schrodinger.protein.reliability module¶

schrodinger.protein.reliability.run_quick_check(ct, binding_site_atoms=None)¶

Runs a quick analysis of protein health.

Parameters:	ct (schrodinger.structure) – protein CT binding_site_asl (atom indices) – list of atom indices to define binding site. Limits checks to area around the binding site.

:rtype str

Returns a Results object of problems spotted in the protein.

schrodinger.protein.reliability.run_check(ct, params)¶: Returns a Results object of problems spotted in the protein.

schrodinger.protein.reliability.find_isolated_water_molecules(ct)¶

Finds water molecules that are isolated (greater than 4.6 A) from other water clusters.

Returns a list of tuples (water_molecule, distance). The water molecule is represented as a set() of atom indexes, and the distance is the minimum distance from another water molecule.

class schrodinger.protein.reliability.ProteinCheckParameters¶

Bases: object

__init__()¶: Initialize self. See help(type(self)) for accurate signature.

enableSidechainPacking()¶

disableSidechainPacking()¶

setBindingSiteASL(site_asl)¶

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.reliability', '__init__': <function ProteinCheckParameters.__init__>, 'enableSidechainPacking': <function ProteinCheckParameters.enableSidechainPacking>, 'disableSidechainPacking': <function ProteinCheckParameters.disableSidechainPacking>, 'setBindingSiteASL': <function ProteinCheckParameters.setBindingSiteASL>, '__dict__': <attribute '__dict__' of 'ProteinCheckParameters' objects>, '__weakref__': <attribute '__weakref__' of 'ProteinCheckParameters' objects>, '__doc__': None})¶

__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.protein.reliability'¶

__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)

class schrodinger.protein.reliability.Results(model)¶

Bases: object

The Results object stores the results from a protein health check.

__init__(model)¶: Initialize self. See help(type(self)) for accurate signature.

getTextSummary()¶

Returns a summary of problems found in the protein. If no problems, returns an empty list.

:rtype list of str

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.reliability', '__doc__': '\n The Results object stores the results from a protein\n health check.\n ', '__init__': <function Results.__init__>, 'getTextSummary': <function Results.getTextSummary>, '__dict__': <attribute '__dict__' of 'Results' objects>, '__weakref__': <attribute '__weakref__' of 'Results' 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).