De-lint parameters.py.
This commit is contained in:
Nathan Baker
@@ -1,232 +1,262 @@
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from __future__ import division
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from __future__ import print_function
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import math
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"""Holds parameters and settings."""
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import pkg_resources
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import propka.lib as lib
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import sys, os
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from propka.lib import info, warning
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import pkg_resources
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# names and types of all key words in configuration file
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matrices = ['interaction_matrix']
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pair_wise_matrices = ['sidechain_cutoffs']
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number_dictionaries = ['VanDerWaalsVolume','charge','model_pkas','ions',
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'valence_electrons','custom_model_pkas']
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list_dictionaries = ['backbone_NH_hydrogen_bond','backbone_CO_hydrogen_bond']
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string_dictionaries = ['protein_group_mapping']
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string_lists = ['ignore_residues','angular_dependent_sidechain_interactions',
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'acid_list','base_list','exclude_sidechain_interactions',
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'backbone_reorganisation_list','write_out_order']
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distances = ['desolv_cutoff','buried_cutoff','coulomb_cutoff1','coulomb_cutoff2']
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parameters = ['Nmin','Nmax','desolvationSurfaceScalingFactor','desolvationPrefactor',
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'desolvationAllowance','coulomb_diel','COO_HIS_exception','OCO_HIS_exception',
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'CYS_HIS_exception','CYS_CYS_exception','min_ligand_model_pka','max_ligand_model_pka',
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'include_H_in_interactions','coupling_max_number_of_bonds',
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'min_bond_distance_for_hydrogen_bonds','coupling_penalty',
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'shared_determinants','common_charge_centre','hide_penalised_group', 'remove_penalised_group',
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'max_intrinsic_pka_diff','min_interaction_energy','max_free_energy_diff','min_swap_pka_shift',
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'min_pka','max_pka','sidechain_interaction']
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strings = ['version','output_file_tag','ligand_typing','pH','reference']
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MATRICES = ['interaction_matrix']
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PAIR_WISE_MATRICES = ['sidechain_cutoffs']
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NUMBER_DICTIONARIES = ['VanDerWaalsVolume', 'charge', 'model_pkas', 'ions',
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'valence_electrons', 'custom_model_pkas']
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LIST_DICTIONARIES = ['backbone_NH_hydrogen_bond', 'backbone_CO_hydrogen_bond']
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STRING_DICTIONARIES = ['protein_group_mapping']
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STRING_LISTS = ['ignore_residues', 'angular_dependent_sidechain_interactions',
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'acid_list', 'base_list', 'exclude_sidechain_interactions',
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'backbone_reorganisation_list', 'write_out_order']
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DISTANCES = ['desolv_cutoff', 'buried_cutoff', 'coulomb_cutoff1',
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'coulomb_cutoff2']
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PARAMETERS = ['Nmin', 'Nmax', 'desolvationSurfaceScalingFactor',
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'desolvationPrefactor', 'desolvationAllowance', 'coulomb_diel',
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'COO_HIS_exception', 'OCO_HIS_exception', 'CYS_HIS_exception',
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'CYS_CYS_exception', 'min_ligand_model_pka',
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'max_ligand_model_pka', 'include_H_in_interactions',
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'coupling_max_number_of_bonds',
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'min_bond_distance_for_hydrogen_bonds', 'coupling_penalty',
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'shared_determinants', 'common_charge_centre',
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'hide_penalised_group', 'remove_penalised_group',
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'max_intrinsic_pka_diff', 'min_interaction_energy',
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'max_free_energy_diff', 'min_swap_pka_shift', 'min_pka',
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'max_pka', 'sidechain_interaction']
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STRINGS = ['version', 'output_file_tag', 'ligand_typing', 'pH', 'reference']
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class Parameters:
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def __init__(self, parameter_file):
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"""PROPKA parameter class."""
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def __init__(self, parameter_file):
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"""Initialize parameter class.
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Args:
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parameter_file: file with parameters
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"""
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# TODO - need to define all members explicitly
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self.model_pkas = {}
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self.interaction_matrix = InteractionMatrix("interaction_matrix")
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self.sidechain_cutoffs = None
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# TODO - it would be nice to rename these but they're defined everywhere
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self.COO_HIS_exception = None
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self.OCO_HIS_exception = None
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self.CYS_HIS_exception = None
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self.CYS_CYS_exception = None
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# These functions set up remaining data structures implicitly
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self.set_up_data_structures()
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self.read_parameters(parameter_file)
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#self.print_interaction_parameters()
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#self.print_interaction_parameters_latex()
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#####self.print_interactions_latex()
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#sys.exit(0)
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def read_parameters(self, file_):
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"""Read parameters from file.
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return
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def read_parameters(self, file):
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Args:
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file_: file to read
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"""
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# try to locate the parameters file
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try:
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ifile = pkg_resources.resource_filename(__name__, file)
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input = lib.open_file_for_reading(ifile)
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except:
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input = lib.open_file_for_reading(file)
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for line in input:
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ifile = pkg_resources.resource_filename(__name__, file_)
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input_ = lib.open_file_for_reading(ifile)
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except (IOError, FileNotFoundError, ValueError):
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input_ = lib.open_file_for_reading(file_)
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for line in input_:
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self.parse_line(line)
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return
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def parse_line(self, line):
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"""Parse parameter file line."""
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# first, remove comments
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comment_pos = line.find('#')
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if comment_pos != -1:
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line = line[:comment_pos]
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# split the line into words
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words = line.split()
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if len(words) == 0:
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return
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# parse the words
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if len(words)==3 and words[0] in number_dictionaries:
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if len(words) == 3 and words[0] in NUMBER_DICTIONARIES:
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self.parse_to_number_dictionary(words)
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elif len(words)==2 and words[0] in string_lists:
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elif len(words) == 2 and words[0] in STRING_LISTS:
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self.parse_to_string_list(words)
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elif len(words)==2 and words[0] in distances:
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elif len(words) == 2 and words[0] in DISTANCES:
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self.parse_distance(words)
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elif len(words)==2 and words[0] in parameters:
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elif len(words) == 2 and words[0] in PARAMETERS:
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self.parse_parameter(words)
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elif len(words)==2 and words[0] in strings:
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elif len(words) == 2 and words[0] in STRINGS:
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self.parse_string(words)
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elif len(words)>2 and words[0] in list_dictionaries:
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elif len(words) > 2 and words[0] in LIST_DICTIONARIES:
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self.parse_to_list_dictionary(words)
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elif words[0] in matrices+pair_wise_matrices:
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elif words[0] in MATRICES+PAIR_WISE_MATRICES:
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self.parse_to_matrix(words)
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elif len(words)==3 and words[0] in string_dictionaries:
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elif len(words) == 3 and words[0] in STRING_DICTIONARIES:
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self.parse_to_string_dictionary(words)
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#info(words)
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return
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def parse_to_number_dictionary(self, words):
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exec('self.%s[\'%s\'] = %s'%tuple(words))
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return
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"""Parse field to number dictionary.
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Args:
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words: strings to parse.
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"""
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dict_ = getattr(self, words[0])
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key = words[1]
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value = words[2]
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dict_[key] = float(value)
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def parse_to_string_dictionary(self, words):
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exec('self.%s[\'%s\'] = \'%s\''%tuple(words))
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return
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"""Parse field to string dictionary.
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Args:
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words: strings to parse
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"""
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dict_ = getattr(self, words[0])
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key = words[1]
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value = words[2]
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dict_[key] = value
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def parse_to_list_dictionary(self, words):
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exec('if not \'%s\' in self.%s.keys(): self.%s[\'%s\'] = []'%(words[1],words[0],words[0],words[1]))
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for word in words[2:]:
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exec('self.%s[\'%s\'].append(%s)'%(words[0],words[1],word))
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"""Parse field to list dictionary.
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return
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Args:
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words: strings to parse.
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"""
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dict_ = getattr(self, words[0])
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key = words[1]
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if not key in dict_:
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dict_[key] = []
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for value in words[2:]:
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if isinstance(value, list):
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dict_[key].append([float(x) for x in value])
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dict_[key].append(float(value))
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def parse_to_string_list(self, words):
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exec('self.%s.append(\'%s\')'%tuple(words))
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return
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"""Parse field to string list.
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Args:
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words: strings to parse
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"""
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list_ = getattr(self, words[0])
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value = words[1]
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list_.append(value)
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def parse_to_matrix(self, words):
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exec('self.%s.add(%s)'%(words[0],tuple(words[1:])))
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return
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"""Parse field to matrix.
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Args:
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words: strings to parse
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"""
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matrix = getattr(self, words[0])
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value = tuple(words[1:])
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matrix.add(value)
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def parse_distance(self, words):
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# float check needed
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exec('self.%s = %s'%tuple(words))
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exec('self.%s_squared = pow(%s,2)'%tuple(words))
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return
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"""Parse field to distance.
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Args:
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words: strings to parse
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"""
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value = float(words[1])
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setattr(self, words[0], value)
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value_sq = value*value
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setattr(self, "%s_squared" % words[0], value_sq)
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def parse_parameter(self, words):
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exec('self.%s = %s'%tuple(words))
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return
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"""Parse field to parameters.
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Args:
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words: strings to parse
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"""
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value = float(words[1])
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setattr(self, words[0], value)
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def parse_string(self, words):
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#info('self.%s = \'%s\''%tuple(words))
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exec('self.%s = \'%s\''%tuple(words))
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return
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"""Parse field to strings.
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Args:
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words: strings to parse
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"""
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setattr(self, words[0], words[1])
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def set_up_data_structures(self):
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for key_word in number_dictionaries+list_dictionaries+string_dictionaries:
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exec('self.%s = {}'%key_word)
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for key_word in string_lists:
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exec('self.%s = []'%key_word)
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for key_word in strings:
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exec('self.%s = \'\''%key_word)
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for key_word in matrices:
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exec('self.%s = Interaction_matrix(\'%s\')'%(key_word,key_word))
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for key_word in pair_wise_matrices:
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exec('self.%s =Pair_wise_matrix(\'%s\')'%(key_word,key_word))
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"""Set up internal data structures.
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return
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TODO - it would be better to make these assignments explicit in __init__.
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"""
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for key_word in NUMBER_DICTIONARIES + LIST_DICTIONARIES \
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+ STRING_DICTIONARIES:
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setattr(self, key_word, {})
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for key_word in STRING_LISTS:
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setattr(self, key_word, [])
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for key_word in STRINGS:
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setattr(self, key_word, "")
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for key_word in MATRICES:
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matrix = InteractionMatrix(key_word)
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setattr(self, key_word, matrix)
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for key_word in PAIR_WISE_MATRICES:
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matrix = PairwiseMatrix(key_word)
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setattr(self, key_word, matrix)
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def print_interaction_parameters(self):
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"""Print interaction parameters."""
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info('--------------- Model pKa values ----------------------')
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for k in self.model_pkas.keys():
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for k in self.model_pkas:
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info('%3s %8.2f' % (k, self.model_pkas[k]))
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info('')
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info('--------------- Interactions --------------------------')
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agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD', 'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
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lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
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map = {
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'CG' :['ARG'],
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'C2N':['ARG'],
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'N30':['N+','LYS'],
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'N31':['N+','LYS'],
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'N32':['N+','LYS'],
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'N33':['N+','LYS'] ,
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'NAR':['HIS'],
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'OCO':['COO'],
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'OP' :[],#['TYR','SER'],
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'SH' :['CYS'] ,
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'NP1':[],
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'OH' :['ROH'],
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'O3' :[] ,
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'CL' :[],
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'F' :[],
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'NAM':['AMD'],
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'N1' :[],
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'O2' :[]}
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for g1 in agroups:
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for g2 in lgroups:
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interaction = '%3s %3s %1s %4s %4s'%(g1,g2,
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self.interaction_matrix[g1][g2],
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self.sidechain_cutoffs.get_value(g1,g2)[0],
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self.sidechain_cutoffs.get_value(g1,g2)[1])
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agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD',
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'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32',
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'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM',
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'N1', 'O2', 'OP', 'SH']
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lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO',
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'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
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map_ = {'CG': ['ARG'], 'C2N': ['ARG'], 'N30': ['N+', 'LYS'],
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'N31': ['N+', 'LYS'], 'N32': ['N+', 'LYS'], 'N33': ['N+', 'LYS'],
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'NAR': ['HIS'], 'OCO': ['COO'], 'OP': [], 'SH': ['CYS'],
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'NP1': [], 'OH': ['ROH'], 'O3': [], 'CL': [], 'F': [],
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'NAM': ['AMD'], 'N1': [], 'O2': []}
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for group1 in agroups:
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for group2 in lgroups:
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interaction = '%3s %3s %1s %4s %4s' \
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% (group1, group2, self.interaction_matrix[group1][group2], \
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self.sidechain_cutoffs.get_value(group1, group2)[0], \
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self.sidechain_cutoffs.get_value(group1, group2)[1])
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map_interaction = ''
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if g2 in map:
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for m in map[g2]:
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map_interaction += '|%3s %3s %1s %4s %4s'%(g1,m,
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self.interaction_matrix[g1][m],
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self.sidechain_cutoffs.get_value(g1,m)[0],
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self.sidechain_cutoffs.get_value(g1,m)[1])
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if self.interaction_matrix[g1][m] != self.interaction_matrix[g1][g2]:
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if group2 in map_:
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for val in map_[group2]:
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map_interaction += '|%3s %3s %1s %4s %4s' \
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% (group1, val, \
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self.interaction_matrix[group1][val], \
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self.sidechain_cutoffs.get_value(group1, val)[0], \
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self.sidechain_cutoffs.get_value(group1, val)[1])
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if self.interaction_matrix[group1][val] \
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!= self.interaction_matrix[group1][group2]:
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map_interaction += '* '
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if self.sidechain_cutoffs.get_value(g1,m)[0] != self.sidechain_cutoffs.get_value(g1,g2)[0] or \
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self.sidechain_cutoffs.get_value(g1,m)[1] != self.sidechain_cutoffs.get_value(g1,g2)[1]:
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if self.sidechain_cutoffs.get_value(group1, val)[0] \
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!= self.sidechain_cutoffs.get_value(group1, group2)[0] \
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or self.sidechain_cutoffs.get_value(group1, val)[1] \
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!= self.sidechain_cutoffs.get_value(group1, group2)[1]:
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map_interaction += '! '
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else:
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map_interaction += ' '
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if len(map[g2])==0 and (self.sidechain_cutoffs.get_value(g1,g2)[0] !=3 or self.sidechain_cutoffs.get_value(g1,g2)[1] != 4):
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if len(map_[group2]) == 0 \
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and (self.sidechain_cutoffs.get_value(group1, group2)[0] \
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!= 3 or self.sidechain_cutoffs.get_value(group1, group2)[1] != 4):
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map_interaction += '? '
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info(interaction, map_interaction)
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if g1==g2:
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if group1 == group2:
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break
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info('-')
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info('--------------- Exceptions ----------------------------')
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info('COO-HIS', self.COO_HIS_exception)
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info('OCO-HIS', self.OCO_HIS_exception)
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info('CYS-HIS', self.CYS_HIS_exception)
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info('CYS-CYS', self.CYS_CYS_exception)
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info('--------------- Mapping -------------------------------')
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info("""
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Titratable:
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@@ -251,45 +281,19 @@ NAM
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N1
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O2
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""")
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return
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def print_interaction_parameters_latex(self):
|
||||
# info('--------------- Model pKa values ----------------------')
|
||||
# for k in self.model_pkas.keys():
|
||||
# info('%3s %8.2f'%(k,self.model_pkas[k]))
|
||||
|
||||
# info('')
|
||||
# info('--------------- Interactions --------------------------')
|
||||
agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD', 'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
|
||||
lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
|
||||
|
||||
map = {
|
||||
'CG' :['ARG'],
|
||||
'C2N':['ARG'],
|
||||
'N30':['N+','LYS'],
|
||||
'N31':['N+','LYS'],
|
||||
'N32':['N+','LYS'],
|
||||
'N33':['N+','LYS'] ,
|
||||
'NAR':['HIS'],
|
||||
'OCO':['COO'],
|
||||
'OP' :[],#['TYR','SER'],
|
||||
'SH' :['CYS'] ,
|
||||
'NP1':['AMD'],
|
||||
'OH' :['ROH'],
|
||||
'O3' :[] ,
|
||||
'CL' :[],
|
||||
'F' :[],
|
||||
'NAM':[],
|
||||
'N1' :[],
|
||||
'O2' :[]}
|
||||
|
||||
|
||||
s = """
|
||||
"""Print interaction parameters in LaTeX format."""
|
||||
# TODO - if these lists and dictionaries are the same as above, then
|
||||
# should be constants at the level of the module
|
||||
agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD',
|
||||
'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32',
|
||||
'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM',
|
||||
'N1', 'O2', 'OP', 'SH']
|
||||
lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO',
|
||||
'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP',
|
||||
'SH']
|
||||
str_ = """
|
||||
\\begin{longtable}{lllll}
|
||||
\\caption{Ligand interaction parameters. For interactions not listed, the default value of %s is applied.}
|
||||
\\label{tab:ligand_interaction_parameters}\\\\
|
||||
@@ -312,33 +316,32 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
|
||||
\\bottomrule
|
||||
\\endlastfoot
|
||||
|
||||
"""%(self.sidechain_cutoffs.default)
|
||||
for g1 in agroups:
|
||||
for g2 in lgroups:
|
||||
if self.interaction_matrix[g1][g2]=='-':
|
||||
""" % (self.sidechain_cutoffs.default)
|
||||
for group1 in agroups:
|
||||
for group2 in lgroups:
|
||||
if self.interaction_matrix[group1][group2] == '-':
|
||||
continue
|
||||
if self.sidechain_cutoffs.get_value(g1,g2)==self.sidechain_cutoffs.default:
|
||||
if self.sidechain_cutoffs.get_value(group1, group2) \
|
||||
== self.sidechain_cutoffs.default:
|
||||
continue
|
||||
|
||||
|
||||
s+= '%3s & %3s & %1s & %4s & %4s\\\\ \n'%(g1,g2,
|
||||
self.interaction_matrix[g1][g2],
|
||||
self.sidechain_cutoffs.get_value(g1,g2)[0],
|
||||
self.sidechain_cutoffs.get_value(g1,g2)[1])
|
||||
|
||||
if g1==g2:
|
||||
str_ += '%3s & %3s & %1s & %4s & %4s\\\\ \n'\
|
||||
% (group1, group2, \
|
||||
self.interaction_matrix[group1][group2], \
|
||||
self.sidechain_cutoffs.get_value(group1, group2)[0], \
|
||||
self.sidechain_cutoffs.get_value(group1, group2)[1])
|
||||
if group1 == group2:
|
||||
break
|
||||
|
||||
s += ' \\end{longtable}\n'
|
||||
info(s)
|
||||
return
|
||||
str_ += ' \\end{longtable}\n'
|
||||
info(str_)
|
||||
|
||||
def print_interactions_latex(self):
|
||||
agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD', 'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
|
||||
lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
|
||||
|
||||
|
||||
s = """
|
||||
"""Print interactions in LaTeX."""
|
||||
# TODO - are these the same lists as above? Convert to module constants.
|
||||
agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD',
|
||||
'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32',
|
||||
'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM',
|
||||
'N1', 'O2', 'OP', 'SH']
|
||||
str_ = """
|
||||
\\begin{longtable}{%s}
|
||||
\\caption{Ligand interaction parameters. For interactions not listed, the default value of %s is applied.}
|
||||
\\label{tab:ligand_interaction_parameters}\\\\
|
||||
@@ -361,174 +364,186 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
|
||||
\\bottomrule
|
||||
\\endlastfoot
|
||||
|
||||
"""%('l'*len(agroups),self.sidechain_cutoffs.default)
|
||||
for g1 in agroups:
|
||||
for g2 in agroups:
|
||||
|
||||
s+= '%3s & %3s & %1s & %4s & %4s\\\\ \n'%(g1,g2,
|
||||
self.interaction_matrix[g1][g2],
|
||||
self.sidechain_cutoffs.get_value(g1,g2)[0],
|
||||
self.sidechain_cutoffs.get_value(g1,g2)[1])
|
||||
|
||||
if g1==g2:
|
||||
""" % ('l'*len(agroups), self.sidechain_cutoffs.default)
|
||||
for group1 in agroups:
|
||||
for group2 in agroups:
|
||||
str_ += '%3s & %3s & %1s & %4s & %4s\\\\ \n' \
|
||||
% (group1, group2, \
|
||||
self.interaction_matrix[group1][group2], \
|
||||
self.sidechain_cutoffs.get_value(group1, group2)[0], \
|
||||
self.sidechain_cutoffs.get_value(group1, group2)[1])
|
||||
if group1 == group2:
|
||||
break
|
||||
|
||||
s += ' \\end{longtable}\n'
|
||||
info(s)
|
||||
return
|
||||
str_ += ' \\end{longtable}\n'
|
||||
info(str_)
|
||||
|
||||
|
||||
class InteractionMatrix:
|
||||
"""Interaction matrix class."""
|
||||
|
||||
|
||||
class Interaction_matrix:
|
||||
def __init__(self, name):
|
||||
"""Initialize with name of matrix.
|
||||
|
||||
Args:
|
||||
name: name of interaction matrix
|
||||
"""
|
||||
self.name = name
|
||||
self.value = None
|
||||
self.ordered_keys = []
|
||||
self.dictionary = {}
|
||||
return
|
||||
|
||||
def add(self,words):
|
||||
def add(self, words):
|
||||
"""Add values to matrix.
|
||||
|
||||
Args:
|
||||
words: values to add
|
||||
"""
|
||||
new_group = words[0]
|
||||
self.ordered_keys.append(new_group)
|
||||
|
||||
if not new_group in self.dictionary.keys():
|
||||
self.dictionary[new_group] = {}
|
||||
|
||||
for i in range(len(self.ordered_keys)):
|
||||
group = self.ordered_keys[i]
|
||||
if len(words)>i+1:
|
||||
for i, group in enumerate(self.ordered_keys):
|
||||
if len(words) > i+1:
|
||||
try:
|
||||
exec('self.value = %s'%words[i+1])
|
||||
except:
|
||||
self.value = float(words[i+1])
|
||||
except ValueError:
|
||||
self.value = words[i+1]
|
||||
self.dictionary[group][new_group] = self.value
|
||||
self.dictionary[new_group][group] = self.value
|
||||
|
||||
|
||||
return
|
||||
|
||||
def get_value(self, item1, item2):
|
||||
"""Get specific matrix value.
|
||||
|
||||
Args:
|
||||
item1: matrix row index
|
||||
item2: matrix column index
|
||||
Returns:
|
||||
matrix value or None
|
||||
"""
|
||||
try:
|
||||
return self.dictionary[item1][item2]
|
||||
except:
|
||||
except KeyError:
|
||||
return None
|
||||
|
||||
def __getitem__(self, group):
|
||||
"""Get specific group from matrix.
|
||||
|
||||
Args:
|
||||
group: group to get
|
||||
"""
|
||||
if group not in self.dictionary.keys():
|
||||
raise Exception('%s not found in interaction matrix %s'%(group,self.name))
|
||||
str_ = '%s not found in interaction matrix %s' % (group, self.name)
|
||||
raise KeyError(str_)
|
||||
return self.dictionary[group]
|
||||
|
||||
|
||||
def keys(self):
|
||||
"""Get keys from matrix.
|
||||
|
||||
Returns:
|
||||
dictionary key list
|
||||
"""
|
||||
return self.dictionary.keys()
|
||||
|
||||
def __str__(self):
|
||||
s = ' '
|
||||
for k1 in self.ordered_keys:
|
||||
s+='%3s '%k1
|
||||
s+='\n'
|
||||
for k1 in self.ordered_keys:
|
||||
s+='%3s '%k1
|
||||
for k2 in self.ordered_keys:
|
||||
s+='%3s '%self[k1][k2]
|
||||
s+='\n'
|
||||
|
||||
return s
|
||||
# ks = ['COO', 'SER', 'ARG', 'LYS', 'HIS', 'AMD', 'CYS', 'TRP','ROH','TYR','N+','CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
|
||||
|
||||
# p = ''
|
||||
# n=0
|
||||
# for i in range(len(ks)):
|
||||
# for j in range(i,len(ks)):
|
||||
# if not [0.0,0.0]==self[ks[i]][ks[j]]:
|
||||
# if not [3.0,4.0]==self[ks[i]][ks[j]]:
|
||||
# p+='sidechain_cutoff %3s %3s %s\n'%(ks[i],ks[j],self[ks[i]][ks[j]])
|
||||
# n+=1
|
||||
|
||||
# info('total',n,len(ks))
|
||||
# return p
|
||||
str_ = ' '
|
||||
for key in self.ordered_keys:
|
||||
str_ += '%3s ' % key
|
||||
str_ += '\n'
|
||||
for key1 in self.ordered_keys:
|
||||
str_ += '%3s ' % key1
|
||||
for key2 in self.ordered_keys:
|
||||
str_ += '%3s ' % self[key1][key2]
|
||||
str_ += '\n'
|
||||
return str_
|
||||
|
||||
|
||||
class PairwiseMatrix:
|
||||
"""Pairwise interaction matrix class."""
|
||||
|
||||
class Pair_wise_matrix:
|
||||
def __init__(self, name):
|
||||
"""Initialize pairwise matrix.
|
||||
|
||||
Args:
|
||||
name: name of pairwise interaction
|
||||
"""
|
||||
self.name = name
|
||||
self.dictionary = {}
|
||||
self.default = [0.0, 0.0]
|
||||
return
|
||||
|
||||
def add(self,words):
|
||||
def add(self, words):
|
||||
"""Add information to the matrix.
|
||||
|
||||
TODO - this function unnecessarily bundles arguments into a tuple
|
||||
|
||||
Args:
|
||||
words: tuple with assignment information and value
|
||||
"""
|
||||
# assign the default value
|
||||
if len(words)==3 and words[0]=='default':
|
||||
if len(words) == 3 and words[0] == 'default':
|
||||
self.default = [float(words[1]), float(words[2])]
|
||||
return
|
||||
|
||||
# assign non-default values
|
||||
g1 = words[0]
|
||||
g2 = words[1]
|
||||
v = [float(words[2]), float(words[3])]
|
||||
group1 = words[0]
|
||||
group2 = words[1]
|
||||
value = [float(words[2]), float(words[3])]
|
||||
self.insert(group1, group2, value)
|
||||
self.insert(group2, group1, value)
|
||||
|
||||
self.insert(g1,g2,v)
|
||||
self.insert(g2,g1,v)
|
||||
def insert(self, key1, key2, value):
|
||||
"""Insert value into matrix.
|
||||
|
||||
return
|
||||
|
||||
def insert(self, k1,k2,v):
|
||||
|
||||
if k1 in self.dictionary.keys() and k2 in self.dictionary[k1].keys():
|
||||
if k1!=k2:
|
||||
warning('Parameter value for %s, %s defined more than once' % (k1, k2))
|
||||
|
||||
if not k1 in self.dictionary:
|
||||
self.dictionary[k1] = {}
|
||||
|
||||
self.dictionary[k1][k2] =v
|
||||
|
||||
return
|
||||
Args:
|
||||
key1: first matrix key (row)
|
||||
key2: second matrix key (column)
|
||||
value: value to insert
|
||||
"""
|
||||
if key1 in self.dictionary and key2 in self.dictionary[key1]:
|
||||
if key1 != key2:
|
||||
str_ = 'Parameter value for %s, %s defined more than once' \
|
||||
% (key1, key2)
|
||||
warning(str_)
|
||||
if not key1 in self.dictionary:
|
||||
self.dictionary[key1] = {}
|
||||
self.dictionary[key1][key2] = value
|
||||
|
||||
def get_value(self, item1, item2):
|
||||
"""Get specified value from matrix.
|
||||
|
||||
Args:
|
||||
item1: row index
|
||||
item2: column index
|
||||
Returns:
|
||||
matrix value (or default)
|
||||
"""
|
||||
try:
|
||||
return self.dictionary[item1][item2]
|
||||
except:
|
||||
except KeyError:
|
||||
return self.default
|
||||
|
||||
def __getitem__(self, group):
|
||||
"""Get item from matrix corresponding to specific group.
|
||||
|
||||
Args:
|
||||
group: group to retrieve
|
||||
Returns:
|
||||
matrix information
|
||||
"""
|
||||
if group not in self.dictionary.keys():
|
||||
raise Exception('%s not found in interaction matrix %s'%(group,self.name))
|
||||
str_ = '%s not found in interaction matrix %s' % (group, self.name)
|
||||
raise KeyError(str_)
|
||||
return self.dictionary[group]
|
||||
|
||||
|
||||
def keys(self):
|
||||
"""Get keys from matrix.
|
||||
|
||||
Returns:
|
||||
dictionary key list
|
||||
"""
|
||||
return self.dictionary.keys()
|
||||
|
||||
def __str__(self):
|
||||
s=''
|
||||
for k1 in self.keys():
|
||||
for k2 in self[k1].keys():
|
||||
s += '%s %s %s\n'%(k1,k2,self[k1][k2])
|
||||
|
||||
return s
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
str_ = ''
|
||||
for key1 in self.keys():
|
||||
for key2 in self[key1].keys():
|
||||
str_ += '%s %s %s\n' % (key1, key2, self[key1][key2])
|
||||
return str_
|
||||
|
||||
Reference in New Issue
Block a user