def to_pdb_ccd_cif_file(path, component: Component, remove_hs=True):
"""Converts structure to the PDB CIF format. Both model and ideal
coordinates are stored. In case ideal coordinates are missing, rdkit
attempts to generate 3D coordinates of the conformer.
Args:
path (str): Path to save cif file.
component (Component): Component to be exported.
remove_hs (bool, optional): Defaults to True.
"""
if not isinstance(component.ccd_cif_dict, dict):
component.ccd_cif_dict = _to_pdb_ccd_cif_dict(component)
cif_copy = copy.deepcopy(component.ccd_cif_dict)
_add_sw_info_cif(cif_copy)
_add_2d_depiction_cif(component, cif_copy)
_add_fragments_and_scaffolds_cif(component, cif_copy)
_add_rdkit_properties_cif(component, cif_copy)
_add_unichem_mapping_cif(component, cif_copy)
_add_rdkit_conformer_cif(component, cif_copy, remove_hs)
if remove_hs:
h_indices: List[int] = [
i for i, x in enumerate(cif_copy['_chem_comp_atom']['type_symbol'])
if x == "H"
]
h_names: List[str] = [
cif_copy['_chem_comp_atom']['atom_id'][i] for i in h_indices
]
hb_indices = []
for key in ('atom_id_1', 'atom_id_2'):
indices = [
i for i, k in enumerate(cif_copy['_chem_comp_bond'][key])
if k in h_names
]
hb_indices += indices
hb_indices = list(set(hb_indices))
# scrap hydrogen atoms
for key in cif_copy['_chem_comp_atom']:
cif_copy['_chem_comp_atom'][key] = ([
k for i, k in enumerate(cif_copy['_chem_comp_atom'][key])
if i not in h_indices
])
# scrap bonds to hydrogen atoms
for key in cif_copy['_chem_comp_bond']:
cif_copy['_chem_comp_bond'][key] = ([
k for i, k in enumerate(cif_copy['_chem_comp_bond'][key])
if i not in hb_indices
])
cfd = mmcif.CifFileWriter(path)
cfd.write({component.id: cif_copy})
def test_plain_cif_write(component: Component, tmpdir, rem_hs):
path = tmpdir.join(f"{component.id}.cif")
to_check = must_have_categories.copy()
component.ccd_cif_dict = None
ccd_writer.write_molecule(str(path), component, remove_hs=rem_hs)
json_obj = reader.read(path)
if component.id == "NA": # Na is an atom!
to_check.pop(2) # remove "_chem_comp_bond"
if component.id == "D3O" and rem_hs: # D3O has single heavy atom
to_check.pop(2)
assert json_obj
assert component.id in json_obj
for c in to_check:
assert c in json_obj[component.id]