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Clean up line breaks in version.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 20:33:34 -07:00
parent c2f362a101
commit 2bb6cf6293
1 changed files with 19 additions and 10 deletions
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27
propka/version.py
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@@ -40,31 +40,38 @@ class Version:
def calculate_pair_weight(self, num_volume1, num_volume2): def calculate_pair_weight(self, num_volume1, num_volume2):
"""Calculate pair weight using assigned model.""" """Calculate pair weight using assigned model."""
return self.weight_pair_method(self.parameters, num_volume1, num_volume2) return self.weight_pair_method(
self.parameters, num_volume1, num_volume2)
def hydrogen_bond_interaction(self, group1, group2): def hydrogen_bond_interaction(self, group1, group2):
"""Calculate H-bond energy using assigned model.""" """Calculate H-bond energy using assigned model."""
return self.hydrogen_bond_interaction_model(group1, group2, self) return self.hydrogen_bond_interaction_model(group1, group2, self)
def calculate_side_chain_energy(self, distance, dpka_max, cutoff, _, f_angle): def calculate_side_chain_energy(self, distance, dpka_max, cutoff, _,
f_angle):
"""Calculate sidechain energy using assigned model.""" """Calculate sidechain energy using assigned model."""
return self.sidechain_interaction_model(distance, dpka_max, cutoff, f_angle) return self.sidechain_interaction_model(
distance, dpka_max, cutoff, f_angle)
def electrostatic_interaction(self, group1, group2, distance): def electrostatic_interaction(self, group1, group2, distance):
"""Calculate electrostatic energy using assigned model.""" """Calculate electrostatic energy using assigned model."""
return self.electrostatic_interaction_model(group1, group2, distance, self) return self.electrostatic_interaction_model(
group1, group2, distance, self)
def calculate_coulomb_energy(self, distance, weight): def calculate_coulomb_energy(self, distance, weight):
"""Calculate Coulomb energy using assigned model.""" """Calculate Coulomb energy using assigned model."""
return self.coulomb_interaction_model(distance, weight, self.parameters) return self.coulomb_interaction_model(
distance, weight, self.parameters)
def check_coulomb_pair(self, group1, group2, distance): def check_coulomb_pair(self, group1, group2, distance):
"""Check Coulomb pair using assigned model.""" """Check Coulomb pair using assigned model."""
return self.check_coulomb_pair_method(self.parameters, group1, group2, distance) return self.check_coulomb_pair_method(
self.parameters, group1, group2, distance)
def calculate_backbone_reorganization(self, conformation): def calculate_backbone_reorganization(self, conformation):
"""Calculate backbone reorganization using assigned model.""" """Calculate backbone reorganization using assigned model."""
return self.backbone_reorganisation_method(self.parameters, conformation) return self.backbone_reorganisation_method(
self.parameters, conformation)
def check_exceptions(self, group1, group2): def check_exceptions(self, group1, group2):
"""Calculate exceptions using assigned model.""" """Calculate exceptions using assigned model."""
@@ -72,7 +79,8 @@ class Version:
def setup_bonding_and_protonation(self, molecular_container): def setup_bonding_and_protonation(self, molecular_container):
"""Setup bonding and protonation using assigned model.""" """Setup bonding and protonation using assigned model."""
return self.molecular_preparation_method(self.parameters, molecular_container) return self.molecular_preparation_method(
self.parameters, molecular_container)
def setup_bonding(self, molecular_container): def setup_bonding(self, molecular_container):
"""Setup bonding using assigned model.""" """Setup bonding using assigned model."""
@@ -242,7 +250,8 @@ class ElementBasedLigandInteractions(VersionA):
res = self.parameters.hydrogen_bonds.get_value( res = self.parameters.hydrogen_bonds.get_value(
elements[0], elements[1]) elements[0], elements[1])
if not res: if not res:
info('Could not determine backbone interaction parameters for:', info(
'Could not determine backbone interaction parameters for:',
backbone_atom, atom) backbone_atom, atom)
return None return None
return None return None