Clean up line breaks in parameters.py
See https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
@@ -7,27 +7,28 @@ from propka.lib import info, warning
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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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NUMBER_DICTIONARIES = [
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'VanDerWaalsVolume', 'charge', 'model_pkas', 'ions', 'valence_electrons',
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'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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STRING_LISTS = [
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'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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PARAMETERS = [
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'Nmin', 'Nmax', 'desolvationSurfaceScalingFactor', 'desolvationPrefactor',
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'desolvationAllowance', 'coulomb_diel', 'COO_HIS_exception',
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'OCO_HIS_exception', 'CYS_HIS_exception', 'CYS_CYS_exception',
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'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',
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'remove_penalised_group', 'max_intrinsic_pka_diff',
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'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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@@ -44,7 +45,7 @@ class Parameters:
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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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# TODO - it would be nice to rename these; 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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@@ -184,10 +185,11 @@ class Parameters:
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def set_up_data_structures(self):
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"""Set up internal data structures.
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TODO - it would be better to make these assignments explicit in __init__.
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TODO - it would be better to make these assignments explicit in
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__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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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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@@ -208,44 +210,52 @@ class Parameters:
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info('')
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info('--------------- Interactions --------------------------')
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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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agroups = [
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'COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD', 'ARG',
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'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR',
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'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
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lgroups = [
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'CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1',
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'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
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map_ = {
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'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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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 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 += '|%3s %3s %1s %4s %4s' % (
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group1, val, 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(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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if (self.sidechain_cutoffs.get_value(group1, val)[0]
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!= self.sidechain_cutoffs.get_value(group1,
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group2)[0]
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or self.sidechain_cutoffs.get_value(group1,
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val)[1]
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!= self.sidechain_cutoffs.get_value(group1,
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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_[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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if (len(map_[group2]) == 0
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and (self.sidechain_cutoffs.get_value(group1,
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group2)[0]
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!= 3
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or self.sidechain_cutoffs.get_value(group1,
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group2)[1]
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!= 4)):
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map_interaction += '? '
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info(interaction, map_interaction)
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if group1 == group2:
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@@ -321,14 +331,16 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
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for group2 in lgroups:
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if self.interaction_matrix[group1][group2] == '-':
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continue
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if self.sidechain_cutoffs.get_value(group1, group2) \
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== self.sidechain_cutoffs.default:
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if (self.sidechain_cutoffs.get_value(group1, group2)
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== self.sidechain_cutoffs.default):
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continue
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str_ += '%3s & %3s & %1s & %4s & %4s\\\\ \n'\
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% (group1, group2, \
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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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str_ += ('%3s & %3s & %1s & %4s & %4s\\\\ \n'
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% (group1, group2,
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self.interaction_matrix[group1][group2],
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self.sidechain_cutoffs.get_value(group1,
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group2)[0],
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self.sidechain_cutoffs.get_value(group1,
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group2)[1]))
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if group1 == group2:
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break
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str_ += ' \\end{longtable}\n'
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@@ -367,11 +379,13 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
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""" % ('l'*len(agroups), self.sidechain_cutoffs.default)
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for group1 in agroups:
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for group2 in agroups:
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str_ += '%3s & %3s & %1s & %4s & %4s\\\\ \n' \
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% (group1, group2, \
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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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str_ += ('%3s & %3s & %1s & %4s & %4s\\\\ \n'
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% (group1, group2,
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self.interaction_matrix[group1][group2],
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self.sidechain_cutoffs.get_value(
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group1, group2)[0],
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self.sidechain_cutoffs.get_value(
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group1, group2)[1]))
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if group1 == group2:
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break
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str_ += ' \\end{longtable}\n'
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@@ -499,8 +513,8 @@ class PairwiseMatrix:
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"""
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if key1 in self.dictionary and key2 in self.dictionary[key1]:
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if key1 != key2:
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str_ = 'Parameter value for %s, %s defined more than once' \
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% (key1, key2)
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str_ = ('Parameter value for %s, %s defined more than once'
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% (key1, key2))
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warning(str_)
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if not key1 in self.dictionary:
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self.dictionary[key1] = {}
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