Official government website icon

bit	Xplor-NIH	VMD-XPLOR

Pydoc: module symmetry

symmetry

Tools for molecular symmetry analysis

Classes

builtins.Exception(builtins.BaseException)

SymmetryViolation

class SymmetryViolation(builtins.Exception)

SymmetryViolation(string)

Method resolution order:: SymmetryViolation; builtins.Exception; builtins.BaseException; builtins.object

Methods defined here:

__init__(s, string): Initialize self. See help(type(self)) for accurate signature.

Data descriptors defined here:

__weakref__: list of weak references to the object (if defined)

Static methods inherited from builtins.Exception:

__new__(*args, **kwargs) from builtins.type: Create and return a new object. See help(type) for accurate signature.

Methods inherited from builtins.BaseException:

__delattr__(self, name, /): Implement delattr(self, name).

__getattribute__(self, name, /): Return getattr(self, name).

__reduce__(...): Helper for pickle.

__repr__(self, /): Return repr(self).

__setattr__(self, name, value, /): Implement setattr(self, name, value).

__setstate__(...)

__str__(self, /): Return str(self).

add_note(...): Exception.add_note(note) --
add a note to the exception

with_traceback(...): Exception.with_traceback(tb) --
set self.__traceback__ to tb and return self.

Data descriptors inherited from builtins.BaseException:

__cause__: exception cause

__context__: exception context

__dict__

__suppress_context__

__traceback__

args

Functions
		testC2(sel1, sel2, rmsdTol=0.01, transTol=0.01, rotTol=0.1) test for C2 Symmetry First, subtract off center of mass of sel1 and sel2. Swap atoms in sel1 and sel2 and rigid-body fit the result to the original. The resulting atomic rmsd should be less than rmsdTol. The norm of the translation should be less than transTol. The resulting rotation matrix should be within rotTol of 180 degrees. Atomic coordinates are not modified by this function. If any tolerance is violated, a SymmetryViolation exception is thrown. A SymmetryResults class is returned, containing: rmsd, trans, rot, and rotVec (the rotation axis)