Partial pylint de-linting of bonds.py.
This commit is contained in:
Nathan Baker
220
propka/bonds.py
220
propka/bonds.py
@@ -1,170 +1,164 @@
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from __future__ import division
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from __future__ import print_function
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import pickle,sys,os,math,propka.calculations
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"""PROPKA representation of bonds."""
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# TODO - is pickle still used?
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import pickle
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# TODO - eliminate use of sys
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import sys
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# TODO - eliminate use of os
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import os
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import math
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import json
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import pkg_resources
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import propka.calculations
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# TODO - replace the info/warning imports with logging functionality
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from propka.lib import info, warning
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# TODO - should these constants be defined higher up in the module?
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# TODO - I don't know what some of these constants mean
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DISULFIDE_DISTANCE = 2.5
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FLUORIDE_DISTANCE = 1.7
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HYDROGEN_DISTANCE = 1.5
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DEFAULT_DISTANCE = 2.0
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class bondmaker:
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"""Makes bonds?
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TODO - the documentation for this class needs to be improved.
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"""
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def __init__(self):
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# predefined bonding distances
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self.distances = {
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'S-S':2.5,
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'F-F':1.7}
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self.distances = {'S-S' : DISULFIDE_DISTANCE, 'F-F' : FLUORIDE_DISTANCE}
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self.distances_squared = {}
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for k in self.distances.keys():
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self.distances_squared[k]=self.distances[k]*self.distances[k]
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self.H_dist = 1.5;
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self.default_dist = 2.0;
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self.H_dist_squared = self.H_dist * self.H_dist
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self.distances_squared[k] = self.distances[k] * self.distances[k]
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self.H_dist = HYDROGEN_DISTANCE
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self.default_dist = DEFAULT_DISTANCE
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self.H_dist_squared = self.H_dist * self.H_dist
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self.default_dist_squared = self.default_dist * self.default_dist
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self.max_sq_distance = max(list(self.distances_squared.values())+[self.default_dist_squared])
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distances = list(self.distances_squared.values()) + [self.default_dist_squared]
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self.max_sq_distance = max(distances)
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# protein bonding data
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self.data_file_name = pkg_resources.resource_filename(__name__, 'protein_bonds.json')
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with open(self.data_file_name,'rt') as json_file:
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with open(self.data_file_name, 'rt') as json_file:
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self.protein_bonds = json.load(json_file)
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self.intra_residue_backbone_bonds = {'N': ['CA'],
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'CA':['N','C'],
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'C': ['CA','O'],
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'O': ['C']}
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self.number_of_pi_electrons_in_bonds_in_backbone = {'C':1,
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'O':1}
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self.number_of_pi_electrons_in_conjugate_bonds_in_backbone = {'N':1}
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self.number_of_pi_electrons_in_bonds_in_sidechains = {'ARG-CZ' :1,
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'ARG-NH1':1,
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'ASN-OD1':1,
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'ASN-CG' :1,
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'ASP-OD1':1,
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'ASP-CG' :1,
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'GLU-OE1':1,
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'GLU-CD' :1,
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'GLN-OE1':1,
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'GLN-CD' :1,
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'HIS-CG' :1,
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'HIS-CD2':1,
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'HIS-ND1':1,
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'HIS-CE1':1,
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'PHE-CG' :1,
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'PHE-CD1':1,
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'PHE-CE1':1,
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'PHE-CZ' :1,
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'PHE-CE2':1,
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'PHE-CD2':1,
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'TRP-CG' :1,
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'TRP-CD1':1,
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'TRP-CE2':1,
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'TRP-CD2':1,
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'TRP-CE3':1,
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'TRP-CZ3':1,
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'TRP-CH2':1,
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'TRP-CZ2':1,
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'TYR-CG' :1,
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'TYR-CD1':1,
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'TYR-CE1':1,
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'TYR-CZ' :1,
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'TYR-CE2':1,
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'TYR-CD2':1}
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self.number_of_pi_electrons_in_conjugate_bonds_in_sidechains = {'ARG-NE' :1,
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'ARG-NH2':1,
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'ASN-ND2':1,
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'GLN-NE2':1,
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'HIS-NE2':1,
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'TRP-NE1':1}
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self.number_of_pi_electrons_in_bonds_ligands = {'C.ar':1,
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'N.pl3':0,
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'C.2':1,
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'O.2':1,
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'O.co2':1,
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'N.ar':1,
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'C.1':2,
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'N.1':2}
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self.number_of_pi_electrons_in_conjugate_bonds_in_ligands = {'N.am':1,'N.pl3':1}
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self.intra_residue_backbone_bonds = {'N': ['CA'], 'CA': ['N', 'C'],
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'C': ['CA', 'O'], 'O': ['C']}
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self.number_of_pi_electrons_in_bonds_in_backbone = {'C': 1, 'O': 1}
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self.number_of_pi_electrons_in_conjugate_bonds_in_backbone = {'N': 1}
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self.number_of_pi_electrons_in_bonds_in_sidechains = {'ARG-CZ' : 1,
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'ARG-NH1': 1,
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'ASN-OD1': 1,
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'ASN-CG' : 1,
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'ASP-OD1': 1,
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'ASP-CG' : 1,
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'GLU-OE1': 1,
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'GLU-CD' : 1,
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'GLN-OE1': 1,
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'GLN-CD' : 1,
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'HIS-CG' : 1,
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'HIS-CD2': 1,
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'HIS-ND1': 1,
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'HIS-CE1': 1,
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'PHE-CG' : 1,
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'PHE-CD1': 1,
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'PHE-CE1': 1,
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'PHE-CZ' : 1,
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'PHE-CE2': 1,
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'PHE-CD2': 1,
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'TRP-CG' : 1,
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'TRP-CD1': 1,
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'TRP-CE2': 1,
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'TRP-CD2': 1,
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'TRP-CE3': 1,
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'TRP-CZ3': 1,
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'TRP-CH2': 1,
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'TRP-CZ2': 1,
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'TYR-CG' : 1,
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'TYR-CD1': 1,
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'TYR-CE1': 1,
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'TYR-CZ' : 1,
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'TYR-CE2': 1,
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'TYR-CD2': 1}
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self.number_of_pi_electrons_in_conjugate_bonds_in_sidechains = {'ARG-NE': 1,
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'ARG-NH2': 1,
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'ASN-ND2': 1,
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'GLN-NE2': 1,
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'HIS-NE2': 1,
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'TRP-NE1': 1}
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self.number_of_pi_electrons_in_bonds_ligands = {'C.ar': 1, 'N.pl3': 0,
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'C.2': 1, 'O.2': 1,
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'O.co2': 1, 'N.ar': 1,
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'C.1': 2, 'N.1': 2}
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self.number_of_pi_electrons_in_conjugate_bonds_in_ligands = {'N.am': 1,
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'N.pl3': 1}
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self.backbone_atoms = list(self.intra_residue_backbone_bonds.keys())
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self.terminal_oxygen_names = ['OXT','O\'\'']
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return
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self.terminal_oxygen_names = ['OXT', 'O\'\'']
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def find_bonds_for_protein(self, protein):
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""" Finds bonds proteins based on the way atoms
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normally bond in proteins"""
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"""Finds bonds proteins based on the way atoms normally bond in proteins.
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Args:
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protein: the protein to search for bonds
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"""
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info('++++ Side chains ++++')
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# side chains
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for chain in protein.chains:
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for residue in chain.residues:
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if residue.resName.replace(' ','') not in ['N+','C-']:
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if residue.resName.replace(' ', '') not in ['N+', 'C-']:
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self.find_bonds_for_side_chain(residue.atoms)
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info('++++ Backbones ++++')
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# backbone
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last_residues = []
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for chain in protein.chains:
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for i in range(1,len(chain.residues)):
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if chain.residues[i-1].resName.replace(' ','') not in ['N+','C-']:
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if chain.residues[i].resName.replace(' ','') not in ['N+','C-']:
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for i in range(1, len(chain.residues)):
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if chain.residues[i-1].resName.replace(' ', '') not in ['N+', 'C-']:
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if chain.residues[i].resName.replace(' ', '') not in ['N+', 'C-']:
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self.connect_backbone(chain.residues[i-1], chain.residues[i])
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last_residues.append(chain.residues[i])
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info('++++ terminal oxygen ++++')
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# terminal OXT
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for last_residue in last_residues:
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self.find_bonds_for_terminal_oxygen(last_residue)
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info('++++ cysteines ++++')
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# Cysteines
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for chain in protein.chains:
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for i in range(0,len(chain.residues)):
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for i in range(0, len(chain.residues)):
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if chain.residues[i].resName == 'CYS':
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for j in range(0,len(chain.residues)):
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for j in range(0, len(chain.residues)):
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if chain.residues[j].resName == 'CYS' and j != i:
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self.check_for_cysteine_bonds(chain.residues[i],
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chain.residues[j])
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return
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def check_for_cysteine_bonds(self, cys1, cys2):
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"""Looks for potential bonds between two cysteines.
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Args:
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cys1: one of the cysteines to check
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cys1: one of the cysteines to check
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"""
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for atom1 in cys1.atoms:
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if atom1.name == 'SG':
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for atom2 in cys2.atoms:
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if atom2.name == 'SG':
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if propka.calculations.squared_distance(atom1,atom2) < self.SS_dist_squared:
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dist = propka.calculations.squared_distance(atom1, atom2)
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# TODO - is SS_dist_squared an attribute of this class?
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if dist < self.SS_dist_squared:
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self.make_bond(atom1, atom2)
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return
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def find_bonds_for_terminal_oxygen(self, residue):
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"""Look for bonds for terminal oxygen.
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Args:
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residue - test residue
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"""
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for atom1 in residue.atoms:
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if atom1.name in self.terminal_oxygen_names:
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for atom2 in residue.atoms:
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if atom2.name == 'C':
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self.make_bond(atom1, atom2)
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return
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# TODO - stopped here.
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def connect_backbone(self, residue1, residue2):
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""" Sets up bonds in the backbone """
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# residue 1
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