mstk.forcefield.typer.Typer

class mstk.forcefield.typer.Typer

Base class for typing engines.

Typing engine assigns atom types for atoms in a molecule or topology by some predefined rules. It is the very first step for force field assignment. It is also the basis of force field development. A well defined typing rule will make the force field development much less painful.

Methods

__init__()
open(filename)	Load a typer from a type definition file.
type(top_or_mol)	Assign types for all atoms in a topology or molecule.

type(top_or_mol)

Assign types for all atoms in a topology or molecule.

The type attribute of all atoms in the topology/molecule will be updated.

Parameters:

top_or_mol (Topology, Molecule) –

static open(filename)

Load a typer from a type definition file.

The typing engine is determined by the TypingEngine line in the file.

Parameters:

filename (str) – Type definition file. If the file does not exist, will search it under directories defined by MSTK_FORCEFIELD_PATH.

Returns:

typer

Return type:

subclass of Typer