omic/propka
1
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases Wiki Activity

De-lint calculations.py.

Browse Source 
Changes were made to function names; impacted functions changed in other
files.  Google searches performed to look for impacts to other software.
This commit is contained in:
Nathan Baker
2020-05-23 15:02:23 -07:00
parent 1611e9d6ea
commit 5ed77a7cf6
4 changed files with 447 additions and 369 deletions
Download Patch File Download Diff File Expand all files Collapse all files

768
propka/calculations.py
View File

File diff suppressed because it is too large Load Diff

2
propka/conformation_container.py
View File

@@ -182,7 +182,7 @@ class Conformation_container:
propka.determinants.setIonDeterminants(self, version) propka.determinants.setIonDeterminants(self, version)
# calculating the back-bone reorganization/desolvation term # calculating the back-bone reorganization/desolvation term
version.calculateBackBoneReorganization(self) version.calculatebackbone_reorganization(self)
# setting remaining non-iterative and iterative side-chain & Coulomb interaction determinants # setting remaining non-iterative and iterative side-chain & Coulomb interaction determinants
propka.determinants.setDeterminants(self.get_sidechain_groups(), version=version, options=options) propka.determinants.setDeterminants(self.get_sidechain_groups(), version=version, options=options)

10
propka/determinants.py
View File

@@ -157,9 +157,9 @@ def setIonDeterminants(conformation_container, version):
for ion_group in conformation_container.get_ions(): for ion_group in conformation_container.get_ions():
squared_distance = propka.calculations.squared_distance(titratable_group, ion_group) squared_distance = propka.calculations.squared_distance(titratable_group, ion_group)
if squared_distance < version.parameters.coulomb_cutoff2_squared: if squared_distance < version.parameters.coulomb_cutoff2_squared:
weight = version.calculatePairWeight(titratable_group.Nmass, ion_group.Nmass) weight = version.calculate_pair_weight(titratable_group.Nmass, ion_group.Nmass)
# the pKa of both acids and bases are shifted up by negative ions (and vice versa) # the pKa of both acids and bases are shifted up by negative ions (and vice versa)
value = (-ion_group.charge) * version.calculateCoulombEnergy(math.sqrt(squared_distance), weight) value = (-ion_group.charge) * version.calculate_coulomb_energy(math.sqrt(squared_distance), weight)
newDeterminant = Determinant(ion_group, value) newDeterminant = Determinant(ion_group, value)
titratable_group.determinants['coulomb'].append(newDeterminant) titratable_group.determinants['coulomb'].append(newDeterminant)
@@ -206,7 +206,7 @@ def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
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
[d1, f_angle, d2] = propka.calculations.AngleFactorX(atom1=heavy_atom, [d1, f_angle, d2] = propka.calculations.angle_distance_factors(atom1=heavy_atom,
atom2=hydrogen_atom, atom2=hydrogen_atom,
atom3=backbone_atom) atom3=backbone_atom)
else: else:
@@ -227,7 +227,7 @@ def setBackBoneDeterminants(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
[d1, f_angle, d2] = propka.calculations.AngleFactorX(atom1=titratable_atom, [d1, f_angle, d2] = propka.calculations.angle_distance_factors(atom1=titratable_atom,
atom2=backbone_H, atom2=backbone_H,
atom3=backbone_N) atom3=backbone_N)
else: else:
@@ -238,7 +238,7 @@ def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
if f_angle > 0.001: if f_angle > 0.001:
value = titratable_group.charge * propka.calculations.HydrogenBondEnergy(distance, dpKa_max, [cutoff1,cutoff2], f_angle) value = titratable_group.charge * propka.calculations.hydrogen_bond_energy(distance, dpKa_max, [cutoff1,cutoff2], f_angle)
newDeterminant = Determinant(backbone_group, value) newDeterminant = Determinant(backbone_group, value)
titratable_group.determinants['backbone'].append(newDeterminant) titratable_group.determinants['backbone'].append(newDeterminant)

36
propka/version.py
View File

@@ -18,7 +18,7 @@ class version:
def calculate_desolvation(self, group): def calculate_desolvation(self, group):
return self.desolvation_model(self.parameters, group) return self.desolvation_model(self.parameters, group)
def calculatePairWeight(self, Nmass1, Nmass2): def calculate_pair_weight(self, Nmass1, Nmass2):
return self.weight_pair_method(self.parameters, Nmass1, Nmass2) return self.weight_pair_method(self.parameters, Nmass1, Nmass2)
# side chains # side chains
@@ -32,18 +32,18 @@ class version:
def electrostatic_interaction(self, group1, group2, distance): def electrostatic_interaction(self, group1, group2, distance):
return self.electrostatic_interaction_model(group1, group2, distance, self) return self.electrostatic_interaction_model(group1, group2, distance, self)
def calculateCoulombEnergy(self, distance, weight): def calculate_coulomb_energy(self, distance, weight):
return self.coulomb_interaction_model(distance, weight, self.parameters) return self.coulomb_interaction_model(distance, weight, self.parameters)
def checkCoulombPair(self, group1, group2, distance): def check_coulomb_pair(self, group1, group2, distance):
return self.check_coulomb_pair_method(self.parameters, group1, group2, distance) return self.check_coulomb_pair_method(self.parameters, group1, group2, distance)
# backbone re-organisation # backbone re-organisation
def calculateBackBoneReorganization(self, conformation): def calculatebackbone_reorganization(self, conformation):
return self.backbone_reorganisation_method(self.parameters, conformation) return self.backbone_reorganisation_method(self.parameters, conformation)
# exceptions # exceptions
def checkExceptions(self, group1, group2): def check_exceptions(self, group1, group2):
return self.exception_check_method(self, group1, group2) return self.exception_check_method(self, group1, group2)
def setup_bonding_and_protonation(self, molecular_container): def setup_bonding_and_protonation(self, molecular_container):
@@ -66,23 +66,23 @@ class version_A(version):
# desolvation related methods # desolvation related methods
self.desolvation_model = calculations.radial_volume_desolvation self.desolvation_model = calculations.radial_volume_desolvation
self.weight_pair_method = calculations.calculatePairWeight self.weight_pair_method = calculations.calculate_pair_weight
# side chain methods # side chain methods
self.sidechain_interaction_model = propka.calculations.HydrogenBondEnergy self.sidechain_interaction_model = propka.calculations.hydrogen_bond_energy
self.hydrogen_bond_interaction_model = propka.calculations.hydrogen_bond_interaction self.hydrogen_bond_interaction_model = propka.calculations.hydrogen_bond_interaction
# colomb methods # colomb methods
self.electrostatic_interaction_model = propka.calculations.electrostatic_interaction self.electrostatic_interaction_model = propka.calculations.electrostatic_interaction
self.check_coulomb_pair_method = propka.calculations.checkCoulombPair self.check_coulomb_pair_method = propka.calculations.check_coulomb_pair
self.coulomb_interaction_model = propka.calculations.CoulombEnergy self.coulomb_interaction_model = propka.calculations.coulomb_energy
#backbone #backbone
self.backbone_interaction_model = propka.calculations.HydrogenBondEnergy self.backbone_interaction_model = propka.calculations.hydrogen_bond_energy
self.backbone_reorganisation_method = propka.calculations.BackBoneReorganization self.backbone_reorganisation_method = propka.calculations.backbone_reorganization
# exception methods # exception methods
self.exception_check_method = propka.calculations.checkExceptions self.exception_check_method = propka.calculations.check_exceptions
return return
def get_hydrogen_bond_parameters(self, atom1, atom2): def get_hydrogen_bond_parameters(self, atom1, atom2):
@@ -188,20 +188,20 @@ class propka30(version):
# desolvation related methods # desolvation related methods
self.desolvation_model = calculations.radial_volume_desolvation self.desolvation_model = calculations.radial_volume_desolvation
self.weight_pair_method = calculations.calculatePairWeight self.weight_pair_method = calculations.calculate_pair_weight
# side chain methods # side chain methods
self.sidechain_interaction_model = propka.calculations.HydrogenBondEnergy self.sidechain_interaction_model = propka.calculations.hydrogen_bond_energy
# colomb methods # colomb methods
self.check_coulomb_pair_method = propka.calculations.checkCoulombPair self.check_coulomb_pair_method = propka.calculations.check_coulomb_pair
self.coulomb_interaction_model = propka.calculations.CoulombEnergy self.coulomb_interaction_model = propka.calculations.coulomb_energy
#backbone #backbone
self.backbone_reorganisation_method = propka.calculations.BackBoneReorganization self.backbone_reorganisation_method = propka.calculations.backbone_reorganization
# exception methods # exception methods
self.exception_check_method = propka.calculations.checkExceptions self.exception_check_method = propka.calculations.check_exceptions
return return