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.
__call__(pos)

Evaluates potentials at pos.

Returns:Potentials acting on probes at position pos.
Return type:list(float)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bindingsite.intfield', '__doc__': '\n Handles computation of the "interaction potentials" generated by\n the "interaction sites" (protein atoms) acting on "probes".\n ', '__init__': <function Field.__init__>, '__call__': <function Field.__call__>, 'nearest_atom_distance': <function Field.nearest_atom_distance>, '__dict__': <attribute '__dict__' of 'Field' objects>, '__weakref__': <attribute '__weakref__' of 'Field' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.bindingsite.intfield'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

nearest_atom_distance(pos)

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