schrodinger.application.desmond.packages.analysis module¶
Classes and functions for trajectory-based analysis
Copyright Schrodinger, LLC. All rights reserved.
-
schrodinger.application.desmond.packages.analysis.
is_small_struc
(atoms)¶ A simple API to determine whether a molecular structure is small. :type atoms:
list
:param atoms: A list of atoms in the structure. The atoms can be atom IDsor atom-class instances.
-
class
schrodinger.application.desmond.packages.analysis.
Pbc
(box)¶ Bases:
object
-
__init__
(box)¶ This implementation supports the general triclinic cell.
Parameters: box ( numpy.ndarray
) – 3x3 matrix whose ROWS are primitive cell vectors. For amsys.System
instance, you can callmsys_model.cell
to get this matrix. For atraj.Frame
instance, you can callfr.box
to get it. For aCms
instance, you can callnumpy.reshape(cms_model.box, [3, 3])
to get it.
-
box
¶
-
volume
¶
-
inv_box
¶
-
calcMinimumImage
(ref_pos, pos)¶ Calculates the minimum image of a position vector
pos
relative to another position vectorref_pos
.pos
andref_pos
can also be arrays of 3D vectors. In this case, they must be of the same size, and minimum images will be calculated for each element inpos
andref_pos
.Parameters: - ref_pos (
numpy.ndarray
. Either 1x3 or Nx3.) – Reference position vector(s) - pos (
numpy.ndarray
. Either 1x3 or Nx3.) – Position vector(s) of which we will calculate the minimum image.
Return type: numpy.ndarray
Returns: The position vector(s) of the mininum image. This function does NOT mutate any of the input vectors.
- ref_pos (
-
calcMinimumDiff
(from_pos, to_pos)¶ Calculates the difference vector from
from_pos
to the minimum image ofto_pos
.pos
andref_pos
can also be arrays of 3D vectors. In this case, they must be of the same size, and minimum image difference will be calculated for each element inpos
andref_pos
.Parameters: - from_pos (
numpy.ndarray
. Either 1x3 or Nx3) – Reference position vector(s) - to_pos (
numpy.ndarray
. Either 1x3 or Nx3) – Position vector(s) of which we will calculate the minimum image.
Return type: numpy.ndarray
Returns: The difference vector(s). This function does NOT mutate any of the input vectors.
- from_pos (
-
wrap
(pos)¶ Puts a coordinate back into the box. If the coordinate is already in the box, this function will return a new position vector that equals the original vector.
Return type: numpy.ndarray
Returns: A new position vector which is within the box. This function does NOT mutate and return the input vector pos
.
-
isWithinCutoff
(pos0, pos1, cutoff_sq)¶ Return True if any of pos0 and pos1 are within the cutoff distance.
Parameters: cutoff_sq ( float
) – = cutoff x cutoff
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__init__': <function Pbc.__init__>, 'box': <property object>, 'volume': <property object>, 'inv_box': <property object>, 'calcMinimumImage': <function Pbc.calcMinimumImage>, 'calcMinimumDiff': <function Pbc.calcMinimumDiff>, 'wrap': <function Pbc.wrap>, 'isWithinCutoff': <function Pbc.isWithinCutoff>, '__dict__': <attribute '__dict__' of 'Pbc' objects>, '__weakref__': <attribute '__weakref__' of 'Pbc' 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.application.desmond.packages.analysis'¶
-
__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.application.desmond.packages.analysis.
Vector
(msys_model, cms_model, from_xid, to_xid)¶ Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Calculate the vector between two xids. Result is a vector for each trajectory frame.
-
__init__
(msys_model, cms_model, from_xid, to_xid)¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate the vector between two xids. Result is a vector for each\n trajectory frame.\n ', '__init__': <function Vector.__init__>, '_precalc': <function Vector._precalc>, '_postcalc': <function Vector._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
Distance
(msys_model, cms_model, xid0, xid1)¶ Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Calculate the distance between two xids. Result is a scalar (distance in Angstroms) for each trajectory frame.
-
__init__
(msys_model, cms_model, xid0, xid1)¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate the distance between two xids. Result is a scalar (distance in\n Angstroms) for each trajectory frame.\n ', '__init__': <function Distance.__init__>, '_precalc': <function Distance._precalc>, '_postcalc': <function Distance._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
Angle
(msys_model, cms_model, xid0, xid1, xid2)¶ Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Calculate the angle formed between three xids. Result is a scalar (angle in degrees) for each trajectory frame.
-
__init__
(msys_model, cms_model, xid0, xid1, xid2)¶ The angle is formed by the vectors
xid1`==>`xid0
andxid1`==>`xid2
.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate the angle formed between three xids. Result is a scalar (angle in\n degrees) for each trajectory frame.\n ', '__init__': <function Angle.__init__>, '_precalc': <function Angle._precalc>, '_postcalc': <function Angle._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
Torsion
(msys_model, cms_model, xid0, xid1, xid2, xid3)¶ Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Calculate the torsion formed between four xids. Result is a scalar (dihedral angle in degrees) for each trajectory frame.
-
__init__
(msys_model, cms_model, xid0, xid1, xid2, xid3)¶ The torsion is defined by the four atoms:
- 0 o o 3
- /
- /
1 o—–o 2
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate the torsion formed between four xids. Result is a scalar\n (dihedral angle in degrees) for each trajectory frame.\n ', '__init__': <function Torsion.__init__>, '_precalc': <function Torsion._precalc>, '_postcalc': <function Torsion._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
PlanarAngle
(msys_model, cms_model, xid0, xid1, xid2, xid3, xid4, xid5)¶ Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Calculate acute planar angle formed among six xids. The first three xids define the first plane and the latter three xids define the second plane.
-
__init__
(msys_model, cms_model, xid0, xid1, xid2, xid3, xid4, xid5)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate acute planar angle formed among six xids. The first three xids\n define the first plane and the latter three xids define the second plane.\n ', '__init__': <function PlanarAngle.__init__>, '_precalc': <function PlanarAngle._precalc>, '_postcalc': <function PlanarAngle._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
CenterOf
(gids, weights=None, return_unwrapped_atompos=False)¶ Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
N.B.: The calculated center is an unwrapped coordinate.
-
__init__
(gids, weights=None, return_unwrapped_atompos=False)¶ Parameters: return_unwrapped_atompos – if False
, return the unwrapped center. Otherwise return both unwrapped center and the unwrapped positions of the selected atoms.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n N.B.: The calculated center is an unwrapped coordinate.\n ', '__init__': <function CenterOf.__init__>, '_precalc': <function CenterOf._precalc>, '_calcCircMean': <function CenterOf._calcCircMean>, '_postcalc': <function CenterOf._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
Com
(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)¶ Bases:
schrodinger.application.desmond.packages.analysis.CenterOf
Class for computing averaged position weighted by atomic mass, under the periodic boundary condition.
- Basic usage:
- ana = Com(msys_model, cms_model, gids=[1, 23, 34, 5, 6]) results = analyze(tr, ana)
where
tr
is a trajectory, andresults
contain alist
of unwrapped centers of mass asfloats
, onefloat
for each frame. If return_unwrapped_atompos isTrue
,results
contain a list of 2-tuples: (unwrapped-center-of-mass, [unwrapped-positions-of-involved-atoms]), and each 2-tuple in the list corresponds to a trajectory frame.-
__init__
(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)¶ Parameters: - asl (
str
) – ASL expression to specify the atom selection - gids (
list
of `int`s) – GIDs of atoms - return_unwrapped_atompos – if
False
, return the unwrapped center. Otherwise return both unwrapped center and the unwrapped positions of the selected atoms.
Both
msys_model
andcms_model
must be previously obtained through theread_cms
function. They both should have the same atom coordinates and the same simulation box matrix.cms_model
is used to obtain atom GIDs from ASL selection.msys_model
is used to retrieve atom attribute from GIDs.Either
asl
orgids
must be specified, but not both.- asl (
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Class for computing averaged position weighted by atomic mass, under the\n periodic boundary condition.\n\n Basic usage:\n ana = Com(msys_model, cms_model, gids=[1, 23, 34, 5, 6])\n results = analyze(tr, ana)\n\n where `tr` is a trajectory, and `results` contain a `list` of unwrapped\n centers of mass as `floats`, one `float` for each frame. If\n return_unwrapped_atompos is `True`, `results` contain a list of 2-tuples:\n (unwrapped-center-of-mass, [unwrapped-positions-of-involved-atoms]), and\n each 2-tuple in the list corresponds to a trajectory frame.\n ', '__init__': <function Com.__init__>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
class
schrodinger.application.desmond.packages.analysis.
Coc
(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)¶ Bases:
schrodinger.application.desmond.packages.analysis.Com
Class for computing center of charge under periodic boundary condition. Pseudo atoms are included.
For each frame, the results will be the unwrapped-center-of-charge. If return_unwrapped_atompos is
True
, the results will be a 2-tuple: (unwrapped-center-of-charge, [unwrapped-positions-of-involved-atoms]).-
__init__
(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)¶ Refer to the docstring of
Com.__init__
.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Class for computing center of charge under periodic boundary condition.\n Pseudo atoms are included.\n\n For each frame, the results will be the unwrapped-center-of-charge. If\n return_unwrapped_atompos is `True`, the results will be a 2-tuple:\n (unwrapped-center-of-charge, [unwrapped-positions-of-involved-atoms]).\n ', '__init__': <function Coc.__init__>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
Centroid
(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)¶ Bases:
schrodinger.application.desmond.packages.analysis.CenterOf
Class for computing centroid under periodic boundary condition.
For each frame, the results will be the unwrapped centroid. If return_unwrapped_atompos is
True
, the results will be a 2-tuple: (unwrapped-centroid, [unwrapped-positions-of-involved-atoms]).-
__init__
(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)¶ Refer to the docstring of
Com.__init__
.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Class for computing centroid under periodic boundary condition.\n\n For each frame, the results will be the unwrapped centroid. If\n return_unwrapped_atompos is `True`, the results will be a 2-tuple:\n (unwrapped-centroid, [unwrapped-positions-of-involved-atoms]).\n ', '__init__': <function Centroid.__init__>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
Gyradius
(msys_model, cms_model, asl=None, gids=None)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Class for computing radius of gyration under periodic boundary condition.
For each frame, the result is the radius of gyration as
float
-
__init__
(msys_model, cms_model, asl=None, gids=None)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Class for computing radius of gyration under periodic boundary condition.\n\n For each frame, the result is the radius of gyration as `float`\n ', '__init__': <function Gyradius.__init__>, '_postcalc': <function Gyradius._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
MassAvgVel
(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)¶ Bases:
schrodinger.application.desmond.packages.analysis.Com
Class for computing mass-averaged velocity. The trajectory should contain velocities data.
For each frame, the result is
numpy.ndarray
of `float`s-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Class for computing mass-averaged velocity.\n The trajectory should contain velocities data.\n\n For each frame, the result is `numpy.ndarray` of `float`s\n ', '_precalc': <function MassAvgVel._precalc>, '_postcalc': <function MassAvgVel._postcalc>})¶
-
__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__
(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)¶ Parameters: - asl (
str
) – ASL expression to specify the atom selection - gids (
list
of `int`s) – GIDs of atoms - return_unwrapped_atompos – if
False
, return the unwrapped center. Otherwise return both unwrapped center and the unwrapped positions of the selected atoms.
Both
msys_model
andcms_model
must be previously obtained through theread_cms
function. They both should have the same atom coordinates and the same simulation box matrix.cms_model
is used to obtain atom GIDs from ASL selection.msys_model
is used to retrieve atom attribute from GIDs.Either
asl
orgids
must be specified, but not both.- asl (
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
PosTrack
(msys_model, cms_model, asl=None, gids=None)¶ Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Class for tracking positions of selected atoms in a trajectory. Pseudo atoms are included.
Since periodic boundary condition is assumed in the MD simulation, the atom positions are wrapped back into the simulation box when they move out of the box. The PosTrack class unwraps the atom positions with respect to their positions in the previous frame. It can be used when atom positions need to be tracked over time, such as diffusion.
-
__init__
(msys_model, cms_model, asl=None, gids=None)¶ Refer to the docstring of
Com.__init__
.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Class for tracking positions of selected atoms in a trajectory.\n Pseudo atoms are included.\n\n Since periodic boundary condition is assumed in the MD simulation, the\n atom positions are wrapped back into the simulation box when they move out\n of the box. The PosTrack class unwraps the atom positions with respect to\n their positions in the previous frame. It can be used when atom positions\n need to be tracked over time, such as diffusion.\n ', '__init__': <function PosTrack.__init__>, '_precalc': <function PosTrack._precalc>, '_postcalc': <function PosTrack._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
schrodinger.application.desmond.packages.analysis.
RadiusOfGyration
¶ alias of
schrodinger.application.desmond.packages.analysis.Gyradius
-
schrodinger.application.desmond.packages.analysis.
CenterOfMotion
¶ alias of
schrodinger.application.desmond.packages.analysis.MassAvgVel
-
schrodinger.application.desmond.packages.analysis.
Position
¶ alias of
schrodinger.application.desmond.packages.analysis.PosTrack
-
class
schrodinger.application.desmond.packages.analysis.
Ramachandran
(msys_model, cms_model, asl)¶ Bases:
schrodinger.application.desmond.packages.analysis._Ramachandran
Calculate the Phi and Psi torsions for selected atoms.
Usage example:
ana = Ramachandran(msys_model, cms_model, ‘protein and res.num 20-30’) results = analyze(tr, ana)where
tr
is a trajectory, andresults
is alist
, and each element in thelist
is alist
: [(phi_0, psi_0), (phi_1, psi_1),] for the corresponding trajectory frame.-
__init__
(msys_model, cms_model, asl)¶ Parameters: asl ( str
) – ASL expression to specify the residues
-
reduce
(results, *_, **__)¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': "\n Calculate the Phi and Psi torsions for selected atoms.\n\n Usage example:\n\n ana = Ramachandran(msys_model, cms_model, 'protein and res.num 20-30')\n results = analyze(tr, ana)\n\n where `tr` is a trajectory, and `results` is a `list`, and each element\n in the `list` is a `list`: [(phi_0, psi_0), (phi_1, psi_1),] for the\n corresponding trajectory frame.\n ", '__init__': <function Ramachandran.__init__>, 'reduce': <function Ramachandran.reduce>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
PosAlign
(msys_model, cms_model, aids, fit_aids, fit_ref_pos)¶ Bases:
schrodinger.application.desmond.packages.staf.CenteredSoluteAnalysis
This analyzer first aligns the geometric center of the solute atoms to that of
cms_model
, then calculates the rotation/translation transformation for converting the structure (fit_aids
) of a centered trajectory frame to a given geometry (fit_ref_pos
) and finally applies the transformation to a position array of only the selected atoms (aids
).If
fit_ref_pos
is not provided, perform centering.-
__init__
(msys_model, cms_model, aids, fit_aids, fit_ref_pos)¶ Parameters: fit_ref_pos (Mx3 numpy.ndarray
orNone
) – positions of reference conformer structure for translation/rotation calculationBoth
msys_model
andcms_model
must be previously obtained through theread_cms
function.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n This analyzer first aligns the geometric center of the solute atoms to that\n of `cms_model`, then calculates the rotation/translation transformation\n for converting the structure (`fit_aids`) of a centered trajectory frame\n to a given geometry (`fit_ref_pos`) and finally applies the transformation\n to a position array of only the selected atoms (`aids`).\n\n If `fit_ref_pos` is not provided, perform centering.\n ', '__init__': <function PosAlign.__init__>, '_postcalc': <function PosAlign._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
RMSD
(msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None, in_place=False)¶ Bases:
schrodinger.application.desmond.packages.analysis.PosAlign
Root Mean Square Deviation from reference positions, with optional alignment fitting.
If spikes are seen, call
topo.make_glued_topology
, see DESMOND-7129.-
__init__
(msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None, in_place=False)¶ See
PosAlign
for parameters.Parameters: - ref_pos (Nx3
numpy.ndarray
) – positions of reference conformer structure - in_place – if
True
, calculate RMSD without applying transformations onref_pos
Typically,
aids
andfit_aids
come from a common source whereasref_pos
andfit_ref_pos
come from another common source.- ref_pos (Nx3
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Root Mean Square Deviation from reference positions, with optional\n alignment fitting.\n\n If spikes are seen, call `topo.make_glued_topology`, see DESMOND-7129.\n ', '__init__': <function RMSD.__init__>, '_precalc': <function RMSD._precalc>, '_postcalc': <function RMSD._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
RMSF
(msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)¶ Bases:
schrodinger.application.desmond.packages.analysis.PosAlign
Root Mean Square Fluctuation from reference positions (averaged position over the trajectory) for each atom, with optional alignment fitting.
If spikes are seen, call
topo.make_glued_topology
, see DESMOND-7129.-
__init__
(msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)¶ Parameters: - fit_ref_pos (Mx3
numpy.ndarray
) – positions of reference conformer structure for translation/rotation calculation - in_place – if
True
, calculate RMSF without applying alignment transformations
Both
msys_model
andcms_model
must be previously obtained through theread_cms
function.- fit_ref_pos (Mx3
-
reduce
(pos_t, *_, **__)¶ Temporal average of the RMSF over the trajectory
Return type: length N numpy.ndarray
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Root Mean Square Fluctuation from reference positions (averaged position\n over the trajectory) for each atom, with optional alignment fitting.\n\n If spikes are seen, call `topo.make_glued_topology`, see DESMOND-7129.\n ', '__init__': <function RMSF.__init__>, '_precalc': <function RMSF._precalc>, '_postcalc': <function RMSF._postcalc>, 'reduce': <function RMSF.reduce>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
LigandRMSD
(msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None)¶ Bases:
schrodinger.application.desmond.packages.analysis.PosAlign
Ligand Root Mean Square Deviation from reference positions, with optional alignment fitting. Taking conformational symmetry into account.
-
__init__
(msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None)¶ see
RMSD.__init__
for parameters
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Ligand Root Mean Square Deviation from reference positions, with optional\n alignment fitting. Taking conformational symmetry into account.\n ', '__init__': <function LigandRMSD.__init__>, '_postcalc': <function LigandRMSD._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
schrodinger.application.desmond.packages.analysis.
get_pdb_protein_bfactor
(fsys_ct, aids)¶ Calculate per-residue b-factor from pdb data for the selected atoms.
Parameters: aids ( list
ofint
) – Atom selectionsReturn type: numpy.ndarray
offloat
-
class
schrodinger.application.desmond.packages.analysis.
ProteinRMSF
(msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)¶ Bases:
schrodinger.application.desmond.packages.analysis.RMSF
Root Mean Square Fluctuation from reference positions (averaged positions over the trajectory) for each residue, with optional alignment fitting
-
__init__
(msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)¶ see
RMSF.__init__
for parameters
-
reduce
(pos_t, *_, **__)¶ :rtype : list[string], list[float] :return: residue tags and RMSF for each residue
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Root Mean Square Fluctuation from reference positions (averaged positions\n over the trajectory) for each residue, with optional alignment fitting\n ', '__init__': <function ProteinRMSF.__init__>, 'reduce': <function ProteinRMSF.reduce>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
Dipole
(msys_model, cms_model, aids)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Electric dipole moment of the selected atoms, in unit of debye.
The result may not be reliable when the structure of the selected atoms are large compared to the simulation box. The unwrapping with respect to periodic boundary condition provided by
CenterOf
is based on circular mean and may not be adequate.-
EA2DEBYE
= 4.802813198¶
-
__init__
(msys_model, cms_model, aids)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Electric dipole moment of the selected atoms, in unit of debye.\n\n The result may not be reliable when the structure of the selected atoms are\n large compared to the simulation box. The unwrapping with respect to\n periodic boundary condition provided by `CenterOf` is based on circular\n mean and may not be adequate.\n ', 'EA2DEBYE': 4.802813198, '__init__': <function Dipole.__init__>, '_postcalc': <function Dipole._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
AxisDirector
(axis)¶ Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Basis vector of 3D axis
-
__init__
(axis)¶ Parameters: axis ( str
) – axis name, ‘X’, ‘Y’ or ‘Z’
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Basis vector of 3D axis\n ', '__init__': <function AxisDirector.__init__>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
MomentOfInertia
(msys_model, cms_model, aids)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Moment of inertia tensor
Result is 3x3
numpy.ndarray
-
__init__
(msys_model, cms_model, aids)¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Moment of inertia tensor\n\n Result is 3x3 `numpy.ndarray`\n ', '__init__': <function MomentOfInertia.__init__>, '_postcalc': <function MomentOfInertia._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
MomentOfInertiaDirector
(msys_model, cms_model, asl)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer
This class calculates the principal moment-of-inertia for each of the selected molecules.
Result: A list of vectors
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n This class calculates the principal moment-of-inertia for each of the\n selected molecules.\n\n Result: A list of vectors\n ', '_dyninit': <function MomentOfInertiaDirector._dyninit>, '__call__': <function MomentOfInertiaDirector.__call__>})¶
-
__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__
(msys_model, cms_model, asl)¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
SmartsDirector
(msys_model, cms_model, asl, smarts)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer
Direction of atom pairs from SMARTS pattern. The SMARTS pattern should pick bonds, i.e., atom pairs, e.g.,
smarts='CC'
.Convention: The vector is pointing from the first atom to the second.
-
__init__
(msys_model, cms_model, asl, smarts)¶
-
__call__
()¶ Call self as a function.
-
reduce_vec
(n, m)¶ Calculate Legendre polynomial P2 using the inner product of n and m as the input.
Parameters: m (N’x3 numpy.array
where N’ is the number of chemical bonds.) – Output ofSmartsDirector
for one frame
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': "\n Direction of atom pairs from SMARTS pattern. The SMARTS pattern should pick\n bonds, i.e., atom pairs, e.g., `smarts='CC'`.\n\n Convention: The vector is pointing from the first atom to the second.\n ", '__init__': <function SmartsDirector.__init__>, '_dyninit': <function SmartsDirector._dyninit>, '__call__': <function SmartsDirector.__call__>, 'reduce_vec': <function SmartsDirector.reduce_vec>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
SystemDipoleDirector
(msys_model, cms_model, asl)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer
Direction of electric dipole moment of all the selected atoms
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Direction of electric dipole moment of all the selected atoms\n ', '_dyninit': <function SystemDipoleDirector._dyninit>, '__call__': <function SystemDipoleDirector.__call__>})¶
-
__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__
(msys_model, cms_model, asl)¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
DipoleDirector
(msys_model, cms_model, asl)¶ Bases:
schrodinger.application.desmond.packages.analysis.SystemDipoleDirector
Dipole direction for each molecule in the selection
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Dipole direction for each molecule in the selection\n ', '_dyninit': <function DipoleDirector._dyninit>})¶
-
__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__
(msys_model, cms_model, asl)¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
LipidDirector
(msys_model, cms_model, asl, tail_type)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Direction of CH bond for carbon atoms on lipid tail
-
__init__
(msys_model, cms_model, asl, tail_type)¶ Parameters: tail_type – ‘sn1’, ‘sn2’, ‘all’
-
__call__
()¶ Return type: list
of Nix3 `numpy.array`s, where Ni is the number of C-H bonds for the i’th lipid C atom over all lipid molecules
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Direction of CH bond for carbon atoms on lipid tail\n ', '__init__': <function LipidDirector.__init__>, '__call__': <function LipidDirector.__call__>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
schrodinger.application.desmond.packages.analysis.
reduce_vec
(n, m)¶ Calculate Legendre polynomial P2 using the inner product of n and m as the input.
-
schrodinger.application.desmond.packages.analysis.
reduce_vec_list
(n, m)¶ Calculate Legendre polynomial P2 using the inner product of n and m as the input.
-
class
schrodinger.application.desmond.packages.analysis.
OrderParameter
(vec1, vec2, reducer)¶ Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Given the director (local or global), and the descriptor (local or global), calculate the order parameter <P2> for each frame
S = 1/N sum_i ((3 * (n dot m_i)^2 -1) / 2)Where n is the director vector and m is the descriptor vector. For example, n is the z axis and m is the electric dipole moment.
- Typical usage includes
- Director Descriptor result Axis Lipid avg over carbon type Axis Smarts avg over bond type Axis Dipole avg over molecule SystemDipole Dipole avg over molecule Dipole Smarts avg over bond type
To extend its functionality, implement to the
GeomAnalyzerBase
interface and provide the reduction rule as callable.-
__init__
(vec1, vec2, reducer)¶ Parameters: - vec1 – a
GeomAnalyzerBase
that computes director - vec2 – a
GeomAnalyzerBase
that computes descriptor
Typically both director and descriptor return Nx3 vectors for each frame, where N depends on the context. In this case, one should make sure that the orders of these vectors match. For example, if both director and descriptor give one vector per molecule, then the implementation should guarantee the molecule orders are the same in vec1() and vec2().
For axis director which returns 1x3 vector, reduction with descriptor is taken care of by numpy broadcasting. For more complicated cases where director and descriptor have incompatible dimensions, the user needs to provide special-purpose reduce function, see
SmartsDirector.reduce_vec
for example.- vec1 – a
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Given the director (local or global), and the descriptor (local or global),\n calculate the order parameter <P2> for each frame\n S = 1/N sum_i ((3 * (n dot m_i)^2 -1) / 2)\n Where n is the director vector and m is the descriptor vector.\n For example, n is the z axis and m is the electric dipole moment.\n\n Typical usage includes\n Director Descriptor result\n Axis Lipid avg over carbon type\n Axis Smarts avg over bond type\n Axis Dipole avg over molecule\n SystemDipole Dipole avg over molecule\n Dipole Smarts avg over bond type\n\n To extend its functionality, implement to the `GeomAnalyzerBase` interface\n and provide the reduction rule as callable.\n ', '__init__': <function OrderParameter.__init__>, '_precalc': <function OrderParameter._precalc>, '_postcalc': <function OrderParameter._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
class
schrodinger.application.desmond.packages.analysis.
MoleculeWiseCom
(msys_model, cms_model, asl)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer
Calculate the center-of-mass for each of the selected molecules.
Result: A list of Nx3 numpy arrays, where N is the number of molecules. Note that the array size N may vary from frame to frame if the ASL is dynamic.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate the center-of-mass for each of the selected molecules.\n\n Result: A list of Nx3 numpy arrays, where N is the number of molecules. Note\n that the array size N may vary from frame to frame if the ASL is dynamic.\n ', '_dyninit': <function MoleculeWiseCom._dyninit>, '__call__': <function MoleculeWiseCom.__call__>})¶
-
__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__
(msys_model, cms_model, asl)¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
AtomicPosition
(msys_model, cms_model, asl=None)¶ Bases:
schrodinger.application.desmond.packages.staf.DynamicAslAnalyzer
Extract the positions of the selected atoms.
Result: A list of Nx3 numpy arrays, where N is the number of atoms. Note that the array size N may vary from frame to frame if the ASL is dynamic.
-
__init__
(msys_model, cms_model, asl=None)¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Extract the positions of the selected atoms.\n\n Result: A list of Nx3 numpy arrays, where N is the number of atoms. Note\n that the array size N may vary from frame to frame if the ASL is dynamic.\n ', '__init__': <function AtomicPosition.__init__>, '_postcalc': <function AtomicPosition._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
SecondaryStructure
(msys_model, cms_model, aids)¶ Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
Calculate the secondary-structure property for selected atoms. The result is a list of
int
numbers, each of which corresponds to a selected atoms and is one of the following values:SecondaryStructure.NONE SecondaryStructure.LOOP SecondaryStructure.HELIX SecondaryStructure.STRAND SecondaryStructure.TURNThe selected atoms can be obtained by calling the
aids
method.-
NONE
= -1¶
-
LOOP
= 0¶
-
HELIX
= 1¶
-
STRAND
= 2¶
-
TURN
= 3¶
-
__init__
(msys_model, cms_model, aids)¶ Parameters: aids ( list
of `int`s) – IDs of atoms to calculate the secondary-structure property for
-
reduce
(results, *_, **__)¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate the secondary-structure property for selected atoms. The result is\n a list of `int` numbers, each of which corresponds to a selected atoms and\n is one of the following values:\n\n SecondaryStructure.NONE\n SecondaryStructure.LOOP\n SecondaryStructure.HELIX\n SecondaryStructure.STRAND\n SecondaryStructure.TURN\n\n The selected atoms can be obtained by calling the `aids` method.\n ', 'NONE': -1, 'LOOP': 0, 'HELIX': 1, 'STRAND': 2, 'TURN': 3, '__init__': <function SecondaryStructure.__init__>, '_postcalc': <function SecondaryStructure._postcalc>, 'reduce': <function SecondaryStructure.reduce>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
SolventAccessibleSurfaceAreaByResidue
(msys_model, cms_model, asl, resolution=None)¶ Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
Calculate the relative SASA broken down by residues. The values are relative to the average SASAs as given by
SolventAccessibleSurfaceAreaByResidue.DIPEPTIDE_SASA
.The result is a 2-tuple: ([residue-names], [relative-SASAs]).
-
DIPEPTIDE_SASA
= {'ACE': (115.4897, 3.5972), 'ALA': (128.7874, 4.715), 'ARG': (271.5978, 9.5583), 'ASH': (175.7041, 5.1167), 'ASN': (179.5393, 4.632), 'ASP': (173.4664, 6.9882), 'CYS': (158.1909, 5.3923), 'CYX': (99.3829, 10.7089), 'GLH': (203.2443, 6.2765), 'GLN': (208.6171, 6.5794), 'GLU': (201.466, 6.9328), 'GLY': (94.1021, 5.1977), 'HID': (208.8269, 5.9202), 'HIE': (218.799, 5.6097), 'HIP': (221.1223, 8.3364), 'HIS': (208.8269, 5.9202), 'ILE': (207.2248, 5.0012), 'LEU': (211.8823, 5.149), 'LYN': (235.5351, 6.8589), 'LYS': (242.8734, 9.351), 'MET': (218.5396, 6.9879), 'NMA': (97.3748, 4.0446), 'PHE': (243.4793, 5.9699), 'PRO': (168.783, 5.5848), 'SER': (140.6706, 4.9089), 'THR': (169.0046, 4.9049), 'TRP': (287.0895, 6.892), 'TYR': (256.8637, 6.2782), 'UNK': (189.961, 6.3732), 'VAL': (181.2543, 4.864)}¶
-
__init__
(msys_model, cms_model, asl, resolution=None)¶ Initialize self. See help(type(self)) for accurate signature.
-
reduce
(results, *_, **__)¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate the relative SASA broken down by residues. The values are relative\n to the average SASAs as given by\n `SolventAccessibleSurfaceAreaByResidue.DIPEPTIDE_SASA`.\n\n The result is a 2-tuple: ([residue-names], [relative-SASAs]).\n ', 'DIPEPTIDE_SASA': {'ACE': (115.4897, 3.5972), 'NMA': (97.3748, 4.0446), 'ALA': (128.7874, 4.715), 'ARG': (271.5978, 9.5583), 'ASH': (175.7041, 5.1167), 'ASN': (179.5393, 4.632), 'ASP': (173.4664, 6.9882), 'CYS': (158.1909, 5.3923), 'CYX': (99.3829, 10.7089), 'GLH': (203.2443, 6.2765), 'GLN': (208.6171, 6.5794), 'GLU': (201.466, 6.9328), 'GLY': (94.1021, 5.1977), 'HIE': (218.799, 5.6097), 'HIS': (208.8269, 5.9202), 'HID': (208.8269, 5.9202), 'HIP': (221.1223, 8.3364), 'ILE': (207.2248, 5.0012), 'LEU': (211.8823, 5.149), 'LYN': (235.5351, 6.8589), 'LYS': (242.8734, 9.351), 'MET': (218.5396, 6.9879), 'PHE': (243.4793, 5.9699), 'PRO': (168.783, 5.5848), 'SER': (140.6706, 4.9089), 'THR': (169.0046, 4.9049), 'TRP': (287.0895, 6.892), 'TYR': (256.8637, 6.2782), 'VAL': (181.2543, 4.864), 'UNK': (189.961, 6.3732)}, '__init__': <function SolventAccessibleSurfaceAreaByResidue.__init__>, '_postcalc': <function SolventAccessibleSurfaceAreaByResidue._postcalc>, 'reduce': <function SolventAccessibleSurfaceAreaByResidue.reduce>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
MolecularSurfaceArea
(msys_model, cms_model, asl, grid_spacing=None)¶ Bases:
schrodinger.application.desmond.packages.staf.CenteredSoluteAnalysis
Calculate the molecular surface area. The result is a single scalar number.
-
__init__
(msys_model, cms_model, asl, grid_spacing=None)¶ Parameters: asl ( str
) – ASL expression to select atoms whose secondary-structure property is of interest.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate the molecular surface area. The result is a single scalar number.\n ', '__init__': <function MolecularSurfaceArea.__init__>, '_postcalc': <function MolecularSurfaceArea._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
SolventAccessibleSurfaceArea
(msys_model, cms_model, asl, exclude_asl=None, resolution=None)¶ Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
Calculate solvent accessible surface area for selected atoms.
-
__init__
(msys_model, cms_model, asl, exclude_asl=None, resolution=None)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate solvent accessible surface area for selected atoms.\n ', '__init__': <function SolventAccessibleSurfaceArea.__init__>, '_postcalc': <function SolventAccessibleSurfaceArea._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
PolarSurfaceArea
(msys_model, cms_model, asl, resolution=None)¶ Bases:
schrodinger.application.desmond.packages.staf.CenteredSoluteAnalysis
Calculate polar surface area for selected atoms.
N.B.: Only O and N atoms are considered as polar atoms in this implementation.
-
__init__
(msys_model, cms_model, asl, resolution=None)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate polar surface area for selected atoms.\n\n N.B.: Only O and N atoms are considered as polar atoms in this\n implementation.\n ', '__init__': <function PolarSurfaceArea.__init__>, '_postcalc': <function PolarSurfaceArea._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
HydrogenBondFinder
(msys_model, cms_model, aids1, aids2, max_dist=2.8, min_donor_angle=120.0, min_acceptor_angle=90.0, max_acceptor_angle=180.0)¶ Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
Find hydrogen bonds between two sets of atoms. The result is a
list
oftuples
, where each tuple is a pair of `schrodinger.structure._StructureAtom`s, i.e., (acceptor, donor).Basic usage:
ana = HydrogenBondFinder(msys_model, cms_model, aids1, aids2) results = analyze(tr, ana)-
__init__
(msys_model, cms_model, aids1, aids2, max_dist=2.8, min_donor_angle=120.0, min_acceptor_angle=90.0, max_acceptor_angle=180.0)¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Find hydrogen bonds between two sets of atoms. The result is a `list` of\n `tuples`, where each tuple is a pair of\n `schrodinger.structure._StructureAtom`s, i.e., (acceptor, donor).\n\n Basic usage:\n\n ana = HydrogenBondFinder(msys_model, cms_model, aids1, aids2)\n results = analyze(tr, ana)\n ', '__init__': <function HydrogenBondFinder.__init__>, '_postcalc': <function HydrogenBondFinder._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
HalogenBondFinder
(msys_model, cms_model, aids1, aids2, max_dist=3.5, min_donor_angle=140.0, min_acceptor_angle=90.0, max_acceptor_angle=170.0)¶ Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
Find halogen bonds between two sets of atoms. The result is a
list
oftuples
, where each tuple is a pair of `schrodinger.structure._StructureAtom`s, i.e., (acceptor, donor).Basic usage:
ana = HalogenBondFinder(msys_model, cms_model, protein_aids, ligand_aids) results = analyze(tr, ana)-
__init__
(msys_model, cms_model, aids1, aids2, max_dist=3.5, min_donor_angle=140.0, min_acceptor_angle=90.0, max_acceptor_angle=170.0)¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Find halogen bonds between two sets of atoms. The result is a `list` of\n `tuples`, where each tuple is a pair of\n `schrodinger.structure._StructureAtom`s, i.e., (acceptor, donor).\n\n Basic usage:\n\n ana = HalogenBondFinder(msys_model, cms_model, protein_aids, ligand_aids)\n results = analyze(tr, ana)\n ', '__init__': <function HalogenBondFinder.__init__>, '_postcalc': <function HalogenBondFinder._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
schrodinger.application.desmond.packages.analysis.
get_ligand_fragments
(lig_ct)¶ Decompose the ligand in several fragments using the murcko rules.
Returns: ligand fragments Return type: list
. Each element is alist
of `int`s.
-
class
schrodinger.application.desmond.packages.analysis.
HydrophobicInter
(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hydrophobic_search_cutoff=3.2, hbond_cutoff=2.8)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Calculate hydrophobic interactions between protein and ligand, with hbonds and pi-pi interactions excluded.
Returns a
list
ofdict
. The length of thislist
is the number of frames. Thedict
key is ‘HydrophobicResult’, and the value is alist
of_HydrophobicInter.Result
, where ca_aid is the AID of alpha carbon, frag_idx is the index of ligand fragment. There are also keys of ‘PiPiResult’, ‘PiCatResult’, ‘HBondResult’ withProtLigPiInter
,ProtLigHbondInter
results as values.-
__init__
(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hydrophobic_search_cutoff=3.2, hbond_cutoff=2.8)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': "\n Calculate hydrophobic interactions between protein and ligand, with hbonds\n and pi-pi interactions excluded.\n\n Returns a `list` of `dict`. The length of this `list` is the number of\n frames. The `dict` key is 'HydrophobicResult', and the value is a `list`\n of `_HydrophobicInter.Result`, where ca_aid is the AID of alpha carbon,\n frag_idx is the index of ligand fragment. There are also keys of\n 'PiPiResult', 'PiCatResult', 'HBondResult' with `ProtLigPiInter`,\n `ProtLigHbondInter` results as values.\n ", '__init__': <function HydrophobicInter.__init__>, '_postcalc': <function HydrophobicInter._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
SaltBridgeFinder
(msys_model, cms_model, aids1, aids2, cutoff=5.0)¶ Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
Find salt bridges present between two sets of atoms. This class wraps around the get_salt_bridges() function.
Return a
list
oftuples
, where each tuple is a pair of `schrodinger.structure._StructureAtom`s, i.e., (anion atom, cation atom).-
__init__
(msys_model, cms_model, aids1, aids2, cutoff=5.0)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Find salt bridges present between two sets of atoms. This class wraps\n around the get_salt_bridges() function.\n\n Return a `list` of `tuples`, where each tuple is a pair of\n `schrodinger.structure._StructureAtom`s, i.e., (anion atom, cation atom).\n ', '__init__': <function SaltBridgeFinder.__init__>, '_postcalc': <function SaltBridgeFinder._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
ProtLigPolarInter
(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, salt_bridge_cutoff=5.0, hbond_cutoff=2.8)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Calculate polar interactions between protein and ligand, with hbonds and water bridges excluded.
Returns a
list
ofdict
. The length of thislist
is the number of frames. Thedict
key is ‘PolarResult’, and the value is alist
of_ProtLigSaltBridges.Result
, where prot_aid and lig_aid are the AID of the protein atom and ligand atom, polar_type is a string that denotes the side chain/backbone information, distance is the distance between the protein atom and the ligand atom. It also contains keys of ‘HBondResult’ and ‘WaterBridgeResult’ withProtLigHbondInter
andWaterBridges
results as values.-
__init__
(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, salt_bridge_cutoff=5.0, hbond_cutoff=2.8)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': "\n Calculate polar interactions between protein and ligand, with hbonds and\n water bridges excluded.\n\n Returns a `list` of `dict`. The length of this `list` is the number of\n frames. The `dict` key is 'PolarResult', and the value is a `list`\n of `_ProtLigSaltBridges.Result`, where prot_aid and lig_aid are the AID of\n the protein atom and ligand atom, polar_type is a string that denotes the\n side chain/backbone information, distance is the distance between the\n protein atom and the ligand atom. It also contains keys of 'HBondResult'\n and 'WaterBridgeResult' with `ProtLigHbondInter` and `WaterBridges`\n results as values.\n ", '__init__': <function ProtLigPolarInter.__init__>, '_postcalc': <function ProtLigPolarInter._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
MetalInter
(msys_model, cms_model, prot_asl, lig_asl, metal_asl=None, contact_cutoff=6.0, metal_cutoff=3.4)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Interactions between metal elements and protein/ligand atoms.
Returns a
list
ofdict
. The length of thislist
is the number of frames. Thedict
key is ‘MetalResult’, and the value is alist
of either_MetalInter.MetalP
or_MetalInter.MetalL
objects, where ion_aid, prot_aid and lig_aid are the AID of the ion atom, protein atom and ligand atom, ion_ele is the ion element string, distance is the distance between the ion atom and the protein/ligand atom.-
MetalP
¶ alias of
_MetalP
-
MetalL
¶ alias of
_MetalL
-
__init__
(msys_model, cms_model, prot_asl, lig_asl, metal_asl=None, contact_cutoff=6.0, metal_cutoff=3.4)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': "\n Interactions between metal elements and protein/ligand atoms.\n\n Returns a `list` of `dict`. The length of this `list` is the number of\n frames. The `dict` key is 'MetalResult', and the value is a `list`\n of either `_MetalInter.MetalP` or `_MetalInter.MetalL` objects, where\n ion_aid, prot_aid and lig_aid are the AID of the ion atom, protein atom and\n ligand atom, ion_ele is the ion element string, distance is the distance\n between the ion atom and the protein/ligand atom.\n ", 'MetalP': <class 'schrodinger.application.desmond.packages.analysis._MetalP'>, 'MetalL': <class 'schrodinger.application.desmond.packages.analysis._MetalL'>, '__init__': <function MetalInter.__init__>, '_isWithinCutoff': <function MetalInter._isWithinCutoff>, '_postcalc': <function MetalInter._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
schrodinger.application.desmond.packages.analysis.
ProtLigPiInter
¶ Compute pi-pi and pi-cation interations between protein and ligand.
Returns a
list
ofdict
. The length of thislist
is the number of frames. Thedict
keys are ‘PiPiResult’, and ‘PiCatResult’. The value is alist
ofProtLigPiInter.Pipi
,ProgLigPiInter.PiLCatP
, orProgLigPiInter.PiPCatL
objects, where frag_idx is the index of the ligand fragment, ca_aid is the AID of alpha carbon, prot_aid and lig_aid are the AID of the protein atom and ligand atom, ring_idx is the ligand ring index, type could be ‘f2f’ or ‘e2f’, distance and angle describe the geometry of the corresponding interaction.
-
schrodinger.application.desmond.packages.analysis.
ProtLigHbondInter
¶ Compute protein-ligand hydrogen bonds.
Returns a
list
ofdict
. The length of thislist
is the number of frames. Thedict
key is ‘HBondResult’, and the value is alist
ofProtLigHbondInter.Result
, where prot_aid is the AID of the protein atom, prot_type is a string that denotes the acceptor/donor, backbone/side chain information, lig_aid is the AID of ligand atom.
-
class
schrodinger.application.desmond.packages.analysis.
WatLigFragDistance
(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hbond_cutoff=2.8)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Distance between water oxygen atom and its closest ligand fragment, with water bridges excluded.
Returns a
list
ofdict
. The length of thislist
is the number of frames. Thedict
key is ‘LigWatResult’, and the value is alist
of_WatLigFragDistance.Result
, where frag_idx is the index of the ligand fragment, wat_res_num is the water residue number, distance is the distance between water oxygen atom and ligand fragment centroid. It also contains the key of ‘WaterBridgeResult’ withWaterBridges
results as value.-
__init__
(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hbond_cutoff=2.8)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': "\n Distance between water oxygen atom and its closest ligand fragment, with\n water bridges excluded.\n\n Returns a `list` of `dict`. The length of this `list` is the number of\n frames. The `dict` key is 'LigWatResult', and the value is a `list`\n of `_WatLigFragDistance.Result`, where frag_idx is the index of the ligand\n fragment, wat_res_num is the water residue number, distance is the distance\n between water oxygen atom and ligand fragment centroid. It also contains\n the key of 'WaterBridgeResult' with `WaterBridges` results as value.\n ", '__init__': <function WatLigFragDistance.__init__>, '_postcalc': <function WatLigFragDistance._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
schrodinger.application.desmond.packages.analysis.
WaterBridges
¶ Find water bridges between protein and ligand
Returns a
list
ofdict
. The length of thislist
is the number of frames. Thedict
key is ‘WaterBridgeResult’, and the value is alist
ofWaterBridges.Result
, where prot_aid and lig_aid are the AID of the protein atom and ligand atom, prot_type and lig_type are strings that denotes the acceptor/donor information, wat_res_num is the water residue number.
-
class
schrodinger.application.desmond.packages.analysis.
ProtLigInter
(msys_model, cms_model, prot_asl, lig_asl, metal_asl=None)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Composition of various protein ligand interactions.
Returns a
list
ofdict
. The length of thislist
is the number of frames. Thedict
keys are ‘WaterBridgeResult’, ‘LigWatResult’, ‘HBondResult’, ‘PiPiResult’, ‘PiCatResult’, ‘MetalResult’, ‘PolarResult’.-
__init__
(msys_model, cms_model, prot_asl, lig_asl, metal_asl=None)¶ Parameters: - prot_asl (
str
) – ASL expression to specify protein atoms - lig_asl (
str
) – ASL expression to specify ligand atoms - metal_asl (
str
orNone
) – ASL expression to specify metal atoms. IfNone
, use default values.
- prot_asl (
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': "\n Composition of various protein ligand interactions.\n\n Returns a `list` of `dict`. The length of this `list` is the number of\n frames. The `dict` keys are 'WaterBridgeResult', 'LigWatResult',\n 'HBondResult', 'PiPiResult', 'PiCatResult', 'MetalResult', 'PolarResult'.\n ", '__init__': <function ProtLigInter.__init__>, '_postcalc': <function ProtLigInter._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
VolumeMapper
(cms_model, asl=None, aids=None, spacing=[1.0, 1.0, 1.0], length=[10.0, 10.0, 10.0], normalize=True)¶ Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
This class calculates the 3D histogram of selected atoms over a trajectory.
- Note: The trajectory provided for this method should already be centered,
- and aligned on the selection of interest. The returned histogram has origin in its central bin.
- Basic usage:
- ana = VolumeMapper(cms_model, ‘mol.num 1’) results = analyze(tr, ana)
-
__init__
(cms_model, asl=None, aids=None, spacing=[1.0, 1.0, 1.0], length=[10.0, 10.0, 10.0], normalize=True)¶ Parameters: asl ( str
) – The ASL selection for which volumetric density map will be constructed
-
reduce
(pos_t, *_, **__)¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': "\n This class calculates the 3D histogram of selected atoms over a trajectory.\n\n Note: The trajectory provided for this method should already be centered,\n and aligned on the selection of interest. The returned histogram has\n origin in its central bin.\n\n Basic usage:\n ana = VolumeMapper(cms_model, 'mol.num 1')\n results = analyze(tr, ana)\n ", '__init__': <function VolumeMapper.__init__>, '_postcalc': <function VolumeMapper._postcalc>, 'reduce': <function VolumeMapper.reduce>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
schrodinger.application.desmond.packages.analysis.
progress_report_frame_number
(i, *_)¶
-
schrodinger.application.desmond.packages.analysis.
analyze
(tr, analyzer, *arg, **kwarg)¶ Do analyses on the given trajectory
tr
, and return the results. The analyses are specified as one or more positional arguements. Each analyzer should satisfy the interface requirements (see the docstring ofGeomCalc.addAnalyzer
).Parameters: - tr (
list
of `traj.Frame`s) – The simulation trajectory to analyze - arg – A list of analyzer objects
- kwarg["progress_feedback"] (callable, e.g., func(i, fr, tr), where
i
is the current frame index,fr
the current frame,tr
the whole trajectory.) – This function will be called at start of analysis on the current frame. This function is intended to report the progress of the analysis.
Return type: list
Returns: For a single analyzer, this function will return a list of analysis results, and each element in the list corresponds to the result of the corresponding frame. For multiple analyzers, this function will return a list of lists, and each element is a list of results of the corresponding analyzer. If an analyzer has a
reduce
method, the reduce method will be called, and its result will be returned.- tr (
-
schrodinger.application.desmond.packages.analysis.
rmsd_matrix
(msys_model, tr, rmsd_gids, fit_gids)¶ For all pairs of frames in the trajectory
tr
, we first superimpose the structures from the two frames on the atoms as specified byfit_gids
, and then we calculate the RMSD for atoms as specified byrmsd_gids
.Parameters: Return type: numpy.ndarray
of `float`sReturns: A symetric square matrix of RMSDs
-
schrodinger.application.desmond.packages.analysis.
cluster
(affinity_matrix)¶ Do clustering using the affinity propagation method.
Parameters: affinity_matrix ( numpy.ndarray
of `float`s) – A square matrix of affinity/similarity values:rtype (
list
-of-int`s, `list
-of-`int`s) :return: The first list is the sample indices of the clusters’ centers, thesecond list is a cluster label of all samples.
-
class
schrodinger.application.desmond.packages.analysis.
Rdf
(msys_model, cms_model, asl0, asl1=None, pos_type0='atom', pos_type1='atom', dr=0.1, rmax=12.0)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Calculate radial distribution function (RDF) of provided selection.
-
__init__
(msys_model, cms_model, asl0, asl1=None, pos_type0='atom', pos_type1='atom', dr=0.1, rmax=12.0)¶ This analyzer calculates the radial distribution function [RDF, also known as g(r)] of specified positions in the system.
In general, we need two groups of positions. The first group are the reference positions, whereas the second the distance group. For example, say we want to calculate the RDF of the distances of water hydrogen atoms with respect to water oxygen atoms, the first group will be all water oxygen atoms’ positions, and the second group all water hydrogen atoms’ positions. The reference and distance groups can be the same, for example, in the case of the RDF of water oxygen atoms.
Each position doesn’t have to be an atom’s position, and it could be a derived position such as the center of mass of the molecule.
Parameters: - asl0 (
str
) – Atom selection for the reference group - asl1 (
str
orNone
) – Atom selection for the distance group. If it’sNone
, it will default toasl0
. - pos_type0 (
str
) – Type of positions of the reference group: “atom” : Use atom’s position directly “com” : Use molecular center of mass “coc” : Use molecular center of charge “centroid”: Use molecular centroid - pos_type1 (
str
) – Type of positions of the distance group. Values are the same as those ofpos_type0
- dr (
float
) – Bin width in the unit of Angstroms - rmax (
float
) – Maximum distance in the unit in Angstroms. The RDF will be calculated untilrmax
.
- asl0 (
-
reduce
(*_, **__)¶ Aggregates the frame-based results (histograms) and returns the final RDF results.
Return type: (list, list)
Returns: Returns the RDF (the first list), and the integral (the second list).
-
bins
()¶
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Calculate radial distribution function (RDF) of provided selection.\n ', '__init__': <function Rdf.__init__>, '_dyncalc': <function Rdf._dyncalc>, '_aids2gids': <staticmethod object>, '_get_slice_volumes': <staticmethod object>, '_postcalc': <function Rdf._postcalc>, 'reduce': <function Rdf.reduce>, 'bins': <function Rdf.bins>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
ProtProtPiInter
(msys_model, cms_model, asl)¶ Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
Protein-protein Pi interaction finder.
Returns a
dict
with two keys: pi-pi and pi-cat. Values arelist
of 2-element `tuple`s-
__init__
(msys_model, cms_model, asl)¶ Parameters: asl ( str
) – ASL expression to select protein atoms
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Protein-protein Pi interaction finder.\n\n Returns a `dict` with two keys: pi-pi and pi-cat. Values are `list` of\n 2-element `tuple`s\n ', '__init__': <function ProtProtPiInter.__init__>, '_postcalc': <function ProtProtPiInter._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
ProtProtHbondInter
(msys_model, cms_model, asl)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Protein-protein hydrogen bond finder.
Returns a
dict
with four keys: hbond_bb, hbond_sb, hbond_bs, hbond_ss, b for backbone and s for sidechain. Values arelist
of 2-element `tuple`s (donor AID, acceptor AID).-
__init__
(msys_model, cms_model, asl)¶ Initialize self. See help(type(self)) for accurate signature.
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Protein-protein hydrogen bond finder.\n\n Returns a `dict` with four keys: hbond_bb, hbond_sb, hbond_bs, hbond_ss,\n b for backbone and s for sidechain. Values are `list` of 2-element\n `tuple`s (donor AID, acceptor AID).\n ', '__init__': <function ProtProtHbondInter.__init__>, '_get_hbond_type': <function ProtProtHbondInter._get_hbond_type>, '_postcalc': <function ProtProtHbondInter._postcalc>})¶
-
__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.desmond.packages.analysis'¶
-
__ne__
¶ Return self!=value.
-
static
__new__
(cls, *args, **kwargs)¶ 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)
-
disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
-
isDynamic
()¶
-
-
class
schrodinger.application.desmond.packages.analysis.
ProtProtInter
(msys_model, cms_model, asl)¶ Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Protein-protein interactions.
Return summary over the whole trajectory. For the same frame, results are unique up to residue level, e.g., even if there are multiple salt-bridges between residue A and B, only 1 is recorded.
-
__init__
(msys_model, cms_model, asl)¶ Parameters: asl ( str
) – ASL expression to select protein atoms
-
__call__
()¶ Call self as a function.
-
__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.desmond.packages.analysis', '__doc__': '\n Protein-protein interactions.\n\n Return summary over the whole trajectory. For the same frame, results are\n unique up to residue level, e.g., even if there are multiple salt-bridges\n between residue A and B, only 1 is recorded.\n ', '__init__': <function ProtProtInter.__init__>, '_get_tag2ca': <function ProtProtInter._get_tag2ca>, '_postcalc': <function ProtProtInter._postcalc>, 'reduce': <function ProtProtInter.reduce>, '_cleanup_hbonds': <function ProtProtInter._cleanup_hbonds>})¶
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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.desmond.packages.analysis'¶
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__ne__
¶ Return self!=value.
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static
__new__
(cls, *args, **kwargs)¶ 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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disableDyncalc
()¶ Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().
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isDynamic
()¶
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