def make_restraints_from_mmcif_dict(cif_file_name_in, comp_id, mogul_dir,
output_dir, output_postfix,
quartet_planes, quartet_hydrogen_planes, use_mmff,
pdb_out_file_name, mmcif_restraints_out_file_name):
if not test_for_mogul():
return [(None, None)]
if comp_id == "TRY_ALL_COMP_IDS":
types = pysw.types_from_mmcif_dictionary(cif_file_name_in)
l = []
for r_type in types:
file_name_stub = r_type + "-" + output_postfix
if options.output_dir != ".":
file_name_stub = os.path.join(options.output_dir, file_name_stub)
pdb_out_file_name_local = file_name_stub + ".pdb"
mmcif_restraints_out_file_name_local = file_name_stub + ".cif"
#
t_mol = make_restraints_from_mmcif_dict_single(cif_file_name_in, r_type, mogul_dir,
output_postfix,
quartet_planes,
quartet_hydrogen_planes, use_mmff,
pdb_out_file_name_local,
mmcif_restraints_out_file_name_local)
l.append((t_mol, r_type))
return l
else:
# just the one
m = 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)
return [(m, comp_id)]
def make_restraints_from_mmcif_dict(cif_file_name_in, comp_id, mogul_dir,
output_dir, output_postfix,
quartet_planes, quartet_hydrogen_planes, use_mmff,
pdb_out_file_name, mmcif_restraints_out_file_name):
if not test_for_mogul():
return [(None, None)]
if comp_id == "TRY_ALL_COMP_IDS":
types = pysw.types_from_mmcif_dictionary(cif_file_name_in)
l = []
for r_type in types:
file_name_stub = r_type + "-" + output_postfix
if options.output_dir != ".":
file_name_stub = os.path.join(options.output_dir, file_name_stub)
pdb_out_file_name_local = file_name_stub + ".pdb"
mmcif_restraints_out_file_name_local = file_name_stub + ".cif"
#
t_mol = make_restraints_from_mmcif_dict_single(cif_file_name_in, r_type, mogul_dir,
output_postfix,
quartet_planes,
quartet_hydrogen_planes, use_mmff,
pdb_out_file_name_local,
mmcif_restraints_out_file_name_local)
l.append((t_mol, r_type))
return l
else:
# just the one
m = 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)
return [(m, comp_id)]
if options.show_tautomers or options.show_smiles:
# ------------------------ 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 ---------------------------------------------------
if options.show_tautomers or options.show_smiles:
# ------------------------ 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 ---------------------------------------------------
