Class ForceField

Create a ForceField instance

Parameters:

• path (str) - The path to the force field file. Not used if data is provided
• data (dict) - The dictionary that defines the force field. If not provided, the database will be read from path.

Raises:

• ValueError - if neither path nor data have been provided

Overrides: object.__init__

Get the force field data for key

Parameters:

• key (str) - A top level key for the force field data dictionary
• fail_on_missing (bool) - True if an exception should be raised if the key is not in the force field data. If False, None will be returned for a missing key

Returns:

the value associated with key, or None if key is missing and fail_on_missing is False

Raises:

• MissingParameterError - If key is missing and fail_on_missing is True

Define the internal coordinates (bonds, angles, dihedrals, included and excluded nonbonds, etc) for the structure

Parameters:

• struct (schrodinger.structure.Structure) - The structure to use when defining internals.

Get the database data of type key for the particles with the given names. The names be ordered in the same way they would be ordered by the coarsegrain.Internals class and the proper number of names must be provided for the desired type - two for bonds, three for angles, etc.

Parameters:

• names (tuple) - The names of the particles to retrieve data for
• key (str) - One of the top level keys in the database dictionary. Should be one of the *_INTERNAL_KEY constants
• fail_on_missing (bool) - Whether missing database data should cause a MissingParameterError. If False, no error is raised and None is returned

Returns: dict or None

A dictionary of database data. The key is the function type and the value is a dictionary of parameter keys and values. None is returned if no data exists and fail_on_missing is False.

Raises:

• MissingParameterError - If fail_on_missing is True and there is no data

Get the FFIOParam object for the given particle names and key

Parameters:

• names (tuple) - The names of the particles to retrieve data for
• key (str) - One of the top level keys in the database dictionary. Should be one of the *_INTERNAL_KEY constants that is a key in the FP_CLASSES dictionary.
• fail_on_missing (bool) - Whether missing database data should cause a MissingParameterError. If False, no error is raised and None is returned

Returns: FFIOParam or None

The FFIOParam object that handles the data for this internal. None is returned if no data exists and fail_on_missing is False.

Add some force field properties to the structure

Parameters:

• struct (schrodinger.structure.Structure) - The structure to add properties to

Determine the nonbond type for this forcefield by inspecting one of the nonbond parameter blocks. We assume all blocks use the same type so an arbitrary block is chosen.

Returns: str

The nonbond type such as coarsegrain.LENNARD_JONES

A generator over all defined shadow bonds in the force field. A shadow bond is a bond that doesn't physically exist in the structure but exists in the forcefield as a bonding attraction between two particles.

Parameters:

• data (dict) - The dictionary defining the force field, such as provided by load_force_field_parameters.

Returns: ShadowData

A ShadowData namedtuple that provides the names of the two particles and the number of bonds that seperate them.

Apply the force field to the structure

Parameters:

• struct (schrodinger.structure.Structure) - The structure to apply the force field
• internals (schrodinger.appliction.matsci.coarsegrain.Internals) - The set of internal coordinates computed from the structure. If not provided, they will be computed.
• filename (str) - If provided, a Cms structure with the applied force field will be written to this file path
• ff_name (str or None) - the name of the forcefield used if self.ff_name is None, if None and self.ff_name is None then the default of FFIO_NAME will be used

Returns: schrodinger.application.desmond.cms.Cms

The CMS structure with the force field applied

Raises:

• MissingParameterError - If required data is missing from the force
• TypeError - If struct is not a coarse grain structure
• KeyError - If struct does not have chorus box PBC properties

FP_CLASSES

Value:

{'angles': <class 'schrodinger.application.matsci.cgforcefield.FFIOAng le'>, 'bonds': <class 'schrodinger.application.matsci.cgforcefield.FFIOBond '>, 'dihedrals': <class 'schrodinger.application.matsci.cgforcefield.FFIO Dihedral'>, 'sites': <class 'schrodinger.application.matsci.cgforcefield.FFIOSite '>}