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De-lint PROPKA #33

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merged 15 commits into from
May 23, 2020
Merged

De-lint PROPKA #33

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22d83ae
Fix some pylint issues for propka.atom.
sobolevnrm May 17, 2020
303aaae
Partial pylint de-linting of bonds.py.
sobolevnrm May 17, 2020
10efc3c
De-lint propka/atom.py
sobolevnrm May 18, 2020
747333d
Merge branch 'master' into nathan/delint
sobolevnrm May 18, 2020
51a59f9
Merge branch 'nathan/tests' into nathan/delint
sobolevnrm May 21, 2020
0131670
De-lint bonds.py
sobolevnrm May 22, 2020
76418a1
De-lint calculations.py up to difficult decision.
sobolevnrm May 22, 2020
80c8cca
Nuke some backwards-compatible PROPKA 3.0 support.
sobolevnrm May 22, 2020
5114442
Merge branch 'master' into nathan/delint
sobolevnrm May 23, 2020
98ad870
Merge branch 'master' into nathan/delint
sobolevnrm May 23, 2020
66e3e55
Add description of hybrid36.
sobolevnrm May 23, 2020
4b3dee5
Simplify bonded atom counting.
sobolevnrm May 23, 2020
69a369c
Remove suggestion for @property method.
sobolevnrm May 23, 2020
df6d849
Simplify bonded atom counting
sobolevnrm May 23, 2020
120718f
Remove property method suggestion.
sobolevnrm May 23, 2020
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538 changes: 281 additions & 257 deletions propka/atom.py
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554 changes: 250 additions & 304 deletions propka/bonds.py
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123 changes: 39 additions & 84 deletions propka/calculations.py
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Original file line number Diff line number Diff line change
@@ -1,97 +1,52 @@

from __future__ import division
from __future__ import print_function

import math, propka.protonate, propka.bonds,copy, sys
"""PROPKA calculations."""
import math
import copy
import sys
import propka.protonate
import propka.bonds
from propka.lib import info, warning


#
# methods for setting up atom naming, bonding, and protonation
#

def setup_bonding_and_protonation(parameters, molecular_container):
"""Set up bonding and protonation for a molecule.

Args:
molecular_container: molecule container.
"""
# make bonds
my_bond_maker = setup_bonding(parameters, molecular_container)

# set up ligand atom names
set_ligand_atom_names(molecular_container)

# apply information on pi electrons
my_bond_maker.add_pi_electron_information(molecular_container)

# Protonate atoms
if molecular_container.options.protonate_all:
my_protonator = propka.protonate.Protonate(verbose=False)
my_protonator.protonate(molecular_container)


return



def setup_bonding(parameters, molecular_container):
# make bonds
my_bond_maker = propka.bonds.bondmaker()
my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)
"""Set up bonding for a molecular container.

Args:
molecular_container: the molecular container in question
Returns:
BondMaker object
"""
my_bond_maker = propka.bonds.BondMaker()
my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)
return my_bond_maker


def set_ligand_atom_names(molecular_container):
for name in molecular_container.conformation_names:
molecular_container.conformations[name].set_ligand_atom_names()
return



#
# The following methods imitates propka3.0 protonation!
#
def setup_bonding_and_protonation_30_style(parameters, molecular_container):
# Protonate atoms
protonate_30_style(molecular_container)
"""Set names for ligands in molecular container.

# make bonds
my_bond_maker = propka.bonds.bondmaker()
my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)

return


def protonate_30_style(molecular_container):
Args:
molecular_container: molecular container for ligand names
"""
for name in molecular_container.conformation_names:
info('Now protonating', name)
# split atom into residues
curres = -1000000
residue = []
O=None
C=None
for atom in molecular_container.conformations[name].atoms:
if atom.resNumb != curres:
curres = atom.resNumb
if len(residue)>0:
#backbone
[O, C]= addBackBoneHydrogen(residue,O,C)
#arginine
if residue[0].resName == 'ARG':
addArgHydrogen(residue)
#histidine
if residue[0].resName == 'HIS':
addHisHydrogen(residue)
#tryptophan
if residue[0].resName == 'TRP':
addTrpHydrogen(residue)
#amides
if residue[0].resName in ['GLN','ASN']:
addAmdHydrogen(residue)


residue = []
if atom.type=='atom':
residue.append(atom)
molecular_container.conformations[name].set_ligand_atom_names()

return

def addArgHydrogen(residue):
"""
Expand Down Expand Up @@ -159,7 +114,7 @@ def addTrpHydrogen(residue):
elif atom.name == "CE2":
CE = atom
if CD == None or NE == None or CE == None:
str = "Did not find all atoms in %s%4d - in %s" % (self.resName, self.resNumb, "addTrpHydrogen()")
str = "Did not find all atoms in %s%4d - in %s" % (self.res_name, self.res_num, "addTrpHydrogen()")
info(str)
sys.exit(0)

Expand All @@ -176,15 +131,15 @@ def addAmdHydrogen(residue):
O = None
N = None
for atom in residue:
if (atom.resName == "GLN" and atom.name == "CD") or (atom.resName == "ASN" and atom.name == "CG"):
if (atom.res_name == "GLN" and atom.name == "CD") or (atom.res_name == "ASN" and atom.name == "CG"):
C = atom
elif (atom.resName == "GLN" and atom.name == "OE1") or (atom.resName == "ASN" and atom.name == "OD1"):
elif (atom.res_name == "GLN" and atom.name == "OE1") or (atom.res_name == "ASN" and atom.name == "OD1"):
O = atom
elif (atom.resName == "GLN" and atom.name == "NE2") or (atom.resName == "ASN" and atom.name == "ND2"):
elif (atom.res_name == "GLN" and atom.name == "NE2") or (atom.res_name == "ASN" and atom.name == "ND2"):
N = atom

if C == None or O == None or N == None:
str = "Did not find N, C and/or O in %s%4d - in %s" % (atom.resName, atom.resNumb, "addAmdHydrogen()")
str = "Did not find N, C and/or O in %s%4d - in %s" % (atom.res_name, atom.res_num, "addAmdHydrogen()")
info(str)
sys.exit(0)

Expand Down Expand Up @@ -222,7 +177,7 @@ def addBackBoneHydrogen(residue, O, C):
return [new_O,new_C]


if N.resName == "PRO":
if N.res_name == "PRO":
""" PRO doesn't have an H-atom; do nothing """
else:
H = protonateDirection([N, O, C])
Expand Down Expand Up @@ -311,11 +266,11 @@ def protonateSP2(list):
def make_new_H(atom, x,y,z):

new_H = propka.atom.Atom()
new_H.setProperty(numb = None,
new_H.set_property(numb = None,
name = 'H%s'%atom.name[1:],
resName = atom.resName,
chainID = atom.chainID,
resNumb = atom.resNumb,
res_name = atom.res_name,
chain_id = atom.chain_id,
res_num = atom.res_num,
x = x,
y = y,
z = z,
Expand All @@ -329,7 +284,7 @@ def make_new_H(atom, x,y,z):
new_H.steric_number = 0
new_H.number_of_lone_pairs = 0
new_H.number_of_protons_to_add = 0
new_H.number_of_pi_electrons_in_double_and_triple_bonds = 0
new_H.num_pi_elec_2_3_bonds = 0

atom.bonded_atoms.append(new_H)
atom.conformation_container.add_atom(new_H)
Expand Down Expand Up @@ -357,7 +312,7 @@ def radial_volume_desolvation(parameters, group):

for atom in all_atoms:
# ignore atoms in the same residue
if atom.resNumb == group.atom.resNumb and atom.chainID == group.atom.chainID:
if atom.res_num == group.atom.res_num and atom.chain_id == group.atom.chain_id:
continue

sq_dist = squared_distance(group, atom)
Expand Down Expand Up @@ -409,15 +364,15 @@ def contactDesolvation(parameters, group):
'N+': 4.5}

all_atoms = group.atom.conformation_container.get_non_hydrogen_atoms()
if residue.resName in version.desolvationRadii:
local_cutoff = version.desolvationRadii[residue.resName]
if residue.res_name in version.desolvationRadii:
local_cutoff = version.desolvationRadii[residue.res_name]
else:
local_cutoff = 0.00
residue.Nmass = 0
residue.Nlocl = 0

for atom in all_atoms:
if atom.resNumb != group.atom.resNumb or atom.chainID != group.atom.chainID:
if atom.res_num != group.atom.res_num or atom.chain_id != group.atom.chain_id:
dX = atom.x - residue.x
dY = atom.y - residue.y
dZ = atom.z - residue.z
Expand Down
14 changes: 7 additions & 7 deletions propka/conformation_container.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@ def init_group(self, group):
titrate_only = self.molecular_container.options.titrate_only
if titrate_only is not None:
at = group.atom
if not (at.chainID, at.resNumb, at.icode) in titrate_only:
if not (at.chain_id, at.res_num, at.icode) in titrate_only:
group.titratable = False
if group.residue_type == 'CYS':
group.exclude_cys_from_results = True
Expand Down Expand Up @@ -376,7 +376,7 @@ def get_heavy_ligand_atoms(self):
return [atom for atom in self.atoms if atom.type=='hetatm' and atom.element != 'H']

def get_chain(self,chain):
return [atom for atom in self.atoms if atom.chainID != chain]
return [atom for atom in self.atoms if atom.chain_id != chain]


def add_atom(self, atom):
Expand All @@ -388,13 +388,13 @@ def add_atom(self, atom):
atom.molecular_container = self.molecular_container

# store chain id for bookkeeping
if not atom.chainID in self.chains:
self.chains.append(atom.chainID)
if not atom.chain_id in self.chains:
self.chains.append(atom.chain_id)

return

def copy_atom(self, atom):
new_atom = atom.makeCopy()
new_atom = atom.make_copy()
self.atoms.append(new_atom)
new_atom.conformation_container = self

Expand Down Expand Up @@ -443,8 +443,8 @@ def sort_atoms(self):
return

def sort_atoms_key(self, atom):
key = ord(atom.chainID)*1e7
key += atom.resNumb*1000
key = ord(atom.chain_id)*1e7
key += atom.res_num*1000
if len(atom.name) > len(atom.element):
key += ord(atom.name[len(atom.element)])
#info(atom,ord(atom.name[len(atom.element)]), '|%s||%s|'%(atom.name,atom.element))
Expand Down
2 changes: 1 addition & 1 deletion propka/determinants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ def addDeterminants(group1, group2, distance, version):
def addSidechainDeterminants(group1, group2, version=None):
"""
adding side-chain determinants/perturbations
Note, resNumb1 > resNumb2
Note, res_num1 > res_num2
"""

hbond_interaction = version.hydrogen_bond_interaction(group1, group2)
Expand Down
26 changes: 13 additions & 13 deletions propka/group.py
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Expand Up @@ -111,22 +111,22 @@ def __init__(self, atom):
self.common_charge_centre = False


self.residue_type = self.atom.resName
self.residue_type = self.atom.res_name
if self.atom.terminal:
self.residue_type = self.atom.terminal

if self.atom.type=='atom':
self.label = '%-3s%4d%2s'%(self.residue_type, atom.resNumb, atom.chainID)
elif self.atom.resName in ['DA ','DC ','DG ','DT ']:
self.label = '%-3s%4d%2s'%(self.residue_type, atom.res_num, atom.chain_id)
elif self.atom.res_name in ['DA ','DC ','DG ','DT ']:
self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1],
atom.element,
atom.name.replace('\'','')[-1],
atom.resNumb,
atom.chainID)
atom.res_num,
atom.chain_id)

# self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1], atom.element,atom.name[-1], atom.resNumb, atom.chainID)
# self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1], atom.element,atom.name[-1], atom.res_num, atom.chain_id)
else:
self.label = '%-3s%4s%2s'%(self.residue_type, atom.name, atom.chainID)
self.label = '%-3s%4s%2s'%(self.residue_type, atom.name, atom.chain_id)


# container for squared distances
Expand Down Expand Up @@ -253,7 +253,7 @@ def __eq__(self, other):
return self.label==other.label
else:
# For heterogene atoms we also need to check the residue number
return self.label==other.label and self.atom.resNumb == other.atom.resNumb
return self.label==other.label and self.atom.res_num == other.atom.res_num

def __hash__(self):
""" Needed together with __eq__ - otherwise we can't make sets of groups """
Expand Down Expand Up @@ -361,7 +361,7 @@ def setup(self):
if not self.model_pka_set:
self.model_pka = self.parameters.model_pkas[self.residue_type]
# check if we should apply a custom model pka
key = '%s-%s'%(self.atom.resName.strip(), self.atom.name.strip())
key = '%s-%s'%(self.atom.res_name.strip(), self.atom.name.strip())
if key in self.parameters.custom_model_pkas.keys():
self.model_pka = self.parameters.custom_model_pkas[key]

Expand Down Expand Up @@ -1122,7 +1122,7 @@ class Ion_group(Group):
def __init__(self, atom):
Group.__init__(self,atom)
self.type = 'ION'
self.residue_type = atom.resName.strip()
self.residue_type = atom.res_name.strip()
info('Found ion group:', atom)
return

Expand Down Expand Up @@ -1201,15 +1201,15 @@ def is_protein_group(parameters,atom):
### Backbone
if atom.type == 'atom' and atom.name == 'N':
# ignore proline backbone nitrogens
if atom.resName != 'PRO':
if atom.res_name != 'PRO':
return BBN_group(atom)
if atom.type == 'atom' and atom.name == 'C':
# ignore C- carboxyl
if atom.count_bonded_elements('O') == 1:
return BBC_group(atom)

### Filters for side chains based on PDB protein atom names
key = '%s-%s'%(atom.resName, atom.name)
key = '%s-%s'%(atom.res_name, atom.name)

if key in parameters.protein_group_mapping.keys():
return eval('%s_group(atom)'%parameters.protein_group_mapping[key])
Expand Down Expand Up @@ -1342,7 +1342,7 @@ def is_ligand_group_by_marvin_pkas(parameters, atom):

def is_ion_group(parameters, atom):

if atom.resName.strip() in parameters.ions.keys():
if atom.res_name.strip() in parameters.ions.keys():
return Ion_group(atom)

return None
12 changes: 6 additions & 6 deletions propka/iterative.py
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Expand Up @@ -124,9 +124,9 @@ def addIterativeIonPair(object1, object2, interaction, version):
Q2 = object2.Q
comp1 = object1.pKa_old + annihilation[0] + Q1*coulomb_value
comp2 = object2.pKa_old + annihilation[1] + Q2*coulomb_value
if object1.resName not in version.parameters.exclude_sidechain_interactions:
if object1.res_name not in version.parameters.exclude_sidechain_interactions:
comp1 += Q1*hbond_value
if object2.resName not in version.parameters.exclude_sidechain_interactions:
if object2.res_name not in version.parameters.exclude_sidechain_interactions:
comp2 += Q2*hbond_value

if Q1 == -1.0 and comp1 < comp2:
Expand Down Expand Up @@ -155,12 +155,12 @@ def addIterativeIonPair(object1, object2, interaction, version):
# Side-chain
if hbond_value > 0.005:
# residue1
if object1.resName not in version.parameters.exclude_sidechain_interactions:
if object1.res_name not in version.parameters.exclude_sidechain_interactions:
interaction = [object2, Q1*hbond_value]
annihilation[0] += -Q1*hbond_value
object1.determinants['sidechain'].append(interaction)
# residue2
if object2.resName not in version.parameters.exclude_sidechain_interactions:
if object2.res_name not in version.parameters.exclude_sidechain_interactions:
interaction = [object1, Q2*hbond_value]
annihilation[1] += -Q2*hbond_value
object2.determinants['sidechain'].append(interaction)
Expand Down Expand Up @@ -309,7 +309,7 @@ def __init__(self, group):

self.label = group.label
self.atom = group.atom
self.resName = group.residue_type
self.res_name = group.residue_type
self.Q = group.charge
self.pKa_old = None
self.pKa_new = None
Expand Down Expand Up @@ -357,7 +357,7 @@ def __eq__(self, other):
return self.label==other.label
else:
# For heterogene atoms we also need to check the residue number
return self.label==other.label and self.atom.resNumb == other.atom.resNumb
return self.label==other.label and self.atom.res_num == other.atom.res_num

def __hash__(self):
""" Needed together with __eq__ - otherwise we can't make sets of groups """
Expand Down
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