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Clean up line breaks.

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See https://github.com/jensengroup/propka-3.1/issues/43.
This commit is contained in:
Nathan Baker
2020-05-25 17:49:52 -07:00
parent 1ce44b77bf
commit 284a33dfe8
1 changed files with 62 additions and 43 deletions
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91
propka/conformation_container.py
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@@ -57,7 +57,8 @@ class ConformationContainer:
"""Generate interaction map and charge centers.""" """Generate interaction map and charge centers."""
# if a group is coupled and we are reading a .propka_input file, then # if a group is coupled and we are reading a .propka_input file, then
# some more configuration might be needed # some more configuration might be needed
map_ = make_interaction_map('Covalent coupling map for %s' % self, map_ = make_interaction_map(
'Covalent coupling map for %s' % self,
self.get_covalently_coupled_groups(), self.get_covalently_coupled_groups(),
lambda g1, g2: g1 in g2.covalently_coupled_groups) lambda g1, g2: g1 in g2.covalently_coupled_groups)
info(map_) info(map_)
@@ -67,13 +68,14 @@ class ConformationContainer:
def set_common_charge_centres(self): def set_common_charge_centres(self):
"""Assign charge centers to groups.""" """Assign charge centers to groups."""
for system in self.get_coupled_systems(self.get_covalently_coupled_groups(), for system in self.get_coupled_systems(
self.get_covalently_coupled_groups(),
Group.get_covalently_coupled_groups): Group.get_covalently_coupled_groups):
# make a list of the charge centre coordinates # make a list of the charge centre coordinates
all_coordinates = list(map(lambda g: [g.x, g.y, g.z], system)) all_coordinates = list(map(lambda g: [g.x, g.y, g.z], system))
# find the common charge center # find the common charge center
ccc = functools.reduce(lambda g1, g2: [g1[0]+g2[0], g1[1]+g2[1], ccc = functools.reduce(
g1[2]+g2[2]], lambda g1, g2: [g1[0]+g2[0], g1[1]+g2[1], g1[2]+g2[2]],
all_coordinates) all_coordinates)
ccc = list(map(lambda c: c/len(system), ccc)) ccc = list(map(lambda c: c/len(system), ccc))
# set the ccc for all coupled groups in this system # set the ccc for all coupled groups in this system
@@ -85,8 +87,8 @@ class ConformationContainer:
"""Find covalently coupled groups and set common charge centres.""" """Find covalently coupled groups and set common charge centres."""
for group in self.get_titratable_groups(): for group in self.get_titratable_groups():
# Find covalently bonded groups # Find covalently bonded groups
bonded_groups = self.find_bonded_titratable_groups(group.atom, 1, bonded_groups = self.find_bonded_titratable_groups(
group.atom) group.atom, 1, group.atom)
# coupled groups # coupled groups
for bond_group in bonded_groups: for bond_group in bonded_groups:
if bond_group in group.covalently_coupled_groups: if bond_group in group.covalently_coupled_groups:
@@ -97,7 +99,8 @@ class ConformationContainer:
if self.parameters.common_charge_centre: if self.parameters.common_charge_centre:
self.set_common_charge_centres() self.set_common_charge_centres()
# print coupling map # print coupling map
map_ = make_interaction_map('Covalent coupling map for %s' % self, map_ = make_interaction_map(
'Covalent coupling map for %s' % self,
self.get_covalently_coupled_groups(), self.get_covalently_coupled_groups(),
lambda g1, g2: g1 in g2.covalently_coupled_groups) lambda g1, g2: g1 in g2.covalently_coupled_groups)
info(map_) info(map_)
@@ -134,14 +137,14 @@ class ConformationContainer:
if bond_atom == original_atom: if bond_atom == original_atom:
continue continue
# check if this atom has a titratable group # check if this atom has a titratable group
if bond_atom.group and bond_atom.group.titratable \ if (bond_atom.group and bond_atom.group.titratable
and num_bonds <= self.parameters.coupling_max_number_of_bonds: and num_bonds
<= self.parameters.coupling_max_number_of_bonds):
res.add(bond_atom.group) res.add(bond_atom.group)
# check for titratable groups bonded to this atom # check for titratable groups bonded to this atom
if num_bonds < self.parameters.coupling_max_number_of_bonds: if num_bonds < self.parameters.coupling_max_number_of_bonds:
res |= self.find_bonded_titratable_groups(bond_atom, res |= self.find_bonded_titratable_groups(
num_bonds+1, bond_atom, num_bonds+1, original_atom)
original_atom)
return res return res
def setup_and_add_group(self, group): def setup_and_add_group(self, group):
@@ -190,22 +193,23 @@ 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
set_backbone_determinants(self.get_titratable_groups(), set_backbone_determinants(
self.get_backbone_groups(), version) self.get_titratable_groups(), self.get_backbone_groups(), version)
# setting ion determinants # setting ion determinants
set_ion_determinants(self, version) set_ion_determinants(self, version)
# calculating the back-bone reorganization/desolvation term # calculating the back-bone reorganization/desolvation term
version.calculate_backbone_reorganization(self) version.calculate_backbone_reorganization(self)
# setting remaining non-iterative and iterative side-chain & Coulomb # setting remaining non-iterative and iterative side-chain & Coulomb
# interaction determinants # interaction determinants
set_determinants(self.get_sidechain_groups(), version=version, set_determinants(
options=options) self.get_sidechain_groups(), version=version, options=options)
# calculating the total pKa values # calculating the total pKa values
for group in self.groups: for group in self.groups:
group.calculate_total_pka() group.calculate_total_pka()
# take coupling effects into account # take coupling effects into account
penalised_labels = self.coupling_effects() penalised_labels = self.coupling_effects()
if self.parameters.remove_penalised_group and len(penalised_labels) > 0: if (self.parameters.remove_penalised_group
and len(penalised_labels) > 0):
info('Removing penalised groups!!!') info('Removing penalised groups!!!')
for group in self.get_titratable_groups(): for group in self.get_titratable_groups():
group.remove_determinants(penalised_labels) group.remove_determinants(penalised_labels)
@@ -227,7 +231,8 @@ class ConformationContainer:
titrate. titrate.
""" """
penalised_labels = [] penalised_labels = []
for all_groups in self.get_coupled_systems(self.get_covalently_coupled_groups(), for all_groups in self.get_coupled_systems(
self.get_covalently_coupled_groups(),
Group.get_covalently_coupled_groups): Group.get_covalently_coupled_groups):
# check if we should share determinants # check if we should share determinants
if self.parameters.shared_determinants: if self.parameters.shared_determinants:
@@ -236,15 +241,19 @@ class ConformationContainer:
first_group = max(all_groups, key=lambda g: g.pka_value) first_group = max(all_groups, key=lambda g: g.pka_value)
# In case of acids # In case of acids
if first_group.charge < 0: if first_group.charge < 0:
first_group.coupled_titrating_group = min(all_groups, key=lambda g: g.pka_value) first_group.coupled_titrating_group = min(
penalised_labels.append(first_group.label) # group with the highest pKa is penalised all_groups, key=lambda g: g.pka_value)
# group with the highest pKa is penalised
penalised_labels.append(first_group.label)
# In case of bases # In case of bases
else: else:
for group in all_groups: for group in all_groups:
if group == first_group: if group == first_group:
continue # group with the highest pKa is allowed to titrate... # group with the highest pKa is allowed to titrate...
continue
group.coupled_titrating_group = first_group group.coupled_titrating_group = first_group
penalised_labels.append(group.label) #... and the rest is penalised #... and the rest are penalised
penalised_labels.append(group.label)
return penalised_labels return penalised_labels
@staticmethod @staticmethod
@@ -287,7 +296,8 @@ class ConformationContainer:
while len(groups) > 0: while len(groups) > 0:
# extract a system of coupled groups ... # extract a system of coupled groups ...
system = set() system = set()
self.get_a_coupled_system_of_groups(groups.pop(), system, get_coupled_groups) self.get_a_coupled_system_of_groups(
groups.pop(), system, get_coupled_groups)
# ... and remove them from the list # ... and remove them from the list
groups -= system groups -= system
yield system yield system
@@ -356,7 +366,8 @@ class ConformationContainer:
Returns: Returns:
list of groups list of groups
""" """
return [group for group in self.groups \ return [
group for group in self.groups
if ('BB' not in group.type and not group.atom.cysteine_bridge)] if ('BB' not in group.type and not group.atom.cysteine_bridge)]
def get_covalently_coupled_groups(self): def get_covalently_coupled_groups(self):
@@ -365,7 +376,8 @@ class ConformationContainer:
Returns: Returns:
list of groups list of groups
""" """
return [g for g in self.groups \ return [
g for g in self.groups
if len(g.covalently_coupled_groups) > 0] if len(g.covalently_coupled_groups) > 0]
def get_non_covalently_coupled_groups(self): def get_non_covalently_coupled_groups(self):
@@ -374,7 +386,8 @@ class ConformationContainer:
Returns: Returns:
list of groups list of groups
""" """
return [g for g in self.groups \ return [
g for g in self.groups
if len(g.non_covalently_coupled_groups) > 0] if len(g.non_covalently_coupled_groups) > 0]
def get_backbone_nh_groups(self): def get_backbone_nh_groups(self):
@@ -401,7 +414,8 @@ class ConformationContainer:
Returns: Returns:
list of groups list of groups
""" """
return [group for group in self.groups if group.residue_type == residue] return [
group for group in self.groups if group.residue_type == residue]
def get_titratable_groups(self): def get_titratable_groups(self):
"""Get all titratable groups needed for pKa calculations. """Get all titratable groups needed for pKa calculations.
@@ -429,8 +443,9 @@ class ConformationContainer:
Returns: Returns:
list of groups list of groups
""" """
return [group for group in self.groups \ return [
if (group.residue_type in self.parameters.acid_list \ group for group in self.groups
if (group.residue_type in self.parameters.acid_list
and not group.atom.cysteine_bridge)] and not group.atom.cysteine_bridge)]
def get_backbone_reorganisation_groups(self): def get_backbone_reorganisation_groups(self):
@@ -439,8 +454,10 @@ class ConformationContainer:
Returns: Returns:
list of groups list of groups
""" """
return [group for group in self.groups \ return [
if (group.residue_type in self.parameters.backbone_reorganisation_list \ group for group in self.groups
if (group.residue_type
in self.parameters.backbone_reorganisation_list
and not group.atom.cysteine_bridge)] and not group.atom.cysteine_bridge)]
def get_ions(self): def get_ions(self):
@@ -449,7 +466,8 @@ class ConformationContainer:
Returns: Returns:
list of groups list of groups
""" """
return [group for group in self.groups \ return [
group for group in self.groups
if group.residue_type in self.parameters.ions.keys()] if group.residue_type in self.parameters.ions.keys()]
def get_group_names(self, group_list): def get_group_names(self, group_list):
@@ -476,7 +494,8 @@ class ConformationContainer:
Returns: Returns:
list of atoms list of atoms
""" """
return [atom for atom in self.atoms \ return [
atom for atom in self.atoms
if atom.type == 'hetatm' and atom.element != 'H'] if atom.type == 'hetatm' and atom.element != 'H']
def get_chain(self, chain): def get_chain(self, chain):
@@ -556,9 +575,9 @@ class ConformationContainer:
def __str__(self): def __str__(self):
"""String that lists statistics of atoms and groups.""" """String that lists statistics of atoms and groups."""
str_ = 'Conformation container %s with %d atoms and %d groups' % (self.name, str_ = (
len(self), 'Conformation container %s with %d atoms and %d groups'
len(self.groups)) % (self.name, len(self), len(self.groups)))
return str_ return str_
def __len__(self): def __len__(self):