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Make mmCIF unit_cell consistent with PDB in case where it is 1,1,1,90…
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…,90,90
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@olegsobolev
olegsobolev committed Nov 26, 2024
1 parent 80c6df1 commit d0d095d
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Showing 4 changed files with 194 additions and 12 deletions.
20 changes: 12 additions & 8 deletions iotbx/pdb/cryst1_interpretation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,11 +113,7 @@ def space_group_info(self, unit_cell=None):
return sgtbx.space_group_info(special[self.symbol])
raise RuntimeError("Programming error (should be unreachable).")

def crystal_symmetry(cryst1_record):
if (isinstance(cryst1_record, str)):
cryst1_record = iotbx.pdb.records.cryst1(pdb_str=cryst1_record)
u = cryst1_record.ucparams
s = cryst1_record.sgroup
def dummy_unit_cell(abc, abg, sg_symbol):
def are_dummy_lengths(abc):
for v in abc:
if (v not in [0, 1]): return False
Expand All @@ -126,11 +122,19 @@ def are_dummy_angles(abg):
for v in abg:
if (v not in [0, 90]): return False
return True
dummy_sg = sg_symbol is None or sg_symbol.replace(" ","") == "P1"
return ( are_dummy_lengths(abc)
and are_dummy_angles(abg)
and dummy_sg)

def crystal_symmetry(cryst1_record):
if (isinstance(cryst1_record, str)):
cryst1_record = iotbx.pdb.records.cryst1(pdb_str=cryst1_record)
u = cryst1_record.ucparams
s = cryst1_record.sgroup
if ( u is not None
and len(u) == 6
and (s is None or s.replace(" ","") == "P1")
and are_dummy_lengths(u[:3])
and are_dummy_angles(u[3:])):
and dummy_unit_cell(u[:3], u[3:], s)):
return crystal.symmetry(
unit_cell=None,
space_group_info=None)
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19 changes: 15 additions & 4 deletions iotbx/pdb/mmcif.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,10 @@
from libtbx.utils import Sorry
from libtbx.str_utils import format_value
import iotbx.pdb
import cctbx.crystal
from iotbx.pdb import hierarchy
from iotbx.pdb import hy36encode
from iotbx.pdb import cryst1_interpretation
from iotbx.pdb.experiment_type import experiment_type
from iotbx.pdb.remark_3_interpretation import \
refmac_range_to_phenix_string_selection, tls
Expand Down Expand Up @@ -426,9 +428,7 @@ def ter_indices(self):
def crystal_symmetry(self,
crystal_symmetry=None,
weak_symmetry=False):
if self.hierarchy is None:
self.construct_hierarchy()
self_symmetry = self.builder.crystal_symmetry
self_symmetry = self.crystal_symmetry_from_cryst1()
if (crystal_symmetry is None):
return self_symmetry
if (self_symmetry is None):
Expand All @@ -440,7 +440,18 @@ def crystal_symmetry(self,
def crystal_symmetry_from_cryst1(self):
if self.hierarchy is None:
self.construct_hierarchy()
return self.builder.crystal_symmetry
builder_cs = self.builder.crystal_symmetry
# check for dummy one
if (builder_cs.unit_cell() is not None and
cryst1_interpretation.dummy_unit_cell(
abc = builder_cs.unit_cell().parameters()[:3],
abg = builder_cs.unit_cell().parameters()[3:],
sg_symbol=str(builder_cs.space_group_info()))):
return cctbx.crystal.symmetry(
unit_cell=None,
space_group_info=None)
return builder_cs


def extract_cryst1_z_columns(self):
return self.cif_model.values()[0].get("_cell.Z_PDB")
Expand Down
166 changes: 166 additions & 0 deletions iotbx/regression/tst_pdb_cif_cells.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,166 @@
from __future__ import absolute_import, division, print_function
import sys
from mmtbx.monomer_library import server
from mmtbx.monomer_library import pdb_interpretation
import iotbx.pdb
from iotbx.pdb.mmcif import cif_input
import inspect
import six

#
# Example from PDB ID 7c9c
#

t_pdb_str = """\
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
ATOM 1 P DT D 1 166.659 153.609 135.182 1.00 61.01 P
ATOM 2 OP1 DT D 1 166.715 152.154 135.422 1.00 61.01 O
ATOM 3 OP2 DT D 1 166.269 154.124 133.851 1.00 61.01 O
ATOM 4 O5' DT D 1 165.696 154.272 136.272 1.00 61.01 O
ATOM 5 C5' DT D 1 166.016 154.187 137.657 1.00 61.01 C
ATOM 6 C4' DT D 1 166.635 155.480 138.154 1.00 61.01 C
ATOM 7 O4' DT D 1 165.721 156.583 137.917 1.00 61.01 O
ATOM 8 C3' DT D 1 166.950 155.515 139.650 1.00 61.01 C
ATOM 9 O3' DT D 1 168.189 156.162 139.861 1.00 61.01 O
ATOM 10 C2' DT D 1 165.801 156.336 140.211 1.00 61.01 C
ATOM 11 C1' DT D 1 165.600 157.334 139.096 1.00 61.01 C
ATOM 12 N1 DT D 1 164.274 157.975 139.127 1.00 61.01 N
ATOM 13 C2 DT D 1 164.180 159.327 138.934 1.00 61.01 C
ATOM 14 O2 DT D 1 165.141 160.036 138.720 1.00 61.01 O
ATOM 15 N3 DT D 1 162.912 159.825 138.994 1.00 61.01 N
ATOM 16 C4 DT D 1 161.753 159.119 139.229 1.00 61.01 C
ATOM 17 O4 DT D 1 160.654 159.657 139.264 1.00 61.01 O
ATOM 18 C5 DT D 1 161.924 157.705 139.429 1.00 61.01 C
ATOM 19 C7 DT D 1 160.735 156.834 139.691 1.00 61.01 C
ATOM 20 C6 DT D 1 163.163 157.207 139.374 1.00 61.01 C
ATOM 21 P DT D 2 168.926 156.085 141.287 1.00 56.21 P
ATOM 22 OP1 DT D 2 170.334 155.745 141.021 1.00 56.21 O
ATOM 23 OP2 DT D 2 168.132 155.242 142.199 1.00 56.21 O
ATOM 24 O5' DT D 2 168.871 157.586 141.817 1.00 56.21 O
ATOM 25 C5' DT D 2 169.222 158.639 140.942 1.00 56.21 C
ATOM 26 C4' DT D 2 168.956 159.998 141.561 1.00 56.21 C
ATOM 27 O4' DT D 2 167.552 160.326 141.452 1.00 56.21 O
ATOM 28 C3' DT D 2 169.313 160.123 143.038 1.00 56.21 C
ATOM 29 O3' DT D 2 170.046 161.312 143.239 1.00 56.21 O
ATOM 30 C2' DT D 2 167.950 160.183 143.722 1.00 56.21 C
ATOM 31 C1' DT D 2 167.118 160.874 142.665 1.00 56.21 C
ATOM 32 N1 DT D 2 165.663 160.625 142.790 1.00 56.21 N
ATOM 33 C2 DT D 2 164.787 161.668 142.631 1.00 56.21 C
ATOM 34 O2 DT D 2 165.142 162.807 142.394 1.00 56.21 O
ATOM 35 N3 DT D 2 163.471 161.332 142.759 1.00 56.21 N
ATOM 36 C4 DT D 2 162.955 160.085 143.024 1.00 56.21 C
ATOM 37 O4 DT D 2 161.753 159.880 143.123 1.00 56.21 O
ATOM 38 C5 DT D 2 163.923 159.037 143.179 1.00 56.21 C
ATOM 39 C7 DT D 2 163.475 157.639 143.468 1.00 56.21 C
ATOM 40 C6 DT D 2 165.218 159.353 143.056 1.00 56.21 C
"""
t_cif_str = """\
data_7C9C
_cell.angle_alpha 90.00
_cell.angle_alpha_esd ?
_cell.angle_beta 90.00
_cell.angle_beta_esd ?
_cell.angle_gamma 90.00
_cell.angle_gamma_esd ?
_cell.entry_id 7C9C
_cell.details ?
_cell.formula_units_Z ?
_cell.length_a 1.00
_cell.length_a_esd ?
_cell.length_b 1.00
_cell.length_b_esd ?
_cell.length_c 1.00
_cell.length_c_esd ?
_cell.volume ?
_cell.volume_esd ?
_cell.Z_PDB ?
#
_symmetry.entry_id 7C9C
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 1
_symmetry.space_group_name_Hall ?
_symmetry.space_group_name_H-M 'P 1'
_symmetry.pdbx_full_space_group_name_H-M ?
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 1 P P . DT A 1 1 ? 166.659 153.609 135.182 1.00 61.01 ? 1 DT D P 1
ATOM 2 O OP1 . DT A 1 1 ? 166.715 152.154 135.422 1.00 61.01 ? 1 DT D OP1 1
ATOM 3 O OP2 . DT A 1 1 ? 166.269 154.124 133.851 1.00 61.01 ? 1 DT D OP2 1
ATOM 4 O "O5'" . DT A 1 1 ? 165.696 154.272 136.272 1.00 61.01 ? 1 DT D "O5'" 1
ATOM 5 C "C5'" . DT A 1 1 ? 166.016 154.187 137.657 1.00 61.01 ? 1 DT D "C5'" 1
ATOM 6 C "C4'" . DT A 1 1 ? 166.635 155.480 138.154 1.00 61.01 ? 1 DT D "C4'" 1
ATOM 7 O "O4'" . DT A 1 1 ? 165.721 156.583 137.917 1.00 61.01 ? 1 DT D "O4'" 1
ATOM 8 C "C3'" . DT A 1 1 ? 166.950 155.515 139.650 1.00 61.01 ? 1 DT D "C3'" 1
ATOM 9 O "O3'" . DT A 1 1 ? 168.189 156.162 139.861 1.00 61.01 ? 1 DT D "O3'" 1
ATOM 10 C "C2'" . DT A 1 1 ? 165.801 156.336 140.211 1.00 61.01 ? 1 DT D "C2'" 1
ATOM 11 C "C1'" . DT A 1 1 ? 165.600 157.334 139.096 1.00 61.01 ? 1 DT D "C1'" 1
ATOM 12 N N1 . DT A 1 1 ? 164.274 157.975 139.127 1.00 61.01 ? 1 DT D N1 1
ATOM 13 C C2 . DT A 1 1 ? 164.180 159.327 138.934 1.00 61.01 ? 1 DT D C2 1
ATOM 14 O O2 . DT A 1 1 ? 165.141 160.036 138.720 1.00 61.01 ? 1 DT D O2 1
ATOM 15 N N3 . DT A 1 1 ? 162.912 159.825 138.994 1.00 61.01 ? 1 DT D N3 1
ATOM 16 C C4 . DT A 1 1 ? 161.753 159.119 139.229 1.00 61.01 ? 1 DT D C4 1
ATOM 17 O O4 . DT A 1 1 ? 160.654 159.657 139.264 1.00 61.01 ? 1 DT D O4 1
ATOM 18 C C5 . DT A 1 1 ? 161.924 157.705 139.429 1.00 61.01 ? 1 DT D C5 1
ATOM 19 C C7 . DT A 1 1 ? 160.735 156.834 139.691 1.00 61.01 ? 1 DT D C7 1
ATOM 20 C C6 . DT A 1 1 ? 163.163 157.207 139.374 1.00 61.01 ? 1 DT D C6 1
ATOM 21 P P . DT A 1 2 ? 168.926 156.085 141.287 1.00 56.21 ? 2 DT D P 1
ATOM 22 O OP1 . DT A 1 2 ? 170.334 155.745 141.021 1.00 56.21 ? 2 DT D OP1 1
ATOM 23 O OP2 . DT A 1 2 ? 168.132 155.242 142.199 1.00 56.21 ? 2 DT D OP2 1
ATOM 24 O "O5'" . DT A 1 2 ? 168.871 157.586 141.817 1.00 56.21 ? 2 DT D "O5'" 1
ATOM 25 C "C5'" . DT A 1 2 ? 169.222 158.639 140.942 1.00 56.21 ? 2 DT D "C5'" 1
ATOM 26 C "C4'" . DT A 1 2 ? 168.956 159.998 141.561 1.00 56.21 ? 2 DT D "C4'" 1
ATOM 27 O "O4'" . DT A 1 2 ? 167.552 160.326 141.452 1.00 56.21 ? 2 DT D "O4'" 1
ATOM 28 C "C3'" . DT A 1 2 ? 169.313 160.123 143.038 1.00 56.21 ? 2 DT D "C3'" 1
ATOM 29 O "O3'" . DT A 1 2 ? 170.046 161.312 143.239 1.00 56.21 ? 2 DT D "O3'" 1
ATOM 30 C "C2'" . DT A 1 2 ? 167.950 160.183 143.722 1.00 56.21 ? 2 DT D "C2'" 1
ATOM 31 C "C1'" . DT A 1 2 ? 167.118 160.874 142.665 1.00 56.21 ? 2 DT D "C1'" 1
ATOM 32 N N1 . DT A 1 2 ? 165.663 160.625 142.790 1.00 56.21 ? 2 DT D N1 1
ATOM 33 C C2 . DT A 1 2 ? 164.787 161.668 142.631 1.00 56.21 ? 2 DT D C2 1
ATOM 34 O O2 . DT A 1 2 ? 165.142 162.807 142.394 1.00 56.21 ? 2 DT D O2 1
ATOM 35 N N3 . DT A 1 2 ? 163.471 161.332 142.759 1.00 56.21 ? 2 DT D N3 1
ATOM 36 C C4 . DT A 1 2 ? 162.955 160.085 143.024 1.00 56.21 ? 2 DT D C4 1
ATOM 37 O O4 . DT A 1 2 ? 161.753 159.880 143.123 1.00 56.21 ? 2 DT D O4 1
ATOM 38 C C5 . DT A 1 2 ? 163.923 159.037 143.179 1.00 56.21 ? 2 DT D C5 1
ATOM 39 C C7 . DT A 1 2 ? 163.475 157.639 143.468 1.00 56.21 ? 2 DT D C7 1
ATOM 40 C C6 . DT A 1 2 ? 165.218 159.353 143.056 1.00 56.21 ? 2 DT D C6 1
"""

def exercise():
pdb_inp = iotbx.pdb.input(lines=t_pdb_str, source_info=None)
cif_inp = iotbx.pdb.input(lines=t_cif_str, source_info=None)
pdb_cs = pdb_inp.crystal_symmetry()
cif_cs = cif_inp.crystal_symmetry()
# print(pdb_cs.unit_cell())
# print(cif_cs.unit_cell())
assert pdb_cs.unit_cell() == cif_cs.unit_cell()

if (__name__ == "__main__"):
exercise()
1 change: 1 addition & 0 deletions iotbx/run_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
"$D/regression/tst_simple_parser.py",
"$D/regression/tst_phil.py",
"$D/regression/tst_pdb_cif_inputs.py",
"$D/regression/tst_pdb_cif_cells.py",
"$D/regression/tst_data_manager.py",
"$D/regression/tst_map_manager_wrapping.py",
"$D/regression/tst_map_manager.py",
Expand Down

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