symmetry
index


 
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)