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Clean up line breaks in determinants.py

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See https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
2020-05-25 18:15:46 -07:00
parent ba8362f514
commit 891fecaab3
1 changed files with 45 additions and 39 deletions
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78
propka/determinants.py
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@@ -39,12 +39,12 @@ def set_determinants(propka_groups, version=None, options=None):
break break
distance = propka.calculations.distance(group1, group2) distance = propka.calculations.distance(group1, group2)
if distance < version.parameters.coulomb_cutoff2: if distance < version.parameters.coulomb_cutoff2:
interaction_type = version.parameters.interaction_matrix.get_value(group1.type, interaction_type = (
group2.type) version.parameters.interaction_matrix.get_value(
group1.type, group2.type))
if interaction_type == 'I': if interaction_type == 'I':
propka.iterative.add_to_determinant_list(group1, group2, propka.iterative.add_to_determinant_list(
distance, group1, group2, distance, iterative_interactions,
iterative_interactions,
version=version) version=version)
elif interaction_type == 'N': elif interaction_type == 'N':
add_determinants(group1, group2, distance, version) add_determinants(group1, group2, distance, version)
@@ -88,8 +88,10 @@ def add_sidechain_determinants(group1, group2, version=None):
new_determinant1 = Determinant(group2, hbond_interaction) new_determinant1 = Determinant(group2, hbond_interaction)
new_determinant2 = Determinant(group1, -hbond_interaction) new_determinant2 = Determinant(group1, -hbond_interaction)
else: else:
new_determinant1 = Determinant(group2, hbond_interaction*group1.charge) new_determinant1 = Determinant(
new_determinant2 = Determinant(group1, hbond_interaction*group2.charge) group2, hbond_interaction*group1.charge)
new_determinant2 = Determinant(
group1, hbond_interaction*group2.charge)
group1.determinants['sidechain'].append(new_determinant1) group1.determinants['sidechain'].append(new_determinant1)
group2.determinants['sidechain'].append(new_determinant2) group2.determinants['sidechain'].append(new_determinant2)
@@ -103,8 +105,8 @@ def add_coulomb_determinants(group1, group2, distance, version):
distance: distance between groups distance: distance between groups
version: version object version: version object
""" """
coulomb_interaction = version.electrostatic_interaction(group1, group2, coulomb_interaction = version.electrostatic_interaction(
distance) group1, group2, distance)
if coulomb_interaction: if coulomb_interaction:
q1 = group1.charge q1 = group1.charge
q2 = group2.charge q2 = group2.charge
@@ -187,13 +189,14 @@ def set_ion_determinants(conformation_container, version):
for ion_group in conformation_container.get_ions(): for ion_group in conformation_container.get_ions():
dist_sq = squared_distance(titratable_group, ion_group) dist_sq = squared_distance(titratable_group, ion_group)
if dist_sq < version.parameters.coulomb_cutoff2_squared: if dist_sq < version.parameters.coulomb_cutoff2_squared:
weight = version.calculate_pair_weight(titratable_group.num_volume, weight = version.calculate_pair_weight(
ion_group.num_volume) titratable_group.num_volume, ion_group.num_volume)
# the pKa of both acids and bases are shifted up by negative # the pKa of both acids and bases are shifted up by negative
# ions (and vice versa) # ions (and vice versa)
value = (-ion_group.charge) \ value = (
* version.calculate_coulomb_energy(math.sqrt(dist_sq), -ion_group.charge
weight) * version.calculate_coulomb_energy(
math.sqrt(dist_sq), weight))
new_det = Determinant(ion_group, value) new_det = Determinant(ion_group, value)
titratable_group.determinants['coulomb'].append(new_det) titratable_group.determinants['coulomb'].append(new_det)
@@ -207,24 +210,26 @@ def set_backbone_determinants(titratable_groups, backbone_groups, version):
version: version object version: version object
""" """
for titratable_group in titratable_groups: for titratable_group in titratable_groups:
titratable_group_interaction_atoms \ titratable_group_interaction_atoms = (
= titratable_group.interaction_atoms_for_acids titratable_group.interaction_atoms_for_acids)
if not titratable_group_interaction_atoms: if not titratable_group_interaction_atoms:
continue continue
# find out which backbone groups this titratable is interacting with # find out which backbone groups this titratable is interacting with
for backbone_group in backbone_groups: for backbone_group in backbone_groups:
# find the interacting atoms # find the interacting atoms
backbone_interaction_atoms \ backbone_interaction_atoms = (
= backbone_group.get_interaction_atoms(titratable_group) backbone_group.get_interaction_atoms(titratable_group))
if not backbone_interaction_atoms: if not backbone_interaction_atoms:
continue continue
# find the smallest distance # find the smallest distance
[backbone_atom, distance, titratable_atom] \ [backbone_atom, distance, titratable_atom] = (
= get_smallest_distance(backbone_interaction_atoms, \ get_smallest_distance(
titratable_group_interaction_atoms) backbone_interaction_atoms,
titratable_group_interaction_atoms))
# get the parameters # get the parameters
parameters = version.get_backbone_hydrogen_bond_parameters(backbone_atom, parameters = (
titratable_atom) version.get_backbone_hydrogen_bond_parameters(
backbone_atom, titratable_atom))
if not parameters: if not parameters:
continue continue
[dpka_max, [cutoff1, cutoff2]] = parameters [dpka_max, [cutoff1, cutoff2]] = parameters
@@ -241,13 +246,13 @@ def set_backbone_determinants(titratable_groups, backbone_groups, version):
# || # ||
# C # C
if backbone_group.type == 'BBC': if backbone_group.type == 'BBC':
if titratable_group.type \ if (titratable_group.type
in version.parameters.angular_dependent_sidechain_interactions: in version.parameters.angular_dependent_sidechain_interactions):
if titratable_atom.element == 'H': if titratable_atom.element == 'H':
heavy_atom = titratable_atom.bonded_atoms[0] heavy_atom = titratable_atom.bonded_atoms[0]
hydrogen_atom = titratable_atom hydrogen_atom = titratable_atom
[_, f_angle, _] = angle_distance_factors(atom1=heavy_atom, [_, f_angle, _] = angle_distance_factors(
atom2=hydrogen_atom, atom1=heavy_atom, atom2=hydrogen_atom,
atom3=backbone_atom) atom3=backbone_atom)
else: else:
# Either the structure is corrupt (no hydrogen), # Either the structure is corrupt (no hydrogen),
@@ -267,19 +272,20 @@ def set_backbone_determinants(titratable_groups, backbone_groups, version):
if backbone_atom.element == 'H': if backbone_atom.element == 'H':
backbone_n = backbone_atom.bonded_atoms[0] backbone_n = backbone_atom.bonded_atoms[0]
backbone_h = backbone_atom backbone_h = backbone_atom
[_, f_angle, _] = angle_distance_factors(atom1=titratable_atom, [_, f_angle, _] = (
atom2=backbone_h, angle_distance_factors(
atom3=backbone_n) atom1=titratable_atom, atom2=backbone_h,
atom3=backbone_n))
else: else:
# Either the structure is corrupt (no hydrogen), or the # Either the structure is corrupt (no hydrogen), or the
# heavy atom is closer to the titratable atom than the # heavy atom is closer to the titratable atom than the
# hydrogen. In either case we set the angle factor to 0 # hydrogen. In either case we set the angle factor to 0
f_angle = 0.0 f_angle = 0.0
if f_angle > FANGLE_MIN: if f_angle > FANGLE_MIN:
value = titratable_group.charge * hydrogen_bond_energy(distance, value = (
dpka_max, titratable_group.charge
[cutoff1, cutoff2], * hydrogen_bond_energy(
f_angle) distance, dpka_max, [cutoff1, cutoff2], f_angle))
new_determinant = Determinant(backbone_group, value) new_determinant = Determinant(backbone_group, value)
titratable_group.determinants['backbone'].append(new_determinant) titratable_group.determinants['backbone'].append(
new_determinant)