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Remove logging abstraction to facilitate debugging and reduce bloat.

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Also performed minor delinting.

Fixes #108
This commit is contained in:
Nathan Baker
2020-11-29 16:09:45 -08:00
parent 67039aabc0
commit 9350799be1
16 changed files with 436 additions and 331 deletions
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71
propka/bonds.py
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@@ -5,12 +5,14 @@ Bonds
PROPKA representation of bonds.
"""
import logging
import math
import json
import pkg_resources
import propka.calculations
# TODO - replace the info/warning imports with logging functionality
from propka.lib import info
_LOGGER = logging.getLogger(__name__)
# TODO - should these constants be defined higher up in the module?
@@ -30,8 +32,8 @@ 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] = (
@@ -53,22 +55,22 @@ class BondMaker:
'C': ['CA', 'O'], 'O': ['C']}
self.num_pi_elec_bonds_backbone = {'C': 1, 'O': 1}
self.num_pi_elec_conj_bonds_backbone = {'N': 1}
self.num_pi_elec_bonds_sidechains = {'ARG-CZ' : 1, 'ARG-NH1': 1,
'ASN-OD1': 1, 'ASN-CG' : 1,
'ASP-OD1': 1, 'ASP-CG' : 1,
'GLU-OE1': 1, 'GLU-CD' : 1,
'GLN-OE1': 1, 'GLN-CD' : 1,
'HIS-CG' : 1, 'HIS-CD2': 1,
self.num_pi_elec_bonds_sidechains = {'ARG-CZ': 1, 'ARG-NH1': 1,
'ASN-OD1': 1, 'ASN-CG': 1,
'ASP-OD1': 1, 'ASP-CG': 1,
'GLU-OE1': 1, 'GLU-CD': 1,
'GLN-OE1': 1, 'GLN-CD': 1,
'HIS-CG': 1, 'HIS-CD2': 1,
'HIS-ND1': 1, 'HIS-CE1': 1,
'PHE-CG' : 1, 'PHE-CD1': 1,
'PHE-CE1': 1, 'PHE-CZ' : 1,
'PHE-CG': 1, 'PHE-CD1': 1,
'PHE-CE1': 1, 'PHE-CZ': 1,
'PHE-CE2': 1, 'PHE-CD2': 1,
'TRP-CG' : 1, 'TRP-CD1': 1,
'TRP-CG': 1, 'TRP-CD1': 1,
'TRP-CE2': 1, 'TRP-CD2': 1,
'TRP-CE3': 1, 'TRP-CZ3': 1,
'TRP-CH2': 1, 'TRP-CZ2': 1,
'TYR-CG' : 1, 'TYR-CD1': 1,
'TYR-CE1': 1, 'TYR-CZ' : 1,
'TYR-CG': 1, 'TYR-CD1': 1,
'TYR-CE1': 1, 'TYR-CZ': 1,
'TYR-CE2': 1, 'TYR-CD2': 1}
self.num_pi_elec_conj_bonds_sidechains = {'ARG-NE': 1, 'ARG-NH2': 1,
'ASN-ND2': 1, 'GLN-NE2': 1,
@@ -90,13 +92,13 @@ class BondMaker:
Args:
protein: the protein to search for bonds
"""
info('++++ Side chains ++++')
_LOGGER.info('++++ Side chains ++++')
# side chains
for chain in protein.chains:
for residue in chain.residues:
if residue.res_name.replace(' ', '') not in ['N+', 'C-']:
self.find_bonds_for_side_chain(residue.atoms)
info('++++ Backbones ++++')
_LOGGER.info('++++ Backbones ++++')
# backbone
last_residues = []
for chain in protein.chains:
@@ -108,11 +110,11 @@ class BondMaker:
self.connect_backbone(chain.residues[i-1],
chain.residues[i])
last_residues.append(chain.residues[i])
info('++++ terminal oxygen ++++')
_LOGGER.info('++++ terminal oxygen ++++')
# terminal OXT
for last_residue in last_residues:
self.find_bonds_for_terminal_oxygen(last_residue)
info('++++ cysteines ++++')
_LOGGER.info('++++ cysteines ++++')
# Cysteines
for chain in protein.chains:
for i in range(0, len(chain.residues)):
@@ -180,7 +182,7 @@ class BondMaker:
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
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])
@@ -204,8 +206,8 @@ class BondMaker:
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])
if not atom1.name in self.backbone_atoms:
if not atom1.name in self.terminal_oxygen_names:
if atom1.name not in self.backbone_atoms:
if atom1.name not in self.terminal_oxygen_names:
for atom2 in atoms:
if atom2.name in (
self
@@ -266,7 +268,6 @@ class BondMaker:
Returns:
list of atoms
"""
#self.find_bonds_for_protein(molecule)
atoms = []
for chain in molecule.chains:
for residue in chain.residues:
@@ -424,9 +425,9 @@ class BondMaker:
"""
if atom1 == atom2:
return
if not atom1 in atom2.bonded_atoms:
if atom1 not in atom2.bonded_atoms:
atom2.bonded_atoms.append(atom1)
if not atom2 in atom1.bonded_atoms:
if atom2 not in atom1.bonded_atoms:
atom1.bonded_atoms.append(atom2)
def generate_protein_bond_dictionary(self, atoms):
@@ -441,21 +442,21 @@ class BondMaker:
name_i = atom.name
resi_j = bonded_atom.res_name
name_j = bonded_atom.name
if not name_i in (
if name_i not in (
self.backbone_atoms
or not name_j in self.backbone_atoms):
if not name_i in (
or name_j not in self.backbone_atoms):
if name_i not in (
self.terminal_oxygen_names
and not name_j in self.terminal_oxygen_names):
if not resi_i in list(self.protein_bonds.keys()):
and name_j not in self.terminal_oxygen_names):
if resi_i not in list(self.protein_bonds.keys()):
self.protein_bonds[resi_i] = {}
if not name_i in self.protein_bonds[resi_i]:
if name_i not in self.protein_bonds[resi_i]:
self.protein_bonds[resi_i][name_i] = []
if not name_j in self.protein_bonds[resi_i][name_i]:
if name_j not in self.protein_bonds[resi_i][name_i]:
self.protein_bonds[resi_i][name_i].append(name_j)
if not resi_j in list(self.protein_bonds.keys()):
if resi_j not in list(self.protein_bonds.keys()):
self.protein_bonds[resi_j] = {}
if not name_j in self.protein_bonds[resi_j]:
if name_j not in self.protein_bonds[resi_j]:
self.protein_bonds[resi_j][name_j] = []
if not name_i in self.protein_bonds[resi_j][name_j]:
if name_i not in self.protein_bonds[resi_j][name_j]:
self.protein_bonds[resi_j][name_j].append(name_i)