downloaded from propka.ki.ku.dk
This commit is contained in:
Jimmy Charnley Kromann
529
Source/parameters.py
Normal file
529
Source/parameters.py
Normal file
@@ -0,0 +1,529 @@
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import math
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import Source.lib as lib
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import sys, os
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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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class Parameters:
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def __init__(self, parameter_file):
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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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return
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def read_parameters(self, file):
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# try to locate the parameters file
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try:
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path = os.path.dirname(__file__)
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ifile = os.path.join(path,'../'+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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self.parse_line(line)
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return
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def parse_line(self, 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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self.parse_to_number_dictionary(words)
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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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self.parse_distance(words)
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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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self.parse_string(words)
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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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self.parse_to_matrix(words)
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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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#print(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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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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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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return
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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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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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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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def parse_parameter(self, words):
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exec('self.%s = %s'%tuple(words))
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return
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def parse_string(self, words):
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#print('self.%s = \'%s\''%tuple(words))
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exec('self.%s = \'%s\''%tuple(words))
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return
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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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return
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def print_interaction_parameters(self):
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print('--------------- Model pKa values ----------------------')
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for k in self.model_pkas.keys():
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print('%3s %8.2f'%(k,self.model_pkas[k]))
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print('')
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print('--------------- 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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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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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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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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map_interaction += '? '
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print(interaction,map_interaction )
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if g1==g2:
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break
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print('-')
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print('--------------- Exceptions ----------------------------')
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print('COO-HIS',self.COO_HIS_exception)
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print('OCO-HIS',self.OCO_HIS_exception)
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print('CYS-HIS',self.CYS_HIS_exception)
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print('CYS-CYS',self.CYS_CYS_exception)
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print('--------------- Mapping -------------------------------')
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print("""
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Titratable:
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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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Non-titratable:
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NP1 AMD?
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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
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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):
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# print('--------------- Model pKa values ----------------------')
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# for k in self.model_pkas.keys():
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# print('%3s %8.2f'%(k,self.model_pkas[k]))
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# print('')
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# print('--------------- 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':['AMD'],
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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':[],
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'N1' :[],
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'O2' :[]}
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s = """
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\\begin{longtable}{lllll}
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\\caption{Ligand interaction parameters. For interactions not listed, the default value of %s is applied.}
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\\label{tab:ligand_interaction_parameters}\\\\
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\\toprule
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Group1 & Group2 & Interaction & c1 &c2 \\\\
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\\midrule
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\\endfirsthead
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\\multicolumn{5}{l}{\\emph{continued from the previous page}}\\\\
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\\toprule
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Group1 & Group2 & Interaction & c1 &c2 \\\\
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\\midrule
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\\endhead
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\\midrule
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\\multicolumn{5}{r}{\\emph{continued on the next page}}\\\\
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\\endfoot
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\\bottomrule
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\\endlastfoot
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"""%(self.sidechain_cutoffs.default)
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for g1 in agroups:
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for g2 in lgroups:
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if self.interaction_matrix[g1][g2]=='-':
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continue
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if self.sidechain_cutoffs.get_value(g1,g2)==self.sidechain_cutoffs.default:
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continue
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s+= '%3s & %3s & %1s & %4s & %4s\\\\ \n'%(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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if g1==g2:
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break
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s += ' \\end{longtable}\n'
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print(s)
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return
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def print_interactions_latex(self):
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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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s = """
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\\begin{longtable}{%s}
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\\caption{Ligand interaction parameters. For interactions not listed, the default value of %s is applied.}
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\\label{tab:ligand_interaction_parameters}\\\\
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\\toprule
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Group1 & Group2 & Interaction & c1 &c2 \\\\
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\\midrule
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\\endfirsthead
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\\multicolumn{5}{l}{\\emph{continued from the previous page}}\\\\
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\\toprule
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Group1 & Group2 & Interaction & c1 &c2 \\\\
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\\midrule
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\\endhead
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\\midrule
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\\multicolumn{5}{r}{\\emph{continued on the next page}}\\\\
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\\endfoot
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\\bottomrule
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\\endlastfoot
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"""%('l'*len(agroups),self.sidechain_cutoffs.default)
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for g1 in agroups:
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for g2 in agroups:
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s+= '%3s & %3s & %1s & %4s & %4s\\\\ \n'%(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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if g1==g2:
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break
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s += ' \\end{longtable}\n'
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print(s)
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return
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class Interaction_matrix:
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def __init__(self, name):
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self.name = name
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self.ordered_keys = []
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self.dictionary = {}
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return
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def add(self,words):
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new_group = words[0]
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self.ordered_keys.append(new_group)
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if not new_group in self.dictionary.keys():
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self.dictionary[new_group] = {}
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for i in range(len(self.ordered_keys)):
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group = self.ordered_keys[i]
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if len(words)>i+1:
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try:
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exec('self.value = %s'%words[i+1])
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except:
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self.value = words[i+1]
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self.dictionary[group][new_group] = self.value
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self.dictionary[new_group][group] = self.value
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return
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def get_value(self, item1, item2):
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try:
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return self.dictionary[item1][item2]
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except:
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return None
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def __getitem__(self, group):
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if group not in self.dictionary.keys():
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raise Exception('%s not found in interaction matrix %s'%(group,self.name))
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return self.dictionary[group]
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def keys(self):
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return self.dictionary.keys()
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def __str__(self):
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s = ' '
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for k1 in self.ordered_keys:
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s+='%3s '%k1
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s+='\n'
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for k1 in self.ordered_keys:
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s+='%3s '%k1
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for k2 in self.ordered_keys:
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s+='%3s '%self[k1][k2]
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s+='\n'
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return s
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# 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']
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# p = ''
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# n=0
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# for i in range(len(ks)):
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# for j in range(i,len(ks)):
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# if not [0.0,0.0]==self[ks[i]][ks[j]]:
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# if not [3.0,4.0]==self[ks[i]][ks[j]]:
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# p+='sidechain_cutoff %3s %3s %s\n'%(ks[i],ks[j],self[ks[i]][ks[j]])
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# n+=1
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# print('total',n,len(ks))
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# return p
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class Pair_wise_matrix:
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def __init__(self, name):
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self.name = name
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self.dictionary = {}
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self.default = [0.0, 0.0]
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return
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|
||||
def add(self,words):
|
||||
# assign the default value
|
||||
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])]
|
||||
|
||||
self.insert(g1,g2,v)
|
||||
self.insert(g2,g1,v)
|
||||
|
||||
return
|
||||
|
||||
def insert(self, k1,k2,v):
|
||||
|
||||
if k1 in self.dictionary.keys() and k2 in self.dictionary[k1].keys():
|
||||
if k1!=k2:
|
||||
print ('Warning: Paramter 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
|
||||
|
||||
def get_value(self, item1, item2):
|
||||
|
||||
try:
|
||||
return self.dictionary[item1][item2]
|
||||
except:
|
||||
return self.default
|
||||
|
||||
def __getitem__(self, group):
|
||||
if group not in self.dictionary.keys():
|
||||
raise Exception('%s not found in interaction matrix %s'%(group,self.name))
|
||||
return self.dictionary[group]
|
||||
|
||||
|
||||
def keys(self):
|
||||
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
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user