BCCGenerator

class openff.recharge.charges.bcc.BCCGenerator[source]

Bases: object

A class for generating the bond charge corrections which should be applied to a molecule.

Methods

__init__()

applied_corrections(*molecules, bcc_collection)

Returns the bond charge corrections which will be applied to a given molecule.

apply_assignment_matrix(assignment_matrix, ...)

Applies an assignment matrix to a list of bond charge corrections yield the final bond-charge corrections for a molecule.

build_assignment_matrix(molecule, bcc_collection)

Generates a matrix that specifies which bond charge corrections have been applied to which atoms in the molecule.

generate(molecule, bcc_collection)

Generate a set of charge increments for a molecule.
__init__()
classmethod applied_corrections(*molecules: Molecule, bcc_collection: BCCCollection) → List[BCCParameter][source]

Returns the bond charge corrections which will be applied to a given molecule.

Parameters

  • molecules – The molecule which the bond charge corrections would be applied to.

  • bcc_collection – The bond charge correction parameters which may be assigned.

classmethod apply_assignment_matrix(assignment_matrix: ndarray, bcc_collection: BCCCollection) → ndarray[source]

Applies an assignment matrix to a list of bond charge corrections yield the final bond-charge corrections for a molecule.

Parameters

  • assignment_matrix – The bond-charge correction matrix constructed using build_assignment_matrix which describes how the bond charge corrections should be applied. This should have shape=(n_atoms, n_bond_charge_corrections)

  • bcc_collection – The bond charge correction parameters which may be assigned.

Return type

The bond-charge corrections with shape=(n_atoms, 1).

classmethod build_assignment_matrix(molecule: Molecule, bcc_collection: BCCCollection) → ndarray[source]

Generates a matrix that specifies which bond charge corrections have been applied to which atoms in the molecule.

The matrix takes the form [atom_index, bcc_index] where atom_index is the index of an atom in the molecule and bcc_index is the index of a bond charge correction. Each value in the matrix can either be positive or negative depending on the direction the BCC was applied in.

Parameters

  • molecule – The molecule to assign the bond charge corrections to.

  • bcc_collection – The bond charge correction parameters that may be assigned.

Returns

  • The assignment matrix with shape=(n_atoms, n_bond_charge_corrections)

  • where n_atoms is the number of atoms in the molecule and

  • n_bond_charge_corrections is the number of bond charges corrections

  • to apply.

classmethod generate(molecule: Molecule, bcc_collection: BCCCollection) → ndarray[source]

Generate a set of charge increments for a molecule.

Parameters

  • molecule – The molecule to generate the bond-charge corrections for.

  • bcc_collection – The bond charge correction parameters which may be assigned.

Returns

  • The bond-charge corrections which should be applied to the

  • molecule.

classmethod build_assignment_matrix(molecule: Molecule, bcc_collection: BCCCollection) → ndarray[source]

Generates a matrix that specifies which bond charge corrections have been applied to which atoms in the molecule.

The matrix takes the form [atom_index, bcc_index] where atom_index is the index of an atom in the molecule and bcc_index is the index of a bond charge correction. Each value in the matrix can either be positive or negative depending on the direction the BCC was applied in.

Parameters

  • molecule – The molecule to assign the bond charge corrections to.

  • bcc_collection – The bond charge correction parameters that may be assigned.

Returns

  • The assignment matrix with shape=(n_atoms, n_bond_charge_corrections)

  • where n_atoms is the number of atoms in the molecule and

  • n_bond_charge_corrections is the number of bond charges corrections

  • to apply.

classmethod apply_assignment_matrix(assignment_matrix: ndarray, bcc_collection: BCCCollection) → ndarray[source]

Applies an assignment matrix to a list of bond charge corrections yield the final bond-charge corrections for a molecule.

Parameters

  • assignment_matrix – The bond-charge correction matrix constructed using build_assignment_matrix which describes how the bond charge corrections should be applied. This should have shape=(n_atoms, n_bond_charge_corrections)

  • bcc_collection – The bond charge correction parameters which may be assigned.

Return type

The bond-charge corrections with shape=(n_atoms, 1).

classmethod applied_corrections(*molecules: Molecule, bcc_collection: BCCCollection) → List[BCCParameter][source]

Returns the bond charge corrections which will be applied to a given molecule.

Parameters

  • molecules – The molecule which the bond charge corrections would be applied to.

  • bcc_collection – The bond charge correction parameters which may be assigned.

classmethod generate(molecule: Molecule, bcc_collection: BCCCollection) → ndarray[source]

Generate a set of charge increments for a molecule.

Parameters

  • molecule – The molecule to generate the bond-charge corrections for.

  • bcc_collection – The bond charge correction parameters which may be assigned.

Returns

  • The bond-charge corrections which should be applied to the

  • molecule.