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Clean up line breaks in group.py and hybrid36.py

Browse Source 
https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
2020-05-25 18:48:24 -07:00
parent 891fecaab3
commit 919305d8a3
2 changed files with 108 additions and 101 deletions
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193
propka/group.py
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@@ -9,40 +9,26 @@ from propka.lib import info, warning
# Constants that start with "UNK_" are a mystery to me # Constants that start with "UNK_" are a mystery to me
UNK_PKA_SCALING = -1.36 UNK_PKA_SCALING = -1.36
PROTONATOR = propka.protonate.Protonate(verbose=False) PROTONATOR = propka.protonate.Protonate(verbose=False)
EXPECTED_ATOMS_ACID_INTERACTIONS = {'COO': {'O': 2}, 'HIS': {'H': 2, 'N': 2}, EXPECTED_ATOMS_ACID_INTERACTIONS = {
'CYS': {'S': 1}, 'TYR': {'O': 1}, 'COO': {'O': 2}, 'HIS': {'H': 2, 'N': 2}, 'CYS': {'S': 1}, 'TYR': {'O': 1},
'LYS': {'N': 1}, 'ARG': {'H': 5, 'N': 3}, 'LYS': {'N': 1}, 'ARG': {'H': 5, 'N': 3}, 'ROH': {'O': 1},
'ROH': {'O': 1}, 'AMD': {'H': 2, 'N': 1}, 'AMD': {'H': 2, 'N': 1}, 'TRP': {'H': 1, 'N': 1}, 'N+': {'N': 1},
'TRP': {'H': 1, 'N': 1}, 'N+': {'N': 1}, 'C-': {'O': 2}, 'BBN': {'H': 1, 'N': 1,}, 'BBC': {'O': 1},
'C-': {'O': 2}, 'BBN': {'H': 1, 'N': 1,}, 'NAR': {'H': 1, 'N': 1}, 'NAM': {'H': 1, 'N': 1}, 'F': {'F': 1},
'BBC': {'O': 1}, 'NAR': {'H': 1, 'N': 1}, 'Cl': {'Cl': 1}, 'OH': {'H': 1, 'O': 1}, 'OP': {'O': 1}, 'O3': {'O': 1},
'NAM': {'H': 1, 'N': 1}, 'F': {'F': 1}, 'O2': {'O': 1}, 'SH': {'S': 1}, 'CG': {'H': 5, 'N': 3},
'Cl': {'Cl': 1}, 'OH': {'H': 1, 'O': 1}, 'C2N': {'H': 4, 'N': 2}, 'OCO': {'O': 2}, 'N30': {'H': 4, 'N': 1},
'OP': {'O': 1}, 'O3': {'O': 1}, 'N31': {'H': 3, 'N': 1}, 'N32': {'H': 2, 'N': 1}, 'N33': {'H': 1, 'N': 1},
'O2': {'O': 1}, 'SH': {'S': 1},
'CG': {'H': 5, 'N': 3},
'C2N': {'H': 4, 'N': 2}, 'OCO': {'O': 2},
'N30': {'H': 4, 'N': 1},
'N31': {'H': 3, 'N': 1},
'N32': {'H': 2, 'N': 1},
'N33': {'H': 1, 'N': 1},
'NP1': {'H': 2, 'N': 1}, 'N1': {'N': 1}} 'NP1': {'H': 2, 'N': 1}, 'N1': {'N': 1}}
EXPECTED_ATOMS_BASE_INTERACTIONS = {'COO': {'O': 2}, 'HIS': {'N': 2}, EXPECTED_ATOMS_BASE_INTERACTIONS = {
'CYS': {'S': 1}, 'TYR': {'O': 1}, 'COO': {'O': 2}, 'HIS': {'N': 2}, 'CYS': {'S': 1}, 'TYR': {'O': 1},
'LYS': {'N': 1}, 'ARG': {'N': 3}, 'LYS': {'N': 1}, 'ARG': {'N': 3}, 'ROH': {'O': 1}, 'AMD': {'O': 1},
'ROH': {'O': 1}, 'AMD': {'O': 1}, 'TRP': {'N': 1}, 'N+': {'N': 1}, 'C-': {'O': 2}, 'BBN': {'H': 1, 'N': 1},
'TRP': {'N': 1}, 'N+': {'N': 1}, 'BBC': {'O': 1}, 'NAR': {'H': 1, 'N': 1}, 'NAM': {'H': 1, 'N': 1},
'C-': {'O': 2}, 'BBN': {'H': 1, 'N': 1}, 'F': {'F': 1}, 'Cl': {'Cl': 1}, 'OH': {'H': 1, 'O': 1}, 'OP': {'O': 1},
'BBC': {'O': 1}, 'NAR': {'H': 1, 'N': 1}, 'O3': {'O': 1}, 'O2': {'O': 1}, 'SH': {'S': 1}, 'CG': {'N': 3},
'NAM': {'H': 1, 'N': 1}, 'F': {'F': 1}, 'C2N': {'N': 2}, 'OCO': {'O': 2}, 'N30': {'N': 1}, 'N31': {'N': 1},
'Cl': {'Cl': 1}, 'OH': {'H': 1, 'O': 1}, 'N32': {'N': 1}, 'N33': {'N': 1}, 'NP1': {'N': 1}, 'N1': {'N': 1}}
'OP': {'O': 1}, 'O3': {'O': 1},
'O2': {'O': 1}, 'SH': {'S': 1},
'CG': {'N': 3}, 'C2N': {'N': 2},
'OCO': {'O': 2}, 'N30': {'N': 1},
'N31': {'N': 1}, 'N32': {'N': 1},
'N33': {'N': 1}, 'NP1': {'N': 1},
'N1': {'N': 1}}
class Group: class Group:
@@ -93,14 +79,12 @@ class Group:
self.label = '%-3s%4d%2s' % (self.residue_type, atom.res_num, self.label = '%-3s%4d%2s' % (self.residue_type, atom.res_num,
atom.chain_id) atom.chain_id)
elif self.atom.res_name in ['DA ', 'DC ', 'DG ', 'DT ']: elif self.atom.res_name in ['DA ', 'DC ', 'DG ', 'DT ']:
self.label = '%1s%1s%1s%4d%2s' % (self.residue_type[1], self.label = '%1s%1s%1s%4d%2s' % (
atom.element, self.residue_type[1], atom.element,
atom.name.replace('\'', '')[-1], atom.name.replace('\'', '')[-1], atom.res_num, atom.chain_id)
atom.res_num,
atom.chain_id)
else: else:
self.label = '%-3s%4s%2s' % (self.residue_type, atom.name, self.label = '%-3s%4s%2s' % (
atom.chain_id) self.residue_type, atom.name, atom.chain_id)
# container for squared distances # container for squared distances
self.squared_distances = {} self.squared_distances = {}
@@ -180,8 +164,8 @@ class Group:
added = True added = True
# otherwise we just add the determinant to our list # otherwise we just add the determinant to our list
if not added: if not added:
self.determinants[type_].append(Determinant(new_determinant.group, self.determinants[type_].append(
new_determinant.value)) Determinant(new_determinant.group, new_determinant.value))
def make_covalently_coupled_line(self): def make_covalently_coupled_line(self):
"""Create line for covalent coupling. """Create line for covalent coupling.
@@ -232,8 +216,9 @@ class Group:
return self.label == other.label return self.label == other.label
else: else:
# For heterogene atoms we also need to check the residue number # For heterogene atoms we also need to check the residue number
return (self.label == other.label) \ return (
and (self.atom.res_num == other.atom.res_num) (self.label == other.label)
and (self.atom.res_num == other.atom.res_num))
def __hash__(self): def __hash__(self):
"""Needed for creating sets of groups.""" """Needed for creating sets of groups."""
@@ -241,8 +226,8 @@ class Group:
def __iadd__(self, other): def __iadd__(self, other):
if self.type != other.type: if self.type != other.type:
errstr = 'Cannot add groups of different types (%s and %s)' \ errstr = ('Cannot add groups of different types (%s and %s)'
% (self.type, other.type) % (self.type, other.type))
raise Exception(errstr) raise Exception(errstr)
# add all values # add all values
self.pka_value += other.pka_value self.pka_value += other.pka_value
@@ -301,8 +286,9 @@ class Group:
labels: list of labels to remove labels: list of labels to remove
""" """
for type_ in ['sidechain', 'backbone', 'coulomb']: for type_ in ['sidechain', 'backbone', 'coulomb']:
matches = list(filter(lambda d: d.label in labels, \ matches = list(
[d for d in self.determinants[type_]])) filter(lambda d: d.label
in labels, [d for d in self.determinants[type_]]))
for match in matches: for match in matches:
self.determinants[type_].remove(match) self.determinants[type_].remove(match)
@@ -354,7 +340,9 @@ class Group:
if not self.model_pka_set: if not self.model_pka_set:
self.model_pka = self.parameters.model_pkas[self.residue_type] self.model_pka = self.parameters.model_pkas[self.residue_type]
# check if we should apply a custom model pka # check if we should apply a custom model pka
key = '%s-%s'%(self.atom.res_name.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(): if key in self.parameters.custom_model_pkas.keys():
self.model_pka = self.parameters.custom_model_pkas[key] self.model_pka = self.parameters.custom_model_pkas[key]
self.model_pka_set = True self.model_pka_set = True
@@ -392,25 +380,31 @@ class Group:
self.interaction_atoms_for_bases, 'base']]: self.interaction_atoms_for_bases, 'base']]:
if self.type in expect.keys(): if self.type in expect.keys():
for elem in expect[self.type].keys(): for elem in expect[self.type].keys():
if len([a for a in found if a.element == elem]) \ if (len([a for a in found if a.element == elem])
!= expect[self.type][elem]: != expect[self.type][elem]):
ok = False ok = False
if not ok: if not ok:
str_ = 'Missing atoms or failed protonation for ' str_ = 'Missing atoms or failed protonation for '
str_ += '%s (%s) -- please check the structure' % (self.label, str_ += ('%s (%s) -- please check the structure'
self.type) % (self.label, self.type))
warning(str_) warning(str_)
warning('%s' % self) warning('%s' % self)
num_acid = sum([EXPECTED_ATOMS_ACID_INTERACTIONS[self.type][e] \ num_acid = sum(
[EXPECTED_ATOMS_ACID_INTERACTIONS[self.type][e]
for e in EXPECTED_ATOMS_ACID_INTERACTIONS[self.type].keys()]) for e in EXPECTED_ATOMS_ACID_INTERACTIONS[self.type].keys()])
num_base = sum([EXPECTED_ATOMS_BASE_INTERACTIONS[self.type][e] \ num_base = sum(
[EXPECTED_ATOMS_BASE_INTERACTIONS[self.type][e]
for e in EXPECTED_ATOMS_BASE_INTERACTIONS[self.type].keys()]) for e in EXPECTED_ATOMS_BASE_INTERACTIONS[self.type].keys()])
warning('Expected %d interaction atoms for acids, found:' % num_acid) warning(
'Expected %d interaction atoms for acids, found:' % num_acid)
for i in range(len(self.interaction_atoms_for_acids)): for i in range(len(self.interaction_atoms_for_acids)):
warning(' %s' % self.interaction_atoms_for_acids[i]) warning(
warning('Expected %d interaction atoms for bases, found:' % num_base) ' %s' % self.interaction_atoms_for_acids[i])
warning(
'Expected %d interaction atoms for bases, found:' % num_base)
for i in range(len(self.interaction_atoms_for_bases)): for i in range(len(self.interaction_atoms_for_bases)):
warning(' %s' % self.interaction_atoms_for_bases[i]) warning(
' %s' % self.interaction_atoms_for_bases[i])
def get_interaction_atoms(self, interacting_group): def get_interaction_atoms(self, interacting_group):
"""Get atoms involved in interaction with other group. """Get atoms involved in interaction with other group.
@@ -507,7 +501,8 @@ class Group:
if self.atom.cysteine_bridge: if self.atom.cysteine_bridge:
self.pka_value = 99.99 self.pka_value = 99.99
return return
self.pka_value = self.model_pka + self.energy_volume + self.energy_local self.pka_value = (
self.model_pka + self.energy_volume + self.energy_local)
for determinant_type in ['sidechain', 'backbone', 'coulomb']: for determinant_type in ['sidechain', 'backbone', 'coulomb']:
for determinant in self.determinants[determinant_type]: for determinant in self.determinants[determinant_type]:
self.pka_value += determinant.value self.pka_value += determinant.value
@@ -523,13 +518,14 @@ class Group:
back_bone += value back_bone += value
side_chain = 0.0 side_chain = 0.0
for determinant in self.determinants['sidechain']: for determinant in self.determinants['sidechain']:
if determinant.label[0:3] not in ['ASP', 'GLU', 'LYS', 'ARG', if determinant.label[0:3] not in [
'HIS', 'CYS', 'TYR', 'C- ', 'ASP', 'GLU', 'LYS', 'ARG', 'HIS', 'CYS', 'TYR', 'C- ',
'N+ ']: 'N+ ']:
value = determinant.value value = determinant.value
side_chain += value side_chain += value
self.intrinsic_pka = self.model_pka + self.energy_volume \ self.intrinsic_pka = (
+ self.energy_local + back_bone + side_chain self.model_pka + self.energy_volume + self.energy_local
+ back_bone + side_chain)
def get_summary_string(self, remove_penalised_group=False): def get_summary_string(self, remove_penalised_group=False):
"""Create summary string for this group. """Create summary string for this group.
@@ -546,13 +542,13 @@ class Group:
ligand_type = self.type ligand_type = self.type
penalty = '' penalty = ''
if self.coupled_titrating_group: if self.coupled_titrating_group:
penalty = ' NB: Discarded due to coupling with %s' \ penalty = (
% self.coupled_titrating_group.label ' NB: Discarded due to coupling with %s'
str_ = " %9s %8.2lf %10.2lf %18s %s\n" % (self.label, % self.coupled_titrating_group.label)
self.pka_value, str_ = (
self.model_pka, " %9s %8.2lf %10.2lf %18s %s\n"
ligand_type, % (self.label, self.pka_value, self.model_pka, ligand_type,
penalty) penalty))
return str_ return str_
def __str__(self): def __str__(self):
@@ -621,8 +617,8 @@ class Group:
titratable and are in that list are included; otherwise all titratable titratable and are in that list are included; otherwise all titratable
residues and CYS residues are included. residues and CYS residues are included.
""" """
return self.titratable or (self.residue_type == 'CYS' and \ return self.titratable or (
not self.exclude_cys_from_results) self.residue_type == 'CYS' and not self.exclude_cys_from_results)
class COOGroup(Group): class COOGroup(Group):
@@ -786,7 +782,8 @@ class CtermGroup(Group):
"""C-terminus group.""" """C-terminus group."""
def __init__(self, atom): def __init__(self, atom):
Group.__init__(self, atom) Group.__init__(self, atom)
self.type = 'COO' # this is to deal with the COO-C- parameter unification. # this is to deal with the COO-C- parameter unification.
self.type = 'COO'
def setup_atoms(self): def setup_atoms(self):
"""Set up atoms in group.""" """Set up atoms in group."""
@@ -820,7 +817,8 @@ class BBNGroup(Group):
the_hydrogen = self.atom.get_bonded_elements('H') the_hydrogen = self.atom.get_bonded_elements('H')
# set the center using the nitrogen # set the center using the nitrogen
self.set_center([self.atom]) self.set_center([self.atom])
self.set_interaction_atoms(the_hydrogen+[self.atom], the_hydrogen+[self.atom]) self.set_interaction_atoms(
the_hydrogen+[self.atom], the_hydrogen+[self.atom])
class BBCGroup(Group): class BBCGroup(Group):
@@ -859,7 +857,8 @@ class NARGroup(Group):
the_hydrogen = self.atom.get_bonded_elements('H') the_hydrogen = self.atom.get_bonded_elements('H')
# set the center using the nitrogen # set the center using the nitrogen
self.set_center([self.atom]) self.set_center([self.atom])
self.set_interaction_atoms(the_hydrogen+[self.atom], the_hydrogen+[self.atom]) self.set_interaction_atoms(
the_hydrogen+[self.atom], the_hydrogen+[self.atom])
class NAMGroup(Group): class NAMGroup(Group):
@@ -881,7 +880,8 @@ class NAMGroup(Group):
the_hydrogen = self.atom.get_bonded_elements('H') the_hydrogen = self.atom.get_bonded_elements('H')
# set the center using the nitrogen # set the center using the nitrogen
self.set_center([self.atom]) self.set_center([self.atom])
self.set_interaction_atoms(the_hydrogen+[self.atom], the_hydrogen+[self.atom]) self.set_interaction_atoms(
the_hydrogen+[self.atom], the_hydrogen+[self.atom])
class FGroup(Group): class FGroup(Group):
@@ -920,7 +920,8 @@ class OHGroup(Group):
the_hydrogen = self.atom.get_bonded_elements('H') the_hydrogen = self.atom.get_bonded_elements('H')
# set the center using the nitrogen # set the center using the nitrogen
self.set_center([self.atom]) self.set_center([self.atom])
self.set_interaction_atoms(the_hydrogen+[self.atom], the_hydrogen+[self.atom]) self.set_interaction_atoms(
the_hydrogen+[self.atom], the_hydrogen+[self.atom])
class OPGroup(Group): class OPGroup(Group):
@@ -938,7 +939,6 @@ class OPGroup(Group):
PROTONATOR.protonate_atom(self.atom) PROTONATOR.protonate_atom(self.atom)
# set the center using the oxygen # set the center using the oxygen
self.set_center([self.atom]) self.set_center([self.atom])
#self.set_interaction_atoms(the_hydrogen+[self.atom], the_hydrogen+[self.atom])
self.set_interaction_atoms([self.atom], [self.atom]) self.set_interaction_atoms([self.atom], [self.atom])
@@ -997,7 +997,8 @@ class CGGroup(Group):
for nitrogen in the_nitrogens: for nitrogen in the_nitrogens:
PROTONATOR.protonate_atom(nitrogen) PROTONATOR.protonate_atom(nitrogen)
the_hydrogens += nitrogen.get_bonded_elements('H') the_hydrogens += nitrogen.get_bonded_elements('H')
self.set_interaction_atoms(the_hydrogens+the_nitrogens, the_nitrogens) self.set_interaction_atoms(
the_hydrogens+the_nitrogens, the_nitrogens)
class C2NGroup(Group): class C2NGroup(Group):
@@ -1013,8 +1014,8 @@ class C2NGroup(Group):
"""Set up atoms in this group.""" """Set up atoms in this group."""
# Identify the nitrogens # Identify the nitrogens
the_nitrogens = self.atom.get_bonded_elements('N') the_nitrogens = self.atom.get_bonded_elements('N')
the_nitrogens = [n for n in the_nitrogens \ the_nitrogens = [
if len(n.get_bonded_heavy_atoms()) == 1] n for n in the_nitrogens if len(n.get_bonded_heavy_atoms()) == 1]
# set the center using the nitrogen # set the center using the nitrogen
self.set_center([self.atom]) self.set_center([self.atom])
the_hydrogens = [] the_hydrogens = []
@@ -1198,12 +1199,14 @@ class TitratableLigandGroup(Group):
self.type = 'BLG' self.type = 'BLG'
self.residue_type = 'BLG' self.residue_type = 'BLG'
else: else:
raise Exception('Unable to determine type of ligand group - charge not set?') raise Exception('Unable to determine type of ligand group - '
'charge not set?')
# check if marvin model pka has been calculated # check if marvin model pka has been calculated
# this is not true if we are reading an input file # this is not true if we are reading an input file
if atom.marvin_pka: if atom.marvin_pka:
self.model_pka = atom.marvin_pka self.model_pka = atom.marvin_pka
info('Titratable ligand group ', atom, self.model_pka, self.charge) info('Titratable ligand group ',
atom, self.model_pka, self.charge)
self.model_pka_set = True self.model_pka_set = True
@@ -1233,8 +1236,8 @@ def is_group(parameters, atom):
elif parameters.ligand_typing == 'groups': elif parameters.ligand_typing == 'groups':
ligand_group = is_ligand_group_by_groups(parameters, atom) ligand_group = is_ligand_group_by_groups(parameters, atom)
else: else:
errstr = 'Unknown ligand typing method \'%s\'' % parameters.ligand_typing raise Exception('Unknown ligand typing method \'%s\''
raise Exception(errstr) % parameters.ligand_typing)
if ligand_group: if ligand_group:
return ligand_group return ligand_group
return None return None
@@ -1314,10 +1317,13 @@ def is_ligand_group_by_groups(_, atom):
if atom.sybyl_type == 'C.2': if atom.sybyl_type == 'C.2':
# Guadinium and amidinium groups # Guadinium and amidinium groups
bonded_nitrogens = atom.get_bonded_elements('N') bonded_nitrogens = atom.get_bonded_elements('N')
npls = [n for n in bonded_nitrogens if (n.sybyl_type == 'N.pl3' \ npls = [
n for n in bonded_nitrogens
if (n.sybyl_type == 'N.pl3'
and len(n.get_bonded_heavy_atoms()) == 1)] and len(n.get_bonded_heavy_atoms()) == 1)]
if len(npls) == 2: if len(npls) == 2:
n_with_max_two_heavy_atom_bonds = [n for n in bonded_nitrogens \ n_with_max_two_heavy_atom_bonds = [
n for n in bonded_nitrogens
if len(n.get_bonded_heavy_atoms()) < 3] if len(n.get_bonded_heavy_atoms()) < 3]
if len(n_with_max_two_heavy_atom_bonds) == 2: if len(n_with_max_two_heavy_atom_bonds) == 2:
return C2NGroup(atom) return C2NGroup(atom)
@@ -1369,16 +1375,17 @@ def is_ligand_group_by_marvin_pkas(parameters, atom):
# TODO - double-check testing coverage of these functions. # TODO - double-check testing coverage of these functions.
if not atom.conformation_container.marvin_pkas_calculated: if not atom.conformation_container.marvin_pkas_calculated:
lpka = LigandPkaValues(parameters) lpka = LigandPkaValues(parameters)
lpka.get_marvin_pkas_for_molecular_container(atom.molecular_container, lpka.get_marvin_pkas_for_molecular_container(
min_ph=parameters.min_ligand_model_pka, atom.molecular_container, min_ph=parameters.min_ligand_model_pka,
max_ph=parameters.max_ligand_model_pka) max_ph=parameters.max_ligand_model_pka)
if atom.marvin_pka: if atom.marvin_pka:
return TitratableLigandGroup(atom) return TitratableLigandGroup(atom)
# Special case of oxygen in carboxyl group not assigned a pka value by marvin # Special case of oxygen in carboxyl group not assigned pka value by marvin
if atom.sybyl_type == 'O.co2': if atom.sybyl_type == 'O.co2':
atom.charge = -1.0 atom.charge = -1.0
other_oxygen = [o for o \ other_oxygen = [
in atom.get_bonded_elements('C')[0].get_bonded_elements('O') \ o for o
in atom.get_bonded_elements('C')[0].get_bonded_elements('O')
if not o == atom][0] if not o == atom][0]
atom.marvin_pka = other_oxygen.marvin_pka atom.marvin_pka = other_oxygen.marvin_pka
return TitratableLigandGroup(atom) return TitratableLigandGroup(atom)

2
propka/hybrid36.py
View File

@@ -1,4 +1,4 @@
"""Provides an alternative PDB format that can transparently encode larger atom numbers. """Provides alternative PDB format that can encode larger atom numbers.
http://cci.lbl.gov/hybrid_36/ http://cci.lbl.gov/hybrid_36/
""" """