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Clean up line breaks in bonds.py.

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See https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
2020-05-25 17:18:57 -07:00
parent 4408b23448
commit 142fa5a004
1 changed files with 63 additions and 43 deletions
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106
propka/bonds.py
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@@ -24,18 +24,23 @@ class BondMaker:
""" """
def __init__(self): def __init__(self):
# predefined bonding distances # 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 = {} self.distances_squared = {}
for key in self.distances: 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 h_dist = HYDROGEN_DISTANCE
self.default_dist = DEFAULT_DISTANCE self.default_dist = DEFAULT_DISTANCE
self.h_dist_squared = h_dist * h_dist self.h_dist_squared = h_dist * h_dist
self.default_dist_squared = self.default_dist * self.default_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) self.max_sq_distance = max(distances)
# protein bonding data # 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: with open(self.data_file_name, 'rt') as json_file:
self.protein_bonds = json.load(json_file) self.protein_bonds = json.load(json_file)
self.intra_residue_backbone_bonds = {'N': ['CA'], 'CA': ['N', 'C'], self.intra_residue_backbone_bonds = {'N': ['CA'], 'CA': ['N', 'C'],
@@ -74,7 +79,7 @@ class BondMaker:
self.num_box_z = None self.num_box_z = None
def find_bonds_for_protein(self, protein): 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: Args:
protein: the protein to search for bonds protein: the protein to search for bonds
@@ -90,9 +95,12 @@ class BondMaker:
last_residues = [] last_residues = []
for chain in protein.chains: for chain in protein.chains:
for i in range(1, len(chain.residues)): for i in range(1, len(chain.residues)):
if chain.residues[i-1].res_name.replace(' ', '') not in ['N+', 'C-']: if (chain.residues[i-1].res_name.replace(' ', '')
if chain.residues[i].res_name.replace(' ', '') not in ['N+', 'C-']: not in ['N+', 'C-']):
self.connect_backbone(chain.residues[i-1], chain.residues[i]) 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]) last_residues.append(chain.residues[i])
info('++++ terminal oxygen ++++') info('++++ terminal oxygen ++++')
# terminal OXT # terminal OXT
@@ -119,7 +127,8 @@ class BondMaker:
if atom1.name == 'SG': if atom1.name == 'SG':
for atom2 in cys2.atoms: for atom2 in cys2.atoms:
if atom2.name == 'SG': 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? # TODO - is SS_dist_squared an attribute of this class?
if dist < self.SS_dist_squared: if dist < self.SS_dist_squared:
self.make_bond(atom1, atom2) self.make_bond(atom1, atom2)
@@ -149,8 +158,8 @@ class BondMaker:
if atom1.name == 'C': if atom1.name == 'C':
for atom2 in residue2.atoms: for atom2 in residue2.atoms:
if atom2.name == 'N': if atom2.name == 'N':
if propka.calculations.squared_distance(atom1, atom2) \ if (propka.calculations.squared_distance(atom1, atom2)
< self.default_dist_squared: < self.default_dist_squared):
self.make_bond(atom1, atom2) self.make_bond(atom1, atom2)
def find_bonds_for_residue_backbone(self, residue): def find_bonds_for_residue_backbone(self, residue):
@@ -161,17 +170,18 @@ class BondMaker:
""" """
for atom1 in residue.atoms: for atom1 in residue.atoms:
if atom1.name in list(self.num_pi_elec_bonds_backbone.keys()): if atom1.name in list(self.num_pi_elec_bonds_backbone.keys()):
atom1.num_pi_elec_2_3_bonds \ atom1.num_pi_elec_2_3_bonds = (
= self.num_pi_elec_bonds_backbone[atom1.name] self.num_pi_elec_bonds_backbone[atom1.name])
if atom1.name in \ if atom1.name in (
list(self.num_pi_elec_conj_bonds_backbone.keys()) \ list(self.num_pi_elec_conj_bonds_backbone.keys())
and len(atom1.bonded_atoms) > 1: # last part to avoid including N-term and len(atom1.bonded_atoms) > 1): # avoid N-term
atom1.num_pi_elec_conj_2_3_bonds \ atom1.num_pi_elec_conj_2_3_bonds = (
= self.num_pi_elec_conj_bonds_backbone[atom1.name] self.num_pi_elec_conj_bonds_backbone[atom1.name])
if atom1.name in self.backbone_atoms: if atom1.name in self.backbone_atoms:
for atom2 in residue.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) self.make_bond(atom1, atom2)
def find_bonds_for_side_chain(self, atoms): def find_bonds_for_side_chain(self, atoms):
@@ -183,16 +193,17 @@ class BondMaker:
for atom1 in atoms: for atom1 in atoms:
key = '%s-%s' % (atom1.res_name, atom1.name) key = '%s-%s' % (atom1.res_name, atom1.name)
if key in list(self.num_pi_elec_bonds_sidechains.keys()): if key in list(self.num_pi_elec_bonds_sidechains.keys()):
atom1.num_pi_elec_2_3_bonds \ atom1.num_pi_elec_2_3_bonds = (
= self.num_pi_elec_bonds_sidechains[key] self.num_pi_elec_bonds_sidechains[key])
if key in list(self.num_pi_elec_conj_bonds_sidechains.keys()): if key in list(self.num_pi_elec_conj_bonds_sidechains.keys()):
atom1.num_pi_elec_conj_2_3_bonds \ atom1.num_pi_elec_conj_2_3_bonds = (
= self.num_pi_elec_conj_bonds_sidechains[key] self.num_pi_elec_conj_bonds_sidechains[key])
if not atom1.name in self.backbone_atoms: if not atom1.name in self.backbone_atoms:
if not atom1.name in self.terminal_oxygen_names: if not atom1.name in self.terminal_oxygen_names:
for atom2 in atoms: 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) self.make_bond(atom1, atom2)
def find_bonds_for_ligand(self, ligand): def find_bonds_for_ligand(self, ligand):
@@ -216,25 +227,30 @@ class BondMaker:
# for ligands # for ligands
if atom.type == 'hetatm': if atom.type == 'hetatm':
if atom.sybyl_type in self.num_pi_elec_bonds_ligands.keys(): 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] atom.num_pi_elec_2_3_bonds = (
if atom.sybyl_type in self.num_pi_elec_conj_bonds_ligands.keys(): self.num_pi_elec_bonds_ligands[atom.sybyl_type])
atom.num_pi_elec_conj_2_3_bonds \ if atom.sybyl_type in (
= self.num_pi_elec_conj_bonds_ligands[atom.sybyl_type] 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 # for protein
if atom.type == 'atom': if atom.type == 'atom':
key = '%s-%s' % (atom.res_name, atom.name) key = '%s-%s' % (atom.res_name, atom.name)
if key in list(self.num_pi_elec_bonds_sidechains.keys()): 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()): 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()): 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] atom.num_pi_elec_2_3_bonds = (
if atom.name in list(self.num_pi_elec_conj_bonds_backbone.keys()) \ self.num_pi_elec_bonds_backbone[atom.name])
and len(atom.bonded_atoms) > 1: 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 # last part to avoid including N-term
atom.num_pi_elec_conj_2_3_bonds \ atom.num_pi_elec_conj_2_3_bonds = (
= self.num_pi_elec_conj_bonds_backbone[atom.name] self.num_pi_elec_conj_bonds_backbone[atom.name])
def find_bonds_for_protein_by_distance(self, molecule): def find_bonds_for_protein_by_distance(self, molecule):
"""Finds bonds for all atoms in the molecule. """Finds bonds for all atoms in the molecule.
@@ -302,7 +318,8 @@ class BondMaker:
molecules: list of molecules for finding bonds. molecules: list of molecules for finding bonds.
""" """
for name in molecules.conformation_names: 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): def add_pi_electron_information(self, molecules):
"""Add pi electron information to a molecule. """Add pi electron information to a molecule.
@@ -311,7 +328,8 @@ class BondMaker:
molecules: list of molecules for adding pi electron information. molecules: list of molecules for adding pi electron information.
""" """
for name in molecules.conformation_names: 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): def find_bonds_for_atoms_using_boxes(self, atoms):
"""Finds all bonds for a list of atoms. """Finds all bonds for a list of atoms.
@@ -417,10 +435,12 @@ class BondMaker:
name_i = atom.name name_i = atom.name
resi_j = bonded_atom.res_name resi_j = bonded_atom.res_name
name_j = bonded_atom.name name_j = bonded_atom.name
if not name_i in self.backbone_atoms or\ if not name_i in (
not name_j in self.backbone_atoms: self.backbone_atoms
if not name_i in self.terminal_oxygen_names and\ or not name_j in self.backbone_atoms):
not name_j in self.terminal_oxygen_names: 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()): if not resi_i in list(self.protein_bonds.keys()):
self.protein_bonds[resi_i] = {} self.protein_bonds[resi_i] = {}
if not name_i in self.protein_bonds[resi_i]: if not name_i in self.protein_bonds[resi_i]: