def average_of_conformations(self):
# make a new configuration to hold the average values
avr_conformation = propka.conformation_container.Conformation_container(name='average',
parameters=self.conformations[self.conformation_names[0]].parameters,
molecular_container=self)
container = self.conformations[self.conformation_names[0]]
for group in container.get_groups_for_calculations():
# new group to hold average values
avr_group = group.clone()
# sum up all groups ...
for name in self.conformation_names:
group_to_add = self.conformations[name].find_group(group)
if group_to_add:
avr_group += group_to_add
else:
warning('Group %s could not be found in conformation %s.' % (group.atom.residue_label, name))
# ... and store the average value
avr_group = avr_group / len(self.conformation_names)
avr_conformation.groups.append(avr_group)
# store information on coupling in the average container
if len(list(filter(lambda c: c.non_covalently_coupled_groups, self.conformations.values()))):
avr_conformation.non_covalently_coupled_groups = True
# store chain info
avr_conformation.chains = self.conformations[self.conformation_names[0]].chains
self.conformations['AVR'] = avr_conformation
return
def setup_atoms(self):
# Find the atoms in the histidine ring
ring_atoms = propka.ligand.is_ring_member(self.atom)
if len(ring_atoms) != 5:
warning('His group does not seem to contain a ring', self)
# protonate ring
for r in ring_atoms:
my_protonator.protonate_atom(r)
# set the center using the ring atoms
if ring_atoms:
self.set_center(ring_atoms)
else:
# Missing side-chain atoms
self.set_center([self.atom])
# FIXME perhaps it would be better to ignore this group completely?
# find the hydrogens on the ring-nitrogens
hydrogens = []
nitrogens = [ra for ra in ring_atoms if ra.element == 'N']
for nitrogen in nitrogens:
hydrogens.extend(nitrogen.get_bonded_elements('H'))
self.set_interaction_atoms(hydrogens+nitrogens, nitrogens)
return
def protein_precheck(conformations, names):
for name in names:
atoms = conformations[name].atoms
# Group the atoms by their residue:
atoms_by_residue = {}
for a in atoms:
if a.element != 'H':
res_id = resid_from_atom(a)
try:
atoms_by_residue[res_id].append(a)
except KeyError:
atoms_by_residue[res_id] = [a]
for res_id, res_atoms in atoms_by_residue.items():
resname = res_atoms[0].resName
residue_label = '%3s%5s'%(resname, res_id)
# ignore ligand residues
if resname not in expected_atom_numbers:
continue
# check for c-terminal
if 'C-' in [a.terminal for a in res_atoms]:
if len(res_atoms) != expected_atom_numbers[resname]+1:
warning('Unexpected number (%d) of atoms in residue %s in conformation %s' % (len(res_atoms), residue_label, name))
continue
# check number of atoms in residue
if len(res_atoms) != expected_atom_numbers[resname]:
warning('Unexpected number (%d) of atoms in residue %s in conformation %s' % (len(res_atoms), residue_label, name))
return
def setup_atoms(self):
# Find the atoms in the histidine ring
ring_atoms = propka.ligand.is_ring_member(self.atom)
if len(ring_atoms) != 5:
warning('His group does not seem to contain a ring', self)
# protonate ring
for r in ring_atoms:
my_protonator.protonate_atom(r)
# set the center using the ring atoms
if ring_atoms:
self.set_center(ring_atoms)
else:
# Missing side-chain atoms
self.set_center([self.atom])
# FIXME perhaps it would be better to ignore this group completely?
# find the hydrogens on the ring-nitrogens
hydrogens = []
nitrogens = [ra for ra in ring_atoms if ra.element == 'N']
for nitrogen in nitrogens:
hydrogens.extend(nitrogen.get_bonded_elements('H'))
self.set_interaction_atoms(hydrogens + nitrogens, nitrogens)
return
def average_of_conformations(self):
"""Generate an average of conformations."""
parameters = self.conformations[self.conformation_names[0]].parameters
# make a new configuration to hold the average values
avr_conformation = ConformationContainer(name='average',
parameters=parameters,
molecular_container=self)
container = self.conformations[self.conformation_names[0]]
for group in container.get_groups_for_calculations():
# new group to hold average values
avr_group = group.clone()
# sum up all groups ...
for name in self.conformation_names:
group_to_add = self.conformations[name].find_group(group)
if group_to_add:
avr_group += group_to_add
else:
str_ = ('Group {0:s} could not be found in '
'conformation {1:s}.'.format(
group.atom.residue_label, name))
warning(str_)
# ... and store the average value
avr_group = avr_group / len(self.conformation_names)
avr_conformation.groups.append(avr_group)
# store information on coupling in the average container
if len(
list(
filter(lambda c: c.non_covalently_coupled_groups,
self.conformations.values()))):
avr_conformation.non_covalently_coupled_groups = True
# store chain info
avr_conformation.chains = self.conformations[
self.conformation_names[0]].chains
self.conformations['AVR'] = avr_conformation
def add_protons(self, atom):
# decide which method to use
debug('PROTONATING',atom)
if atom.steric_number in list(self.protonation_methods.keys()):
self.protonation_methods[atom.steric_number](atom)
else:
warning('Do not have a method for protonating', atom, '(steric number: %d)' % atom.steric_number)
return
def add_protons(self, atom):
# decide which method to use
debug('PROTONATING', atom)
if atom.steric_number in list(self.protonation_methods.keys()):
self.protonation_methods[atom.steric_number](atom)
else:
warning('Do not have a method for protonating', atom,
'(steric number: %d)' % atom.steric_number)
return
def set_bond_distance(self, a, element):
d = 1.0
if element in list(self.bond_lengths.keys()):
d = self.bond_lengths[element]
else:
warning('Bond length for %s not found, using the standard value of %f' % (element, d))
a = a.rescale(d)
return a
def get_marvin_pkas_for_molecule(self,
atoms,
filename='__tmp_ligand.mol2',
reuse=False,
no_pkas=10,
min_pH=-10,
max_pH=20):
# print out structure unless we are using user-modified structure
if not reuse:
propka.pdb.write_mol2_for_atoms(atoms, filename)
# check that we actually have a file to work with
if not os.path.isfile(filename):
warning(
'Didn\'t find a user-modified file \'%s\' - generating one' %
filename)
propka.pdb.write_mol2_for_atoms(atoms, filename)
# Marvin
# calculate pKa values
options = 'pka -a %d -b %d --min %f --max %f -d large' % (
no_pkas, no_pkas, min_pH, max_pH)
(output,
errors) = subprocess.Popen([self.cxcalc, filename] + options.split(),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()
if len(errors) > 0:
info(
'********************************************************************************************************'
)
info(
'* Warning: Marvin execution failed: *'
)
info('* %-100s *' % errors)
info(
'* *'
)
info(
'* Please edit the ligand mol2 file and re-run PropKa with the -l option: %29s *'
% filename)
info(
'********************************************************************************************************'
)
sys.exit(-1)
# extract calculated pkas
indices, pkas, types = self.extract_pkas(output)
# store calculated pka values
for i in range(len(indices)):
atoms[indices[i]].marvin_pka = pkas[i]
atoms[indices[i]].charge = {'a': -1, 'b': +1}[types[i]]
info('%s model pKa: %.2f' % (atoms[indices[i]], pkas[i]))
return
def get_marvin_pkas_for_molecule(self, atoms, filename='__tmp_ligand.mol2',
reuse=False, num_pkas=10, min_ph=-10,
max_ph=20):
"""Use Marvin executables to calculate pKas for a molecule.
Args:
molecule: the molecule
name: filename
reuse: flag to reuse the structure files
num_pkas: number of pKas to calculate
min_ph: minimum pH value
max_ph: maximum pH value
"""
# print out structure unless we are using user-modified structure
if not reuse:
write_mol2_for_atoms(atoms, filename)
# check that we actually have a file to work with
if not os.path.isfile(filename):
errstr = (
"Didn't find a user-modified file '{0:s}' "
"- generating one".format(
filename))
warning(errstr)
write_mol2_for_atoms(atoms, filename)
# Marvin calculate pKa values
fmt = (
'pka -a {num1} -b {num2} --min {min_ph} '
'--max {max_ph} -d large')
options = (
fmt.format(
num1=num_pkas, num2=num_pkas, min_ph=min_ph, max_ph=max_ph))
(output, errors) = subprocess.Popen(
[self.cxcalc, filename]+options.split(), stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()
if len(errors) > 0:
info('***********************************************************'
'*********************************************')
info('* Warning: Marvin execution failed: '
' *')
info('* {0:<100s} *'.format(errors))
info('* '
' *')
info('* Please edit the ligand mol2 file and re-run PropKa with '
'the -l option: {0:>29s} *'.format(filename))
info('***********************************************************'
'*********************************************')
sys.exit(-1)
# extract calculated pkas
indices, pkas, types = self.extract_pkas(output)
# store calculated pka values
for i, index in enumerate(indices):
atoms[index].marvin_pka = pkas[i]
atoms[index].charge = {'a': -1, 'b': 1}[types[i]]
info('{0:s} model pKa: {1:<.2f}'.format(atoms[index], pkas[i]))
def set_bond_distance(self, a, element):
d = 1.0
if element in list(self.bond_lengths.keys()):
d = self.bond_lengths[element]
else:
warning(
'Bond length for %s not found, using the standard value of %f'
% (element, d))
a = a.rescale(d)
return a
def insert(self, k1, k2, v):
if k1 in self.dictionary.keys() and k2 in self.dictionary[k1].keys():
if k1 != k2:
warning("Parameter value for %s, %s defined more than once" % (k1, k2))
if not k1 in self.dictionary:
self.dictionary[k1] = {}
self.dictionary[k1][k2] = v
return
def add_protons(self, atom):
"""Add protons to atom.
Args:
atom: atom for calculation
"""
# decide which method to use
debug('PROTONATING', atom)
if atom.steric_number in list(self.protonation_methods.keys()):
self.protonation_methods[atom.steric_number](atom)
else:
warning('Do not have a method for protonating', atom,
'(steric number: {0:d})'.format(atom.steric_number))
def insert(self, k1, k2, v):
if k1 in self.dictionary.keys() and k2 in self.dictionary[k1].keys():
if k1 != k2:
warning('Parameter value for %s, %s defined more than once' %
(k1, k2))
if not k1 in self.dictionary:
self.dictionary[k1] = {}
self.dictionary[k1][k2] = v
return
def insert(self, key1, key2, value):
"""Insert value into matrix.
Args:
key1: first matrix key (row)
key2: second matrix key (column)
value: value to insert
"""
if key1 in self.dictionary and key2 in self.dictionary[key1]:
if key1 != key2:
str_ = ('Parameter value for {0:s}, {1:s} defined more '
'than once'.format(key1, key2))
warning(str_)
if not key1 in self.dictionary:
self.dictionary[key1] = {}
self.dictionary[key1][key2] = value
def set_bond_distance(self, bvec, element):
"""Set bond distance between atom and element.
Args:
bvec: bond vector
element: bonded element
Returns:
scaled bond vector
"""
dist = 1.0
if element in list(self.bond_lengths.keys()):
dist = self.bond_lengths[element]
else:
str_ = (
'Bond length for {0:s} not found, using the standard value '
'of {1:f}'.format(element, dist))
warning(str_)
bvec = bvec.rescale(dist)
return bvec
def protein_precheck(conformations, names):
for name in names:
atoms = conformations[name].atoms
# Group the atoms by their residue:
atoms_by_residue = {}
for a in atoms:
if a.element != 'H':
res_id = resid_from_atom(a)
try:
atoms_by_residue[res_id].append(a)
except KeyError:
atoms_by_residue[res_id] = [a]
for res_id, res_atoms in atoms_by_residue.items():
resname = res_atoms[0].resName
residue_label = '%3s%5s' % (resname, res_id)
# ignore ligand residues
if resname not in expected_atom_numbers:
continue
# check for c-terminal
if 'C-' in [a.terminal for a in res_atoms]:
if len(res_atoms) != expected_atom_numbers[resname] + 1:
warning(
'Unexpected number (%d) of atoms in residue %s in conformation %s'
% (len(res_atoms), residue_label, name))
continue
# check number of atoms in residue
if len(res_atoms) != expected_atom_numbers[resname]:
warning(
'Unexpected number (%d) of atoms in residue %s in conformation %s'
% (len(res_atoms), residue_label, name))
return
def get_marvin_pkas_for_molecule(self, atoms, filename='__tmp_ligand.mol2', reuse=False, no_pkas=10, min_pH =-10, max_pH=20):
# print out structure unless we are using user-modified structure
if not reuse:
propka.pdb.write_mol2_for_atoms(atoms, filename)
# check that we actually have a file to work with
if not os.path.isfile(filename):
warning('Didn\'t find a user-modified file \'%s\' - generating one' % filename)
propka.pdb.write_mol2_for_atoms(atoms, filename)
# Marvin
# calculate pKa values
options = 'pka -a %d -b %d --min %f --max %f -d large'%(no_pkas, no_pkas, min_pH, max_pH)
(output,errors) = subprocess.Popen([self.cxcalc, filename]+options.split(),
stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
if len(errors)>0:
info('********************************************************************************************************')
info('* Warning: Marvin execution failed: *')
info('* %-100s *' % errors)
info('* *')
info('* Please edit the ligand mol2 file and re-run PropKa with the -l option: %29s *' % filename)
info('********************************************************************************************************')
sys.exit(-1)
# extract calculated pkas
indices,pkas,types = self.extract_pkas(output)
# store calculated pka values
for i in range(len(indices)):
atoms[indices[i]].marvin_pka = pkas[i]
atoms[indices[i]].charge = {'a':-1,'b':+1}[types[i]]
info('%s model pKa: %.2f' % (atoms[indices[i]], pkas[i]))
return
def set_interaction_atoms(self, interaction_atoms_for_acids, interaction_atoms_for_bases):
[a.set_group_type(self.type) for a in interaction_atoms_for_acids+interaction_atoms_for_bases]
self.interaction_atoms_for_acids = interaction_atoms_for_acids
self.interaction_atoms_for_bases = interaction_atoms_for_bases
# check if all atoms have been identified
ok = True
for [expect, found, t] in [[expected_atoms_acid_interactions, self.interaction_atoms_for_acids, 'acid'],
[expected_atoms_base_interactions, self.interaction_atoms_for_bases, 'base']]:
if self.type in expect.keys():
for e in expect[self.type].keys():
if len([a for a in found if a.element==e]) != expect[self.type][e]:
ok = False
if not ok:
warning('Missing atoms or failed protonation for %s (%s) -- please check the structure' % (self.label, self.type))
warning('%s' % self)
Na = sum([expected_atoms_acid_interactions[self.type][e] for e in expected_atoms_acid_interactions[self.type].keys()])
Nb = sum([expected_atoms_base_interactions[self.type][e] for e in expected_atoms_base_interactions[self.type].keys()])
warning('Expected %d interaction atoms for acids, found:' % Na)
for i in range(len(self.interaction_atoms_for_acids)):
warning(' %s' % self.interaction_atoms_for_acids[i])
warning('Expected %d interaction atoms for bases, found:' % Nb)
for i in range(len(self.interaction_atoms_for_bases)):
warning(' %s' % self.interaction_atoms_for_bases[i])
#return
return
def hydrogen_bond_interaction(group1, group2, version):
# find the smallest distance between interacting atoms
atoms1 = group1.get_interaction_atoms(group2)
atoms2 = group2.get_interaction_atoms(group1)
[closest_atom1, distance, closest_atom2
] = propka.calculations.get_smallest_distance(atoms1, atoms2)
if None in [closest_atom1, closest_atom2]:
warning('Side chain interaction failed for %s and %s' %
(group1.label, group2.label))
return None
# get the parameters
[dpka_max,
cutoff] = version.get_hydrogen_bond_parameters(closest_atom1,
closest_atom2)
if dpka_max == None or None in cutoff:
return None
# check that the closest atoms are close enough
if distance >= cutoff[1]:
return None
# check that bond distance criteria is met
bond_distance_too_short = group1.atom.is_atom_within_bond_distance(
group2.atom, version.parameters.min_bond_distance_for_hydrogen_bonds,
1)
if bond_distance_too_short:
return None
# set the angle factor
#
# ---closest_atom1/2
# .
# .
# the_hydrogen---closest_atom2/1---
f_angle = 1.0
if group2.type in version.parameters.angular_dependent_sidechain_interactions:
if closest_atom2.element == 'H':
heavy_atom = closest_atom2.bonded_atoms[0]
hydrogen = closest_atom2
distance, f_angle, nada = propka.calculations.AngleFactorX(
closest_atom1, hydrogen, heavy_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
elif group1.type in version.parameters.angular_dependent_sidechain_interactions:
if closest_atom1.element == 'H':
heavy_atom = closest_atom1.bonded_atoms[0]
hydrogen = closest_atom1
distance, f_angle, nada = propka.calculations.AngleFactorX(
closest_atom2, hydrogen, heavy_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
weight = version.calculatePairWeight(group1.Nmass, group2.Nmass)
exception, value = version.checkExceptions(group1, group2)
#exception = False # circumventing exception
if exception == True:
""" do nothing, value should have been assigned """
#info(" exception for %s %s %6.2lf" % (group1.label, group2.label, value))
else:
value = version.calculateSideChainEnergy(distance, dpka_max, cutoff,
weight, f_angle)
# info('distance',distance)
# info('dpka_max',dpka_max)
# info('cutoff',cutoff)
# info('f_angle',f_angle)
# info('weight',weight)
# info('value',value)
# info('===============================================')
return value
def set_interaction_atoms(self, interaction_atoms_for_acids,
interaction_atoms_for_bases):
[
a.set_group_type(self.type)
for a in interaction_atoms_for_acids + interaction_atoms_for_bases
]
self.interaction_atoms_for_acids = interaction_atoms_for_acids
self.interaction_atoms_for_bases = interaction_atoms_for_bases
# check if all atoms have been identified
ok = True
for [expect, found, t] in [[
expected_atoms_acid_interactions,
self.interaction_atoms_for_acids, 'acid'
],
[
expected_atoms_base_interactions,
self.interaction_atoms_for_bases, 'base'
]]:
if self.type in expect.keys():
for e in expect[self.type].keys():
if len([a for a in found if a.element == e
]) != expect[self.type][e]:
ok = False
if not ok:
warning(
'Missing atoms or failed protonation for %s (%s) -- please check the structure'
% (self.label, self.type))
warning('%s' % self)
Na = sum([
expected_atoms_acid_interactions[self.type][e]
for e in expected_atoms_acid_interactions[self.type].keys()
])
Nb = sum([
expected_atoms_base_interactions[self.type][e]
for e in expected_atoms_base_interactions[self.type].keys()
])
warning('Expected %d interaction atoms for acids, found:' % Na)
for i in range(len(self.interaction_atoms_for_acids)):
warning(' %s' %
self.interaction_atoms_for_acids[i])
warning('Expected %d interaction atoms for bases, found:' % Nb)
for i in range(len(self.interaction_atoms_for_bases)):
warning(' %s' %
self.interaction_atoms_for_bases[i])
#return
return
def set_interaction_atoms(self, interaction_atoms_for_acids,
interaction_atoms_for_bases):
"""Set interacting atoms and group types.
Args:
interaction_atoms_for_acids: list of atoms for acid interactions
interaction_atoms_for_base: list of atoms for base interactions
"""
for atom in interaction_atoms_for_acids + interaction_atoms_for_bases:
atom.set_group_type(self.type)
self.interaction_atoms_for_acids = interaction_atoms_for_acids
self.interaction_atoms_for_bases = interaction_atoms_for_bases
# check if all atoms have been identified
ok = True
for [expect, found, _] in [[
EXPECTED_ATOMS_ACID_INTERACTIONS,
self.interaction_atoms_for_acids, 'acid'
],
[
EXPECTED_ATOMS_BASE_INTERACTIONS,
self.interaction_atoms_for_bases, 'base'
]]:
if self.type in expect.keys():
for elem in expect[self.type].keys():
if (len([a for a in found if a.element == elem]) !=
expect[self.type][elem]):
ok = False
if not ok:
str_ = 'Missing atoms or failed protonation for '
str_ += '{0:s} ({1:s}) -- please check the structure'.format(
self.label, self.type)
warning(str_)
warning('{0:s}'.format(str(self)))
num_acid = sum([
EXPECTED_ATOMS_ACID_INTERACTIONS[self.type][e]
for e in EXPECTED_ATOMS_ACID_INTERACTIONS[self.type].keys()
])
num_base = sum([
EXPECTED_ATOMS_BASE_INTERACTIONS[self.type][e]
for e in EXPECTED_ATOMS_BASE_INTERACTIONS[self.type].keys()
])
warning(
'Expected {0:d} interaction atoms for acids, found:'.format(
num_acid))
for i in range(len(self.interaction_atoms_for_acids)):
warning(' {0:s}'.format(
str(self.interaction_atoms_for_acids[i])))
warning(
'Expected {0:d} interaction atoms for bases, found:'.format(
num_base))
for i in range(len(self.interaction_atoms_for_bases)):
warning(' {0:s}'.format(
str(self.interaction_atoms_for_bases[i])))
def hydrogen_bond_interaction(group1, group2, version):
"""Calculate energy for hydrogen bond interactions between two groups.
Args:
group1: first interacting group
group2: second interacting group
version: an object that contains version-specific parameters
Returns:
hydrogen bond interaction energy
"""
# find the smallest distance between interacting atoms
atoms1 = group1.get_interaction_atoms(group2)
atoms2 = group2.get_interaction_atoms(group1)
[closest_atom1, dist,
closest_atom2] = get_smallest_distance(atoms1, atoms2)
if None in [closest_atom1, closest_atom2]:
warning('Side chain interaction failed for {0:s} and {1:s}'.format(
group1.label, group2.label))
return None
# get the parameters
[dpka_max,
cutoff] = version.get_hydrogen_bond_parameters(closest_atom1,
closest_atom2)
if (dpka_max is None) or (None in cutoff):
return None
# check that the closest atoms are close enough
if dist >= cutoff[1]:
return None
# check that bond distance criteria is met
min_hbond_dist = version.parameters.min_bond_distance_for_hydrogen_bonds
if group1.atom.is_atom_within_bond_distance(group2.atom, min_hbond_dist,
1):
return None
# set angle factor
f_angle = 1.0
if group2.type in version.parameters.angular_dependent_sidechain_interactions:
if closest_atom2.element == 'H':
heavy_atom = closest_atom2.bonded_atoms[0]
hydrogen = closest_atom2
dist, f_angle, _ = angle_distance_factors(closest_atom1, hydrogen,
heavy_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
elif group1.type in version.parameters.angular_dependent_sidechain_interactions:
if closest_atom1.element == 'H':
heavy_atom = closest_atom1.bonded_atoms[0]
hydrogen = closest_atom1
dist, f_angle, _ = angle_distance_factors(closest_atom2, hydrogen,
heavy_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
weight = version.calculate_pair_weight(group1.num_volume,
group2.num_volume)
exception, value = version.check_exceptions(group1, group2)
if exception:
# Do nothing, value should have been assigned.
pass
else:
value = version.calculate_side_chain_energy(dist, dpka_max, cutoff,
weight, f_angle)
return value
def hydrogen_bond_interaction(group1, group2, version):
# find the smallest distance between interacting atoms
atoms1 = group1.get_interaction_atoms(group2)
atoms2 = group2.get_interaction_atoms(group1)
[closest_atom1, distance, closest_atom2] = propka.calculations.get_smallest_distance(atoms1, atoms2)
if None in [closest_atom1, closest_atom2]:
warning('Side chain interaction failed for %s and %s' % (group1.label, group2.label))
return None
# get the parameters
[dpka_max, cutoff] = version.get_hydrogen_bond_parameters(closest_atom1,closest_atom2)
if dpka_max==None or None in cutoff:
return None
# check that the closest atoms are close enough
if distance >= cutoff[1]:
return None
# check that bond distance criteria is met
bond_distance_too_short = group1.atom.is_atom_within_bond_distance(group2.atom,
version.parameters.min_bond_distance_for_hydrogen_bonds,1)
if bond_distance_too_short:
return None
# set the angle factor
#
# ---closest_atom1/2
# .
# .
# the_hydrogen---closest_atom2/1---
f_angle = 1.0
if group2.type in version.parameters.angular_dependent_sidechain_interactions:
if closest_atom2.element == 'H':
heavy_atom = closest_atom2.bonded_atoms[0]
hydrogen = closest_atom2
distance, f_angle, nada = propka.calculations.AngleFactorX(closest_atom1, hydrogen, heavy_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
elif group1.type in version.parameters.angular_dependent_sidechain_interactions:
if closest_atom1.element == 'H':
heavy_atom = closest_atom1.bonded_atoms[0]
hydrogen = closest_atom1
distance, f_angle, nada = propka.calculations.AngleFactorX(closest_atom2, hydrogen, heavy_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
weight = version.calculatePairWeight(group1.Nmass, group2.Nmass)
exception, value = version.checkExceptions(group1, group2)
#exception = False # circumventing exception
if exception == True:
""" do nothing, value should have been assigned """
#info(" exception for %s %s %6.2lf" % (group1.label, group2.label, value))
else:
value = version.calculateSideChainEnergy(distance, dpka_max, cutoff, weight, f_angle)
# info('distance',distance)
# info('dpka_max',dpka_max)
# info('cutoff',cutoff)
# info('f_angle',f_angle)
# info('weight',weight)
# info('value',value)
# info('===============================================')
return value