@](CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(CC(CC)(C)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(C[C@](CC)(C)C4)C3)C2)C1)C.C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:0,2,9,18,22,29,36,54,74,76,83,93,96,98,106,109,119,122,124,126,128,138,141,143,145,w:40,47,58,65,86,111,147,r| 1807 C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] C(C(C(C(C(C(C(C(C(C(C(C(O[H])(C(C(=O)N(C1(C(OP(=O)(O[H])O[H])([H])OC(C(OC2(C(N(C(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(/C(=C(/C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])\[H])/[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])([H])C(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])(OC(=O)C(C(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])([H])C(OP(O[H])(O[H])=O)([H])C(C(OC3(C([H])([H])C(OC4(OC(C(O[H])(C(O[H])([H])[H])[H])([H])C(O[H])([H])C(O[H])([H])C4([H])[H])C(O[H])=O)([H])C(O[H])([H])C(C(O[H])(C(O[H])([H])[H])[H])([H])O3)C(O[H])=O)([H])[H])([H])O2)[H])([H])[H])([H])C(O[H])([H])C1(OC(=O)C(C(O[H])(C(C(C(C(C(C(C(C(C(C(C([H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])([H])[H])[H])[H])[H])([H])[H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])([H])([H])[H] - 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(O[C@H]5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,11,16,18,24,27,29,33,34,w:9,r| + 1827 [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| [C@]12(C)CC[C@@]3([C@@]4(C)CCC(OC5C(O)C(O)[C@H](O)[C@@H](C(=O)O)O5)C[C@@]4(CC[C@@]3([H])[C@]1([H])CC[C@@]2([C@H](C)CCCC(C)C)[H])[H])[H] |&1:0,4,5,16,18,24,27,29,33,34,w:9,11,r| 1856 [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| [C@@H]12CC34C[C@@H]5CCC67[C@]83C(C5)(C1)CC[C@H](C6)CC8(C[C@@H](CC4)C7)CC2 |&1:0,4,8,14,19,r| 1866 C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,w:10,r| C([C@]1(C)C[C@]2(C[C@@]3(C[C@]4(CC(CC)(C)C4)C3)C2)C1)C |&1:1,4,6,8,w:10,r| 1869 [12C@H]12[C@]34C([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| [12C@H]12[C@]34C([C@H](C[C@H]3[C@@H](CC4[C@H](C1)C)C)C)C[C@H]2C |&1:0,1,3,5,6,9,15,r| diff --git a/api/tests/integration/ref/formats/cdx.py.out b/api/tests/integration/ref/formats/cdx.py.out index 7d4af98b27..bf2bd4bdf4 100644 --- a/api/tests/integration/ref/formats/cdx.py.out +++ b/api/tests/integration/ref/formats/cdx.py.out @@ -2,7 +2,7 @@ ***** 0 Smiles: -C1(N[C@@H](C(N[C@H](C(O[C@H](C)[C@@H](C(NCC1)=O)NC(CC1=CC=CC=C1)=O)=O)CC1C2C=CC=CC=2NC=1)=O)CC1C2C=CC=CC=2NC=1)=O |wU:10.16,2.41,wD:8.7,5.28,(9.70,-2.74,;10.26,-7.33,;11.13,-7.82,;11.99,-7.32,;10.12,-7.33,;10.99,-7.82,;11.85,-7.32,;9.22,-4.60,;8.69,-5.44,;9.16,-6.33,;7.69,-5.40,;7.16,-6.25,;7.10,-3.24,;7.97,-2.74,;8.83,-3.24,;6.16,-6.21,;7.22,-4.52,;7.76,-3.67,;7.29,-2.79,;7.83,-1.94,;7.36,-1.06,;7.89,-0.21,;8.89,-0.25,;9.36,-1.14,;8.83,-1.98,;8.76,-3.71,;11.85,-6.32,;10.99,-8.82,;10.12,-9.33,;10.02,-10.32,;10.69,-11.07,;10.38,-12.01,;9.40,-12.22,;8.74,-11.48,;9.05,-10.53,;8.55,-9.67,;9.22,-8.93,;11.99,-6.32,;11.13,-8.82,;10.26,-9.33,;10.16,-10.32,;10.83,-11.07,;10.52,-12.01,;9.55,-12.22,;8.88,-11.48,;9.19,-10.53,;8.69,-9.67,;9.36,-8.93,;9.70,-1.74,)| +C1(N[C@@H](C(N[C@H](C(O[C@H](C)[C@@H](C(NCC1)=O)NC(CC1=CC=CC=C1)=O)=O)CC1C2C=CC=CC=2NC=1)=O)CC1C2C=CC=CC=2NC=1)=O Molfile: -INDIGO-01000000002D @@ -138,7 +138,7 @@ Properties: ***** 1 Smiles: -C1(=O)CCNC(=O)[C@H]([C@H](OC(=O)[C@@H](NC(=O)[C@H](N1)CC1=CNC2=C1C=CC=C2)CC1=CNC2=C1C=CC=C2)C)NC(CC1=CC=CC=C1)=O |wU:7.43,wD:8.8,16.18,12.30,(4.99,-17.89,;4.99,-16.89,;4.12,-18.39,;3.26,-17.89,;2.39,-18.39,;13.92,-17.89,;13.92,-16.89,;13.05,-18.39,;12.19,-17.89,;11.32,-18.39,;10.45,-17.89,;10.45,-16.89,;9.59,-18.39,;8.72,-17.89,;7.72,-18.39,;7.72,-19.39,;6.86,-17.89,;5.99,-18.39,;6.86,-16.89,;7.72,-16.39,;8.63,-16.79,;9.30,-16.05,;8.80,-15.19,;7.83,-15.40,;7.16,-14.65,;7.47,-13.70,;8.45,-13.50,;9.11,-14.24,;9.59,-19.39,;10.45,-19.89,;11.36,-19.49,;12.03,-20.23,;11.53,-21.09,;10.56,-20.89,;9.90,-21.63,;10.21,-22.58,;11.18,-22.78,;11.84,-22.04,;12.19,-16.89,;13.05,-19.39,;13.92,-19.89,;14.78,-19.39,;15.65,-19.89,;16.52,-19.39,;17.38,-19.89,;17.38,-20.89,;16.52,-21.39,;15.65,-20.89,;13.92,-20.89,)| +C1(=O)CCNC(=O)[C@H]([C@H](OC(=O)[C@@H](NC(=O)[C@H](N1)CC1=CNC2=C1C=CC=C2)CC1=CNC2=C1C=CC=C2)C)NC(CC1=CC=CC=C1)=O Molfile: -INDIGO-01000000002D diff --git a/api/tests/integration/tests/formats/ref/acd2d_err.ket b/api/tests/integration/tests/formats/ref/acd2d_err.ket index 5e6c9f6c4b..3f3f732ee1 100644 --- a/api/tests/integration/tests/formats/ref/acd2d_err.ket +++ b/api/tests/integration/tests/formats/ref/acd2d_err.ket @@ -14781,8 +14781,7 @@ 7.0, 2.6600000858306886, 0.0 - ], - "stereoLabel": "abs" + ] }, { "label": "N", @@ -14790,8 +14789,7 @@ 7.130000114440918, 1.090000033378601, 0.0 - ], - "stereoLabel": "abs" + ] }, { "label": "C", @@ -14823,8 +14821,7 @@ 6.019999980926514, 0.0, 0.0 - ], - "stereoLabel": "abs" + ] }, { "label": "C", @@ -14882,8 +14879,7 @@ 6.409999847412109, 2.190000057220459, 0.0 - ], - "stereoLabel": "abs" + ] }, { "label": "C", @@ -30958,8 +30954,7 @@ 2.975600004196167, -2.3452000617980959, 0.0 - ], - "stereoLabel": "abs" + ] }, { "label": "C", @@ -38279,8 +38274,7 @@ 4.26639986038208, -1.8983999490737916, 0.0 - ], - "stereoLabel": "abs" + ] }, { "label": "C", @@ -38835,8 +38829,7 @@ 8.11620044708252, -2.767199993133545, 0.0 - ], - "stereoLabel": "abs" + ] }, { "label": "C", @@ -52309,8 +52302,7 @@ 2.358599901199341, -0.25519999861717226, 0.0 - ], - "stereoLabel": "abs" + ] }, { "label": "O", @@ -78537,8 +78529,7 @@ 3.516700029373169, -1.7541999816894532, 0.0 - ], - "stereoLabel": "&1" + ] }, { "label": "C", @@ -78571,8 +78562,7 @@ 2.575000047683716, -5.112500190734863, 0.0 - ], - "stereoLabel": "&1" + ] }, { "label": "C", @@ -117814,8 +117804,7 @@ 0.7069000005722046, 1.2137999534606934, 0.0 - ], - "stereoLabel": "abs" + ] }, { "label": "C", diff --git a/api/tests/integration/tests/formats/ref/acd2d_err3.sdf b/api/tests/integration/tests/formats/ref/acd2d_err3.sdf index 05cea7c00f..ade3ac61b4 100644 --- a/api/tests/integration/tests/formats/ref/acd2d_err3.sdf +++ b/api/tests/integration/tests/formats/ref/acd2d_err3.sdf @@ -12400,7 +12400,6 @@ M V30 35 2 16 18 M V30 END BOND M V30 BEGIN COLLECTION M V30 MDLV30/STERAC1 ATOMS=(5 1 2 3 6 10) -M V30 MDLV30/STEABS ATOMS=(2 5 9) M V30 END COLLECTION M V30 END CTAB M END diff --git a/core/indigo-core/molecule/src/molecule_stereocenters.cpp b/core/indigo-core/molecule/src/molecule_stereocenters.cpp index feac98aa2f..3a7b6bbe7b 100644 --- a/core/indigo-core/molecule/src/molecule_stereocenters.cpp +++ b/core/indigo-core/molecule/src/molecule_stereocenters.cpp @@ -235,22 +235,25 @@ bool MoleculeStereocenters::isPossibleAtropocenter(BaseMolecule& baseMolecule, i for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) { auto bond_idx = v.neiEdge(i); - if (baseMolecule.getEdgeTopology(bond_idx) == TOPOLOGY_CHAIN) + if (baseMolecule.getEdgeTopology(bond_idx) == TOPOLOGY_CHAIN && baseMolecule.vertexInRing(v.neiVertex(i))) { std::unordered_set visited; RedBlackMap dir_map; visited.insert(bond_idx); if (findAtropoStereobonds(baseMolecule, dir_map, atom_idx, visited, true)) { - visited.clear(); - dir_map.clear(); - visited.insert(bond_idx); - if (hasRing(baseMolecule, v.neiVertex(i), visited)) - { - possible_atropo_bond = bond_idx; - return true; - } + possible_atropo_bond = bond_idx; + return true; } + //{ // advanced rings search. currently not in use. + // visited.clear(); + // visited.insert(bond_idx); + // if (hasRing(baseMolecule, v.neiVertex(i), visited)) + // { + // possible_atropo_bond = bond_idx; + // return true; + // } + //} } } break; From 7a84a674706bbc98045046ad19c3ba14a357c3a9 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 4 Oct 2023 05:14:05 +0200 Subject: [PATCH 22/36] wiggly bonds fix --- .../integration/ref/formats/smiles.py.out | 3 + .../integration/ref/standardize/basic.py.out | 14 ++-- api/tests/integration/tests/formats/smiles.py | 1 + core/indigo-core/molecule/smiles_saver.h | 1 + .../molecule/src/molecule_stereocenters.cpp | 67 +++++++++++------- .../molecule/src/smiles_loader.cpp | 27 +++---- .../indigo-core/molecule/src/smiles_saver.cpp | 70 +++++++++---------- utils/indigo-depict/main.c | 2 +- 8 files changed, 97 insertions(+), 88 deletions(-) diff --git a/api/tests/integration/ref/formats/smiles.py.out b/api/tests/integration/ref/formats/smiles.py.out index e08b627bce..27d92a67c4 100644 --- a/api/tests/integration/ref/formats/smiles.py.out +++ b/api/tests/integration/ref/formats/smiles.py.out @@ -78,3 +78,6 @@ C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4,(2.40,-1.39,;3.20,-0.00,;2.40, atropisomer: C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |wU:3.12,wD:3.3| C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |wU:3.12,wD:3.3,(-2.40,1.39,;-0.80,1.39,;-0.00,2.77,;0.00,0.00,;1.60,0.00,;2.40,1.39,;4.00,1.39,;4.80,0.00,;6.40,0.00,;4.00,-1.39,;2.40,-1.39,;1.60,-2.77,;-0.80,-1.39,;0.00,-2.77,;-2.40,-1.39,;-3.20,-0.00,)| +atropisomer: +C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |w:3.3,3.12| +C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |w:3.3,3.12,(-2.40,1.39,;-0.80,1.39,;-0.00,2.77,;0.00,0.00,;1.60,0.00,;2.40,1.39,;4.00,1.39,;4.80,0.00,;6.40,0.00,;4.00,-1.39,;2.40,-1.39,;1.60,-2.77,;-0.80,-1.39,;0.00,-2.77,;-2.40,-1.39,;-3.20,-0.00,)| diff --git a/api/tests/integration/ref/standardize/basic.py.out b/api/tests/integration/ref/standardize/basic.py.out index 55e9d14b1e..24d4e8a98b 100644 --- a/api/tests/integration/ref/standardize/basic.py.out +++ b/api/tests/integration/ref/standardize/basic.py.out @@ -1115,8 +1115,8 @@ M END 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 + 2 1 1 4 0 0 0 + 2 3 1 4 0 0 0 2 4 1 0 0 0 0 4 5 4 0 0 0 0 5 6 4 0 0 0 0 @@ -1153,7 +1153,7 @@ M END 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 + 2 1 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 4 0 0 0 0 @@ -1192,8 +1192,8 @@ M END 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 + 2 1 1 4 0 0 0 + 2 3 1 4 0 0 0 2 4 1 0 0 0 0 4 5 4 0 0 0 0 5 6 4 0 0 0 0 @@ -1230,8 +1230,8 @@ M END 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 + 2 1 1 4 0 0 0 + 2 3 1 4 0 0 0 2 4 1 0 0 0 0 4 5 4 0 0 0 0 5 6 4 0 0 0 0 diff --git a/api/tests/integration/tests/formats/smiles.py b/api/tests/integration/tests/formats/smiles.py index 09dce8fd0c..96692466e1 100644 --- a/api/tests/integration/tests/formats/smiles.py +++ b/api/tests/integration/tests/formats/smiles.py @@ -120,6 +120,7 @@ mols_smiles = [ "C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12|", "C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |wU:5.4,wD:5.5|", + "C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |w:5.4,5.5|" ] for sm in mols_smiles: print("atropisomer:") diff --git a/core/indigo-core/molecule/smiles_saver.h b/core/indigo-core/molecule/smiles_saver.h index 65981dff94..bd3c668e9c 100644 --- a/core/indigo-core/molecule/smiles_saver.h +++ b/core/indigo-core/molecule/smiles_saver.h @@ -129,6 +129,7 @@ namespace indigo void _writeUnsaturated(); void _writeSubstitutionCounts(); void _writeWedges(); + void _writeBondDirs(const std::string& tag, const std::vector>& bonds); bool _shouldWriteAromaticBond(int bond_idx); void _startExtension(); diff --git a/core/indigo-core/molecule/src/molecule_stereocenters.cpp b/core/indigo-core/molecule/src/molecule_stereocenters.cpp index 3a7b6bbe7b..54ffd3e107 100644 --- a/core/indigo-core/molecule/src/molecule_stereocenters.cpp +++ b/core/indigo-core/molecule/src/molecule_stereocenters.cpp @@ -434,7 +434,6 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom for (int i = vertex.neiBegin(); i != vertex.neiEnd(); i = vertex.neiNext(i)) { - int e_idx = vertex.neiEdge(i); int v_idx = vertex.neiVertex(i); @@ -487,19 +486,19 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom return _getDirection(baseMolecule, from, to, bidirectional_mode); }; - if (is_either) + if (stereocenter.is_tetrahydral) { - stereocenter.type = ATOM_ANY; - for (int i = 0; i < degree; i++) + if (is_either) { - stereocenter.pyramid[i] = edge_ids[i].nei_idx; - if (getDir(atom_idx, edge_ids[i].nei_idx) > 0) - sensible_bonds_out[edge_ids[i].edge_idx] = 1; + stereocenter.type = ATOM_ANY; + for (int i = 0; i < degree; i++) + { + stereocenter.pyramid[i] = edge_ids[i].nei_idx; + if (getDir(atom_idx, edge_ids[i].nei_idx) > 0) + sensible_bonds_out[edge_ids[i].edge_idx] = 1; + } } - } - else - { - if (stereocenter.is_tetrahydral) + else { if (degree == 4) { @@ -732,6 +731,7 @@ bool MoleculeStereocenters::_buildOneCenter(BaseMolecule& baseMolecule, int atom sensible_bonds_out[edge_ids[i].edge_idx] = 1; } } + if (stereocenter.is_tetrahydral) { if (_stereocenters.find(atom_idx)) @@ -1398,6 +1398,7 @@ void MoleculeStereocenters::buildOnSubmolecule(BaseMolecule& baseMolecule, const new_stereocenter.is_atropisomeric = super_stereocenter.is_atropisomeric; new_stereocenter.is_tetrahydral = super_stereocenter.is_tetrahydral; + // copy tetrahydral center if (new_stereocenter.is_tetrahydral) { for (j = 0; j < 4; j++) @@ -1416,25 +1417,39 @@ void MoleculeStereocenters::buildOnSubmolecule(BaseMolecule& baseMolecule, const } moveMinimalToEnd(new_stereocenter.pyramid); - if (new_stereocenter.pyramid[0] == -1 || new_stereocenter.pyramid[1] == -1 || new_stereocenter.pyramid[2] == -1) - // pyramid is not mapped completely - continue; - } - - _stereocenters.insert(sub_idx, new_stereocenter); + // copy bond directions for tetrahydral center + const Vertex& super_vertex = super.getVertex(super_idx); + for (j = super_vertex.neiBegin(); j != super_vertex.neiEnd(); j = super_vertex.neiNext(j)) + { + int super_edge = super_vertex.neiEdge(j); + if (mapping[super_vertex.neiVertex(j)] == -1) + continue; - const Vertex& super_vertex = super.getVertex(super_idx); + int bdir = super.getBondDirection(super_edge); + if (bdir) + baseMolecule.setBondDirection(baseMolecule.findEdgeIndex(sub_idx, mapping[super_vertex.neiVertex(j)]), bdir); + } + } - for (j = super_vertex.neiBegin(); j != super_vertex.neiEnd(); j = super_vertex.neiNext(j)) + // copy atropocenter + if (new_stereocenter.is_atropisomeric && super.stereocenters._atropocenters.find(super_idx)) { - int super_edge = super_vertex.neiEdge(j); - if (mapping[super_vertex.neiVertex(j)] == -1) - continue; - - int dir = super.getBondDirection(super_edge); - if (dir != 0) - baseMolecule.setBondDirection(baseMolecule.findEdgeIndex(sub_idx, mapping[super_vertex.neiVertex(j)]), dir); + const auto& ac_super = super.stereocenters._atropocenters.at(super_idx); + auto& ac_new = baseMolecule.stereocenters._atropocenters.findOrInsert(sub_idx); + const auto& e = super.getEdge(ac_super.atropo_bond); + ac_new.atropo_bond = baseMolecule.findEdgeIndex(mapping[e.beg], mapping[e.end]); + // copy bond directions for atropisomeric center + ac_new.bond_directions.clear(); + for (j = ac_super.bond_directions.begin(); j != ac_super.bond_directions.end(); j = ac_super.bond_directions.next(j)) + { + const auto& atropo_edge = super.getEdge(ac_super.bond_directions.key(j)); + int atropo_edge_idx = baseMolecule.findEdgeIndex(mapping[atropo_edge.beg], mapping[atropo_edge.end]); + int bdir = ac_super.bond_directions.value(j); + ac_new.bond_directions.insert(atropo_edge_idx, bdir); + baseMolecule.setBondDirection(atropo_edge_idx, bdir); + } } + _stereocenters.insert(sub_idx, new_stereocenter); } } diff --git a/core/indigo-core/molecule/src/smiles_loader.cpp b/core/indigo-core/molecule/src/smiles_loader.cpp index 019a27a9e3..5a37c27665 100644 --- a/core/indigo-core/molecule/src/smiles_loader.cpp +++ b/core/indigo-core/molecule/src/smiles_loader.cpp @@ -318,6 +318,7 @@ void SmilesLoader::_readOtherStuff() while (isdigit(_scanner.lookNext())) { int atom_idx = _scanner.readUnsigned(); + // handle wiggly bonds if (!wmode) { // This either bond can mark stereocenter or cis-trans double bond @@ -327,7 +328,7 @@ void SmilesLoader::_readOtherStuff() for (int nei : v.neighbors()) { int edge_idx = v.neiEdge(nei); - if (_bmol->getBondOrder(edge_idx) == BOND_DOUBLE) + if (_bmol->getBondOrder(edge_idx) == BOND_DOUBLE && _bmol->getBondTopology(edge_idx) != TOPOLOGY_RING) { cis_trans.ignore(edge_idx); found = true; @@ -336,12 +337,7 @@ void SmilesLoader::_readOtherStuff() if (!found) { - if (!_bmol->isPossibleStereocenter(atom_idx)) - { - if (!stereochemistry_options.ignore_errors) - throw Error("chirality not possible on atom #%d", atom_idx); - } - else + if (_bmol->isPossibleStereocenter(atom_idx)) { // Check if the stereocenter has already been marked as any // For example [H]C1(O)c2ccnn2[C@@H](O)c2ccnn12 |r,w:1.0,1.1| @@ -357,19 +353,14 @@ void SmilesLoader::_readOtherStuff() auto bond_idx = _scanner.readUnsigned(); if (!_has_directions_on_rings) _has_directions_on_rings = _bmol->getBondTopology(bond_idx) == TOPOLOGY_RING; - if (wmode) + if (bond_idx < _bmol->edgeCount() && atom_idx < _bmol->vertexCount()) { - if (bond_idx < _bmol->edgeCount() && atom_idx < _bmol->vertexCount()) - { - auto& v = _bmol->getEdge(bond_idx); - if (v.end == atom_idx) - _bmol->swapEdgeEnds(bond_idx); + auto& v = _bmol->getEdge(bond_idx); + if (v.end == atom_idx) + _bmol->swapEdgeEnds(bond_idx); - if (v.beg == atom_idx) - { - _bmol->setBondDirection(bond_idx, wmode == 'U' ? BOND_UP : BOND_DOWN); - } - } + if (v.beg == atom_idx) + _bmol->setBondDirection(bond_idx, wmode == 'U' ? BOND_UP : (wmode == 'D' ? BOND_DOWN : BOND_EITHER)); } } diff --git a/core/indigo-core/molecule/src/smiles_saver.cpp b/core/indigo-core/molecule/src/smiles_saver.cpp index 52970fda21..c75b660e98 100644 --- a/core/indigo-core/molecule/src/smiles_saver.cpp +++ b/core/indigo-core/molecule/src/smiles_saver.cpp @@ -1839,59 +1839,57 @@ void SmilesSaver::_writeSubstitutionCounts() } } +void SmilesSaver::_writeBondDirs(const std::string& tag, const std::vector>& bonds) +{ + bool is_first = true; + for (const auto& kvp : bonds) + { + if (is_first) + { + _startExtension(); + _output.writeString(tag.c_str()); + is_first = false; + } + else + _output.writeString(","); + _output.printf("%d.%d", kvp.first, kvp.second); + } +} + void SmilesSaver::_writeWedges() { if (_bmol) { - std::vector> down_dirs, up_dirs; + std::vector> down_dirs, up_dirs, wiggy_dirs; for (int i = 0; i < _written_bonds.size(); ++i) { auto bond_idx = _written_bonds[i]; auto& e = _bmol->getEdge(bond_idx); auto bdir = _bmol->getBondDirection(bond_idx); - if (bdir && bdir < BOND_EITHER) + if (bdir) { const auto& edge = _bmol->getEdge(bond_idx); auto wa_idx = _written_atoms.find(edge.beg); - if (bdir == BOND_UP) + switch (bdir) + { + case BOND_UP: up_dirs.emplace_back(wa_idx, i); - else + break; + case BOND_DOWN: down_dirs.emplace_back(wa_idx, i); - } - } - bool is_first = true; - if (up_dirs.size()) - { - for (const auto& kvp : up_dirs) - { - if (is_first) - { - _startExtension(); - _output.writeString("wU:"); - is_first = false; - } - else - _output.writeString(","); - _output.printf("%d.%d", kvp.first, kvp.second); - } - } - is_first = true; - if (down_dirs.size()) - { - for (const auto& kvp : down_dirs) - { - if (is_first) - { - _startExtension(); - _output.writeString("wD:"); - is_first = false; + break; + case BOND_EITHER: + wiggy_dirs.emplace_back(wa_idx, i); + break; } - else - _output.writeString(","); - _output.printf("%d.%d", kvp.first, kvp.second); } } - if ((down_dirs.size() || up_dirs.size()) && BaseMolecule::hasCoord(*_mol)) + + _writeBondDirs("wU:", up_dirs); + _writeBondDirs("wD:", down_dirs); + _writeBondDirs("w:", wiggy_dirs); + + if ((down_dirs.size() || up_dirs.size() || wiggy_dirs.size()) && BaseMolecule::hasCoord(*_mol)) { _output.writeString(",("); for (int i = 0; i < _written_atoms.size(); ++i) diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index c97759bcf9..fb993cc893 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -917,7 +917,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - indigoLayout(obj); + //indigoLayout(obj); if (p.out_ext == OEXT_MOL) indigoSaveMolfileToFile(obj, p.outfile); else if (p.out_ext == OEXT_KET) From a2f39abb135674b430b8af41e3d9abcb8ba0e810 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 4 Oct 2023 05:18:37 +0200 Subject: [PATCH 23/36] wiggly bonds fix --- utils/indigo-depict/main.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index fb993cc893..c97759bcf9 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -917,7 +917,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - //indigoLayout(obj); + indigoLayout(obj); if (p.out_ext == OEXT_MOL) indigoSaveMolfileToFile(obj, p.outfile); else if (p.out_ext == OEXT_KET) From b693ab9997500d44a26d600888d5abe3594034c2 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 4 Oct 2023 05:23:00 +0200 Subject: [PATCH 24/36] py format --- api/tests/integration/tests/formats/smiles.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/api/tests/integration/tests/formats/smiles.py b/api/tests/integration/tests/formats/smiles.py index 96692466e1..e650df5a2c 100644 --- a/api/tests/integration/tests/formats/smiles.py +++ b/api/tests/integration/tests/formats/smiles.py @@ -120,7 +120,7 @@ mols_smiles = [ "C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12|", "C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |wU:5.4,wD:5.5|", - "C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |w:5.4,5.5|" + "C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |w:5.4,5.5|", ] for sm in mols_smiles: print("atropisomer:") From 5ff9efe3cb00bf1dadd0592ac839ebdca622761d Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Wed, 4 Oct 2023 05:36:53 +0200 Subject: [PATCH 25/36] wiggly bonds fix --- core/indigo-core/molecule/src/molecule_automorphism_search.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/indigo-core/molecule/src/molecule_automorphism_search.cpp b/core/indigo-core/molecule/src/molecule_automorphism_search.cpp index 247ae82766..0823185cf7 100644 --- a/core/indigo-core/molecule/src/molecule_automorphism_search.cpp +++ b/core/indigo-core/molecule/src/molecule_automorphism_search.cpp @@ -733,7 +733,7 @@ int MoleculeAutomorphismSearch::_validStereocenterByAtom(int atom_index, Array Date: Sun, 8 Oct 2023 14:55:11 +0200 Subject: [PATCH 26/36] fix double bond as atropobond --- api/tests/integration/ref/bingo/molecules.py.out | 6 +++--- core/indigo-core/molecule/src/molecule_stereocenters.cpp | 3 ++- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/api/tests/integration/ref/bingo/molecules.py.out b/api/tests/integration/ref/bingo/molecules.py.out index d42b33ee08..38878c04e3 100644 --- a/api/tests/integration/ref/bingo/molecules.py.out +++ b/api/tests/integration/ref/bingo/molecules.py.out @@ -154,7 +154,7 @@ Structure 916 excluded: stereocenters: stereo types of the opposite bonds mismat Structure 931 excluded: stereocenters: one bond up, one bond down -- indefinite case near atom 1 Structure 936 excluded: molfile loader: direction of bond #2 makes no sense Structure 940 excluded: element: bad valence on Ar having 0 drawn bonds, charge 0, and 2 radical electrons -Structure 941 excluded: molfile loader: direction of bond #4 makes no sense +Structure 941 excluded: molfile loader: direction of bond #3 makes no sense Structure 943 excluded: element: bad valence on H having 2 drawn bonds, charge -2, and 0 radical electrons Structure 948 excluded: molfile loader: direction of bond #15 makes no sense Structure 955 excluded: element: bad valence on H having 0 drawn bonds, charge -3, and 0 radical electrons @@ -231,7 +231,7 @@ Structure 1492 excluded: stereocenters: directions of neighbor stereo bonds matc Structure 1498 excluded: molfile loader: direction of bond #3 makes no sense Structure 1501 excluded: stereocenters: directions of neighbor stereo bonds match near atom 0 Structure 1505 excluded: element: bad valence on C having 4 drawn bonds, charge -1, and 1 radical electrons -Structure 1514 excluded: molfile loader: direction of bond #4 makes no sense +Structure 1514 excluded: molfile loader: direction of bond #3 makes no sense Structure 1552 excluded: element: bad valence on H having 1 drawn bonds, charge 1, and 0 radical electrons Structure 1564 excluded: stereocenters: all 3 bonds up near stereoatom 97 Structure 1567 excluded: molfile loader: direction of bond #5 makes no sense @@ -270,7 +270,7 @@ Structure 1831 excluded: molfile loader: direction of bond #9 makes no sense Structure 1842 excluded: element: bad valence on I having 2 drawn bonds, charge 0, and 0 radical electrons Structure 1843 excluded: molfile loader: direction of bond #8 makes no sense Structure 1844 excluded: molfile loader: direction of bond #13 makes no sense -Structure 1846 excluded: molfile loader: direction of bond #4 makes no sense +Structure 1846 excluded: molfile loader: direction of bond #3 makes no sense Structure 1848 excluded: molfile loader: direction of bond #9 makes no sense Structure 1851 excluded: stereocenters: 2 hydrogens near stereocenter 8 Structure 1857 excluded: molfile loader: direction of bond #1 makes no sense diff --git a/core/indigo-core/molecule/src/molecule_stereocenters.cpp b/core/indigo-core/molecule/src/molecule_stereocenters.cpp index 54ffd3e107..c00b564a14 100644 --- a/core/indigo-core/molecule/src/molecule_stereocenters.cpp +++ b/core/indigo-core/molecule/src/molecule_stereocenters.cpp @@ -235,7 +235,8 @@ bool MoleculeStereocenters::isPossibleAtropocenter(BaseMolecule& baseMolecule, i for (int i = v.neiBegin(); i != v.neiEnd(); i = v.neiNext(i)) { auto bond_idx = v.neiEdge(i); - if (baseMolecule.getEdgeTopology(bond_idx) == TOPOLOGY_CHAIN && baseMolecule.vertexInRing(v.neiVertex(i))) + if (baseMolecule.getEdgeTopology(bond_idx) == TOPOLOGY_CHAIN && baseMolecule.getBondOrder(bond_idx) == BOND_SINGLE && + baseMolecule.vertexInRing(v.neiVertex(i))) { std::unordered_set visited; RedBlackMap dir_map; From efe5cd26e557f70fee87a2068e941671aa8c43dc Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Sun, 8 Oct 2023 19:57:18 +0200 Subject: [PATCH 27/36] inchi fix --- core/indigo-core/molecule/src/inchi_wrapper.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/core/indigo-core/molecule/src/inchi_wrapper.cpp b/core/indigo-core/molecule/src/inchi_wrapper.cpp index 5da196f263..073da92622 100644 --- a/core/indigo-core/molecule/src/inchi_wrapper.cpp +++ b/core/indigo-core/molecule/src/inchi_wrapper.cpp @@ -523,6 +523,8 @@ void InchiWrapper::generateInchiInput(Molecule& mol, inchi_Input& input, Array Date: Sun, 8 Oct 2023 20:15:52 +0200 Subject: [PATCH 28/36] inchi fix --- core/indigo-core/molecule/src/inchi_wrapper.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/indigo-core/molecule/src/inchi_wrapper.cpp b/core/indigo-core/molecule/src/inchi_wrapper.cpp index 073da92622..214a634cb9 100644 --- a/core/indigo-core/molecule/src/inchi_wrapper.cpp +++ b/core/indigo-core/molecule/src/inchi_wrapper.cpp @@ -523,7 +523,7 @@ void InchiWrapper::generateInchiInput(Molecule& mol, inchi_Input& input, Array Date: Sun, 8 Oct 2023 20:51:11 +0200 Subject: [PATCH 29/36] cml fix --- core/indigo-core/molecule/src/cml_saver.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/indigo-core/molecule/src/cml_saver.cpp b/core/indigo-core/molecule/src/cml_saver.cpp index fe5c90487d..f034b01d4e 100644 --- a/core/indigo-core/molecule/src/cml_saver.cpp +++ b/core/indigo-core/molecule/src/cml_saver.cpp @@ -368,7 +368,7 @@ void CmlSaver::_addMoleculeElement(XMLElement* elem, BaseMolecule& mol, bool que } } - if (_mol->stereocenters.getType(i) > MoleculeStereocenters::ATOM_ANY) + if (_mol->stereocenters.getType(i) > MoleculeStereocenters::ATOM_ANY && _mol->stereocenters.isTetrahydral(i)) { XMLElement* atomparity = _doc->NewElement("atomParity"); atom->LinkEndChild(atomparity); From 434a81b3e4d96b4db7ef4a1d408d14cb52cc2d6e Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 9 Oct 2023 01:27:08 +0200 Subject: [PATCH 30/36] free center fix --- core/indigo-core/molecule/src/smiles_loader.cpp | 2 +- utils/indigo-depict/main.c | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/core/indigo-core/molecule/src/smiles_loader.cpp b/core/indigo-core/molecule/src/smiles_loader.cpp index 5a37c27665..4e03d9144b 100644 --- a/core/indigo-core/molecule/src/smiles_loader.cpp +++ b/core/indigo-core/molecule/src/smiles_loader.cpp @@ -341,7 +341,7 @@ void SmilesLoader::_readOtherStuff() { // Check if the stereocenter has already been marked as any // For example [H]C1(O)c2ccnn2[C@@H](O)c2ccnn12 |r,w:1.0,1.1| - if (_bmol->stereocenters.getType(atom_idx) != MoleculeStereocenters::ATOM_ANY) + if (!_bmol->stereocenters.exists(atom_idx)) _bmol->addStereocenters(atom_idx, MoleculeStereocenters::ATOM_ANY, 0, false); } } diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index c97759bcf9..fb993cc893 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -917,7 +917,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - indigoLayout(obj); + //indigoLayout(obj); if (p.out_ext == OEXT_MOL) indigoSaveMolfileToFile(obj, p.outfile); else if (p.out_ext == OEXT_KET) From e1f5f74a8830a051ce174398f6819af43d67014b Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 9 Oct 2023 01:27:39 +0200 Subject: [PATCH 31/36] free center fix --- utils/indigo-depict/main.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c index fb993cc893..c97759bcf9 100644 --- a/utils/indigo-depict/main.c +++ b/utils/indigo-depict/main.c @@ -917,7 +917,7 @@ int main(int argc, char* argv[]) _prepare(obj, p.aromatization); if (p.action == ACTION_LAYOUT) { - //indigoLayout(obj); + indigoLayout(obj); if (p.out_ext == OEXT_MOL) indigoSaveMolfileToFile(obj, p.outfile); else if (p.out_ext == OEXT_KET) From 6089687a71ed17599a88066f853084ac9d65dc98 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 9 Oct 2023 01:31:46 +0200 Subject: [PATCH 32/36] bingo fixes --- bingo/tests/data/molecules/cml/std.json | 2 +- bingo/tests/data/molecules/compactmolecule/std.json | 2 +- bingo/tests/data/reactions/compactreaction/std.json | 2 +- bingo/tests/test_rsmiles/test_rsmiles.py | 6 +++++- 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/bingo/tests/data/molecules/cml/std.json b/bingo/tests/data/molecules/cml/std.json index 023a75fd81..082ab2079a 100644 --- a/bingo/tests/data/molecules/cml/std.json +++ b/bingo/tests/data/molecules/cml/std.json @@ -3722,7 +3722,7 @@ { "query_id": 745, "query_type": "cml", - "expected": "\n\n \n \n \n \n \n 1\n \n \n 1\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 1\n \n \n \n \n \n 1\n \n \n 1\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 1\n \n \n 1\n \n \n \n \n \n 1\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 1\n \n \n 1\n \n \n \n \n 1\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n T\n \n \n \n \n C\n \n \n \n C\n \n \n C\n \n \n \n C\n \n \n \n C\n \n \n \n C\n \n \n C\n \n \n \n C\n \n \n \n \n W\n \n \n \n \n \n W\n \n \n W\n \n \n \n \n \n \n \n W\n \n \n \n \n \n W\n \n \n W\n \n \n \n \n \n \n \n \n T\n \n \n \n T\n \n \n \n \n C\n \n \n \n C\n \n \n C\n \n \n \n C\n \n \n \n \n \n T\n \n \n \n T\n \n \n \n \n \n W\n \n \n \n \n \n W\n \n \n W\n \n \n \n \n \n \n \n \n T\n \n \n \n \n W\n \n \n \n \n \n W\n \n \n W\n \n \n \n \n \n \n \n \n T\n \n \n \n T\n \n \n \n \n C\n \n \n \n C\n \n \n C\n \n \n \n C\n \n \n \n \n\n" + "expected": "111111111111111TCCCCCCCCWWWWWWTTCCCCTTWWWTWWWTTCCCC\n" }, { "query_id": 746, diff --git a/bingo/tests/data/molecules/compactmolecule/std.json b/bingo/tests/data/molecules/compactmolecule/std.json index 3402f39342..2a715c6499 100644 --- a/bingo/tests/data/molecules/compactmolecule/std.json +++ b/bingo/tests/data/molecules/compactmolecule/std.json @@ -3722,7 +3722,7 @@ { "query_id": 745, "query_type": "compactmolecule(0)", - "expected": "942f6642b01222a2a8d1b953c4477764" + "expected": "757a56ddfcbfe7e377b87037fb415a40" }, { "query_id": 746, diff --git a/bingo/tests/data/reactions/compactreaction/std.json b/bingo/tests/data/reactions/compactreaction/std.json index 3e71814fab..cd8d134a43 100644 --- a/bingo/tests/data/reactions/compactreaction/std.json +++ b/bingo/tests/data/reactions/compactreaction/std.json @@ -1447,7 +1447,7 @@ { "query_id": 290, "query_type": "compactreaction(0)", - "expected": "871fbada43b7c6c4b1c7a3298791bb1d" + "expected": "b0deb28fd1bd4350908254566b88b994" }, { "query_id": 291, diff --git a/bingo/tests/test_rsmiles/test_rsmiles.py b/bingo/tests/test_rsmiles/test_rsmiles.py index a6e774b14a..d63b34fa2f 100644 --- a/bingo/tests/test_rsmiles/test_rsmiles.py +++ b/bingo/tests/test_rsmiles/test_rsmiles.py @@ -1,11 +1,15 @@ import pytest from ..helpers import assert_calculate_query, query_cases - +from ..logger import logger class TestRsmiles: @pytest.mark.parametrize("query_id, expected", query_cases("rsmiles")) def test_molecular_weight(self, db, entities, query_id, expected): reaction = entities.get(query_id) result = db.rsmiles(reaction) + if result != expected: + logger.info(query_id) + logger.info(result) + logger.info(expected) assert_calculate_query(result, expected) From 0651b1550f7132bac82ccfe2c8c682b0bca98988 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 9 Oct 2023 03:39:27 +0200 Subject: [PATCH 33/36] cml fix --- bingo/tests/data/molecules/cml/std.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bingo/tests/data/molecules/cml/std.json b/bingo/tests/data/molecules/cml/std.json index 082ab2079a..3462218872 100644 --- a/bingo/tests/data/molecules/cml/std.json +++ b/bingo/tests/data/molecules/cml/std.json @@ -3722,7 +3722,7 @@ { "query_id": 745, "query_type": "cml", - "expected": "111111111111111TCCCCCCCCWWWWWWTTCCCCTTWWWTWWWTTCCCC\n" + "expected": "11111111111TCCCCCCCCWWWWWWTTCCCCTTWWWTWWWTTCCCC\n" }, { "query_id": 746, From 3f3395a544f6c9c45e2f293284f00fe69a409bb7 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 9 Oct 2023 05:40:55 +0200 Subject: [PATCH 34/36] tests fixed --- .../basic/buffer_string_load_iterate.py.out | 8 +++---- .../integration/ref/bingo/molecules.py.out | 6 +++--- .../ref/stereo/bidirectional.py.out | 16 +++++++------- bingo/tests/test_rsmiles/test_rsmiles.py | 4 ---- .../molecule/src/molecule_stereocenters.cpp | 21 ++++++++++++------- 5 files changed, 29 insertions(+), 26 deletions(-) diff --git a/api/tests/integration/ref/basic/buffer_string_load_iterate.py.out b/api/tests/integration/ref/basic/buffer_string_load_iterate.py.out index dcd6e78794..9ef808c527 100644 --- a/api/tests/integration/ref/basic/buffer_string_load_iterate.py.out +++ b/api/tests/integration/ref/basic/buffer_string_load_iterate.py.out @@ -10230,10 +10230,10 @@ O=C(N)[C@H]1[C@@H](C(N[2H])=O)C1C([NH-])=O [C@@H]1(C)[C@H](C)[C@H]1C [C@@H]1(C)[C@H](C)[C@@H]1C O1[C@H]([C@@H]1[2H])CCCC -[C@@H]12OC(O[C@@H]1C([C@@H]([C@@H]1OC(OC1)(C)C)O2)=O)(C)C |wU:6.15,wD:0.0,4.3,7.8,(2.26,0.59,;3.82,0.58,;4.30,-0.91,;3.02,-1.82,;1.76,-0.89,;0.27,-0.89,;-0.20,0.58,;-1.67,1.05,;-2.91,0.15,;-4.17,1.08,;-3.70,2.51,;-2.15,2.50,;-5.68,1.41,;-5.22,-0.05,;1.02,1.49,;-0.64,-2.14,;5.32,-2.07,;5.81,-0.60,)| +[C@@H]12OC(O[C@@H]1C([C@@H]([C@@H]1OC(OC1)(C)C)O2)=O)(C)C [P@@](C(C)(C)C)(C1C=CC=CC=1)C1=CC=CC=C1OC [P@](C(C)(C)C)(C1C=CC=CC=1)C1=CC=CC=C1OC -[C@H]12OC(O[C@H]1O[C@H](C1COC(C)(C)O1)C2=O)(C)C |wU:6.7,wD:0.0,4.3,(5.93,-3.99,;6.58,-4.47,;7.24,-4.00,;6.99,-3.22,;6.18,-3.22,;5.49,-2.73,;4.82,-3.22,;4.04,-2.97,;3.57,-2.30,;2.78,-2.54,;2.77,-3.37,;1.95,-3.44,;2.43,-4.12,;3.55,-3.63,;5.09,-3.99,;4.61,-4.67,;8.04,-3.83,;7.79,-4.62,)| +[C@H]12OC(O[C@H]1O[C@H](C1COC(C)(C)O1)C2=O)(C)C C[C@H]([C@H](Cl)CC)Cl CC([C@H](Cl)CC)Cl C1[C@H](C)[C@](O)(CO)C(OCC2[C@]3([H])[C@@H](CCN3CC=2)OC(/C/1=C\C)=O)=O @@ -10468,10 +10468,10 @@ O=C(N)[C@H]1[C@@H](C(N[2H])=O)C1C([NH-])=O [C@@H]1(C)[C@H](C)[C@H]1C [C@@H]1(C)[C@H](C)[C@@H]1C O1[C@H]([C@@H]1[2H])CCCC -[C@@H]12OC(O[C@@H]1C([C@@H]([C@@H]1OC(OC1)(C)C)O2)=O)(C)C |wU:6.15,wD:0.0,4.3,7.8,(2.26,0.59,;3.82,0.58,;4.30,-0.91,;3.02,-1.82,;1.76,-0.89,;0.27,-0.89,;-0.20,0.58,;-1.67,1.05,;-2.91,0.15,;-4.17,1.08,;-3.70,2.51,;-2.15,2.50,;-5.68,1.41,;-5.22,-0.05,;1.02,1.49,;-0.64,-2.14,;5.32,-2.07,;5.81,-0.60,)| +[C@@H]12OC(O[C@@H]1C([C@@H]([C@@H]1OC(OC1)(C)C)O2)=O)(C)C [P@@](C(C)(C)C)(C1C=CC=CC=1)C1=CC=CC=C1OC [P@](C(C)(C)C)(C1C=CC=CC=1)C1=CC=CC=C1OC -[C@H]12OC(O[C@H]1O[C@H](C1COC(C)(C)O1)C2=O)(C)C |wU:6.7,wD:0.0,4.3,(5.93,-3.99,;6.58,-4.47,;7.24,-4.00,;6.99,-3.22,;6.18,-3.22,;5.49,-2.73,;4.82,-3.22,;4.04,-2.97,;3.57,-2.30,;2.78,-2.54,;2.77,-3.37,;1.95,-3.44,;2.43,-4.12,;3.55,-3.63,;5.09,-3.99,;4.61,-4.67,;8.04,-3.83,;7.79,-4.62,)| +[C@H]12OC(O[C@H]1O[C@H](C1COC(C)(C)O1)C2=O)(C)C C[C@H]([C@H](Cl)CC)Cl CC([C@H](Cl)CC)Cl C1[C@H](C)[C@](O)(CO)C(OCC2[C@]3([H])[C@@H](CCN3CC=2)OC(/C/1=C\C)=O)=O diff --git a/api/tests/integration/ref/bingo/molecules.py.out b/api/tests/integration/ref/bingo/molecules.py.out index 38878c04e3..6c1a060fc8 100644 --- a/api/tests/integration/ref/bingo/molecules.py.out +++ b/api/tests/integration/ref/bingo/molecules.py.out @@ -39,7 +39,7 @@ Structure 275 excluded: molfile loader: direction of bond #7 makes no sense Structure 276 excluded: element: bad valence on H having 1 drawn bonds, charge 1, and 0 radical electrons Structure 283 excluded: element: bad valence on N having 4 drawn bonds, charge 0, and 0 radical electrons Structure 286 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 0 -Structure 294 excluded: molfile loader: direction of bond #22 makes no sense +Structure 294 excluded: molfile loader: direction of bond #185 makes no sense Structure 295 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 0 Structure 301 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 1 Structure 316 excluded: stereocenters: stereo types of non-opposite bonds match near atom 30 @@ -263,7 +263,7 @@ Structure 1785 excluded: stereocenters: one bond up, one bond down -- indefinite Structure 1792 excluded: stereocenters: 2 hydrogens near stereocenter 6 Structure 1797 excluded: element: bad valence on N having 5 drawn bonds, charge 1, and 0 radical electrons Structure 1799 excluded: molfile loader: direction of bond #45 makes no sense -Structure 1800 excluded: molfile loader: direction of bond #177 makes no sense +Structure 1800 excluded: molfile loader: direction of bond #185 makes no sense Structure 1823 excluded: molfile loader: direction of bond #0 makes no sense Structure 1830 excluded: molfile loader: direction of bond #1 makes no sense Structure 1831 excluded: molfile loader: direction of bond #9 makes no sense @@ -288,7 +288,7 @@ Structure 1926 excluded: molfile loader: direction of bond #7 makes no sense Structure 1931 excluded: element: bad valence on H having 4 drawn bonds, charge 0, and 0 radical electrons Structure 1939 excluded: element: bad valence on C having 5 drawn bonds, charge 0, and 0 radical electrons Structure 1945 excluded: molfile loader: direction of bond #5 makes no sense -Structure 1948 excluded: molfile loader: direction of bond #22 makes no sense +Structure 1948 excluded: molfile loader: direction of bond #185 makes no sense Structure 1952 excluded: molfile loader: direction of bond #3 makes no sense Structure 1953 excluded: stereocenters: stereo types of the opposite bonds mismatch near atom 0 Structure 1956 excluded: element: bad valence on C having 4 drawn bonds, charge -1, and 1 radical electrons diff --git a/api/tests/integration/ref/stereo/bidirectional.py.out b/api/tests/integration/ref/stereo/bidirectional.py.out index e1cdb013f8..6f337825d7 100644 --- a/api/tests/integration/ref/stereo/bidirectional.py.out +++ b/api/tests/integration/ref/stereo/bidirectional.py.out @@ -3,8 +3,8 @@ 02.mol C1CCC([C@@H]2C=CC(N([H])C2=O)=O)O1 |&1:4,r| 03.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 04.mol C1CCC([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:4,r| -05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r,wU:4.3,wD:3.2,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| -06.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r,wD:3.2,3.3,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| +05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| +06.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 07.mol stereocenters: one bond up, one bond down -- indefinite case near atom 3 08.mol C1CC[C@@](C)(C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 09.mol C1CC[C@@](C)(C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| @@ -26,8 +26,8 @@ test2.mol stereocenters: one bond up, one bond down -- indefinite case near atom 02.mol C1CCC([C@@H]2C=CC(N([H])C2=O)=O)O1 |&1:4,r| 03.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 04.mol C1CCC([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:4,r| -05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r,wU:4.3,wD:3.2,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| -06.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r,wD:3.2,3.3,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| +05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| +06.mol C1CC[C@@H](C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 07.mol C1CCC(C2C=CC(N([H])C2=O)=O)O1 |&1:3,r,wU:3.2,wD:3.3,(-2.06,-0.81,;-1.79,-1.62,;-0.94,-1.62,;-0.70,-0.78,;0.04,-0.14,;-0.15,0.64,;0.46,1.24,;1.22,1.01,;1.53,0.12,;2.06,-0.05,;0.82,-0.39,;1.04,-1.18,;1.84,1.62,;-1.41,-0.31,)| 08.mol C1CC[C@@](C)(C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| 09.mol C1CC[C@@](C)(C2C=CC(N([H])C2=O)=O)O1 |&1:3,r| @@ -49,8 +49,8 @@ test2.mol C1(CCCO1)N 02.mol C1CC[C@H]([C@@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| 03.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| 04.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| -05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r,wU:4.3,wD:3.2,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| -06.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r,wD:3.2,3.3,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| +05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| +06.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,4,r| 07.mol stereocenters: one bond up, one bond down -- indefinite case near atom 3 08.mol C1CC[C@@](C)([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,5,r| 09.mol C1CC[C@@](C)([C@H]2C=CC(N([H])C2=O)=O)O1 |&1:3,5,r| @@ -72,8 +72,8 @@ test2.mol stereocenters: one bond up, one bond down -- indefinite case near atom 02.mol C1CC[C@H]([C@@H]2C=CC(N([H])C2=O)=O)O1 03.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 04.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 -05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |wU:4.10,wD:3.13,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| -06.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 |wU:4.10,wD:3.13,(-1.86,-1.61,;-1.59,-2.42,;-0.75,-2.42,;-0.50,-1.58,;0.42,-0.09,;-0.27,0.30,;-0.28,1.17,;0.41,1.55,;1.27,1.16,;1.75,1.43,;1.14,0.30,;1.86,-0.09,;0.40,2.42,;-1.21,-1.12,)| +05.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 +06.mol C1CC[C@@H]([C@H]2C=CC(N([H])C2=O)=O)O1 07.mol stereocenters: one bond up, one bond down -- indefinite case near atom 3 08.mol C1CC[C@@](C)([C@H]2C=CC(N([H])C2=O)=O)O1 09.mol C1CC[C@@](C)([C@H]2C=CC(N([H])C2=O)=O)O1 diff --git a/bingo/tests/test_rsmiles/test_rsmiles.py b/bingo/tests/test_rsmiles/test_rsmiles.py index d63b34fa2f..e3989f50bc 100644 --- a/bingo/tests/test_rsmiles/test_rsmiles.py +++ b/bingo/tests/test_rsmiles/test_rsmiles.py @@ -8,8 +8,4 @@ class TestRsmiles: def test_molecular_weight(self, db, entities, query_id, expected): reaction = entities.get(query_id) result = db.rsmiles(reaction) - if result != expected: - logger.info(query_id) - logger.info(result) - logger.info(expected) assert_calculate_query(result, expected) diff --git a/core/indigo-core/molecule/src/molecule_stereocenters.cpp b/core/indigo-core/molecule/src/molecule_stereocenters.cpp index c00b564a14..072751255d 100644 --- a/core/indigo-core/molecule/src/molecule_stereocenters.cpp +++ b/core/indigo-core/molecule/src/molecule_stereocenters.cpp @@ -98,13 +98,20 @@ void MoleculeStereocenters::buildFromBonds(BaseMolecule& baseMolecule, const Ste int atom_idx = _stereocenters.key(i); _AtropoCenter& ac = _atropocenters.at(atom_idx); std::unordered_set visited_bonds; - findAtropoStereobonds(baseMolecule, ac.bond_directions, atom_idx, visited_bonds, false, sensible_bonds_out); - auto bdir = baseMolecule.getBondDirection(ac.atropo_bond); - // include possible atropobond itself if its direction is not sensible, but direction is set - if (bdir && !sensible_bonds_out[ac.atropo_bond]) + if (findAtropoStereobonds(baseMolecule, ac.bond_directions, atom_idx, visited_bonds, false, sensible_bonds_out)) { - ac.bond_directions.insert(ac.atropo_bond, bdir); - sensible_bonds_out[ac.atropo_bond] = 1; + auto bdir = baseMolecule.getBondDirection(ac.atropo_bond); + // include possible atropobond itself if its direction is not sensible, but direction is set + if (bdir && !sensible_bonds_out[ac.atropo_bond]) + { + ac.bond_directions.insert(ac.atropo_bond, bdir); + sensible_bonds_out[ac.atropo_bond] = 1; + } + } + else + { + atom.is_atropisomeric = false; + _atropocenters.remove(atom_idx); } } } @@ -291,7 +298,7 @@ bool MoleculeStereocenters::findAtropoStereobonds(BaseMolecule& baseMolecule, Re if (first_only) return true; } - findAtropoStereobonds(baseMolecule, directions_map, v.neiVertex(i), visited_bonds); + findAtropoStereobonds(baseMolecule, directions_map, v.neiVertex(i), visited_bonds, first_only, sensible_bonds_out); } } } From 5dc3c8c9df552f120b9e1aa9136d0bf749661aab Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 9 Oct 2023 06:13:25 +0200 Subject: [PATCH 35/36] bingo fix --- bingo/tests/data/molecules/checkmolecule/std.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bingo/tests/data/molecules/checkmolecule/std.json b/bingo/tests/data/molecules/checkmolecule/std.json index 975559c2ee..a4d438ba0d 100644 --- a/bingo/tests/data/molecules/checkmolecule/std.json +++ b/bingo/tests/data/molecules/checkmolecule/std.json @@ -8352,17 +8352,17 @@ { "query_id": 1671, "query_type": "checkmolecule", - "expected": "molfile loader: direction of bond #22 makes no sense" + "expected": "molfile loader: direction of bond #185 makes no sense" }, { "query_id": 1672, "query_type": "checkmolecule", - "expected": "molfile loader: direction of bond #22 makes no sense" + "expected": "molfile loader: direction of bond #185 makes no sense" }, { "query_id": 1673, "query_type": "checkmolecule", - "expected": "molfile loader: direction of bond #177 makes no sense" + "expected": "molfile loader: direction of bond #185 makes no sense" }, { "query_id": 1674, From a1c1502f48f9edf4cb217a53ea4de52e00a33ac4 Mon Sep 17 00:00:00 2001 From: Roman Porozhnetov Date: Mon, 9 Oct 2023 10:36:37 +0200 Subject: [PATCH 36/36] bingo fix --- .github/workflows/indigo-ci.yaml | 2 +- bingo/tests/data/reactions/rsmiles/std.json | 2 +- bingo/tests/test_rsmiles/test_rsmiles.py | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/indigo-ci.yaml b/.github/workflows/indigo-ci.yaml index 4a7a05e49b..a3a13af246 100644 --- a/.github/workflows/indigo-ci.yaml +++ b/.github/workflows/indigo-ci.yaml @@ -676,7 +676,7 @@ jobs: python setup.py bdist_wheel cp dist/*.whl ${GITHUB_WORKSPACE}/dist/ - name: Run pylint - run: pylint bingo_elastic + run: pylint --max-args 10 bingo_elastic working-directory: bingo/bingo-elastic/python - name: Run tests run: pytest tests diff --git a/bingo/tests/data/reactions/rsmiles/std.json b/bingo/tests/data/reactions/rsmiles/std.json index df1ee6bb33..d2014162c3 100644 --- a/bingo/tests/data/reactions/rsmiles/std.json +++ b/bingo/tests/data/reactions/rsmiles/std.json @@ -1447,7 +1447,7 @@ { "query_id": 290, "query_type": "rsmiles", - "expected": "[C:1]1([O:48][CH2:4]1)([C@@:3]1([H])[CH2:9][CH2:17][C@@:14]2([H])[C@:24]3([H])[CH2:27][CH:29]=[C:30]4[CH2:33][C@H:35]([CH2:34][CH2:31][C@:28]4([CH3:32])[C@@:26]3([H])[CH2:25][CH2:15][C@:8]12[CH3:16])[O:36][Si](C)(C)C(C)(C)C)[CH:2](OS(=O)(=O)C)[C:6]1([Si](C)(C)C)[O:49][CH2:10]1>>[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10]F)=[CH:2]1.[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10][OH:49])=[CH:2]1 |w:0,34,40,a:3,7,9,15,18,20,24,47,51,53,57,63,65,69,78,82,84,88,94,96,100|" + "expected": "[C@:1]1([O:48][CH2:4]1)([C@@:3]1([H])[CH2:9][CH2:17][C@@:14]2([H])[C@:24]3([H])[CH2:27][CH:29]=[C:30]4[CH2:33][C@H:35]([CH2:34][CH2:31][C@:28]4([CH3:32])[C@@:26]3([H])[CH2:25][CH2:15][C@:8]12[CH3:16])[O:36][Si](C)(C)C(C)(C)C)[CH:2](OS(=O)(=O)C)[C:6]1([Si](C)(C)C)[O:49][CH2:10]1>>[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10]F)=[CH:2]1.[C@:8]12([CH3:16])[CH2:15][CH2:25][C@:26]3([H])[C@@:28]4([CH3:32])[CH2:31][CH2:34][C@H:35]([OH:36])[CH2:33][C:30]4=[CH:29][CH2:27][C@@:24]3([H])[C@:14]1([H])[CH2:17][CH2:9][C@:3]2([H])[C:1]1=[CH:4][O:48][C:6]([CH2:10][OH:49])=[CH:2]1 |a:0,3,7,9,15,18,20,24,47,51,53,57,63,65,69,78,82,84,88,94,96,100,w:34,40|" }, { "query_id": 291, diff --git a/bingo/tests/test_rsmiles/test_rsmiles.py b/bingo/tests/test_rsmiles/test_rsmiles.py index e3989f50bc..2d98f7639d 100644 --- a/bingo/tests/test_rsmiles/test_rsmiles.py +++ b/bingo/tests/test_rsmiles/test_rsmiles.py @@ -1,7 +1,6 @@ import pytest from ..helpers import assert_calculate_query, query_cases -from ..logger import logger class TestRsmiles: @pytest.mark.parametrize("query_id, expected", query_cases("rsmiles"))