26a5ab042e
- use autosummary (with custom module template) - updated module docs for all modules so that they are included with sphinx autodocs
302 lines
11 KiB
Python
302 lines
11 KiB
Python
"""
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Working with Determinants
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=========================
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Functions to manipulate :class:`propka.determinant.Determinant` objects.
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.. TODO::
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It is confusing to have both `determinant.py` and `determinants.py`.
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Should these be merged?
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.. SeeAlso::
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:mod:`propka.determinant`
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"""
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import math
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import propka.iterative
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import propka.lib
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import propka.vector_algebra
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from propka.calculations import squared_distance, get_smallest_distance
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from propka.energy import angle_distance_factors, hydrogen_bond_energy
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from propka.determinant import Determinant
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# Cutoff for angle factor
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# TODO - this constant appears elsewhere in the package.
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# It should be moved to a configuration file.
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FANGLE_MIN = 0.001
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def set_determinants(propka_groups, version=None, options=None):
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"""Add side-chain and coulomb determinants/perturbations to all residues.
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NOTE - backbone determinants are set separately
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Args:
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propka_groups: groups to adjust
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version: version object
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options: options object
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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 = propka.calculations.distance(group1, group2)
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if distance < version.parameters.coulomb_cutoff2:
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interaction_type = (
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version.parameters.interaction_matrix.get_value(
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group1.type, group2.type))
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if interaction_type == 'I':
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propka.iterative.add_to_determinant_list(
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group1, group2, distance, iterative_interactions,
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version=version)
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elif interaction_type == 'N':
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add_determinants(group1, group2, distance, version)
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# --- Iterative section ---#
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propka.iterative.add_determinants(iterative_interactions, version)
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def add_determinants(group1, group2, distance, version):
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"""Add determinants and perturbations for distance(R1,R2) < coulomb_cutoff.
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Args:
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group1: first group to add
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group2: second group to add
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distance: distance between groups
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version: version object
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"""
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# side-chain determinant
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add_sidechain_determinants(group1, group2, version)
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# Coulomb determinant
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add_coulomb_determinants(group1, group2, distance, version)
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def add_sidechain_determinants(group1, group2, version=None):
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"""Add side-chain determinants and perturbations.
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NOTE - res_num1 > res_num2
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Args:
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group1: first group to add
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group2: second group to add
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version: version object
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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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new_determinant1 = Determinant(group2, -hbond_interaction)
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new_determinant2 = Determinant(group1, hbond_interaction)
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else:
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new_determinant1 = Determinant(group2, hbond_interaction)
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new_determinant2 = Determinant(group1, -hbond_interaction)
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else:
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new_determinant1 = Determinant(
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group2, hbond_interaction*group1.charge)
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new_determinant2 = Determinant(
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group1, hbond_interaction*group2.charge)
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group1.determinants['sidechain'].append(new_determinant1)
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group2.determinants['sidechain'].append(new_determinant2)
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def add_coulomb_determinants(group1, group2, distance, version):
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"""Add non-iterative Coulomb determinants and perturbations.
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Args:
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group1: first group to add
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group2: second group to add
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distance: distance between groups
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version: version object
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"""
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coulomb_interaction = version.electrostatic_interaction(
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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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add_coulomb_acid_pair(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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add_coulomb_base_pair(group1, group2, coulomb_interaction)
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else:
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# one of each
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add_coulomb_ion_pair(group1, group2, coulomb_interaction)
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def add_coulomb_acid_pair(object1, object2, value):
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"""Add the Coulomb interaction (an acid pair).
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The higher pKa is raised.
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Args:
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object1: first part of pair
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object2: second part of pair
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value: determinant value
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"""
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if object1.model_pka > object2.model_pka:
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new_determinant = Determinant(object2, value)
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object1.determinants['coulomb'].append(new_determinant)
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else:
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new_determinant = Determinant(object1, value)
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object2.determinants['coulomb'].append(new_determinant)
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def add_coulomb_base_pair(object1, object2, value):
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"""Add the Coulomb interaction (a base pair).
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The lower pKa is lowered.
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Args:
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object1: first part of pair
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object2: second part of pair
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value: determinant value
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"""
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if object1.model_pka < object2.model_pka:
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new_determinant = Determinant(object2, -value)
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object1.determinants['coulomb'].append(new_determinant)
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else:
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new_determinant = Determinant(object1, -value)
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object2.determinants['coulomb'].append(new_determinant)
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def add_coulomb_ion_pair(object1, object2, value):
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"""Add 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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Args:
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object1: first part of pair
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object2: second part of pair
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value: determinant value
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"""
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# residue1
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q1 = object1.charge
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new_determinant = Determinant(object2, q1*value)
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object1.determinants['coulomb'].append(new_determinant)
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# residue2
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q2 = object2.charge
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new_determinant = Determinant(object1, q2*value)
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object2.determinants['coulomb'].append(new_determinant)
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def set_ion_determinants(conformation_container, version):
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"""Add ion determinants and perturbations.
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Args:
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conformation_container: conformation to set
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version: version object
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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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dist_sq = squared_distance(titratable_group, ion_group)
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if dist_sq < version.parameters.coulomb_cutoff2_squared:
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weight = version.calculate_pair_weight(
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titratable_group.num_volume, ion_group.num_volume)
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# the pKa of both acids and bases are shifted up by negative
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# ions (and vice versa)
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value = (
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-ion_group.charge
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* version.calculate_coulomb_energy(
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math.sqrt(dist_sq), weight))
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new_det = Determinant(ion_group, value)
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titratable_group.determinants['coulomb'].append(new_det)
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def set_backbone_determinants(titratable_groups, backbone_groups, version):
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"""Set determinants between titrable and backbone groups.
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Args:
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titratable_groups: list of titratable groups
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backbone_groups: list of backbone groups
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version: version object
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"""
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for titratable_group in titratable_groups:
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titratable_group_interaction_atoms = (
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titratable_group.interaction_atoms_for_acids)
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if not titratable_group_interaction_atoms:
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continue
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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 = (
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backbone_group.get_interaction_atoms(titratable_group))
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if not backbone_interaction_atoms:
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continue
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# find the smallest distance
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[backbone_atom, distance, titratable_atom] = (
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get_smallest_distance(
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backbone_interaction_atoms,
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titratable_group_interaction_atoms))
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# get the parameters
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parameters = (
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version.get_backbone_hydrogen_bond_parameters(
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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
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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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[_, f_angle, _] = angle_distance_factors(
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atom1=heavy_atom, 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),
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# or the heavy atom is closer to the titratable
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# atom than the hydrogen. In either case we set the
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# angle factor 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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[_, f_angle, _] = (
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angle_distance_factors(
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atom1=titratable_atom, 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
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# heavy atom is closer to the titratable atom than the
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# hydrogen. In either case we set the angle factor to 0
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f_angle = 0.0
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if f_angle > FANGLE_MIN:
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value = (
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titratable_group.charge
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* hydrogen_bond_energy(
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distance, dpka_max, [cutoff1, cutoff2], f_angle))
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new_determinant = Determinant(backbone_group, value)
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titratable_group.determinants['backbone'].append(
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new_determinant)
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