From 891fecaab3a2d435212316cee7f3990f1e678c93 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Mon, 25 May 2020 18:15:46 -0700 Subject: [PATCH] Clean up line breaks in determinants.py See https://github.com/jensengroup/propka-3.1/issues/43 --- propka/determinants.py | 84 ++++++++++++++++++++++-------------------- 1 file changed, 45 insertions(+), 39 deletions(-) diff --git a/propka/determinants.py b/propka/determinants.py index fa80763..9a82e33 100644 --- a/propka/determinants.py +++ b/propka/determinants.py @@ -39,13 +39,13 @@ def set_determinants(propka_groups, version=None, options=None): break distance = propka.calculations.distance(group1, group2) if distance < version.parameters.coulomb_cutoff2: - interaction_type = version.parameters.interaction_matrix.get_value(group1.type, - group2.type) + interaction_type = ( + version.parameters.interaction_matrix.get_value( + group1.type, group2.type)) if interaction_type == 'I': - propka.iterative.add_to_determinant_list(group1, group2, - distance, - iterative_interactions, - version=version) + propka.iterative.add_to_determinant_list( + group1, group2, distance, iterative_interactions, + version=version) elif interaction_type == 'N': add_determinants(group1, group2, distance, version) # --- Iterative section ---# @@ -53,7 +53,7 @@ def set_determinants(propka_groups, version=None, options=None): def add_determinants(group1, group2, distance, version): - """Add determinants and perturbations for distance(R1, R2) < coulomb_cutoff. + """Add determinants and perturbations for distance(R1,R2) < coulomb_cutoff. Args: group1: first group to add @@ -88,8 +88,10 @@ def add_sidechain_determinants(group1, group2, version=None): new_determinant1 = Determinant(group2, hbond_interaction) new_determinant2 = Determinant(group1, -hbond_interaction) else: - new_determinant1 = Determinant(group2, hbond_interaction*group1.charge) - new_determinant2 = Determinant(group1, hbond_interaction*group2.charge) + new_determinant1 = Determinant( + group2, hbond_interaction*group1.charge) + new_determinant2 = Determinant( + group1, hbond_interaction*group2.charge) group1.determinants['sidechain'].append(new_determinant1) group2.determinants['sidechain'].append(new_determinant2) @@ -103,8 +105,8 @@ def add_coulomb_determinants(group1, group2, distance, version): distance: distance between groups version: version object """ - coulomb_interaction = version.electrostatic_interaction(group1, group2, - distance) + coulomb_interaction = version.electrostatic_interaction( + group1, group2, distance) if coulomb_interaction: q1 = group1.charge q2 = group2.charge @@ -187,13 +189,14 @@ def set_ion_determinants(conformation_container, version): for ion_group in conformation_container.get_ions(): dist_sq = squared_distance(titratable_group, ion_group) if dist_sq < version.parameters.coulomb_cutoff2_squared: - weight = version.calculate_pair_weight(titratable_group.num_volume, - ion_group.num_volume) + weight = version.calculate_pair_weight( + titratable_group.num_volume, ion_group.num_volume) # the pKa of both acids and bases are shifted up by negative # ions (and vice versa) - value = (-ion_group.charge) \ - * version.calculate_coulomb_energy(math.sqrt(dist_sq), - weight) + value = ( + -ion_group.charge + * version.calculate_coulomb_energy( + math.sqrt(dist_sq), weight)) new_det = Determinant(ion_group, value) titratable_group.determinants['coulomb'].append(new_det) @@ -207,24 +210,26 @@ def set_backbone_determinants(titratable_groups, backbone_groups, version): version: version object """ for titratable_group in titratable_groups: - titratable_group_interaction_atoms \ - = titratable_group.interaction_atoms_for_acids + titratable_group_interaction_atoms = ( + titratable_group.interaction_atoms_for_acids) if not titratable_group_interaction_atoms: continue # find out which backbone groups this titratable is interacting with for backbone_group in backbone_groups: # find the interacting atoms - backbone_interaction_atoms \ - = backbone_group.get_interaction_atoms(titratable_group) + backbone_interaction_atoms = ( + backbone_group.get_interaction_atoms(titratable_group)) if not backbone_interaction_atoms: continue # find the smallest distance - [backbone_atom, distance, titratable_atom] \ - = get_smallest_distance(backbone_interaction_atoms, \ - titratable_group_interaction_atoms) + [backbone_atom, distance, titratable_atom] = ( + get_smallest_distance( + backbone_interaction_atoms, + titratable_group_interaction_atoms)) # get the parameters - parameters = version.get_backbone_hydrogen_bond_parameters(backbone_atom, - titratable_atom) + parameters = ( + version.get_backbone_hydrogen_bond_parameters( + backbone_atom, titratable_atom)) if not parameters: continue [dpka_max, [cutoff1, cutoff2]] = parameters @@ -241,14 +246,14 @@ def set_backbone_determinants(titratable_groups, backbone_groups, version): # || # C if backbone_group.type == 'BBC': - if titratable_group.type \ - in version.parameters.angular_dependent_sidechain_interactions: + if (titratable_group.type + in version.parameters.angular_dependent_sidechain_interactions): if titratable_atom.element == 'H': heavy_atom = titratable_atom.bonded_atoms[0] hydrogen_atom = titratable_atom - [_, f_angle, _] = angle_distance_factors(atom1=heavy_atom, - atom2=hydrogen_atom, - atom3=backbone_atom) + [_, f_angle, _] = angle_distance_factors( + atom1=heavy_atom, atom2=hydrogen_atom, + atom3=backbone_atom) else: # Either the structure is corrupt (no hydrogen), # or the heavy atom is closer to the titratable @@ -267,19 +272,20 @@ def set_backbone_determinants(titratable_groups, backbone_groups, version): if backbone_atom.element == 'H': backbone_n = backbone_atom.bonded_atoms[0] backbone_h = backbone_atom - [_, f_angle, _] = angle_distance_factors(atom1=titratable_atom, - atom2=backbone_h, - atom3=backbone_n) + [_, f_angle, _] = ( + angle_distance_factors( + atom1=titratable_atom, atom2=backbone_h, + atom3=backbone_n)) else: # Either the structure is corrupt (no hydrogen), or the # heavy atom is closer to the titratable atom than the # hydrogen. In either case we set the angle factor to 0 f_angle = 0.0 if f_angle > FANGLE_MIN: - value = titratable_group.charge * hydrogen_bond_energy(distance, - dpka_max, - [cutoff1, cutoff2], - f_angle) + value = ( + titratable_group.charge + * hydrogen_bond_energy( + distance, dpka_max, [cutoff1, cutoff2], f_angle)) new_determinant = Determinant(backbone_group, value) - titratable_group.determinants['backbone'].append(new_determinant) - \ No newline at end of file + titratable_group.determinants['backbone'].append( + new_determinant)