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#2195 - Indigo functions doesn't work if query atom and monomer on the canvas at the same time #2710

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Dec 24, 2024
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#2195 - Indigo functions doesn't work if query atom and monomer on the canvas at the same time #2710

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5 changes: 5 additions & 0 deletions api/c/indigo/src/indigo_savers.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -207,6 +207,11 @@ void IndigoSmilesSaver::generateSmarts(IndigoObject& obj, Array<char>& out_buffe
{
BaseMolecule& mol = obj.getBaseMolecule();

if (mol.tgroups.getTGroupCount())
{
mol.transformTemplatesToSuperatoms();
}

SmilesSaver saver(output);
saver.smarts_mode = true;
if (mol.isQueryMolecule())
Expand Down
10 changes: 6 additions & 4 deletions api/tests/integration/ref/formats/ket_to_ket.py.out
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
*** KET to KET ***
images.ket:SUCCEED
ambiguous_monomer.ket doc: SUCCEED
ambiguous_monomer.ket mol: SUCCEED
monomer_shape.ket doc: SUCCEED
monomer_shape.ket mol: SUCCEED
ambiguous_monomer.ket doc loadKetDocument: SUCCEED
ambiguous_monomer.ket mol loadMolecule: SUCCEED
ambiguous_monomer.ket mol loadQueryMolecule: SUCCEED
monomer_shape.ket doc loadKetDocument: SUCCEED
monomer_shape.ket mol loadMolecule: SUCCEED
monomer_shape.ket mol loadQueryMolecule: SUCCEED
7 changes: 6 additions & 1 deletion api/tests/integration/tests/formats/custom_query.py
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Expand Up @@ -27,7 +27,12 @@ def test_smarts_to_ket(smarts_in, expected_str):


def test_ket_to_smarts(filename, expected_str):
mol = indigo.loadQueryMoleculeFromFile(os.path.join(ref_path, filename))
try:
mol = indigo.loadMoleculeFromFile(os.path.join(ref_path, filename))
except IndigoException as e:
mol = indigo.loadQueryMoleculeFromFile(
os.path.join(ref_path, filename)
)
smarts = mol.smarts()
if smarts == expected_str:
print(
Expand Down
15 changes: 8 additions & 7 deletions api/tests/integration/tests/formats/ket_to_ket.py
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Expand Up @@ -59,16 +59,17 @@ def check_res(filename, format, ket_ref, ket):
"ambiguous_monomer",
]
formats = {
"doc": indigo.loadKetDocument,
"mol": indigo.loadMolecule,
"doc": [indigo.loadKetDocument],
"mol": [indigo.loadMolecule, indigo.loadQueryMolecule],
}
for filename in sorted(files):
for format in sorted(formats.keys()):
file_path = os.path.join(ref_path, filename)
with open("{}_{}.ket".format(file_path, format), "r") as file:
ket_ref = file.read()
mol = formats[format](ket_ref)
# with open("{}_{}.ket".format(file_path, format), "w") as file:
# file.write(mol.json())
ket = mol.json()
check_res(filename, format, ket_ref, ket)
for loader in formats[format]:
mol = loader(ket_ref)
# with open("{}_{}.ket".format(file_path, format), "w") as file:
# file.write(mol.json())
ket = mol.json()
check_res(filename, format + " " + loader.__name__, ket_ref, ket)
55 changes: 49 additions & 6 deletions core/indigo-core/molecule/base_molecule.h
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Expand Up @@ -215,13 +215,55 @@ namespace indigo
virtual bool isPseudoAtom(int idx) = 0;
virtual const char* getPseudoAtom(int idx) = 0;

struct _AttachOrder
{
int ap_idx;
Array<char> ap_id;
};

struct _TemplateOccurrence
{
int name_idx; // index in _template_names
int class_idx; // index in _template_classes
int seq_id; // sequence id
int template_idx; // template idx
Array<char> seq_name; // sequence name
DisplayOption contracted; // display option (-1 if undefined, 0 - expanded, 1 - contracted)
Array<_AttachOrder> order; // attach order info
_TemplateOccurrence() : name_idx(-1), class_idx(-1), seq_id(-1), template_idx(-1), contracted(DisplayOption::Undefined)
{
}
_TemplateOccurrence(const _TemplateOccurrence& other)
: name_idx(other.name_idx), class_idx(other.class_idx), seq_id(other.seq_id), template_idx(other.template_idx), contracted(other.contracted)
{
seq_name.copy(other.seq_name);
order.copy(other.order);
}
};
ObjPool<_TemplateOccurrence> _template_occurrences;

StringPool _template_classes;
StringPool _template_names;

virtual int addTemplateAtom(const char* text) = 0;
virtual bool isTemplateAtom(int idx) = 0;
virtual const char* getTemplateAtom(int idx) = 0;
virtual const int getTemplateAtomSeqid(int idx) = 0;
virtual const char* getTemplateAtomSeqName(int idx) = 0;
virtual const char* getTemplateAtomClass(int idx) = 0;
virtual const int getTemplateAtomDisplayOption(int idx) = 0;
virtual const int getTemplateAtomTemplateIndex(int idx) = 0;
virtual int getTemplateAtomOccurrence(int idx) = 0;

const char* getTemplateAtom(int idx);
const int getTemplateAtomSeqid(int idx);
const char* getTemplateAtomSeqName(int idx);
const char* getTemplateAtomClass(int idx);
const int getTemplateAtomDisplayOption(int idx);
const int getTemplateAtomTemplateIndex(int idx);

void renameTemplateAtom(int idx, const char* text);
void setTemplateAtomName(int idx, const char* text);
void setTemplateAtomClass(int idx, const char* text);
void setTemplateAtomSeqid(int idx, int seq_id);
void setTemplateAtomSeqName(int idx, const char* seq_name);

void setTemplateAtomDisplayOption(int idx, int contracted);
void setTemplateAtomTemplateIndex(int idx, int temp_idx);

bool getUnresolvedTemplatesList(BaseMolecule& bmol, std::string& unresolved);

Expand Down Expand Up @@ -313,6 +355,7 @@ namespace indigo
virtual int addAtom(int label) = 0;

virtual int addBond(int beg, int end, int order) = 0;
virtual int addBond_Silent(int beg, int end, int order) = 0;

void unfoldHydrogens(Array<int>* markers_out, int max_h_cnt = -1, bool impl_h_no_throw = false, bool only_selected = false);

Expand Down
42 changes: 4 additions & 38 deletions core/indigo-core/molecule/molecule.h
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Expand Up @@ -45,18 +45,13 @@ namespace indigo

void setPseudoAtom(int idx, const char* text);

void renameTemplateAtom(int idx, const char* text);
bool isTemplateAtom(int idx) override;
int getTemplateAtomOccurrence(int idx) override;
virtual int addTemplateAtom(const char* text) override;
void setTemplateAtom(int idx, const char* text);
void setTemplateAtomName(int idx, const char* text);
void setTemplateAtomClass(int idx, const char* text);
void setTemplateAtomSeqid(int idx, int seq_id);
void setTemplateAtomSeqName(int idx, const char* seq_name);

void setTemplateAtomDisplayOption(int idx, int contracted);
void setTemplateAtomTemplateIndex(int idx, int temp_idx);

int addBond(int beg, int end, int order) override;
int addBond_Silent(int beg, int end, int order);
int addBond_Silent(int beg, int end, int order) override;

void setAtomCharge(int idx, int charge);
void setAtomCharge_Silent(int idx, int charge);
Expand Down Expand Up @@ -98,14 +93,6 @@ namespace indigo
bool isPseudoAtom(int idx) override;
const char* getPseudoAtom(int idx) override;

bool isTemplateAtom(int idx) override;
const char* getTemplateAtom(int idx) override;
const int getTemplateAtomSeqid(int idx) override;
const char* getTemplateAtomSeqName(int idx) override;
const char* getTemplateAtomClass(int idx) override;
const int getTemplateAtomTemplateIndex(int idx) override;
const int getTemplateAtomDisplayOption(int idx) override;

bool isRSite(int atom_idx) override;
dword getRSiteBits(int atom_idx) override;
void allowRGroupOnRSite(int atom_idx, int rg_idx) override;
Expand Down Expand Up @@ -202,27 +189,6 @@ namespace indigo

StringPool _pseudo_atom_values;

struct _AttachOrder
{
int ap_idx;
Array<char> ap_id;
};

struct _TemplateOccurrence
{
int name_idx; // index in _template_names
int class_idx; // index in _template_classes
int seq_id; // sequence id
int template_idx; // template idx
Array<char> seq_name; // sequence name
DisplayOption contracted; // display option (-1 if undefined, 0 - expanded, 1 - contracted)
Array<_AttachOrder> order; // attach order info
};
ObjPool<_TemplateOccurrence> _template_occurrences;

StringPool _template_classes;
StringPool _template_names;

bool _aromatized;

bool _ignore_bad_valence;
Expand Down
10 changes: 3 additions & 7 deletions core/indigo-core/molecule/molecule_layered_molecules.h
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Expand Up @@ -97,14 +97,9 @@ namespace indigo
bool isPseudoAtom(int idx) override;
const char* getPseudoAtom(int idx) override;

int addTemplateAtom(const char* text) override;
bool isTemplateAtom(int idx) override;
const char* getTemplateAtom(int idx) override;
const int getTemplateAtomSeqid(int idx) override;
const char* getTemplateAtomSeqName(int idx) override;
const int getTemplateAtomTemplateIndex(int idx) override;

const char* getTemplateAtomClass(int idx) override;
const int getTemplateAtomDisplayOption(int idx) override;
int getTemplateAtomOccurrence(int idx) override;

bool isRSite(int atom_idx) override;
dword getRSiteBits(int atom_idx) override;
Expand Down Expand Up @@ -132,6 +127,7 @@ namespace indigo

int addAtom(int label) override;
int addBond(int beg, int end, int order) override;
int addBond_Silent(int beg, int end, int order) override;

int getImplicitH(int idx, bool impl_h_no_throw) override;
void setImplicitH(int idx, int impl_h) override;
Expand Down
10 changes: 4 additions & 6 deletions core/indigo-core/molecule/query_molecule.h
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Expand Up @@ -215,6 +215,7 @@ namespace indigo

int value_min;
int value_max;
int occurrence_idx;

// available only when type is ATOM_PSEUDO or ATOM_TEMPLATE or ATOM_TEMPLATE_CLASS
Array<char> alias;
Expand Down Expand Up @@ -319,13 +320,9 @@ namespace indigo
bool isPseudoAtom(int idx) override;
const char* getPseudoAtom(int idx) override;

int addTemplateAtom(const char* text) override;
bool isTemplateAtom(int idx) override;
const char* getTemplateAtom(int idx) override;
const int getTemplateAtomSeqid(int idx) override;
const char* getTemplateAtomSeqName(int idx) override;
const char* getTemplateAtomClass(int idx) override;
const int getTemplateAtomDisplayOption(int idx) override;
const int getTemplateAtomTemplateIndex(int idx) override;
int getTemplateAtomOccurrence(int idx) override;

bool isRSite(int atom_idx) override;
dword getRSiteBits(int atom_idx) override;
Expand Down Expand Up @@ -411,6 +408,7 @@ namespace indigo

int addAtom(int label) override;
int addBond(int beg, int end, int order) override;
int addBond_Silent(int beg, int end, int order) override;

int getImplicitH(int idx, bool impl_h_no_throw) override;
void setImplicitH(int idx, int impl_h) override;
Expand Down
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