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De-lint determinants.py.

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Public methods/members names were changed.  These were checked against
Google for potential impact on other packages.
This commit is contained in:
Nathan Baker
2020-05-24 08:53:51 -07:00
parent 25648327ce
commit 476ab1f276
4 changed files with 185 additions and 150 deletions
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2
propka/calculations.py
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@@ -636,7 +636,7 @@ def check_coulomb_pair(parameters, group1, group2, dist):
num_volume = group1.Nmass + group2.Nmass num_volume = group1.Nmass + group2.Nmass
do_coulomb = True do_coulomb = True
# check if both groups are titratable (ions are taken care of in # check if both groups are titratable (ions are taken care of in
# determinants::setIonDeterminants) # determinants::set_ion_determinants)
if not (group1.titratable and group2.titratable): if not (group1.titratable and group2.titratable):
do_coulomb = False do_coulomb = False
# check if the distance is not too big # check if the distance is not too big

10
propka/conformation_container.py
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@@ -4,8 +4,8 @@ import propka.ligand
from propka.output import make_interaction_map from propka.output import make_interaction_map
from propka.determinant import Determinant from propka.determinant import Determinant
from propka.coupled_groups import NCCG from propka.coupled_groups import NCCG
from propka.determinants import setBackBoneDeterminants, setIonDeterminants from propka.determinants import set_backbone_determinants, set_ion_determinants
from propka.determinants import setDeterminants from propka.determinants import set_determinants
from propka.group import Group, is_group from propka.group import Group, is_group
from propka.lib import info from propka.lib import info
@@ -190,15 +190,15 @@ class ConformationContainer:
for group in self.get_titratable_groups() + self.get_ions(): for group in self.get_titratable_groups() + self.get_ions():
version.calculate_desolvation(group) version.calculate_desolvation(group)
# calculate backbone interactions # calculate backbone interactions
setBackBoneDeterminants(self.get_titratable_groups(), set_backbone_determinants(self.get_titratable_groups(),
self.get_backbone_groups(), version) self.get_backbone_groups(), version)
# setting ion determinants # setting ion determinants
setIonDeterminants(self, version) set_ion_determinants(self, version)
# calculating the back-bone reorganization/desolvation term # calculating the back-bone reorganization/desolvation term
version.calculatebackbone_reorganization(self) version.calculatebackbone_reorganization(self)
# setting remaining non-iterative and iterative side-chain & Coulomb # setting remaining non-iterative and iterative side-chain & Coulomb
# interaction determinants # interaction determinants
setDeterminants(self.get_sidechain_groups(), version=version, set_determinants(self.get_sidechain_groups(), version=version,
options=options) options=options)
# calculating the total pKa values # calculating the total pKa values
for group in self.groups: for group in self.groups:

321
propka/determinants.py
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@@ -1,23 +1,33 @@
"""Functions to manipulate Determinant objects.
from __future__ import division TODO - it is confusing to have both `determinant.py` and `determinants.py`.
from __future__ import print_function Should these be merged?
"""
import math, time import math
import propka.iterative
import propka.iterative, propka.lib, propka.vector_algebra import propka.lib
import propka.calculations import propka.vector_algebra
from propka.calculations import squared_distance, get_smallest_distance
from propka.calculations import angle_distance_factors, hydrogen_bond_energy
from propka.determinant import Determinant from propka.determinant import Determinant
# TODO - it is confusing to have both `determinant.py` and `determinants.py`. # Cutoff for angle factor
# Should these be merged? # TODO - this constant appears elsewhere in the package.
# It should be moved to a configuration file.
FANGLE_MIN = 0.001
def setDeterminants(propka_groups, version=None, options=None): def set_determinants(propka_groups, version=None, options=None):
"""Add side-chain and coulomb determinants/perturbations to all residues.
NOTE - backbone determinants are set separately
Args:
propka_groups: groups to adjust
version: version object
options: options object
""" """
adding side-chain and coulomb determinants/perturbations to all residues - note, backbone determinants are set separately
"""
iterative_interactions = [] iterative_interactions = []
# --- NonIterative section ---# # --- NonIterative section ---#
for group1 in propka_groups: for group1 in propka_groups:
@@ -27,172 +37,198 @@ def setDeterminants(propka_groups, version=None, options=None):
# do not calculate interactions for coupled groups # do not calculate interactions for coupled groups
if group2 in group1.covalently_coupled_groups: if group2 in group1.covalently_coupled_groups:
break break
distance = propka.calculations.distance(group1, group2) distance = propka.calculations.distance(group1, group2)
if distance < version.parameters.coulomb_cutoff2: if distance < version.parameters.coulomb_cutoff2:
interaction_type = version.parameters.interaction_matrix.get_value(group1.type,group2.type) interaction_type = version.parameters.interaction_matrix.get_value(group1.type,
group2.type)
if interaction_type == 'I': if interaction_type == 'I':
propka.iterative.addtoDeterminantList(group1, group2, distance, iterative_interactions, version=version) propka.iterative.addtoDeterminantList(group1, group2,
distance,
iterative_interactions,
version=version)
elif interaction_type == 'N': elif interaction_type == 'N':
addDeterminants(group1, group2, distance, version) add_determinants(group1, group2, distance, version)
# --- Iterative section ---# # --- Iterative section ---#
propka.iterative.addDeterminants(iterative_interactions, version, options=options) propka.iterative.add_determinants(iterative_interactions, version,
options=options)
def addDeterminants(group1, group2, distance, version): def add_determinants(group1, group2, distance, version):
"""Add determinants and perturbations for distance(R1, R2) < coulomb_cutoff.
Args:
group1: first group to add
group2: second group to add
distance: distance between groups
version: version object
""" """
adding determinants/perturbations, distance(R1, R2) < coulomb_cutoff always
"""
# side-chain determinant # side-chain determinant
addSidechainDeterminants(group1, group2, version) add_sidechain_determinants(group1, group2, version)
# Coulomb determinant # Coulomb determinant
addCoulombDeterminants(group1, group2, distance, version) add_coulomb_determinants(group1, group2, distance, version)
return
def addSidechainDeterminants(group1, group2, version=None): def add_sidechain_determinants(group1, group2, version=None):
"""Add side-chain determinants and perturbations.
NOTE - res_num1 > res_num2
Args:
group1: first group to add
group2: second group to add
version: version object
""" """
adding side-chain determinants/perturbations
Note, res_num1 > res_num2
"""
hbond_interaction = version.hydrogen_bond_interaction(group1, group2) hbond_interaction = version.hydrogen_bond_interaction(group1, group2)
if hbond_interaction: if hbond_interaction:
if group1.charge == group2.charge: if group1.charge == group2.charge:
# acid pair or base pair # acid pair or base pair
if group1.model_pka < group2.model_pka: if group1.model_pka < group2.model_pka:
newDeterminant1 = Determinant(group2, -hbond_interaction) new_determinant1 = Determinant(group2, -hbond_interaction)
newDeterminant2 = Determinant(group1, hbond_interaction) new_determinant2 = Determinant(group1, hbond_interaction)
else: else:
newDeterminant1 = Determinant(group2, hbond_interaction) new_determinant1 = Determinant(group2, hbond_interaction)
newDeterminant2 = Determinant(group1, -hbond_interaction) new_determinant2 = Determinant(group1, -hbond_interaction)
else: else:
newDeterminant1 = Determinant(group2, hbond_interaction*group1.charge) new_determinant1 = Determinant(group2, hbond_interaction*group1.charge)
newDeterminant2 = Determinant(group1, hbond_interaction*group2.charge) new_determinant2 = Determinant(group1, hbond_interaction*group2.charge)
group1.determinants['sidechain'].append(new_determinant1)
group2.determinants['sidechain'].append(new_determinant2)
group1.determinants['sidechain'].append(newDeterminant1)
group2.determinants['sidechain'].append(newDeterminant2)
return def add_coulomb_determinants(group1, group2, distance, version):
"""Add non-iterative Coulomb determinants and perturbations.
def addCoulombDeterminants(group1, group2, distance, version): Args:
group1: first group to add
group2: second group to add
distance: distance between groups
version: version object
""" """
adding NonIterative Coulomb determinants/perturbations coulomb_interaction = version.electrostatic_interaction(group1, group2,
""" distance)
coulomb_interaction = version.electrostatic_interaction(group1, group2, distance)
if coulomb_interaction: if coulomb_interaction:
Q1 = group1.charge q1 = group1.charge
Q2 = group2.charge q2 = group2.charge
# assigning the Coulombic interaction # assigning the Coulombic interaction
if Q1 < 0.0 and Q2 < 0.0: if q1 < 0.0 and q2 < 0.0:
""" both are acids """ # both are acids
addCoulombAcidPair(group1, group2, coulomb_interaction) add_coulomb_acid_pair(group1, group2, coulomb_interaction)
elif Q1 > 0.0 and Q2 > 0.0: elif q1 > 0.0 and q2 > 0.0:
""" both are bases """ # both are bases
addCoulombBasePair(group1, group2, coulomb_interaction) add_coulomb_base_pair(group1, group2, coulomb_interaction)
else: else:
""" one of each """ # one of each
addCoulombIonPair(group1, group2, coulomb_interaction) add_coulomb_ion_pair(group1, group2, coulomb_interaction)
return
def addCoulombAcidPair(object1, object2, value): def add_coulomb_acid_pair(object1, object2, value):
"""Add the Coulomb interaction (an acid pair).
The higher pKa is raised.
Args:
object1: first part of pair
object2: second part of pair
value: determinant value
""" """
Adding the Coulomb interaction (an acid pair):
the higher pKa is raised
"""
if object1.model_pka > object2.model_pka: if object1.model_pka > object2.model_pka:
newDeterminant = Determinant(object2, value) new_determinant = Determinant(object2, value)
object1.determinants['coulomb'].append(newDeterminant) object1.determinants['coulomb'].append(new_determinant)
else: else:
newDeterminant = Determinant(object1, value) new_determinant = Determinant(object1, value)
object2.determinants['coulomb'].append(newDeterminant) object2.determinants['coulomb'].append(new_determinant)
def addCoulombBasePair(object1, object2, value): def add_coulomb_base_pair(object1, object2, value):
""" """Add the Coulomb interaction (a base pair).
Adding the Coulomb interaction (a base pair):
the lower pKa is lowered The lower pKa is lowered.
Args:
object1: first part of pair
object2: second part of pair
value: determinant value
""" """
if object1.model_pka < object2.model_pka: if object1.model_pka < object2.model_pka:
newDeterminant = Determinant(object2, -value) new_determinant = Determinant(object2, -value)
object1.determinants['coulomb'].append(newDeterminant) object1.determinants['coulomb'].append(new_determinant)
else: else:
newDeterminant = Determinant(object1, -value) new_determinant = Determinant(object1, -value)
object2.determinants['coulomb'].append(newDeterminant) object2.determinants['coulomb'].append(new_determinant)
def addCoulombIonPair(object1, object2, value): def add_coulomb_ion_pair(object1, object2, value):
"""Add the Coulomb interaction (an acid-base pair).
The pKa of the acid is lowered & the pKa of the base is raised.
Args:
object1: first part of pair
object2: second part of pair
value: determinant value
""" """
Adding the Coulomb interaction (an acid-base pair):
the pKa of the acid is lowered & the pKa of the base is raised
"""
# residue1 # residue1
Q1 = object1.charge q1 = object1.charge
newDeterminant = Determinant(object2, Q1*value) new_determinant = Determinant(object2, q1*value)
object1.determinants['coulomb'].append(newDeterminant) object1.determinants['coulomb'].append(new_determinant)
# residue2 # residue2
Q2 = object2.charge q2 = object2.charge
newDeterminant = Determinant(object1, Q2*value) new_determinant = Determinant(object1, q2*value)
object2.determinants['coulomb'].append(newDeterminant) object2.determinants['coulomb'].append(new_determinant)
def set_ion_determinants(conformation_container, version):
"""Add ion determinants and perturbations.
Args:
def setIonDeterminants(conformation_container, version): conformation_container: conformation to set
""" version: version object
adding ion determinants/perturbations
""" """
for titratable_group in conformation_container.get_titratable_groups(): for titratable_group in conformation_container.get_titratable_groups():
for ion_group in conformation_container.get_ions(): for ion_group in conformation_container.get_ions():
squared_distance = propka.calculations.squared_distance(titratable_group, ion_group) dist_sq = squared_distance(titratable_group, ion_group)
if squared_distance < version.parameters.coulomb_cutoff2_squared: if dist_sq < version.parameters.coulomb_cutoff2_squared:
weight = version.calculate_pair_weight(titratable_group.Nmass, ion_group.Nmass) weight = version.calculate_pair_weight(titratable_group.Nmass,
# the pKa of both acids and bases are shifted up by negative ions (and vice versa) ion_group.Nmass)
value = (-ion_group.charge) * version.calculate_coulomb_energy(math.sqrt(squared_distance), weight) # the pKa of both acids and bases are shifted up by negative
newDeterminant = Determinant(ion_group, value) # ions (and vice versa)
titratable_group.determinants['coulomb'].append(newDeterminant) value = (-ion_group.charge) \
* version.calculate_coulomb_energy(math.sqrt(dist_sq),
weight)
new_det = Determinant(ion_group, value)
titratable_group.determinants['coulomb'].append(new_det)
return
def setBackBoneDeterminants(titratable_groups, backbone_groups, version): def set_backbone_determinants(titratable_groups, backbone_groups, version):
"""Set determinants between titrable and backbone groups.
Args:
titratable_groups: list of titratable groups
backbone_groups: list of backbone groups
version: version object
"""
for titratable_group in titratable_groups: for titratable_group in titratable_groups:
titratable_group_interaction_atoms = titratable_group.interaction_atoms_for_acids titratable_group_interaction_atoms \
= titratable_group.interaction_atoms_for_acids
if not titratable_group_interaction_atoms: if not titratable_group_interaction_atoms:
continue continue
# find out which backbone groups this titratable is interacting with # find out which backbone groups this titratable is interacting with
for backbone_group in backbone_groups: for backbone_group in backbone_groups:
# find the interacting atoms # find the interacting atoms
backbone_interaction_atoms = backbone_group.get_interaction_atoms(titratable_group) backbone_interaction_atoms \
= backbone_group.get_interaction_atoms(titratable_group)
if not backbone_interaction_atoms: if not backbone_interaction_atoms:
continue continue
# find the smallest distance # find the smallest distance
[backbone_atom, distance, titratable_atom] = propka.calculations.get_smallest_distance(backbone_interaction_atoms, [backbone_atom, distance, titratable_atom] \
titratable_group_interaction_atoms) = get_smallest_distance(backbone_interaction_atoms, \
titratable_group_interaction_atoms)
# get the parameters # get the parameters
parameters = version.get_backbone_hydrogen_bond_parameters(backbone_atom, titratable_atom) parameters = version.get_backbone_hydrogen_bond_parameters(backbone_atom,
titratable_atom)
if not parameters: if not parameters:
continue continue
[dpKa_max, [cutoff1, cutoff2]] = parameters [dpka_max, [cutoff1, cutoff2]] = parameters
if distance < cutoff2: if distance < cutoff2:
# calculate angle factor # calculate angle factor
f_angle = 1.0 f_angle = 1.0
@@ -206,19 +242,20 @@ def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
# || # ||
# C # C
if backbone_group.type == 'BBC': if backbone_group.type == 'BBC':
if titratable_group.type in version.parameters.angular_dependent_sidechain_interactions: if titratable_group.type \
in version.parameters.angular_dependent_sidechain_interactions:
if titratable_atom.element == 'H': if titratable_atom.element == 'H':
heavy_atom = titratable_atom.bonded_atoms[0] heavy_atom = titratable_atom.bonded_atoms[0]
hydrogen_atom = titratable_atom hydrogen_atom = titratable_atom
[d1, f_angle, d2] = propka.calculations.angle_distance_factors(atom1=heavy_atom, [_, f_angle, _] = angle_distance_factors(atom1=heavy_atom,
atom2=hydrogen_atom, atom2=hydrogen_atom,
atom3=backbone_atom) atom3=backbone_atom)
else: else:
# Either the structure is corrupt (no hydrogen), or the heavy atom is closer to # Either the structure is corrupt (no hydrogen),
# the titratable atom than the hydrogen. In either case we set the angle factor # or the heavy atom is closer to the titratable
# to 0 # atom than the hydrogen. In either case we set the
# angle factor to 0
f_angle = 0.0 f_angle = 0.0
# for BBN groups, the hydrogen is on the backbone group # for BBN groups, the hydrogen is on the backbone group
# #
# Titra. # Titra.
@@ -229,23 +266,21 @@ def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
# / \ # / \
if backbone_group.type == 'BBN': if backbone_group.type == 'BBN':
if backbone_atom.element == 'H': if backbone_atom.element == 'H':
backbone_N = backbone_atom.bonded_atoms[0] backbone_n = backbone_atom.bonded_atoms[0]
backbone_H = backbone_atom backbone_h = backbone_atom
[d1, f_angle, d2] = propka.calculations.angle_distance_factors(atom1=titratable_atom, [_, f_angle, _] = angle_distance_factors(atom1=titratable_atom,
atom2=backbone_H, atom2=backbone_h,
atom3=backbone_N) atom3=backbone_n)
else: else:
# Either the structure is corrupt (no hydrogen), or the heavy atom is closer to # Either the structure is corrupt (no hydrogen), or the
# the titratable atom than the hydrogen. In either case we set the angle factor # heavy atom is closer to the titratable atom than the
# to 0 # hydrogen. In either case we set the angle factor to 0
f_angle = 0.0 f_angle = 0.0
if f_angle > FANGLE_MIN:
value = titratable_group.charge * hydrogen_bond_energy(distance,
if f_angle > 0.001: dpka_max,
value = titratable_group.charge * propka.calculations.hydrogen_bond_energy(distance, dpKa_max, [cutoff1,cutoff2], f_angle) [cutoff1, cutoff2],
f_angle)
newDeterminant = Determinant(backbone_group, value) new_determinant = Determinant(backbone_group, value)
titratable_group.determinants['backbone'].append(newDeterminant) titratable_group.determinants['backbone'].append(new_determinant)
return

2
propka/iterative.py
View File

@@ -166,7 +166,7 @@ def addIterativeIonPair(object1, object2, interaction, version):
object2.determinants['sidechain'].append(interaction) object2.determinants['sidechain'].append(interaction)
def addDeterminants(iterative_interactions, version, options=None): def add_determinants(iterative_interactions, version, options=None):
""" """
The iterative pKa scheme. Later it is all added in 'calculateTotalPKA' The iterative pKa scheme. Later it is all added in 'calculateTotalPKA'
""" """