Advanced usage

Adding or removing contacts between atoms

Altering the contacts between two atom can be achieved using the PatchedForceField. It wraps another ForceField and applied custom changes to it. As example the contact between the first and second residue should be removed.

ff = springcraft.PatchedForceField(
    springcraft.InvariantForceField(cutoff_distance=13.0),
    contact_pair_off=[(0,1)]
)
anm = springcraft.ANM(atoms, ff)

Defining a custom force field

To implement a custom force field, the ForceField base class needs to be inherited. In the most basic case, only the method ForceField.force_constant() must be overridden. For atom pairs within cutoff distance this function must return the spring force constant. Furthermore, some properties can be overridden, to further customize the force field:

• cutoff_distance defines at which maximum distance atom pairs are considered. By default, no cutoff is applied.

• contact_shutdown, contact_pair_off and contact_pair_on are used to add or remove atom pairs. For these atoms the cutoff distance is ignored. These are mainly used by the PatchedForceField.

• natoms gives the number of atoms in the model, if the ForceField requires an AtomArray. This is simply used to check whether the model used for the force field fits the coordinates given for Kirchhoff and Hessian calculation.

For the purpose of an example a chimeric force field is created

class ChimericForceField(springcraft.ForceField):
    """
    Uses a mixture of amino acid type and distance dependency.
    """

    def __init__(self, atoms):
        self._type_ff = springcraft.TabulatedForceField.s_enm_13(atoms)
        self._dist_ff = springcraft.ParameterFreeForceField()

    def force_constant(self, atom_i, atom_j, sq_distance):
        return (
            self._type_ff(atom_i, atom_j, sq_distance) *
            self._dist_ff(atom_i, atom_j, sq_distance)
        )

    @property
    def natoms(self):
        return self._type_ff.natoms


ff = ChimericForceField(atoms)