Clean up line breaks in molecular_container.py.
This commit is contained in:
Nathan Baker
@@ -56,10 +56,11 @@ class Molecular_container:
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if input_file_extension[0:4] == '.pdb':
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# input is a pdb file. read in atoms and top up containers to make
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# sure that all atoms are present in all conformations
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[self.conformations, self.conformation_names] \
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= propka.pdb.read_pdb(input_file, self.version.parameters, self)
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[self.conformations, self.conformation_names] = (
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propka.pdb.read_pdb(input_file, self.version.parameters, self))
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if len(self.conformations) == 0:
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info('Error: The pdb file does not seems to contain any molecular conformations')
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info('Error: The pdb file does not seems to contain any '
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'molecular conformations')
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sys.exit(-1)
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self.top_up_conformations()
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# make a structure precheck
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@@ -79,9 +80,9 @@ class Molecular_container:
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propka.pdb.write_input(self, filename)
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elif input_file_extension == '.propka_input':
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#input is a propka_input file
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[self.conformations, self.conformation_names] \
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= propka.pdb.read_input(input_file, self.version.parameters,
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self)
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[self.conformations, self.conformation_names] = (
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propka.pdb.read_input(input_file, self.version.parameters,
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self))
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# Extract groups - this merely sets up the groups found in the
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# input file
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self.extract_groups()
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@@ -94,8 +95,8 @@ class Molecular_container:
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def top_up_conformations(self):
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"""Makes sure that all atoms are present in all conformations."""
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for name in self.conformation_names:
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if name != '1A' and (len(self.conformations[name]) \
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< len(self.conformations['1A'])):
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if (name != '1A' and (len(self.conformations[name])
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< len(self.conformations['1A']))):
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self.conformations[name].top_up(self.conformations['1A'])
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def find_covalently_coupled_groups(self):
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@@ -109,7 +110,8 @@ class Molecular_container:
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info('-' * 103)
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verbose = self.options.display_coupled_residues
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for name in self.conformation_names:
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self.conformations[name].find_non_covalently_coupled_groups(verbose=verbose)
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self.conformations[name].find_non_covalently_coupled_groups(
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verbose=verbose)
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def extract_groups(self):
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"""Identify the groups needed for pKa calculation."""
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@@ -125,7 +127,8 @@ class Molecular_container:
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"""Calculate pKa values."""
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# calculate for each conformation
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for name in self.conformation_names:
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self.conformations[name].calculate_pka(self.version, self.options)
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self.conformations[name].calculate_pka(
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self.version, self.options)
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# find non-covalently coupled groups
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self.find_non_covalently_coupled_groups()
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# find the average of the conformations
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@@ -137,9 +140,8 @@ class Molecular_container:
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"""Generate an average of conformations."""
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parameters = self.conformations[self.conformation_names[0]].parameters
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# make a new configuration to hold the average values
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avr_conformation = ConformationContainer(name='average',
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parameters=parameters,
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molecular_container=self)
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avr_conformation = ConformationContainer(
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name='average', parameters=parameters, molecular_container=self)
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container = self.conformations[self.conformation_names[0]]
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for group in container.get_groups_for_calculations():
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# new group to hold average values
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@@ -150,8 +152,8 @@ class Molecular_container:
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if group_to_add:
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avr_group += group_to_add
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else:
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str_ = 'Group %s could not be found in conformation %s.' \
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% (group.atom.residue_label, name)
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str_ = ('Group %s could not be found in conformation %s.'
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% (group.atom.residue_label, name))
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warning(str_)
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# ... and store the average value
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avr_group = avr_group / len(self.conformation_names)
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@@ -161,7 +163,8 @@ class Molecular_container:
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self.conformations.values()))):
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avr_conformation.non_covalently_coupled_groups = True
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# store chain info
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avr_conformation.chains = self.conformations[self.conformation_names[0]].chains
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avr_conformation.chains = self.conformations[
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self.conformation_names[0]].chains
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self.conformations['AVR'] = avr_conformation
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def write_pka(self, filename=None, reference="neutral",
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@@ -180,11 +183,13 @@ class Molecular_container:
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# to an alternative pka file
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if self.options.display_coupled_residues:
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filename = os.path.join('%s_alt_state.pka' % (self.name))
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if hasattr(self.version.parameters, 'output_file_tag') \
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and len(self.version.parameters.output_file_tag) > 0:
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filename = os.path.join('%s_%s.pka' % (self.name,
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if (hasattr(self.version.parameters, 'output_file_tag')
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and len(self.version.parameters.output_file_tag) > 0):
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filename = os.path.join(
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'%s_%s.pka' % (self.name,
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self.version.parameters.output_file_tag))
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propka.output.write_pka(self, self.version.parameters, filename=filename,
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propka.output.write_pka(
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self, self.version.parameters, filename=filename,
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conformation='AVR', reference=reference)
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def get_folding_profile(self, conformation='AVR', reference="neutral",
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@@ -238,8 +243,8 @@ class Molecular_container:
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charge_profile = []
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for ph in propka.lib.make_grid(*grid):
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conf = self.conformations[conformation]
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q_unfolded, q_folded = conf.calculate_charge(self.version.parameters,
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ph=ph)
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q_unfolded, q_folded = conf.calculate_charge(
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self.version.parameters, ph=ph)
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charge_profile.append([ph, q_unfolded, q_folded])
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return charge_profile
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@@ -254,8 +259,8 @@ class Molecular_container:
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1. Folded state PI
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2. Unfolded state PI
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"""
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charge_profile = self.get_charge_profile(conformation=conformation,
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grid=grid)
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charge_profile = self.get_charge_profile(
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conformation=conformation, grid=grid)
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pi_folded = pi_unfolded = [None, 1e6, 1e6]
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for point in charge_profile:
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pi_folded = min(pi_folded, point, key=lambda v: abs(v[2]))
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@@ -266,16 +271,14 @@ class Molecular_container:
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pi_unfolded_value = pi_unfolded[0]
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step = grid[2]
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# TODO - need to warn if maximum number of iterations is exceeded
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if (pi_folded[2] > UNK_PI_CUTOFF or pi_unfolded[1] > UNK_PI_CUTOFF) \
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and iteration < MAX_ITERATION:
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pi_folded_value, _ = self.get_pi(conformation=conformation,
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grid=[pi_folded[0]-step,
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pi_folded[0]+step,
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step/10.0],
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if ((pi_folded[2] > UNK_PI_CUTOFF
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or pi_unfolded[1] > UNK_PI_CUTOFF) and iteration < MAX_ITERATION):
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pi_folded_value, _ = self.get_pi(
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conformation=conformation,
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grid=[pi_folded[0]-step, pi_folded[0]+step, step/10.0],
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iteration=iteration+1)
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_, pi_unfolded_value = self.get_pi(conformation=conformation,
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grid=[pi_unfolded[0]-step,
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pi_unfolded[0]+step,
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step/10.0],
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_, pi_unfolded_value = self.get_pi(
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conformation=conformation,
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grid=[pi_unfolded[0]-step, pi_unfolded[0]+step, step/10.0],
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iteration=iteration+1)
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return pi_folded_value, pi_unfolded_value
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