Clean up line breaks in version.py
See https://github.com/jensengroup/propka-3.1/issues/43
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@@ -40,31 +40,38 @@ class Version:
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def calculate_pair_weight(self, num_volume1, num_volume2):
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"""Calculate pair weight using assigned model."""
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return self.weight_pair_method(self.parameters, num_volume1, num_volume2)
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return self.weight_pair_method(
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self.parameters, num_volume1, num_volume2)
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def hydrogen_bond_interaction(self, group1, group2):
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"""Calculate H-bond energy using assigned model."""
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return self.hydrogen_bond_interaction_model(group1, group2, self)
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def calculate_side_chain_energy(self, distance, dpka_max, cutoff, _, f_angle):
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def calculate_side_chain_energy(self, distance, dpka_max, cutoff, _,
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f_angle):
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"""Calculate sidechain energy using assigned model."""
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return self.sidechain_interaction_model(distance, dpka_max, cutoff, f_angle)
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return self.sidechain_interaction_model(
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distance, dpka_max, cutoff, f_angle)
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def electrostatic_interaction(self, group1, group2, distance):
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"""Calculate electrostatic energy using assigned model."""
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return self.electrostatic_interaction_model(group1, group2, distance, self)
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return self.electrostatic_interaction_model(
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group1, group2, distance, self)
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def calculate_coulomb_energy(self, distance, weight):
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"""Calculate Coulomb energy using assigned model."""
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return self.coulomb_interaction_model(distance, weight, self.parameters)
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return self.coulomb_interaction_model(
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distance, weight, self.parameters)
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def check_coulomb_pair(self, group1, group2, distance):
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"""Check Coulomb pair using assigned model."""
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return self.check_coulomb_pair_method(self.parameters, group1, group2, distance)
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return self.check_coulomb_pair_method(
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self.parameters, group1, group2, distance)
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def calculate_backbone_reorganization(self, conformation):
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"""Calculate backbone reorganization using assigned model."""
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return self.backbone_reorganisation_method(self.parameters, conformation)
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return self.backbone_reorganisation_method(
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self.parameters, conformation)
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def check_exceptions(self, group1, group2):
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"""Calculate exceptions using assigned model."""
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@@ -72,7 +79,8 @@ class Version:
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def setup_bonding_and_protonation(self, molecular_container):
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"""Setup bonding and protonation using assigned model."""
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return self.molecular_preparation_method(self.parameters, molecular_container)
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return self.molecular_preparation_method(
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self.parameters, molecular_container)
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def setup_bonding(self, molecular_container):
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"""Setup bonding using assigned model."""
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@@ -242,8 +250,9 @@ class ElementBasedLigandInteractions(VersionA):
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res = self.parameters.hydrogen_bonds.get_value(
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elements[0], elements[1])
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if not res:
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info('Could not determine backbone interaction parameters for:',
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backbone_atom, atom)
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info(
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'Could not determine backbone interaction parameters for:',
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backbone_atom, atom)
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return None
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return None
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