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Remove logging abstraction to facilitate debugging and reduce bloat.
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Also performed minor delinting.

Fixes #108
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@sobolevnrm
sobolevnrm committed Nov 30, 2020
1 parent 67039aa commit 9350799
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71 changes: 36 additions & 35 deletions propka/bonds.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,12 +5,14 @@
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?
Expand All @@ -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] = (
Expand All @@ -53,22 +55,22 @@ def __init__(self):
'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,
Expand All @@ -90,13 +92,13 @@ def find_bonds_for_protein(self, protein):
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:
Expand All @@ -108,11 +110,11 @@ def find_bonds_for_protein(self, protein):
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)):
Expand Down Expand Up @@ -180,7 +182,7 @@ def find_bonds_for_residue_backbone(self, residue):
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])

Expand All @@ -204,8 +206,8 @@ def find_bonds_for_side_chain(self, atoms):
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
Expand Down Expand Up @@ -266,7 +268,6 @@ def find_bonds_for_protein_by_distance(self, molecule):
Returns:
list of atoms
"""
#self.find_bonds_for_protein(molecule)
atoms = []
for chain in molecule.chains:
for residue in chain.residues:
Expand Down Expand Up @@ -424,9 +425,9 @@ def make_bond(atom1, atom2):
"""
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):
Expand All @@ -441,21 +442,21 @@ def generate_protein_bond_dictionary(self, atoms):
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)
36 changes: 21 additions & 15 deletions propka/conformation_container.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
Container data structure for molecular conformations.
"""
import logging
import functools
import propka.ligand
from propka.output import make_interaction_map
Expand All @@ -12,11 +13,14 @@
from propka.determinants import set_backbone_determinants, set_ion_determinants
from propka.determinants import set_determinants
from propka.group import Group, is_group
from propka.lib import info


_LOGGER = logging.getLogger(__name__)


#: A large number that gets multipled with the integer obtained from applying
#: :func:`ord` to the atom chain ID. Used in calculating atom keys for sorting.
#: :func:`ord` to the atom chain ID. Used in calculating atom keys for
#: sorting.
UNICODE_MULTIPLIER = 1e7

#: A number that gets mutiplied with an atom's residue number. Used in
Expand Down Expand Up @@ -54,7 +58,8 @@ def extract_groups(self):
else:
group = atom.group
# if the atom has been checked in a another conformation, check
# if it has a group that should be used in this conformation as well
# if it has a group that should be used in this conformation
# as well
if group:
self.setup_and_add_group(group)

Expand All @@ -66,7 +71,7 @@ def additional_setup_when_reading_input_file(self):
'Covalent coupling map for {0:s}'.format(str(self)),
self.get_covalently_coupled_groups(),
lambda g1, g2: g1 in g2.covalently_coupled_groups)
info(map_)
_LOGGER.info(map_)
# check if we should set a common charge centre as well
if self.parameters.common_charge_centre:
self.set_common_charge_centres()
Expand Down Expand Up @@ -108,15 +113,16 @@ def find_covalently_coupled_groups(self):
'Covalent coupling map for {0:s}'.format(str(self)),
self.get_covalently_coupled_groups(),
lambda g1, g2: g1 in g2.covalently_coupled_groups)
info(map_)
_LOGGER.info("Coupling map:\n%s", map_)

def find_non_covalently_coupled_groups(self, verbose=False):
"""Find non-covalently coupled groups and set common charge centres.
Args:
verbose: verbose output
"""
# check if non-covalent coupling has already been set up in an input file
# check if non-covalent coupling has already been set up in an input
# file
if len(list(filter(lambda g: len(g.non_covalently_coupled_groups) > 0,
self.get_titratable_groups()))) > 0:
self.non_covalently_coupled_groups = True
Expand Down Expand Up @@ -193,7 +199,7 @@ def calculate_pka(self, version, options):
version: version object
options: option object
"""
info('\nCalculating pKas for', self)
_LOGGER.info('Calculating pKas for %s', self)
# calculate desolvation
for group in self.get_titratable_groups() + self.get_ions():
version.calculate_desolvation(group)
Expand All @@ -215,7 +221,7 @@ def calculate_pka(self, version, options):
penalised_labels = self.coupling_effects()
if (self.parameters.remove_penalised_group
and len(penalised_labels) > 0):
info('Removing penalised groups!!!')
_LOGGER.info('Removing penalised groups!!!')
for group in self.get_titratable_groups():
group.remove_determinants(penalised_labels)
# re-calculating the total pKa values
Expand Down Expand Up @@ -257,7 +263,7 @@ def coupling_effects(self):
# group with the highest pKa is allowed to titrate...
continue
group.coupled_titrating_group = first_group
#... and the rest are penalised
# ... and the rest are penalised
penalised_labels.append(group.label)
return penalised_labels

Expand All @@ -282,7 +288,7 @@ def share_determinants(groups):
max_dets[det.group] = max(det.value,
max_dets[det.group],
key=lambda v: abs(v))
# overwrite/add maximum value for each determinant
# overwrite/add maximum value for each determinant
for det_group in max_dets:
new_determinant = Determinant(det_group, max_dets[det_group])
for group in groups:
Expand Down Expand Up @@ -433,9 +439,9 @@ def get_titratable_groups(self):
def get_groups_for_calculations(self):
"""Get a list of groups that should be included in results report.
If --titrate_only option is specified, only residues that are titratable
and are in that list are included; otherwise all titratable residues
and CYS residues are included.
If --titrate_only option is specified, only residues that are
titratable and are in that list are included; otherwise all titratable
residues and CYS residues are included.
Returns:
list of groups
Expand Down Expand Up @@ -525,7 +531,7 @@ def add_atom(self, atom):
if not atom.molecular_container:
atom.molecular_container = self.molecular_container
# store chain id for bookkeeping
if not atom.chain_id in self.chains:
if atom.chain_id not in self.chains:
self.chains.append(atom.chain_id)

def copy_atom(self, atom):
Expand Down Expand Up @@ -556,7 +562,7 @@ def top_up(self, other):
"""
my_residue_labels = {a.residue_label for a in self.atoms}
for atom in other.atoms:
if not atom.residue_label in my_residue_labels:
if atom.residue_label not in my_residue_labels:
self.copy_atom(atom)

def find_group(self, group):
Expand Down
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