Atom-typing Options

The primary data structure in foyer is the Forcefield class, which inherits from the OpenMM class of the same name. The primary operation on this class is the .apply() function, which takes a chemical topology and returns a parametrized ParmEd Structure. The user may pass some otions to this function based on a particular use case.

Forcefield

class foyer.forcefield.Forcefield(forcefield_files=None, name=None, validation=True, debug=False)[source]

Specialization of OpenMM’s Forcefield allowing SMARTS based atomtyping.

Parameters
  • forcefield_files (list of str, optional, default None) – List of forcefield files to load.

  • name (str, optional, default None) – Name of a forcefield to load that is packaged within foyer.

apply(structure, references_file=None, use_residue_map=True, assert_bond_params=True, assert_angle_params=True, assert_dihedral_params=True, assert_improper_params=False, combining_rule='geometric', verbose=False, *args, **kwargs)[source]

Apply the force field to a molecular structure

Parameters
  • structure (parmed.Structure or mbuild.Compound) – Molecular structure to apply the force field to

  • references_file (str, optional, default None) – Name of file where force field references will be written (in Bibtex format)

  • use_residue_map (boolean, optional, default True) – Store atomtyped topologies of residues to a dictionary that maps them to residue names. Each topology, including atomtypes, will be copied to other residues with the same name. This avoids repeatedly calling the subgraph isomorphism on idential residues and should result in better performance for systems with many identical residues, i.e. a box of water. Note that for this to be applied to independent molecules, they must each be saved as different residues in the topology.

  • assert_bond_params (bool, optional, default True) – If True, Foyer will exit if parameters are not found for all system bonds.

  • assert_angle_params (bool, optional, default True) – If True, Foyer will exit if parameters are not found for all system angles.

  • assert_dihedral_params (bool, optional, default True) – If True, Foyer will exit if parameters are not found for all system proper dihedrals.

  • assert_improper_params (bool, optional, default False) – If True, Foyer will exit if parameters are not found for all system improper dihedrals.

  • combining_rule (str, optional, default 'geometric') – The combining rule of the system, stored as an attribute of the ParmEd structure. Accepted arguments are geometric and lorentz.

  • verbose (bool, optional, default False) – If True, Foyer will print debug-level information about notable or potentially problematic details it encounters.

createSystem(topology, nonbondedMethod=NoCutoff, nonbondedCutoff=Quantity(value=1.0, unit=nanometer), constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, switchDistance=None, **args)[source]

Construct an OpenMM System representing a Topology with this force field.

Parameters
  • topology (Topology) – The Topology for which to create a System

  • nonbondedMethod (object=NoCutoff) – The method to use for nonbonded interactions. Allowed values are NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.

  • nonbondedCutoff (distance=1*nanometer) – The cutoff distance to use for nonbonded interactions

  • constraints (object=None) – Specifies which bonds and angles should be implemented with constraints. Allowed values are None, HBonds, AllBonds, or HAngles.

  • rigidWater (boolean=True) – If true, water molecules will be fully rigid regardless of the value passed for the constraints argument

  • removeCMMotion (boolean=True) – If true, a CMMotionRemover will be added to the System

  • hydrogenMass (mass=None) – The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is subtracted from the heavy atom to keep their total mass the same.

  • switchDistance (float=None) – The distance at which the potential energy switching function is turned on for

  • args – Arbitrary additional keyword arguments may also be specified. This allows extra parameters to be specified that are specific to particular force fields.

Returns

the newly created System

Return type

system

registerAtomType(parameters)[source]

Register a new atom type.

run_atomtyping(structure, use_residue_map=True, **kwargs)[source]

Atomtype the topology

Parameters
  • structure (parmed.structure.Structure) – Molecular structure to find atom types of

  • use_residue_map (boolean, optional, default True) – Store atomtyped topologies of residues to a dictionary that maps them to residue names. Each topology, including atomtypes, will be copied to other residues with the same name. This avoids repeatedly calling the subgraph isomorphism on idential residues and should result in better performance for systems with many identical residues, i.e. a box of water. Note that for this to be applied to independent molecules, they must each be saved as different residues in the topology.