mstk.forcefield.typer.GaffTyper

class mstk.forcefield.typer.GaffTyper(file=None)

GaffTyper is specifically designed for GAFF atom type assignment. By default, it uses the type definition file gaff.smt

Compared with SmartsTyper, this class will handle conjugated atom types according to the GAFF convention, e.g. cc/cd, ce/cf etc…

The official tool for GAFF - antechamber has several issues: - Mysterious aromatic assignment - A lost of parameters missing. parmchk2 gives unreasonable guess for torsion parameters, e.g. biphenyl

Parameters:

file (str or file-like object, optional) – Type definition file.

Notes

• SMARTS is parsed by using RDKit package. Make sure it is installed.

• In type definition file, empty lines are ignored, and comments should start with ##.

Methods

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