From a27f054ac7f7d531007f6014811a349521a7f826 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Mon, 25 May 2020 19:43:32 -0700 Subject: [PATCH] Clean up line breaks in molecular_container.py. --- propka/molecular_container.py | 79 ++++++++++++++++++----------------- 1 file changed, 41 insertions(+), 38 deletions(-) diff --git a/propka/molecular_container.py b/propka/molecular_container.py index 3ef1478..0c97448 100644 --- a/propka/molecular_container.py +++ b/propka/molecular_container.py @@ -56,10 +56,11 @@ class Molecular_container: if input_file_extension[0:4] == '.pdb': # input is a pdb file. read in atoms and top up containers to make # sure that all atoms are present in all conformations - [self.conformations, self.conformation_names] \ - = propka.pdb.read_pdb(input_file, self.version.parameters, self) + [self.conformations, self.conformation_names] = ( + propka.pdb.read_pdb(input_file, self.version.parameters, self)) 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) self.top_up_conformations() # make a structure precheck @@ -79,9 +80,9 @@ class Molecular_container: propka.pdb.write_input(self, filename) elif input_file_extension == '.propka_input': #input is a propka_input file - [self.conformations, self.conformation_names] \ - = propka.pdb.read_input(input_file, self.version.parameters, - self) + [self.conformations, self.conformation_names] = ( + propka.pdb.read_input(input_file, self.version.parameters, + self)) # Extract groups - this merely sets up the groups found in the # input file self.extract_groups() @@ -94,8 +95,8 @@ class Molecular_container: def top_up_conformations(self): """Makes sure that all atoms are present in all conformations.""" for name in self.conformation_names: - if name != '1A' and (len(self.conformations[name]) \ - < len(self.conformations['1A'])): + if (name != '1A' and (len(self.conformations[name]) + < len(self.conformations['1A']))): self.conformations[name].top_up(self.conformations['1A']) def find_covalently_coupled_groups(self): @@ -109,7 +110,8 @@ class Molecular_container: info('-' * 103) verbose = self.options.display_coupled_residues 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): """Identify the groups needed for pKa calculation.""" @@ -125,7 +127,8 @@ class Molecular_container: """Calculate pKa values.""" # calculate for each conformation 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 self.find_non_covalently_coupled_groups() # find the average of the conformations @@ -137,9 +140,8 @@ class Molecular_container: """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) + 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 @@ -150,8 +152,8 @@ class Molecular_container: if group_to_add: avr_group += group_to_add else: - str_ = 'Group %s could not be found in conformation %s.' \ - % (group.atom.residue_label, name) + str_ = ('Group %s could not be found in conformation %s.' + % (group.atom.residue_label, name)) warning(str_) # ... and store the average value avr_group = avr_group / len(self.conformation_names) @@ -161,7 +163,8 @@ class Molecular_container: self.conformations.values()))): avr_conformation.non_covalently_coupled_groups = True # 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 def write_pka(self, filename=None, reference="neutral", @@ -180,12 +183,14 @@ class Molecular_container: # to an alternative pka file if self.options.display_coupled_residues: filename = os.path.join('%s_alt_state.pka' % (self.name)) - if hasattr(self.version.parameters, 'output_file_tag') \ - and len(self.version.parameters.output_file_tag) > 0: - filename = os.path.join('%s_%s.pka' % (self.name, - self.version.parameters.output_file_tag)) - propka.output.write_pka(self, self.version.parameters, filename=filename, - conformation='AVR', reference=reference) + if (hasattr(self.version.parameters, 'output_file_tag') + and len(self.version.parameters.output_file_tag) > 0): + filename = os.path.join( + '%s_%s.pka' % (self.name, + self.version.parameters.output_file_tag)) + propka.output.write_pka( + self, self.version.parameters, filename=filename, + conformation='AVR', reference=reference) def get_folding_profile(self, conformation='AVR', reference="neutral", grid=[0., 14., 0.1]): @@ -238,8 +243,8 @@ class Molecular_container: charge_profile = [] for ph in propka.lib.make_grid(*grid): conf = self.conformations[conformation] - q_unfolded, q_folded = conf.calculate_charge(self.version.parameters, - ph=ph) + q_unfolded, q_folded = conf.calculate_charge( + self.version.parameters, ph=ph) charge_profile.append([ph, q_unfolded, q_folded]) return charge_profile @@ -254,8 +259,8 @@ class Molecular_container: 1. Folded state PI 2. Unfolded state PI """ - charge_profile = self.get_charge_profile(conformation=conformation, - grid=grid) + charge_profile = self.get_charge_profile( + conformation=conformation, grid=grid) pi_folded = pi_unfolded = [None, 1e6, 1e6] for point in charge_profile: 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] step = grid[2] # 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) \ - and iteration < MAX_ITERATION: - pi_folded_value, _ = self.get_pi(conformation=conformation, - grid=[pi_folded[0]-step, - pi_folded[0]+step, - step/10.0], - iteration=iteration+1) - _, pi_unfolded_value = self.get_pi(conformation=conformation, - grid=[pi_unfolded[0]-step, - pi_unfolded[0]+step, - step/10.0], - iteration=iteration+1) + if ((pi_folded[2] > UNK_PI_CUTOFF + or pi_unfolded[1] > UNK_PI_CUTOFF) and iteration < MAX_ITERATION): + pi_folded_value, _ = self.get_pi( + conformation=conformation, + grid=[pi_folded[0]-step, pi_folded[0]+step, step/10.0], + iteration=iteration+1) + _, pi_unfolded_value = self.get_pi( + conformation=conformation, + grid=[pi_unfolded[0]-step, pi_unfolded[0]+step, step/10.0], + iteration=iteration+1) return pi_folded_value, pi_unfolded_value