Force fields

Module that contains the classes for evaluating classical molecular force fields to compute the energy of atomistic systems

class topsearch.potentials.force_fields.MMFF94(xyz_file: str)

Description

Evaluate the energy and force of a molecular system using the MMFF94 empirical force field through RDKit.

xyz_file

The filename for the xyz file that contains the molecular or atomic system

Type:

string

molecule

rdkit object that stores the information about the molecule

Type:

class instance

conf

stores the particular atomic positions for the molecule

Type:

class instance

n_atoms

Store the number of atoms in the molecule or cluster

Type:

int

force_field

the force field object that contains parameters to allow evaluation of the potential energy from the molecule object

Type:

class instance

function(position: NDArray[Any, Any]) → float

Compute the potential energy

function_gradient(position: NDArray[Any, Any]) → tuple

Compute the potential energy and its gradient

gradient(position: NDArray[Any, Any]) → NDArray[Any, Any]

Compute the atomic forces in the molecule

set_xyz(position: NDArray[Any, Any]) → None

Put the xyz coordinates provided in position into the molecule object