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Clean up line breaks in molecular_container.py.

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This commit is contained in:
Nathan Baker
2020-05-25 19:43:32 -07:00
parent 2658f80906
commit a27f054ac7
1 changed files with 41 additions and 38 deletions
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79
propka/molecular_container.py
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@@ -56,10 +56,11 @@ class Molecular_container:
if input_file_extension[0:4] == '.pdb': if input_file_extension[0:4] == '.pdb':
# input is a pdb file. read in atoms and top up containers to make # input is a pdb file. read in atoms and top up containers to make
# sure that all atoms are present in all conformations # sure that all atoms are present in all conformations
[self.conformations, self.conformation_names] \ [self.conformations, self.conformation_names] = (
= propka.pdb.read_pdb(input_file, self.version.parameters, self) propka.pdb.read_pdb(input_file, self.version.parameters, self))
if len(self.conformations) == 0: if len(self.conformations) == 0:
info('Error: The pdb file does not seems to contain any molecular conformations') info('Error: The pdb file does not seems to contain any '
'molecular conformations')
sys.exit(-1) sys.exit(-1)
self.top_up_conformations() self.top_up_conformations()
# make a structure precheck # make a structure precheck
@@ -79,9 +80,9 @@ class Molecular_container:
propka.pdb.write_input(self, filename) propka.pdb.write_input(self, filename)
elif input_file_extension == '.propka_input': elif input_file_extension == '.propka_input':
#input is a propka_input file #input is a propka_input file
[self.conformations, self.conformation_names] \ [self.conformations, self.conformation_names] = (
= propka.pdb.read_input(input_file, self.version.parameters, propka.pdb.read_input(input_file, self.version.parameters,
self) self))
# Extract groups - this merely sets up the groups found in the # Extract groups - this merely sets up the groups found in the
# input file # input file
self.extract_groups() self.extract_groups()
@@ -94,8 +95,8 @@ class Molecular_container:
def top_up_conformations(self): def top_up_conformations(self):
"""Makes sure that all atoms are present in all conformations.""" """Makes sure that all atoms are present in all conformations."""
for name in self.conformation_names: for name in self.conformation_names:
if name != '1A' and (len(self.conformations[name]) \ if (name != '1A' and (len(self.conformations[name])
< len(self.conformations['1A'])): < len(self.conformations['1A']))):
self.conformations[name].top_up(self.conformations['1A']) self.conformations[name].top_up(self.conformations['1A'])
def find_covalently_coupled_groups(self): def find_covalently_coupled_groups(self):
@@ -109,7 +110,8 @@ class Molecular_container:
info('-' * 103) info('-' * 103)
verbose = self.options.display_coupled_residues verbose = self.options.display_coupled_residues
for name in self.conformation_names: for name in self.conformation_names:
self.conformations[name].find_non_covalently_coupled_groups(verbose=verbose) self.conformations[name].find_non_covalently_coupled_groups(
verbose=verbose)
def extract_groups(self): def extract_groups(self):
"""Identify the groups needed for pKa calculation.""" """Identify the groups needed for pKa calculation."""
@@ -125,7 +127,8 @@ class Molecular_container:
"""Calculate pKa values.""" """Calculate pKa values."""
# calculate for each conformation # calculate for each conformation
for name in self.conformation_names: for name in self.conformation_names:
self.conformations[name].calculate_pka(self.version, self.options) self.conformations[name].calculate_pka(
self.version, self.options)
# find non-covalently coupled groups # find non-covalently coupled groups
self.find_non_covalently_coupled_groups() self.find_non_covalently_coupled_groups()
# find the average of the conformations # find the average of the conformations
@@ -137,9 +140,8 @@ class Molecular_container:
"""Generate an average of conformations.""" """Generate an average of conformations."""
parameters = self.conformations[self.conformation_names[0]].parameters parameters = self.conformations[self.conformation_names[0]].parameters
# make a new configuration to hold the average values # make a new configuration to hold the average values
avr_conformation = ConformationContainer(name='average', avr_conformation = ConformationContainer(
parameters=parameters, name='average', parameters=parameters, molecular_container=self)
molecular_container=self)
container = self.conformations[self.conformation_names[0]] container = self.conformations[self.conformation_names[0]]
for group in container.get_groups_for_calculations(): for group in container.get_groups_for_calculations():
# new group to hold average values # new group to hold average values
@@ -150,8 +152,8 @@ class Molecular_container:
if group_to_add: if group_to_add:
avr_group += group_to_add avr_group += group_to_add
else: else:
str_ = 'Group %s could not be found in conformation %s.' \ str_ = ('Group %s could not be found in conformation %s.'
% (group.atom.residue_label, name) % (group.atom.residue_label, name))
warning(str_) warning(str_)
# ... and store the average value # ... and store the average value
avr_group = avr_group / len(self.conformation_names) avr_group = avr_group / len(self.conformation_names)
@@ -161,7 +163,8 @@ class Molecular_container:
self.conformations.values()))): self.conformations.values()))):
avr_conformation.non_covalently_coupled_groups = True avr_conformation.non_covalently_coupled_groups = True
# store chain info # store chain info
avr_conformation.chains = self.conformations[self.conformation_names[0]].chains avr_conformation.chains = self.conformations[
self.conformation_names[0]].chains
self.conformations['AVR'] = avr_conformation self.conformations['AVR'] = avr_conformation
def write_pka(self, filename=None, reference="neutral", def write_pka(self, filename=None, reference="neutral",
@@ -180,12 +183,14 @@ class Molecular_container:
# to an alternative pka file # to an alternative pka file
if self.options.display_coupled_residues: if self.options.display_coupled_residues:
filename = os.path.join('%s_alt_state.pka' % (self.name)) filename = os.path.join('%s_alt_state.pka' % (self.name))
if hasattr(self.version.parameters, 'output_file_tag') \ if (hasattr(self.version.parameters, 'output_file_tag')
and len(self.version.parameters.output_file_tag) > 0: and len(self.version.parameters.output_file_tag) > 0):
filename = os.path.join('%s_%s.pka' % (self.name, filename = os.path.join(
self.version.parameters.output_file_tag)) '%s_%s.pka' % (self.name,
propka.output.write_pka(self, self.version.parameters, filename=filename, self.version.parameters.output_file_tag))
conformation='AVR', reference=reference) propka.output.write_pka(
self, self.version.parameters, filename=filename,
conformation='AVR', reference=reference)
def get_folding_profile(self, conformation='AVR', reference="neutral", def get_folding_profile(self, conformation='AVR', reference="neutral",
grid=[0., 14., 0.1]): grid=[0., 14., 0.1]):
@@ -238,8 +243,8 @@ class Molecular_container:
charge_profile = [] charge_profile = []
for ph in propka.lib.make_grid(*grid): for ph in propka.lib.make_grid(*grid):
conf = self.conformations[conformation] conf = self.conformations[conformation]
q_unfolded, q_folded = conf.calculate_charge(self.version.parameters, q_unfolded, q_folded = conf.calculate_charge(
ph=ph) self.version.parameters, ph=ph)
charge_profile.append([ph, q_unfolded, q_folded]) charge_profile.append([ph, q_unfolded, q_folded])
return charge_profile return charge_profile
@@ -254,8 +259,8 @@ class Molecular_container:
1. Folded state PI 1. Folded state PI
2. Unfolded state PI 2. Unfolded state PI
""" """
charge_profile = self.get_charge_profile(conformation=conformation, charge_profile = self.get_charge_profile(
grid=grid) conformation=conformation, grid=grid)
pi_folded = pi_unfolded = [None, 1e6, 1e6] pi_folded = pi_unfolded = [None, 1e6, 1e6]
for point in charge_profile: for point in charge_profile:
pi_folded = min(pi_folded, point, key=lambda v: abs(v[2])) pi_folded = min(pi_folded, point, key=lambda v: abs(v[2]))
@@ -266,16 +271,14 @@ class Molecular_container:
pi_unfolded_value = pi_unfolded[0] pi_unfolded_value = pi_unfolded[0]
step = grid[2] step = grid[2]
# TODO - need to warn if maximum number of iterations is exceeded # TODO - need to warn if maximum number of iterations is exceeded
if (pi_folded[2] > UNK_PI_CUTOFF or pi_unfolded[1] > UNK_PI_CUTOFF) \ if ((pi_folded[2] > UNK_PI_CUTOFF
and iteration < MAX_ITERATION: or pi_unfolded[1] > UNK_PI_CUTOFF) and iteration < MAX_ITERATION):
pi_folded_value, _ = self.get_pi(conformation=conformation, pi_folded_value, _ = self.get_pi(
grid=[pi_folded[0]-step, conformation=conformation,
pi_folded[0]+step, grid=[pi_folded[0]-step, pi_folded[0]+step, step/10.0],
step/10.0], iteration=iteration+1)
iteration=iteration+1) _, pi_unfolded_value = self.get_pi(
_, pi_unfolded_value = self.get_pi(conformation=conformation, conformation=conformation,
grid=[pi_unfolded[0]-step, grid=[pi_unfolded[0]-step, pi_unfolded[0]+step, step/10.0],
pi_unfolded[0]+step, iteration=iteration+1)
step/10.0],
iteration=iteration+1)
return pi_folded_value, pi_unfolded_value return pi_folded_value, pi_unfolded_value