schrodinger.application.bindingsite.intfield module

Logic to compute “interaction fields” between (protein) atoms and “probe” particles.

schrodinger.application.bindingsite.intfield.get_hbond_direction(atom)

Returns direction of “ideal” hydrogen bond that would be formed by the given atom. It is not always right, e.g. for O in C-O-H. This needs to be refined or proven irrelevant.

schrodinger.application.bindingsite.intfield.get_interaction_sites(st, atom_indices=None, probes=None, logger=None)

Identifies interaction sites among the protein atoms according to their atom types.

Parameters

  • st (schrodinger.structure.Structure) – Structure.

  • atom_indices (iterable over int) – Iterable over the contributing atom indices.

  • probes (container of str) – Probes of interest.

Returns

List of atoms that interact with the requested probes. Individual atom contributions are given by tuples that hold the -1/0/1 integers (see INTERACTIONS) associated with the corresponding probe.

Return type

list(tuple(schrodinger.structure._StructureAtom, tuple(int)))

class schrodinger.application.bindingsite.intfield.Field(st, atom_indices=None, probes=None, alpha=1.0, r_cut=4.0, a_cut=60.0, logger=None)

Bases: object

Handles computation of the “interaction potentials” generated by the “interaction sites” (protein atoms) acting on “probes”.

__init__(st, atom_indices=None, probes=None, alpha=1.0, r_cut=4.0, a_cut=60.0, logger=None)
Parameters

  • st (schrodinger.structure.Structure) – Structure.

  • atom_indices (iterable over int) – Iterable over the contributing atom indices.

  • probes (container of str) – Probes of interest.

  • alpha (float) – Interaction range (length scale of exponential decay).

  • r_cut (float) – Ignore contributions from atoms further than r_cut from a probe.

  • a_cut (float) – Ignore hydrogen bond interactions for angles exceeding a_cut.

nearest_atom_distance(pos)

Returns distance to the nearest atom that contributes to the potentials.