def make_restraints_from_mmcif_dict_single(cif_file_name_in, comp_id,
mogul_dir, output_postfix,
quartet_planes,
quartet_hydrogen_planes, use_mmff,
pdb_out_file_name,
mmcif_restraints_out_file_name):
# print 'in make_restraints_from_mmcif_dict_single() comp_id is ', comp_id
# print 'in make_restraints_from_mmcif_dict_single() cif_file_name_in is ', cif_file_name_in
if not test_for_mogul():
return [(None, None)]
mogul_file_name_stub = comp_id + '-' + output_postfix # file component of files within mogul_dir
m = pyrogen_boost.rdkit_mol_chem_comp_pdbx(cif_file_name_in, comp_id)
if False: # debugging
for atom in m.GetAtoms():
try:
name = atom.GetProp('name')
chir = atom.GetProp('_CIPCode')
print ' atom', atom, 'name', name, 'chir', chir
except KeyError as e:
print 'pyrogen.py:: atom', atom, " with name ", name, ' has no _CIPCode property'
pass
# maybe user didn't select the correct comp_id for the given dictionary mmcif
if m.GetNumAtoms() == 0:
print 'No atoms for comp_id', comp_id
return False
else:
name = ''
try:
name = m.GetProp('_Name')
except KeyError:
print 'caught KeyError in make_restraints_from_mmcif_dict_single() trying GetProp _Name'
return make_restraints(m, comp_id, mogul_dir, mogul_file_name_stub,
pdb_out_file_name,
mmcif_restraints_out_file_name, quartet_planes,
quartet_hydrogen_planes, use_mmff, False, False,
False)
def make_restraints_from_mmcif_dict_single(cif_file_name_in, comp_id, mogul_dir, output_postfix,
quartet_planes, quartet_hydrogen_planes, use_mmff,
pdb_out_file_name, mmcif_restraints_out_file_name):
# print 'in make_restraints_from_mmcif_dict_single() comp_id is ', comp_id
# print 'in make_restraints_from_mmcif_dict_single() cif_file_name_in is ', cif_file_name_in
if not test_for_mogul():
return [(None, None)]
mogul_file_name_stub = comp_id + '-' + output_postfix # file component of files within mogul_dir
m = pyrogen_boost.rdkit_mol_chem_comp_pdbx(cif_file_name_in, comp_id)
if False: # debugging
for atom in m.GetAtoms():
try:
name = atom.GetProp('name')
chir = atom.GetProp('_CIPCode')
print ' atom', atom, 'name', name, 'chir', chir
except KeyError as e:
print 'pyrogen.py:: atom', atom, " with name ", name, ' has no _CIPCode property'
pass
# maybe user didn't select the correct comp_id for the given dictionary mmcif
if m.GetNumAtoms() == 0:
print 'No atoms for comp_id', comp_id
return False
else :
name = ''
try:
name = m.GetProp('_Name')
except KeyError:
print 'caught KeyError in make_restraints_from_mmcif_dict_single() trying GetProp _Name'
return make_restraints(m, comp_id, mogul_dir, mogul_file_name_stub,
pdb_out_file_name, mmcif_restraints_out_file_name,
quartet_planes, quartet_hydrogen_planes, use_mmff, False, False, False)
# ------------------------ Tautomers and SMILES ---------------------------------------------
mol = False
if len(args) > 0:
smi_raw = args[0]
smiles,compound_name = smiles_and_name_from(smi_raw)
mol = Chem.MolFromSmiles(smiles)
else:
if options.sdf_file != None:
mol = Chem.MolFromMolFile(options.sdf_file)
else:
if options.mmcif_file_name != None:
types = pysw.types_from_mmcif_dictionary(options.mmcif_file_name)
print '-- tautomer mode: mmcif file types:', types
for type in types:
mol_local = pyrogen_boost.rdkit_mol_chem_comp_pdbx(options.mmcif_file_name, type)
score_and_print_tautomers(mol_local, type, options.output_postfix, options.drawing)
if mol:
if options.show_tautomers:
score_and_print_tautomers(mol, comp_id, options.output_postfix, options.drawing)
if options.show_smiles:
s = Chem.MolToSmiles(mol);
print s
else:
# ------------------------ dict-build-mode ---------------------------------------------------
mmcif_file_name = options.mmcif_file_name
# shall we go get the dictionary?
# ------------------------ Tautomers and SMILES ---------------------------------------------
mol = False
if len(args) > 0:
smi_raw = args[0]
smiles,compound_name = smiles_and_name_from(smi_raw)
mol = Chem.MolFromSmiles(smiles)
else:
if options.sdf_file != None:
mol = Chem.MolFromMolFile(options.sdf_file)
else:
if options.mmcif_file_name != None:
types = pysw.types_from_mmcif_dictionary(options.mmcif_file_name)
print '-- tautomer mode: mmcif file types:', types
for type in types:
mol_local = pyrogen_boost.rdkit_mol_chem_comp_pdbx(options.mmcif_file_name, type)
score_and_print_tautomers(mol_local, type, options.output_postfix, options.drawing)
if mol:
if options.show_tautomers:
score_and_print_tautomers(mol, comp_id, options.output_postfix, options.drawing)
if options.show_smiles:
s = Chem.MolToSmiles(mol);
print s
else:
# ------------------------ dict-build-mode ---------------------------------------------------
mmcif_file_name = options.mmcif_file_name
# shall we go get the dictionary?
