def atom_match_dictionary(restraints, sane_H_mol, comp_id_list_for_names_match, dict_files_for_names_match):
template_comp_ids = ['CYS', 'ASP', 'GLU', 'HIS', 'ILE', 'LYS', 'LEU', 'MET',
'ASN', 'PRO', 'GLN', 'ARG', 'SER', 'THR', 'VAL', 'TRP', 'TYR',
'G', 'C', 'GLC', 'MAN']
if isinstance(comp_id_list_for_names_match, basestring):
template_comp_ids = comp_id_list_for_names_match.split(',')
template_cif_dict_files_names = []
if isinstance(dict_files_for_names_match, basestring):
template_cif_dict_files_names = dict_files_for_names_match.split(',')
# don't use my set of comp_ids then
template_comp_ids = []
success,new_restraints,at_name_list = pysw.match_restraints_to_dictionaries(restraints,
template_comp_ids,
template_cif_dict_files_names)
if success:
n = len(sane_H_mol.GetAtoms())
if len(restraints['_chem_comp_atom']) == n:
restraints = new_restraints
for iat in range(n):
name = sane_H_mol.GetAtomWithIdx(iat).GetProp('name')
if name != restraints['_chem_comp_atom'][iat][0]:
# print " changing name from", name, "to", restraints['_chem_comp_atom'][iat][0]
sane_H_mol.GetAtomWithIdx(iat).SetProp('name', restraints['_chem_comp_atom'][iat][0]);
return restraints
def atom_match_dictionary(restraints, sane_H_mol, comp_id_list_for_names_match, dict_files_for_names_match):
template_comp_ids = ['CYS', 'ASP', 'GLU', 'HIS', 'ILE', 'LYS', 'LEU', 'MET',
'ASN', 'PRO', 'GLN', 'ARG', 'SER', 'THR', 'VAL', 'TRP', 'TYR',
'G', 'C', 'GLC', 'MAN']
if isinstance(comp_id_list_for_names_match, basestring):
template_comp_ids = comp_id_list_for_names_match.split(',')
template_cif_dict_files_names = []
if isinstance(dict_files_for_names_match, basestring):
template_cif_dict_files_names = dict_files_for_names_match.split(',')
# don't use my set of comp_ids then
template_comp_ids = []
success,new_restraints,at_name_list = pysw.match_restraints_to_dictionaries(restraints,
template_comp_ids,
template_cif_dict_files_names)
if success:
n = len(sane_H_mol.GetAtoms())
if len(restraints['_chem_comp_atom']) == n:
restraints = new_restraints
for iat in range(n):
name = sane_H_mol.GetAtomWithIdx(iat).GetProp('name')
if name != restraints['_chem_comp_atom'][iat][0]:
# print " changing name from", name, "to", restraints['_chem_comp_atom'][iat][0]
sane_H_mol.GetAtomWithIdx(iat).SetProp('name', restraints['_chem_comp_atom'][iat][0]);
return restraints