De-lint molecular_container.py.
This commit is contained in:
Nathan Baker
@@ -1,145 +1,140 @@
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#!/usr/bin/python
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#
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# Molecular container for storing all contents of pdb files
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#
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#
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from __future__ import division
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from __future__ import print_function
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import os, sys
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import propka.pdb, propka.version, propka.output, propka.conformation_container, propka.group, propka.lib
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"""Molecular container for storing all contents of PDB files."""
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import os
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import sys
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import propka.pdb
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import propka.version
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import propka.output
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import propka.group
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import propka.lib
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from propka.conformation_container import ConformationContainer
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from propka.lib import info, warning
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# TODO - these are constants whose origins are a little murky
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UNK_PI_CUTOFF = 0.01
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# Maximum number of iterations for finding PI
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MAX_ITERATION = 4
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class Molecular_container:
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"""Container for storing molecular contents of PDB files."""
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def __init__(self, input_file, options=None):
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"""Initialize molecular container.
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Args:
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input_file: molecular input file
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options: options object
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"""
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# printing out header before parsing input
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propka.output.printHeader()
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# set up some values
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self.options = options
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self.input_file = input_file
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# TODO - replace this indelicate os.path code with pathlib
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self.dir = os.path.split(input_file)[0]
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self.file = os.path.split(input_file)[1]
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self.name = self.file[0:self.file.rfind('.')]
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input_file_extension = input_file[input_file.rfind('.'):]
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# set the version
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if options:
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parameters = propka.parameters.Parameters(self.options.parameters)
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else:
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parameters = propka.parameters.Parameters('propka.cfg')
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try:
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exec('self.version = propka.version.%s(parameters)'%parameters.version)
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version_class = getattr(propka.version, parameters.version)
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self.version = version_class(parameters)
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except:
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raise Exception('Error: Version %s does not exist'%parameters.version)
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errstr = 'Error: Version %s does not exist' % parameters.version
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raise Exception(errstr)
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# read the input file
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if input_file_extension[0:4] == '.pdb':
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# input is a pdb file
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# read in atoms and top up containers to make sure that all atoms are present in all conformations
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[self.conformations, self.conformation_names] = propka.pdb.read_pdb(input_file, self.version.parameters,self)
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if len(self.conformations)==0:
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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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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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sys.exit(-1)
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self.top_up_conformations()
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# make a structure precheck
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propka.pdb.protein_precheck(self.conformations, self.conformation_names)
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propka.pdb.protein_precheck(self.conformations,
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self.conformation_names)
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# set up atom bonding and protonation
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self.version.setup_bonding_and_protonation(self)
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# Extract groups
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self.extract_groups()
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# sort atoms
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for name in self.conformation_names:
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self.conformations[name].sort_atoms()
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# find coupled groups
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self.find_covalently_coupled_groups()
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# write out the input file
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filename = self.file.replace(input_file_extension,'.propka_input')
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filename = self.file.replace(input_file_extension, '.propka_input')
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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] = propka.pdb.read_input(input_file, self.version.parameters, self)
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# Extract groups - this merely sets up the groups found in the 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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# 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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# do some additional set up
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self.additional_setup_when_reading_input_file()
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else:
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info('Unrecognized input file:%s' % input_file)
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sys.exit(-1)
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return
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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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"""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]) < 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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return
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def find_covalently_coupled_groups(self):
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"""Find covalently coupled groups."""
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info('-' * 103)
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for name in self.conformation_names:
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self.conformations[name].find_covalently_coupled_groups()
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return
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def find_non_covalently_coupled_groups(self):
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"""Find non-covalently coupled groups."""
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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=self.options.display_coupled_residues)
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return
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self.conformations[name].find_non_covalently_coupled_groups(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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"""Identify the groups needed for pKa calculation."""
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for name in self.conformation_names:
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self.conformations[name].extract_groups()
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return
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def additional_setup_when_reading_input_file(self):
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"""Additional setup."""
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for name in self.conformation_names:
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self.conformations[name].additional_setup_when_reading_input_file()
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return
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def calculate_pka(self):
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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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# 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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self.average_of_conformations()
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# print out the conformation-average results
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propka.output.printResult(self, 'AVR', self.version.parameters)
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return
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def average_of_conformations(self):
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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 = propka.conformation_container.ConformationContainer(name='average',
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parameters=self.conformations[self.conformation_names[0]].parameters,
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molecular_container=self)
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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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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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@@ -150,104 +145,133 @@ 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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warning('Group %s could not be found in conformation %s.' % (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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avr_conformation.groups.append(avr_group)
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# store information on coupling in the average container
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if len(list(filter(lambda c: c.non_covalently_coupled_groups, self.conformations.values()))):
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if len(list(filter(lambda c: c.non_covalently_coupled_groups,
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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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self.conformations['AVR'] = avr_conformation
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return
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def write_pka(self, filename=None, reference="neutral", direction="folding", options=None):
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#for name in self.conformation_names:
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# propka.output.writePKA(self, self.version.parameters, filename='%s_3.1_%s.pka'%(self.name, name),
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# conformation=name,reference=reference,
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# direction=direction, options=options)
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def write_pka(self, filename=None, reference="neutral",
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direction="folding", options=None):
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"""Write pKa information to a file.
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Args:
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filename: file to write to
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reference: reference state
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direction: folding vs. unfolding
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options: options object
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"""
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# write out the average conformation
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filename=os.path.join('%s.pka'%(self.name))
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# if the display_coupled_residues option is true,
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# write the results out to an alternative pka file
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filename = os.path.join('%s.pka' % (self.name))
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# if the display_coupled_residues option is true, write the results out
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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') and len(self.version.parameters.output_file_tag)>0:
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filename=os.path.join('%s_%s.pka'%(self.name,self.version.parameters.output_file_tag))
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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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self.version.parameters.output_file_tag))
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propka.output.writePKA(self, self.version.parameters, filename=filename,
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conformation='AVR',reference=reference,
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conformation='AVR', reference=reference,
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direction=direction, options=options)
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return
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def get_folding_profile(self, conformation='AVR', reference="neutral",
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grid=[0., 14., 0.1]):
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"""Get a folding profile.
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def getFoldingProfile(self, conformation='AVR',reference="neutral", direction="folding", grid=[0., 14., 0.1], options=None):
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Args:
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conformation: conformation to select
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reference: reference state
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direction: folding direction (folding)
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grid: the grid of pH values [min, max, step_size]
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options: options object
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Returns:
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TODO - figure out what these are
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1. profile
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2. opt
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3. range_80pct
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4. stability_range
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"""
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# calculate stability profile
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profile = []
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for ph in propka.lib.make_grid(*grid):
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ddg = self.conformations[conformation].calculate_folding_energy( ph=ph, reference=reference)
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#info(ph,ddg)
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conf = self.conformations[conformation]
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ddg = conf.calculate_folding_energy(ph=ph, reference=reference)
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profile.append([ph, ddg])
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# find optimum
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opt =[None, 1e6]
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opt = [None, 1e6]
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for point in profile:
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opt = min(opt, point, key=lambda v:v[1])
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opt = min(opt, point, key=lambda v: v[1])
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# find values within 80 % of optimum
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range_80pct = [None, None]
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values_within_80pct = [p[0] for p in profile if p[1]< 0.8*opt[1]]
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if len(values_within_80pct)>0:
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values_within_80pct = [p[0] for p in profile if p[1] < 0.8*opt[1]]
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if len(values_within_80pct) > 0:
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range_80pct = [min(values_within_80pct), max(values_within_80pct)]
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# find stability range
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stability_range = [None, None]
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stable_values = [p[0] for p in profile if p[1]< 0.0]
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if len(stable_values)>0:
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stable_values = [p[0] for p in profile if p[1] < 0.0]
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if len(stable_values) > 0:
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stability_range = [min(stable_values), max(stable_values)]
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return profile, opt, range_80pct, stability_range
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def get_charge_profile(self, conformation='AVR', grid=[0., 14., .1]):
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"""Get charge profile for conformation as function of pH.
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def getChargeProfile(self, conformation='AVR', grid=[0., 14., .1]):
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Args:
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conformation: conformation to test
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grid: grid of pH values [min, max, step]
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Returns:
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list of charge state values
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"""
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charge_profile = []
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for ph in propka.lib.make_grid(*grid):
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q_unfolded, q_folded = self.conformations[conformation].calculate_charge(self.version.parameters, ph=ph)
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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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charge_profile.append([ph, q_unfolded, q_folded])
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return charge_profile
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def getPI(self, conformation='AVR', grid=[0., 14., 1], iteration=0):
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#info('staring',grid, iteration)
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# search
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charge_profile = self.getChargeProfile(conformation=conformation, grid=grid)
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pi = []
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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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pi_unfolded = min(pi_unfolded, point, key=lambda v:abs(v[1]))
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def get_pi(self, conformation='AVR', grid=[0., 14., 1], iteration=0):
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"""Get the isoelectric points for folded and unfolded states.
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# If results are not good enough, do it again with a higher sampling resolution
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pi_folded_value = pi_folded[0]
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Args:
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conformation: conformation to test
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grid: grid of pH values [min, max, step]
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iteration: iteration number of process
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Returns:
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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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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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pi_unfolded = min(pi_unfolded, point, key=lambda v: abs(v[1]))
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# If results are not good enough, do it again with a higher sampling
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# resolution
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pi_folded_value = pi_folded[0]
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pi_unfolded_value = pi_unfolded[0]
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step = grid[2]
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if (pi_folded[2] > 0.01 or pi_unfolded[1] > 0.01) and iteration<4:
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pi_folded_value, x = self.getPI(conformation=conformation, grid=[pi_folded[0]-step, pi_folded[0]+step, step/10.0], iteration=iteration+1)
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x, pi_unfolded_value = self.getPI(conformation=conformation, grid=[pi_unfolded[0]-step, pi_unfolded[0]+step, step/10.0], iteration=iteration+1)
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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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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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iteration=iteration+1)
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return pi_folded_value, pi_unfolded_value
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if __name__ == '__main__':
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input_file = sys.argv[1]
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mc = Molecular_container(input_file)
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@@ -76,10 +76,10 @@ def writePKA(protein, parameters, filename=None, conformation ='1A',reference="n
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str += "%s\n" % ( getTheLine() )
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# printing Folding Profile
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str += getFoldingProfileSection(protein, conformation=conformation, reference=reference, direction=direction, window=[0., 14., 1.0], options=options)
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str += get_folding_profileSection(protein, conformation=conformation, reference=reference, window=[0., 14., 1.0])
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# printing Protein Charge Profile
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str += getChargeProfileSection(protein, conformation=conformation)
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str += get_charge_profileSection(protein, conformation=conformation)
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# now, writing the pka text to file
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file.write(str)
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@@ -156,7 +156,7 @@ def getSummarySection(protein, conformation, parameters):
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return str
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def getFoldingProfileSection(protein, conformation='AVR', direction="folding", reference="neutral", window=[0., 14., 1.0], verbose=False, options=None):
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def get_folding_profileSection(protein, conformation='AVR', direction="folding", reference="neutral", window=[0., 14., 1.0], verbose=False, options=None):
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"""
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returns the protein-folding-profile section
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"""
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@@ -164,9 +164,9 @@ def getFoldingProfileSection(protein, conformation='AVR', direction="folding", r
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str += "\n"
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str += "Free energy of %9s (kcal/mol) as a function of pH (using %s reference)\n" % (direction, reference)
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profile, [pH_opt, dG_opt], [dG_min, dG_max], [pH_min, pH_max] = protein.getFoldingProfile(conformation=conformation,
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profile, [pH_opt, dG_opt], [dG_min, dG_max], [pH_min, pH_max] = protein.get_folding_profile(conformation=conformation,
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reference=reference,
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direction=direction, grid=[0., 14., 0.1], options=options)
|
||||
grid=[0., 14., 0.1])
|
||||
if profile == None:
|
||||
str += "Could not determine folding profile\n"
|
||||
else:
|
||||
@@ -195,13 +195,13 @@ def getFoldingProfileSection(protein, conformation='AVR', direction="folding", r
|
||||
|
||||
|
||||
|
||||
def getChargeProfileSection(protein, conformation='AVR', options=None):
|
||||
def get_charge_profileSection(protein, conformation='AVR', options=None):
|
||||
"""
|
||||
returns the protein-folding-profile section
|
||||
"""
|
||||
str = "Protein charge of folded and unfolded state as a function of pH\n"
|
||||
|
||||
profile = protein.getChargeProfile(conformation=conformation,grid=[0., 14., 1.])
|
||||
profile = protein.get_charge_profile(conformation=conformation,grid=[0., 14., 1.])
|
||||
if profile == None:
|
||||
str += "Could not determine charge profile\n"
|
||||
else:
|
||||
@@ -210,7 +210,7 @@ def getChargeProfileSection(protein, conformation='AVR', options=None):
|
||||
str += "%6.2lf%10.2lf%8.2lf\n" % (pH, Q_mod, Q_pro)
|
||||
|
||||
|
||||
pI_pro, pI_mod = protein.getPI(conformation=conformation)
|
||||
pI_pro, pI_mod = protein.get_pi(conformation=conformation)
|
||||
if pI_pro == None or pI_mod == None:
|
||||
str += "Could not determine the pI\n\n"
|
||||
else:
|
||||
|
||||
Reference in New Issue
Block a user