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)))
- st (
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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
.
- st (
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__call__
(pos)¶ Evaluates potentials at
pos
.Returns: Potentials acting on probes at position pos
.Return type: list(float)
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__class__
¶ alias of
builtins.type
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__delattr__
¶ Implement delattr(self, name).
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__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>})¶
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__dir__
() → list¶ default dir() implementation
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__eq__
¶ Return self==value.
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__format__
()¶ default object formatter
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__ge__
¶ Return self>=value.
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__getattribute__
¶ Return getattr(self, name).
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__gt__
¶ Return self>value.
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__hash__
¶ Return hash(self).
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__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
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__le__
¶ Return self<=value.
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__lt__
¶ Return self<value.
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__module__
= 'schrodinger.application.bindingsite.intfield'¶
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__ne__
¶ Return self!=value.
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__new__
()¶ Create and return a new object. See help(type) for accurate signature.
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__reduce__
()¶ helper for pickle
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__reduce_ex__
()¶ helper for pickle
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__repr__
¶ Return repr(self).
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__setattr__
¶ Implement setattr(self, name, value).
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__sizeof__
() → int¶ size of object in memory, in bytes
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__str__
¶ Return str(self).
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__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).
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__weakref__
¶ list of weak references to the object (if defined)
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nearest_atom_distance
(pos)¶ Returns distance to the nearest atom that contributes to the potentials.
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