def getResidueID(res):
if Biomol.getChainID(res) != ' ':
return Biomol.getResidueCode(res) + '_' + str(
Biomol.getResidueSequenceNumber(res)) + '_' + Biomol.getChainID(
res)
return Biomol.getResidueCode(res) + '_' + str(
Biomol.getResidueSequenceNumber(res))
def __init__(self, lig_feature, env_feature):
ftype_names = {
Pharm.FeatureType.H_BOND_ACCEPTOR: 'HBA',
Pharm.FeatureType.H_BOND_DONOR: 'HBD',
Pharm.FeatureType.POS_IONIZABLE: 'PI',
Pharm.FeatureType.NEG_IONIZABLE: 'NI',
Pharm.FeatureType.AROMATIC: 'AR',
Pharm.FeatureType.HYDROPHOBIC: 'H',
Pharm.FeatureType.X_VOLUME: 'XV'
}
lig_feature_type = ftype_names[Pharm.getType(lig_feature)]
lig_residue_code = Biomol.getResidueCode(
Pharm.getSubstructure(lig_feature).atoms[0])
lig_residue_number = Biomol.getResidueSequenceNumber(
Pharm.getSubstructure(lig_feature).atoms[0])
lig_residue_chain = Biomol.getChainID(
Pharm.getSubstructure(lig_feature).atoms[0])
env_feature_type = ftype_names[Pharm.getType(env_feature)]
env_residue_code = Biomol.getResidueCode(
Pharm.getSubstructure(env_feature).atoms[0])
env_residue_number = Biomol.getResidueSequenceNumber(
Pharm.getSubstructure(env_feature).atoms[0])
env_residue_chain = Biomol.getChainID(
Pharm.getSubstructure(env_feature).atoms[0])
self.interaction_type = '{}-{}'.format(lig_feature_type,
env_feature_type)
self.lig_residue = '{}_{}_{}'.format(lig_residue_code,
lig_residue_number,
lig_residue_chain)
self.env_residue = '{}_{}_{}'.format(env_residue_code,
env_residue_number,
env_residue_chain)
atoms = []
for atom in Pharm.getSubstructure(lig_feature).atoms:
key_atom = '{}:{}'.format(Chem.getSymbol(atom),
Biomol.getSerialNumber(atom))
atoms.append(key_atom)
self.lig_atom = sorted(atoms, key=lambda k: int(k.split(':')[1]))
atoms = []
for atom in Pharm.getSubstructure(env_feature).atoms:
key_atom = '{}:{}'.format(Chem.getSymbol(atom),
Biomol.getSerialNumber(atom))
atoms.append(key_atom)
self.env_atom = sorted(atoms, key=lambda k: int(k.split(':')[1]))
def fixResidueSeqNumbers(mol):
curr_seq_no = 0
res_start = 0
res_end = 0
num_atoms = mol.getNumAtoms()
old_res_seq_nos = []
old_to_new_seq_no_map = {}
for atom in mol.atoms:
old_res_seq_nos.append(Biomol.getResidueSequenceNumber(atom))
while res_start < num_atoms:
while res_end < num_atoms and (old_res_seq_nos[res_start]
== old_res_seq_nos[res_end]):
res_end += 1
if not old_res_seq_nos[res_start] in old_to_new_seq_no_map:
old_to_new_seq_no_map[old_res_seq_nos[res_start]] = curr_seq_no
while res_start < res_end:
Biomol.setResidueSequenceNumber(mol.getAtom(res_start),
curr_seq_no)
res_start += 1
curr_seq_no += 1
return old_res_seq_nos, old_to_new_seq_no_map
def filterResidues(residues, res_subset):
if len(res_subset) == 0:
return
i = 0
while i < len(residues):
seq_no = Biomol.getResidueSequenceNumber(residues[i])
if seq_no in res_subset:
i += 1
continue
del residues[i]
def generate_key(ftr):
first_atom = Pharm.getSubstructure(ftr).atoms[0]
base = str(ftype_names[Pharm.getType(ftr)]) + '[' + str(
Biomol.getResidueCode(first_atom)) + '_' + str(
Biomol.getResidueSequenceNumber(first_atom)) + '_' + str(
Biomol.getChainID(first_atom))
atoms_list = []
for a in Pharm.getSubstructure(ftr).atoms:
if Biomol.hasSerialNumber(a) == False:
continue
atom_id = str(Biomol.getSerialNumber(a))
atoms_list.append(atom_id)
atom_key = ""
for k in sorted(atoms_list, key=natural_sort_key, reverse=True):
atom_key += '_' + k
key = base + atom_key + ']'
return key