schrodinger.application.bindingsite.intfield module¶
Logic to compute “interaction fields” between (protein) atoms and “probe” particles.
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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.
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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)))
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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”.
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__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
.
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nearest_atom_distance
(pos)¶ Returns distance to the nearest atom that contributes to the potentials.
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