propka.version

Version-based configuration

Contains version-specific methods and parameters.

TODO - this module unnecessarily confuses the code. Can we eliminate it?

Classes

ElementBasedLigandInteractions(parameters)	TODO - figure out what this is.
Propka30(parameters)	Version class for PROPKA 3.0.
SimpleHB(parameters)	A simple hydrogen bond version.
Version(parameters)	Store version-specific methods and parameters.
VersionA(parameters)	TODO - figure out what this is.

class propka.version.ElementBasedLigandInteractions(parameters)

TODO - figure out what this is.

get_backbone_hydrogen_bond_parameters(backbone_atom, atom)

Get hydrogen bond parameters between backbone atom and other atom.

Parameters:

• backbone_atom – backbone atom

• atom – other atom

Returns

[v, [c1, c3]] TODO - figure out what this is

get_hydrogen_bond_parameters(atom1, atom2)

Get hydrogen bond parameters for two atoms.

Parameters:

• atom1 – first atom

• atom2 – second atom

Returns:

[dpka_max, cutoff]

class propka.version.Propka30(parameters)

Version class for PROPKA 3.0.

get_hydrogen_bond_parameters(atom1, atom2)

Get hydrogen bond parameters for two atoms.

Parameters:

• atom1 – first atom

• atom2 – second atom

Returns:

[dpka_max, cutoff]

class propka.version.SimpleHB(parameters)

A simple hydrogen bond version.

get_backbone_hydrogen_bond_parameters(backbone_atom, atom)

Get hydrogen bond parameters between backbone atom and other atom.

Parameters:

• backbone_atom – backbone atom

• atom – other atom

Returns

[v, [c1, c3]] TODO - figure out what this is

get_hydrogen_bond_parameters(atom1, atom2)

Get hydrogen bond parameters for two atoms.

Parameters:

• atom1 – first atom

• atom2 – second atom

Returns:

[dpka_max, cutoff]

class propka.version.Version(parameters: Parameters)

Store version-specific methods and parameters.

calculate_backbone_reorganization(conformation)

Calculate backbone reorganization using assigned model.

calculate_coulomb_energy(distance, weight)

Calculate Coulomb energy using assigned model.

calculate_desolvation(group)

Calculate desolvation energy using assigned model.

calculate_pair_weight(num_volume1, num_volume2)

Calculate pair weight using assigned model.

calculate_side_chain_energy(distance, dpka_max, cutoff, _, f_angle)

Calculate sidechain energy using assigned model.

check_coulomb_pair(group1, group2, distance)

Check Coulomb pair using assigned model.

check_exceptions(group1, group2)

Calculate exceptions using assigned model.

electrostatic_interaction(group1, group2, distance)

Calculate electrostatic energy using assigned model.

static empty_function(*args)

Placeholder function so we don’t use uninitialized variables.

Parameters:

args – whatever arguments would have been passed to the function

Raises:

NotImplementedError –

get_hydrogen_bond_parameters(atom1: Atom, atom2: Atom) → Tuple[float, Sequence[float]]

Get hydrogen bond parameters for two atoms.

hydrogen_bond_interaction(group1, group2)

Calculate H-bond energy using assigned model.

setup_bonding(molecular_container)

Setup bonding using assigned model.

setup_bonding_and_protonation(molecular_container)

Setup bonding and protonation using assigned model.

class propka.version.VersionA(parameters)

TODO - figure out what this is.

get_backbone_hydrogen_bond_parameters(backbone_atom, atom)

Get hydrogen bond parameters between backbone atom and other atom.

Parameters:

• backbone_atom – backbone atom

• atom – other atom

Returns

[v, [c1, c3]] TODO - figure out what this is

get_hydrogen_bond_parameters(atom1, atom2)

Get hydrogen bond parameters for two atoms.

Parameters:

• atom1 – first atom

• atom2 – second atom

Returns:

[dpka_max, cutoff]