Clean up line breaks in bonds.py.
See https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
106
propka/bonds.py
106
propka/bonds.py
@@ -24,18 +24,23 @@ class BondMaker:
|
||||
"""
|
||||
def __init__(self):
|
||||
# predefined bonding distances
|
||||
self.distances = {'S-S' : DISULFIDE_DISTANCE, 'F-F' : FLUORIDE_DISTANCE}
|
||||
self.distances = {'S-S' : DISULFIDE_DISTANCE,
|
||||
'F-F' : FLUORIDE_DISTANCE}
|
||||
self.distances_squared = {}
|
||||
for key in self.distances:
|
||||
self.distances_squared[key] = self.distances[key] * self.distances[key]
|
||||
self.distances_squared[key] = (
|
||||
self.distances[key] * self.distances[key])
|
||||
h_dist = HYDROGEN_DISTANCE
|
||||
self.default_dist = DEFAULT_DISTANCE
|
||||
self.h_dist_squared = h_dist * h_dist
|
||||
self.default_dist_squared = self.default_dist * self.default_dist
|
||||
distances = list(self.distances_squared.values()) + [self.default_dist_squared]
|
||||
distances = (
|
||||
list(self.distances_squared.values())
|
||||
+ [self.default_dist_squared])
|
||||
self.max_sq_distance = max(distances)
|
||||
# protein bonding data
|
||||
self.data_file_name = pkg_resources.resource_filename(__name__, 'protein_bonds.json')
|
||||
self.data_file_name = (
|
||||
pkg_resources.resource_filename(__name__, 'protein_bonds.json'))
|
||||
with open(self.data_file_name, 'rt') as json_file:
|
||||
self.protein_bonds = json.load(json_file)
|
||||
self.intra_residue_backbone_bonds = {'N': ['CA'], 'CA': ['N', 'C'],
|
||||
@@ -74,7 +79,7 @@ class BondMaker:
|
||||
self.num_box_z = None
|
||||
|
||||
def find_bonds_for_protein(self, protein):
|
||||
"""Finds bonds proteins based on the way atoms normally bond in proteins.
|
||||
"""Bonds proteins based on the way atoms normally bond.
|
||||
|
||||
Args:
|
||||
protein: the protein to search for bonds
|
||||
@@ -90,9 +95,12 @@ class BondMaker:
|
||||
last_residues = []
|
||||
for chain in protein.chains:
|
||||
for i in range(1, len(chain.residues)):
|
||||
if chain.residues[i-1].res_name.replace(' ', '') not in ['N+', 'C-']:
|
||||
if chain.residues[i].res_name.replace(' ', '') not in ['N+', 'C-']:
|
||||
self.connect_backbone(chain.residues[i-1], chain.residues[i])
|
||||
if (chain.residues[i-1].res_name.replace(' ', '')
|
||||
not in ['N+', 'C-']):
|
||||
if (chain.residues[i].res_name.replace(' ', '')
|
||||
not in ['N+', 'C-']):
|
||||
self.connect_backbone(chain.residues[i-1],
|
||||
chain.residues[i])
|
||||
last_residues.append(chain.residues[i])
|
||||
info('++++ terminal oxygen ++++')
|
||||
# terminal OXT
|
||||
@@ -119,7 +127,8 @@ class BondMaker:
|
||||
if atom1.name == 'SG':
|
||||
for atom2 in cys2.atoms:
|
||||
if atom2.name == 'SG':
|
||||
dist = propka.calculations.squared_distance(atom1, atom2)
|
||||
dist = propka.calculations.squared_distance(atom1,
|
||||
atom2)
|
||||
# TODO - is SS_dist_squared an attribute of this class?
|
||||
if dist < self.SS_dist_squared:
|
||||
self.make_bond(atom1, atom2)
|
||||
@@ -149,8 +158,8 @@ class BondMaker:
|
||||
if atom1.name == 'C':
|
||||
for atom2 in residue2.atoms:
|
||||
if atom2.name == 'N':
|
||||
if propka.calculations.squared_distance(atom1, atom2) \
|
||||
< self.default_dist_squared:
|
||||
if (propka.calculations.squared_distance(atom1, atom2)
|
||||
< self.default_dist_squared):
|
||||
self.make_bond(atom1, atom2)
|
||||
|
||||
def find_bonds_for_residue_backbone(self, residue):
|
||||
@@ -161,17 +170,18 @@ class BondMaker:
|
||||
"""
|
||||
for atom1 in residue.atoms:
|
||||
if atom1.name in list(self.num_pi_elec_bonds_backbone.keys()):
|
||||
atom1.num_pi_elec_2_3_bonds \
|
||||
= self.num_pi_elec_bonds_backbone[atom1.name]
|
||||
if atom1.name in \
|
||||
list(self.num_pi_elec_conj_bonds_backbone.keys()) \
|
||||
and len(atom1.bonded_atoms) > 1: # last part to avoid including N-term
|
||||
atom1.num_pi_elec_conj_2_3_bonds \
|
||||
= self.num_pi_elec_conj_bonds_backbone[atom1.name]
|
||||
atom1.num_pi_elec_2_3_bonds = (
|
||||
self.num_pi_elec_bonds_backbone[atom1.name])
|
||||
if atom1.name in (
|
||||
list(self.num_pi_elec_conj_bonds_backbone.keys())
|
||||
and len(atom1.bonded_atoms) > 1): # avoid N-term
|
||||
atom1.num_pi_elec_conj_2_3_bonds = (
|
||||
self.num_pi_elec_conj_bonds_backbone[atom1.name])
|
||||
|
||||
if atom1.name in self.backbone_atoms:
|
||||
for atom2 in residue.atoms:
|
||||
if atom2.name in self.intra_residue_backbone_bonds[atom1.name]:
|
||||
if atom2.name in (
|
||||
self.intra_residue_backbone_bonds[atom1.name]):
|
||||
self.make_bond(atom1, atom2)
|
||||
|
||||
def find_bonds_for_side_chain(self, atoms):
|
||||
@@ -183,16 +193,17 @@ class BondMaker:
|
||||
for atom1 in atoms:
|
||||
key = '%s-%s' % (atom1.res_name, atom1.name)
|
||||
if key in list(self.num_pi_elec_bonds_sidechains.keys()):
|
||||
atom1.num_pi_elec_2_3_bonds \
|
||||
= self.num_pi_elec_bonds_sidechains[key]
|
||||
atom1.num_pi_elec_2_3_bonds = (
|
||||
self.num_pi_elec_bonds_sidechains[key])
|
||||
if key in list(self.num_pi_elec_conj_bonds_sidechains.keys()):
|
||||
atom1.num_pi_elec_conj_2_3_bonds \
|
||||
= self.num_pi_elec_conj_bonds_sidechains[key]
|
||||
|
||||
atom1.num_pi_elec_conj_2_3_bonds = (
|
||||
self.num_pi_elec_conj_bonds_sidechains[key])
|
||||
if not atom1.name in self.backbone_atoms:
|
||||
if not atom1.name in self.terminal_oxygen_names:
|
||||
for atom2 in atoms:
|
||||
if atom2.name in self.protein_bonds[atom1.res_name][atom1.name]:
|
||||
if atom2.name in (
|
||||
self
|
||||
.protein_bonds[atom1.res_name][atom1.name]):
|
||||
self.make_bond(atom1, atom2)
|
||||
|
||||
def find_bonds_for_ligand(self, ligand):
|
||||
@@ -216,25 +227,30 @@ class BondMaker:
|
||||
# for ligands
|
||||
if atom.type == 'hetatm':
|
||||
if atom.sybyl_type in self.num_pi_elec_bonds_ligands.keys():
|
||||
atom.num_pi_elec_2_3_bonds = self.num_pi_elec_bonds_ligands[atom.sybyl_type]
|
||||
if atom.sybyl_type in self.num_pi_elec_conj_bonds_ligands.keys():
|
||||
atom.num_pi_elec_conj_2_3_bonds \
|
||||
= self.num_pi_elec_conj_bonds_ligands[atom.sybyl_type]
|
||||
atom.num_pi_elec_2_3_bonds = (
|
||||
self.num_pi_elec_bonds_ligands[atom.sybyl_type])
|
||||
if atom.sybyl_type in (
|
||||
self.num_pi_elec_conj_bonds_ligands.keys()):
|
||||
atom.num_pi_elec_conj_2_3_bonds = (
|
||||
self.num_pi_elec_conj_bonds_ligands[atom.sybyl_type])
|
||||
# for protein
|
||||
if atom.type == 'atom':
|
||||
key = '%s-%s' % (atom.res_name, atom.name)
|
||||
if key in list(self.num_pi_elec_bonds_sidechains.keys()):
|
||||
atom.num_pi_elec_2_3_bonds = self.num_pi_elec_bonds_sidechains[key]
|
||||
atom.num_pi_elec_2_3_bonds = (
|
||||
self.num_pi_elec_bonds_sidechains[key])
|
||||
if key in list(self.num_pi_elec_conj_bonds_sidechains.keys()):
|
||||
atom.num_pi_elec_conj_2_3_bonds = self.num_pi_elec_conj_bonds_sidechains[key]
|
||||
|
||||
atom.num_pi_elec_conj_2_3_bonds = (
|
||||
self.num_pi_elec_conj_bonds_sidechains[key])
|
||||
if atom.name in list(self.num_pi_elec_bonds_backbone.keys()):
|
||||
atom.num_pi_elec_2_3_bonds = self.num_pi_elec_bonds_backbone[atom.name]
|
||||
if atom.name in list(self.num_pi_elec_conj_bonds_backbone.keys()) \
|
||||
and len(atom.bonded_atoms) > 1:
|
||||
atom.num_pi_elec_2_3_bonds = (
|
||||
self.num_pi_elec_bonds_backbone[atom.name])
|
||||
if atom.name in list(
|
||||
self.num_pi_elec_conj_bonds_backbone.keys()) and (
|
||||
len(atom.bonded_atoms) > 1):
|
||||
# last part to avoid including N-term
|
||||
atom.num_pi_elec_conj_2_3_bonds \
|
||||
= self.num_pi_elec_conj_bonds_backbone[atom.name]
|
||||
atom.num_pi_elec_conj_2_3_bonds = (
|
||||
self.num_pi_elec_conj_bonds_backbone[atom.name])
|
||||
|
||||
def find_bonds_for_protein_by_distance(self, molecule):
|
||||
"""Finds bonds for all atoms in the molecule.
|
||||
@@ -302,7 +318,8 @@ class BondMaker:
|
||||
molecules: list of molecules for finding bonds.
|
||||
"""
|
||||
for name in molecules.conformation_names:
|
||||
self.find_bonds_for_atoms_using_boxes(molecules.conformations[name].atoms)
|
||||
self.find_bonds_for_atoms_using_boxes(
|
||||
molecules.conformations[name].atoms)
|
||||
|
||||
def add_pi_electron_information(self, molecules):
|
||||
"""Add pi electron information to a molecule.
|
||||
@@ -311,7 +328,8 @@ class BondMaker:
|
||||
molecules: list of molecules for adding pi electron information.
|
||||
"""
|
||||
for name in molecules.conformation_names:
|
||||
self.add_pi_electron_table_info(molecules.conformations[name].atoms)
|
||||
self.add_pi_electron_table_info(
|
||||
molecules.conformations[name].atoms)
|
||||
|
||||
def find_bonds_for_atoms_using_boxes(self, atoms):
|
||||
"""Finds all bonds for a list of atoms.
|
||||
@@ -417,10 +435,12 @@ class BondMaker:
|
||||
name_i = atom.name
|
||||
resi_j = bonded_atom.res_name
|
||||
name_j = bonded_atom.name
|
||||
if not name_i in self.backbone_atoms or\
|
||||
not name_j in self.backbone_atoms:
|
||||
if not name_i in self.terminal_oxygen_names and\
|
||||
not name_j in self.terminal_oxygen_names:
|
||||
if not name_i in (
|
||||
self.backbone_atoms
|
||||
or not name_j in self.backbone_atoms):
|
||||
if not name_i in (
|
||||
self.terminal_oxygen_names
|
||||
and not name_j in self.terminal_oxygen_names):
|
||||
if not resi_i in list(self.protein_bonds.keys()):
|
||||
self.protein_bonds[resi_i] = {}
|
||||
if not name_i in self.protein_bonds[resi_i]:
|
||||
|
||||
Reference in New Issue
Block a user