2079259884
Use python3 version of the print function when running under python2. Also added "from __future__ import division" to a few more module files.
243 lines
9.5 KiB
Python
243 lines
9.5 KiB
Python
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from __future__ import division
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from __future__ import print_function
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import math, time
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import Source.iterative, Source.lib, Source.vector_algebra
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import Source.calculations
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from Source.determinant import Determinant
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def setDeterminants(propka_groups, version=None, options=None):
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"""
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adding side-chain and coulomb determinants/perturbations to all residues - note, backbone determinants are set separately
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"""
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iterative_interactions = []
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# --- NonIterative section ---#
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for group1 in propka_groups:
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for group2 in propka_groups:
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if group1 == group2:
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break
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# do not calculate interactions for coupled groups
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if group2 in group1.covalently_coupled_groups:
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break
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distance = Source.calculations.distance(group1, group2)
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if distance < version.parameters.coulomb_cutoff2:
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interaction_type = version.parameters.interaction_matrix.get_value(group1.type,group2.type)
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if interaction_type == 'I':
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Source.iterative.addtoDeterminantList(group1, group2, distance, iterative_interactions, version=version)
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elif interaction_type == 'N':
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addDeterminants(group1, group2, distance, version)
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# --- Iterative section ---#
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Source.iterative.addDeterminants(iterative_interactions, version, options=options)
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def addDeterminants(group1, group2, distance, version):
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"""
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adding determinants/perturbations, distance(R1, R2) < coulomb_cutoff always
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"""
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# side-chain determinant
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addSidechainDeterminants(group1, group2, version)
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# Coulomb determinant
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addCoulombDeterminants(group1, group2, distance, version)
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return
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def addSidechainDeterminants(group1, group2, version=None):
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"""
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adding side-chain determinants/perturbations
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Note, resNumb1 > resNumb2
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"""
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hbond_interaction = version.hydrogen_bond_interaction(group1, group2)
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if hbond_interaction:
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if group1.charge == group2.charge:
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# acid pair or base pair
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if group1.model_pka < group2.model_pka:
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newDeterminant1 = Determinant(group2, -hbond_interaction)
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newDeterminant2 = Determinant(group1, hbond_interaction)
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else:
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newDeterminant1 = Determinant(group2, hbond_interaction)
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newDeterminant2 = Determinant(group1, -hbond_interaction)
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else:
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newDeterminant1 = Determinant(group2, hbond_interaction*group1.charge)
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newDeterminant2 = Determinant(group1, hbond_interaction*group2.charge)
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group1.determinants['sidechain'].append(newDeterminant1)
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group2.determinants['sidechain'].append(newDeterminant2)
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return
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def addCoulombDeterminants(group1, group2, distance, version):
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"""
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adding NonIterative Coulomb determinants/perturbations
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"""
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coulomb_interaction = version.electrostatic_interaction(group1, group2, distance)
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if coulomb_interaction:
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Q1 = group1.charge
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Q2 = group2.charge
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# assigning the Coulombic interaction
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if Q1 < 0.0 and Q2 < 0.0:
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""" both are acids """
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addCoulombAcidPair(group1, group2, coulomb_interaction)
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elif Q1 > 0.0 and Q2 > 0.0:
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""" both are bases """
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addCoulombBasePair(group1, group2, coulomb_interaction)
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else:
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""" one of each """
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addCoulombIonPair(group1, group2, coulomb_interaction)
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return
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def addCoulombAcidPair(object1, object2, value):
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"""
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Adding the Coulomb interaction (an acid pair):
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the higher pKa is raised
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"""
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if object1.model_pka > object2.model_pka:
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newDeterminant = Determinant(object2, value)
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object1.determinants['coulomb'].append(newDeterminant)
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else:
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newDeterminant = Determinant(object1, value)
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object2.determinants['coulomb'].append(newDeterminant)
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def addCoulombBasePair(object1, object2, value):
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"""
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Adding the Coulomb interaction (a base pair):
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the lower pKa is lowered
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"""
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if object1.model_pka < object2.model_pka:
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newDeterminant = Determinant(object2, -value)
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object1.determinants['coulomb'].append(newDeterminant)
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else:
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newDeterminant = Determinant(object1, -value)
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object2.determinants['coulomb'].append(newDeterminant)
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def addCoulombIonPair(object1, object2, value):
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"""
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Adding the Coulomb interaction (an acid-base pair):
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the pKa of the acid is lowered & the pKa of the base is raised
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"""
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# residue1
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Q1 = object1.charge
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newDeterminant = Determinant(object2, Q1*value)
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object1.determinants['coulomb'].append(newDeterminant)
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# residue2
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Q2 = object2.charge
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newDeterminant = Determinant(object1, Q2*value)
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object2.determinants['coulomb'].append(newDeterminant)
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def setIonDeterminants(conformation_container, version):
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"""
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adding ion determinants/perturbations
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"""
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for titratable_group in conformation_container.get_titratable_groups():
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for ion_group in conformation_container.get_ions():
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squared_distance = Source.calculations.squared_distance(titratable_group, ion_group)
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if squared_distance < version.parameters.coulomb_cutoff2_squared:
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weight = version.calculatePairWeight(titratable_group.Nmass, ion_group.Nmass)
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# the pKa of both acids and bases are shifted up by negative ions (and vice versa)
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value = (-ion_group.charge) * version.calculateCoulombEnergy(math.sqrt(squared_distance), weight)
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newDeterminant = Determinant(ion_group, value)
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titratable_group.determinants['coulomb'].append(newDeterminant)
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return
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def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
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for titratable_group in titratable_groups:
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# find out which backbone groups this titratable is interacting with
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for backbone_group in backbone_groups:
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# find the interacting atoms
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backbone_interaction_atoms = backbone_group.get_interaction_atoms(titratable_group)
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titratable_group_interaction_atoms = titratable_group.interaction_atoms_for_acids
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# find the smallest distance
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[backbone_atom, distance, titratable_atom] = Source.calculations.get_smallest_distance(backbone_interaction_atoms,
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titratable_group_interaction_atoms)
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# get the parameters
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parameters = version.get_backbone_hydrogen_bond_parameters(backbone_atom, titratable_atom)
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if not parameters:
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continue
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[dpKa_max, [cutoff1, cutoff2]] = parameters
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if distance < cutoff2:
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# calculate angle factor
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f_angle = 1.0
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# for BBC groups, the hydrogen is on the titratable group
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#
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# Titra.
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# /
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# H
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# .
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# O
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# ||
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# C
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if backbone_group.type == 'BBC':
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if titratable_group.type in version.parameters.angular_dependent_sidechain_interactions:
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if titratable_atom.element == 'H':
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heavy_atom = titratable_atom.bonded_atoms[0]
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hydrogen_atom = titratable_atom
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[d1, f_angle, d2] = Source.calculations.AngleFactorX(atom1=heavy_atom,
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atom2=hydrogen_atom,
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atom3=backbone_atom)
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else:
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# Either the structure is corrupt (no hydrogen), or the heavy atom is closer to
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# the titratable atom than the hydrogen. In either case we set the angle factor
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# to 0
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f_angle = 0.0
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# for BBN groups, the hydrogen is on the backbone group
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#
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# Titra.
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# .
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# H
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# |
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# N
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# / \
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if backbone_group.type == 'BBN':
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if backbone_atom.element == 'H':
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backbone_N = backbone_atom.bonded_atoms[0]
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backbone_H = backbone_atom
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[d1, f_angle, d2] = Source.calculations.AngleFactorX(atom1=titratable_atom,
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atom2=backbone_H,
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atom3=backbone_N)
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else:
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# Either the structure is corrupt (no hydrogen), or the heavy atom is closer to
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# the titratable atom than the hydrogen. In either case we set the angle factor
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# to 0
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f_angle = 0.0
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if f_angle > 0.001:
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value = titratable_group.charge * Source.calculations.HydrogenBondEnergy(distance, dpKa_max, [cutoff1,cutoff2], f_angle)
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newDeterminant = Determinant(backbone_group, value)
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titratable_group.determinants['backbone'].append(newDeterminant)
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return
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