def addCoulombBasePair(object1, object2, value):
"""
Adding the Coulomb interaction (a base pair):
the lower pKa is lowered
"""
if object1.model_pka < object2.model_pka:
newDeterminant = Determinant(object2, -value)
object1.determinants['coulomb'].append(newDeterminant)
else:
newDeterminant = Determinant(object1, -value)
object2.determinants['coulomb'].append(newDeterminant)
def addCoulombAcidPair(object1, object2, value):
"""
Adding the Coulomb interaction (an acid pair):
the higher pKa is raised
"""
if object1.model_pka > object2.model_pka:
newDeterminant = Determinant(object2, value)
object1.determinants['coulomb'].append(newDeterminant)
else:
newDeterminant = Determinant(object1, value)
object2.determinants['coulomb'].append(newDeterminant)
def addCoulombIonPair(object1, object2, value):
"""
Adding the Coulomb interaction (an acid-base pair):
the pKa of the acid is lowered & the pKa of the base is raised
"""
# residue1
Q1 = object1.charge
newDeterminant = Determinant(object2, Q1 * value)
object1.determinants['coulomb'].append(newDeterminant)
# residue2
Q2 = object2.charge
newDeterminant = Determinant(object1, Q2 * value)
object2.determinants['coulomb'].append(newDeterminant)
def share_determinants(groups):
"""Share sidechain, backbone, and Coloumb determinants between groups.
Args:
groups: groups to share between
"""
# make a list of the determinants to share
types = ['sidechain', 'backbone', 'coulomb']
for type_ in types:
# find maximum value for each determinant
max_dets = {}
for group in groups:
for det in group.determinants[type_]:
# update max dets
if det.group not in max_dets.keys():
max_dets[det.group] = det.value
else:
max_dets[det.group] = max(det.value,
max_dets[det.group],
key=lambda v: abs(v))
# 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:
group.set_determinant(new_determinant, type_)
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
"""
if object1.model_pka > object2.model_pka:
new_determinant = Determinant(object2, value)
object1.determinants['coulomb'].append(new_determinant)
else:
new_determinant = Determinant(object1, value)
object2.determinants['coulomb'].append(new_determinant)
def add_coulomb_base_pair(object1, object2, value):
"""Add the Coulomb interaction (a base pair).
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:
new_determinant = Determinant(object2, -value)
object1.determinants['coulomb'].append(new_determinant)
else:
new_determinant = Determinant(object1, -value)
object2.determinants['coulomb'].append(new_determinant)
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
"""
# residue1
q1 = object1.charge
new_determinant = Determinant(object2, q1 * value)
object1.determinants['coulomb'].append(new_determinant)
# residue2
q2 = object2.charge
new_determinant = Determinant(object1, q2 * value)
object2.determinants['coulomb'].append(new_determinant)
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
"""
hbond_interaction = version.hydrogen_bond_interaction(group1, group2)
if hbond_interaction:
if group1.charge == group2.charge:
# acid pair or base pair
if group1.model_pka < group2.model_pka:
new_determinant1 = Determinant(group2, -hbond_interaction)
new_determinant2 = Determinant(group1, hbond_interaction)
else:
new_determinant1 = Determinant(group2, hbond_interaction)
new_determinant2 = Determinant(group1, -hbond_interaction)
else:
new_determinant1 = Determinant(group2,
hbond_interaction * group1.charge)
new_determinant2 = Determinant(group1,
hbond_interaction * group2.charge)
group1.determinants['sidechain'].append(new_determinant1)
group2.determinants['sidechain'].append(new_determinant2)
def addSidechainDeterminants(group1, group2, version=None):
"""
adding side-chain determinants/perturbations
Note, resNumb1 > resNumb2
"""
hbond_interaction = version.hydrogen_bond_interaction(group1, group2)
if hbond_interaction:
if group1.charge == group2.charge:
# acid pair or base pair
if group1.model_pka < group2.model_pka:
newDeterminant1 = Determinant(group2, -hbond_interaction)
newDeterminant2 = Determinant(group1, hbond_interaction)
else:
newDeterminant1 = Determinant(group2, hbond_interaction)
newDeterminant2 = Determinant(group1, -hbond_interaction)
else:
newDeterminant1 = Determinant(group2,
hbond_interaction * group1.charge)
newDeterminant2 = Determinant(group1,
hbond_interaction * group2.charge)
group1.determinants['sidechain'].append(newDeterminant1)
group2.determinants['sidechain'].append(newDeterminant2)
return
def set_determinant(self, new_determinant, type_):
"""Overwrite current and create non-present determinants.
Args:
new_determinant: new determinant to add
type_: determinant type
"""
# first check if we already have a determinant with this label
for own_determinant in self.determinants[type_]:
if own_determinant.group == new_determinant.group:
# if so, overwrite the value
own_determinant.value = new_determinant.value
return
# otherwise we just add the determinant to our list
self.determinants[type_].append(
Determinant(new_determinant.group, new_determinant.value))
def setIonDeterminants(conformation_container, version):
"""
adding ion determinants/perturbations
"""
for titratable_group in conformation_container.get_titratable_groups():
for ion_group in conformation_container.get_ions():
squared_distance = propka.calculations.squared_distance(
titratable_group, ion_group)
if squared_distance < version.parameters.coulomb_cutoff2_squared:
weight = version.calculatePairWeight(titratable_group.Nmass,
ion_group.Nmass)
# the pKa of both acids and bases are shifted up by negative ions (and vice versa)
value = (-ion_group.charge) * version.calculateCoulombEnergy(
math.sqrt(squared_distance), weight)
newDeterminant = Determinant(ion_group, value)
titratable_group.determinants['coulomb'].append(newDeterminant)
return
def set_ion_determinants(conformation_container, version):
"""Add ion determinants and perturbations.
Args:
conformation_container: conformation to set
version: version object
"""
for titratable_group in conformation_container.get_titratable_groups():
for ion_group in conformation_container.get_ions():
dist_sq = squared_distance(titratable_group, ion_group)
if dist_sq < version.parameters.coulomb_cutoff2_squared:
weight = version.calculate_pair_weight(
titratable_group.num_volume, ion_group.num_volume)
# the pKa of both acids and bases are shifted up by negative
# ions (and vice versa)
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)
def share_determinant(self, new_determinant, type_):
"""Add determinant to this group's list of determinants.
Args:
new_determinant: determinant to add
type_: type of determinant
"""
added = False
# first check if we already have a determinant with this label
for own_determinant in self.determinants[type_]:
if own_determinant.group == new_determinant.group:
# if so, find the average value
avr = 0.5 * (own_determinant.value + new_determinant.value)
own_determinant.value = avr
new_determinant.value = avr
added = True
# otherwise we just add the determinant to our list
if not added:
self.determinants[type_].append(
Determinant(new_determinant.group, new_determinant.value))
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:
titratable_group_interaction_atoms = (
titratable_group.interaction_atoms_for_acids)
if not titratable_group_interaction_atoms:
continue
# find out which backbone groups this titratable is interacting with
for backbone_group in backbone_groups:
# find the interacting atoms
backbone_interaction_atoms = (
backbone_group.get_interaction_atoms(titratable_group))
if not backbone_interaction_atoms:
continue
# find the smallest distance
[backbone_atom, distance, titratable_atom
] = (get_smallest_distance(backbone_interaction_atoms,
titratable_group_interaction_atoms))
# get the parameters
parameters = (version.get_backbone_hydrogen_bond_parameters(
backbone_atom, titratable_atom))
if not parameters:
continue
[dpka_max, [cutoff1, cutoff2]] = parameters
if distance < cutoff2:
# calculate angle factor
f_angle = 1.0
# for BBC groups, the hydrogen is on the titratable group
#
# Titra.
# /
# H
# .
# O
# ||
# C
if backbone_group.type == 'BBC':
if (titratable_group.type in version.parameters.
angular_dependent_sidechain_interactions):
if titratable_atom.element == 'H':
heavy_atom = titratable_atom.bonded_atoms[0]
hydrogen_atom = titratable_atom
[_, f_angle,
_] = angle_distance_factors(atom1=heavy_atom,
atom2=hydrogen_atom,
atom3=backbone_atom)
else:
# Either the structure is corrupt (no hydrogen),
# or the heavy atom is closer to the titratable
# atom than the hydrogen. In either case we set the
# angle factor to 0
f_angle = 0.0
# for BBN groups, the hydrogen is on the backbone group
#
# Titra.
# .
# H
# |
# N
# / \
if backbone_group.type == 'BBN':
if backbone_atom.element == 'H':
backbone_n = backbone_atom.bonded_atoms[0]
backbone_h = backbone_atom
[_, f_angle,
_] = (angle_distance_factors(atom1=titratable_atom,
atom2=backbone_h,
atom3=backbone_n))
else:
# Either the structure is corrupt (no hydrogen), or the
# heavy atom is closer to the titratable atom than the
# hydrogen. In either case we set the angle factor to 0
f_angle = 0.0
if f_angle > FANGLE_MIN:
value = (titratable_group.charge * hydrogen_bond_energy(
distance, dpka_max, [cutoff1, cutoff2], f_angle))
new_determinant = Determinant(backbone_group, value)
titratable_group.determinants['backbone'].append(
new_determinant)
def addDeterminants(iterative_interactions, version, options=None):
"""
The iterative pKa scheme. Later it is all added in 'calculateTotalPKA'
"""
# --- setup ---
iteratives = []
done_group = []
# creating iterative objects with references to their real group counterparts
for interaction in iterative_interactions:
pair = interaction[0]
for group in pair:
if group in done_group:
#print "done already"
""" do nothing - already have an iterative object for this group """
else:
newIterative = Iterative(group)
iteratives.append(newIterative)
done_group.append(group)
# Initialize iterative scheme
debug("\n --- pKa iterations (%d groups, %d interactions) ---" %
(len(iteratives), len(iterative_interactions)))
converged = False
iteration = 0
# set non-iterative pka values as first step
for itres in iteratives:
itres.pKa_iter.append(itres.pKa_NonIterative)
# --- starting pKa iterations ---
while converged == False:
# initialize pKa_new
iteration += 1
for itres in iteratives:
itres.determinants = {
'sidechain': [],
'backbone': [],
'coulomb': []
}
itres.pKa_new = itres.pKa_NonIterative
# Adding interactions to temporary determinant container
for interaction in iterative_interactions:
pair = interaction[0]
values = interaction[1]
annihilation = interaction[2]
#print "len(interaction) = %d" % (len(interaction))
object1, object2 = findIterative(pair, iteratives)
Q1 = object1.Q
Q2 = object2.Q
if Q1 < 0.0 and Q2 < 0.0:
""" both are acids """
addIterativeAcidPair(object1, object2, interaction)
elif Q1 > 0.0 and Q2 > 0.0:
""" both are bases """
addIterativeBasePair(object1, object2, interaction)
else:
""" one of each """
addIterativeIonPair(object1, object2, interaction, version)
# Calculating pKa_new values
for itres in iteratives:
for type in ['sidechain', 'backbone', 'coulomb']:
for determinant in itres.determinants[type]:
itres.pKa_new += determinant[1]
# Check convergence
converged = True
for itres in iteratives:
if itres.pKa_new == itres.pKa_old:
itres.converged = True
else:
itres.converged = False
converged = False
# reset pKa_old & storing pKa_new in pKa_iter
for itres in iteratives:
itres.pKa_old = itres.pKa_new
itres.pKa_iter.append(itres.pKa_new)
if iteration == 10:
info("did not converge in %d iterations" % (iteration))
break
# --- Iterations finished ---
# printing pKa iterations
# formerly was conditioned on if options.verbosity >= 2 - now unnecessary
str = "%12s" % (" ")
for index in range(0, iteration + 1):
str += "%8d" % (index)
debug(str)
for itres in iteratives:
str = "%s " % (itres.label)
for pKa in itres.pKa_iter:
str += "%8.2lf" % (pKa)
if itres.converged == False:
str += " *"
debug(str)
# creating real determinants and adding them to group object
for itres in iteratives:
for type in ['sidechain', 'backbone', 'coulomb']:
for interaction in itres.determinants[type]:
#info('done',itres.group.label,interaction[0],interaction[1])
value = interaction[1]
if value > 0.005 or value < -0.005:
g = interaction[0]
newDeterminant = Determinant(g, value)
itres.group.determinants[type].append(newDeterminant)
def add_determinants(iterative_interactions, version, _=None):
"""Add determinants iteratively.
The iterative pKa scheme. Later it is all added in 'calculateTotalPKA'
Args:
iterative_interactions: list of iterative interactions
version: version object
_: options object
"""
# --- setup ---
iteratives = []
done_group = []
# create iterative objects with references to their real group counterparts
for interaction in iterative_interactions:
pair = interaction[0]
for group in pair:
if group in done_group:
# do nothing - already have an iterative object for this group
pass
else:
new_iterative = Iterative(group)
iteratives.append(new_iterative)
done_group.append(group)
# Initialize iterative scheme
debug(
"\n --- pKa iterations ({0:d} groups, {1:d} interactions) ---".format(
len(iteratives), len(iterative_interactions)))
converged = False
iteration = 0
# set non-iterative pka values as first step
for iter_ in iteratives:
iter_.pka_iter.append(iter_.pka_noniterative)
# --- starting pKa iterations ---
while not converged:
# initialize pka_new
iteration += 1
for itres in iteratives:
itres.determinants = {'sidechain': [], 'backbone': [],
'coulomb': []}
itres.pka_new = itres.pka_noniterative
# Adding interactions to temporary determinant container
for interaction in iterative_interactions:
pair = interaction[0]
object1, object2 = find_iterative(pair, iteratives)
q1 = object1.q
q2 = object2.q
if q1 < 0.0 and q2 < 0.0:
# both are acids
add_iterative_acid_pair(object1, object2, interaction)
elif q1 > 0.0 and q2 > 0.0:
# both are bases
add_iterative_base_pair(object1, object2, interaction)
else:
# one of each
add_iterative_ion_pair(object1, object2, interaction, version)
# Calculating pka_new values
for itres in iteratives:
for type_ in ['sidechain', 'backbone', 'coulomb']:
for determinant in itres.determinants[type_]:
itres.pka_new += determinant[1]
# Check convergence
converged = True
for itres in iteratives:
if itres.pka_new == itres.pka_old:
itres.converged = True
else:
itres.converged = False
converged = False
# reset pka_old & storing pka_new in pka_iter
for itres in iteratives:
itres.pka_old = itres.pka_new
itres.pka_iter.append(itres.pka_new)
if iteration == 10:
info("did not converge in {0:d} iterations".format(iteration))
break
# printing pKa iterations
# formerly was conditioned on if options.verbosity >= 2 - now unnecessary
str_ = ' '
for index in range(iteration+1):
str_ += "{0:>8d}".format(index)
debug(str_)
for itres in iteratives:
str_ = "{0:s} ".format(itres.label)
for pka in itres.pka_iter:
str_ += "{0:>8.2f}".format(pka)
if not itres.converged:
str_ += " *"
debug(str_)
# creating real determinants and adding them to group object
for itres in iteratives:
for type_ in ['sidechain', 'backbone', 'coulomb']:
for interaction in itres.determinants[type_]:
#info('done',itres.group.label,interaction[0],interaction[1])
value = interaction[1]
if value > UNK_MIN_VALUE or value < -UNK_MIN_VALUE:
group = interaction[0]
new_det = Determinant(group, value)
itres.group.determinants[type_].append(new_det)
def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
for titratable_group in titratable_groups:
titratable_group_interaction_atoms = titratable_group.interaction_atoms_for_acids
if not titratable_group_interaction_atoms:
continue
# find out which backbone groups this titratable is interacting with
for backbone_group in backbone_groups:
# find the interacting atoms
backbone_interaction_atoms = backbone_group.get_interaction_atoms(
titratable_group)
if not backbone_interaction_atoms:
continue
# find the smallest distance
[backbone_atom, distance,
titratable_atom] = propka.calculations.get_smallest_distance(
backbone_interaction_atoms,
titratable_group_interaction_atoms)
# get the parameters
parameters = version.get_backbone_hydrogen_bond_parameters(
backbone_atom, titratable_atom)
if not parameters:
continue
[dpKa_max, [cutoff1, cutoff2]] = parameters
if distance < cutoff2:
# calculate angle factor
f_angle = 1.0
# for BBC groups, the hydrogen is on the titratable group
#
# Titra.
# /
# H
# .
# O
# ||
# C
if backbone_group.type == 'BBC':
if titratable_group.type in version.parameters.angular_dependent_sidechain_interactions:
if titratable_atom.element == 'H':
heavy_atom = titratable_atom.bonded_atoms[0]
hydrogen_atom = titratable_atom
[d1, f_angle,
d2] = propka.calculations.AngleFactorX(
atom1=heavy_atom,
atom2=hydrogen_atom,
atom3=backbone_atom)
else:
# Either the structure is corrupt (no hydrogen), or the heavy atom is closer to
# the titratable atom than the hydrogen. In either case we set the angle factor
# to 0
f_angle = 0.0
# for BBN groups, the hydrogen is on the backbone group
#
# Titra.
# .
# H
# |
# N
# / \
if backbone_group.type == 'BBN':
if backbone_atom.element == 'H':
backbone_N = backbone_atom.bonded_atoms[0]
backbone_H = backbone_atom
[d1, f_angle, d2] = propka.calculations.AngleFactorX(
atom1=titratable_atom,
atom2=backbone_H,
atom3=backbone_N)
else:
# Either the structure is corrupt (no hydrogen), or the heavy atom is closer to
# the titratable atom than the hydrogen. In either case we set the angle factor
# to 0
f_angle = 0.0
if f_angle > 0.001:
value = titratable_group.charge * propka.calculations.HydrogenBondEnergy(
distance, dpKa_max, [cutoff1, cutoff2], f_angle)
newDeterminant = Determinant(backbone_group, value)
titratable_group.determinants['backbone'].append(
newDeterminant)
return