213 lines
8.2 KiB
Python
213 lines
8.2 KiB
Python
import math
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import Source.lib as lib
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import sys, os
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import Source.calculations as calculations
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import Source.parameters
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class version:
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def __init__(self,parameters):
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self.parameters = parameters
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return
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# desolvation
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def calculate_desolvation(self, group):
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return self.desolvation_model(self.parameters, group)
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def calculatePairWeight(self, Nmass1, Nmass2):
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return self.weight_pair_method(self.parameters, Nmass1, Nmass2)
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# side chains
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def hydrogen_bond_interaction(self, group1, group2):
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return self.hydrogen_bond_interaction_model(group1, group2, self)
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def calculateSideChainEnergy(self, distance, dpka_max, cutoff, weight, f_angle):
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return self.sidechain_interaction_model(distance, dpka_max, cutoff, f_angle) # weight is ignored in 3.0 Sep07
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# coulomb
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def electrostatic_interaction(self, group1, group2, distance):
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return self.electrostatic_interaction_model(group1, group2, distance, self)
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def calculateCoulombEnergy(self, distance, weight):
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return self.coulomb_interaction_model(distance, weight, self.parameters)
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def checkCoulombPair(self, group1, group2, distance):
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return self.check_coulomb_pair_method(self.parameters, group1, group2, distance)
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# backbone re-organisation
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def calculateBackBoneReorganization(self, conformation):
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return self.backbone_reorganisation_method(self.parameters, conformation)
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# exceptions
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def checkExceptions(self, group1, group2):
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return self.exception_check_method(self, group1, group2)
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def setup_bonding_and_protonation(self, molecular_container):
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return self.molecular_preparation_method(self.parameters, molecular_container)
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def setup_bonding(self, molecular_container):
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return self.prepare_bonds(self.parameters, molecular_container)
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class version_A(version):
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def __init__(self, parameters):
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# set the calculation rutines used in this version
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version.__init__(self, parameters)
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# atom naming, bonding, and protonation
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self.molecular_preparation_method = Source.calculations.setup_bonding_and_protonation
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self.prepare_bonds = Source.calculations.setup_bonding
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# desolvation related methods
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self.desolvation_model = calculations.radial_volume_desolvation
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self.weight_pair_method = calculations.calculatePairWeight
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# side chain methods
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self.sidechain_interaction_model = Source.calculations.HydrogenBondEnergy
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self.hydrogen_bond_interaction_model = Source.calculations.hydrogen_bond_interaction
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# colomb methods
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self.electrostatic_interaction_model = Source.calculations.electrostatic_interaction
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self.check_coulomb_pair_method = Source.calculations.checkCoulombPair
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self.coulomb_interaction_model = Source.calculations.CoulombEnergy
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#backbone
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self.backbone_interaction_model = Source.calculations.HydrogenBondEnergy
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self.backbone_reorganisation_method = Source.calculations.BackBoneReorganization
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# exception methods
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self.exception_check_method = Source.calculations.checkExceptions
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return
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def get_hydrogen_bond_parameters(self, atom1, atom2):
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dpka_max = self.parameters.sidechain_interaction
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cutoff = self.parameters.sidechain_cutoffs.get_value(atom1.group_type, atom2.group_type)
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return [dpka_max, cutoff]
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def get_backbone_hydrogen_bond_parameters(self, backbone_atom, atom):
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if backbone_atom.group_type == 'BBC':
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if atom.group_type in self.parameters.backbone_CO_hydrogen_bond.keys():
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[v,c1,c2] = self.parameters.backbone_CO_hydrogen_bond[atom.group_type]
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return [v,[c1,c2]]
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if backbone_atom.group_type == 'BBN':
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if atom.group_type in self.parameters.backbone_NH_hydrogen_bond.keys():
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[v,c1,c2] = self.parameters.backbone_NH_hydrogen_bond[atom.group_type]
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return [v,[c1,c2]]
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return None
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class simple_hb(version_A):
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def __init__(self, parameters):
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# set the calculation rutines used in this version
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version_A.__init__(self, parameters)
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print('Using simple hb model')
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return
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def get_hydrogen_bond_parameters(self, atom1, atom2):
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return self.parameters.hydrogen_bonds.get_value(atom1.element, atom2.element)
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def get_backbone_hydrogen_bond_parameters(self, backbone_atom, atom):
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return self.parameters.hydrogen_bonds.get_value(backbone_atom.element, atom.element)
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class element_based_ligand_interactions(version_A):
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def __init__(self, parameters):
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# set the calculation rutines used in this version
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version_A.__init__(self, parameters)
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print('Using detailed SC model!')
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return
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def get_hydrogen_bond_parameters(self, atom1, atom2):
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if not 'hetatm' in [atom1.type, atom2.type]:
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# this is a protein-protein interaction
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dpka_max = self.parameters.sidechain_interaction.get_value(atom1.group_type, atom2.group_type)
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cutoff = self.parameters.sidechain_cutoffs.get_value(atom1.group_type, atom2.group_type)
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return [dpka_max, cutoff]
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# at least one ligand atom is involved in this interaction
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# make sure that we are using the heavy atoms for finding paramters
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elements = []
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for a in [atom1, atom2]:
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if a.element == 'H': elements.append(a.bonded_atoms[0].element)
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else: elements.append(a.element)
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return self.parameters.hydrogen_bonds.get_value(elements[0], elements[1])
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def get_backbone_hydrogen_bond_parameters(self, backbone_atom, atom):
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if atom.type == 'atom':
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# this is a backbone-protein interaction
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if backbone_atom.group_type == 'BBC' and\
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atom.group_type in self.parameters.backbone_CO_hydrogen_bond.keys():
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[v,c1,c2] = self.parameters.backbone_CO_hydrogen_bond[atom.group_type]
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return [v,[c1,c2]]
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if backbone_atom.group_type == 'BBN' and\
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atom.group_type in self.parameters.backbone_NH_hydrogen_bond.keys():
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[v,c1,c2] = self.parameters.backbone_NH_hydrogen_bond[atom.group_type]
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return [v,[c1,c2]]
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else:
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# this is a backbone-ligand interaction
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# make sure that we are using the heavy atoms for finding paramters
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elements = []
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for a in [backbone_atom, atom]:
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if a.element == 'H': elements.append(a.bonded_atoms[0].element)
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else: elements.append(a.element)
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res = self.parameters.hydrogen_bonds.get_value(elements[0], elements[1])
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if not res:
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print('Could not determine backbone interaction parameters for:',
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backbone_atom,atom)
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return
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return None
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class propka30(version):
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def __init__(self, parameters):
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# set the calculation rutines used in this version
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version.__init__(self, parameters)
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# atom naming, bonding, and protonation
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self.molecular_preparation_method = Source.calculations.setup_bonding_and_protonation_30_style
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# desolvation related methods
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self.desolvation_model = calculations.radial_volume_desolvation
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self.weight_pair_method = calculations.calculatePairWeight
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# side chain methods
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self.sidechain_interaction_model = Source.calculations.HydrogenBondEnergy
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# colomb methods
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self.check_coulomb_pair_method = Source.calculations.checkCoulombPair
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self.coulomb_interaction_model = Source.calculations.CoulombEnergy
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#backbone
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self.backbone_reorganisation_method = Source.calculations.BackBoneReorganization
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# exception methods
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self.exception_check_method = Source.calculations.checkExceptions
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return
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def get_hydrogen_bond_parameters(self, atom1, atom2):
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dpka_max = self.parameters.sidechain_interaction.get_value(atom1.group_type, atom2.group_type)
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cutoff = self.parameters.sidechain_cutoffs.get_value(atom1.group_type, atom2.group_type)
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return [dpka_max, cutoff]
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