Xplor-NIH: module symmetry

symmetry

Tools for molecular symmetry analysis

Classes



exceptions.Exception(exceptions.BaseException)

SymmetryViolation

class SymmetryViolation(exceptions.Exception)


Method resolution order:

SymmetryViolation

exceptions.Exception

exceptions.BaseException

__builtin__.object

Methods defined here:

__init__(s, string)

Data and other attributes defined here:

__weakref__ = <attribute '__weakref__' of 'SymmetryViolation' objects>
list of weak references to the object (if defined)

Data and other attributes inherited from exceptions.Exception:

__new__ = <built-in method __new__ of type object at 0x2b2baf9bfe00>
T.__new__(S, ...) -> a new object with type S, a subtype of T

Methods inherited from exceptions.BaseException:

__delattr__(...)
x.__delattr__('name') <==> del x.name

__getattribute__(...)
x.__getattribute__('name') <==> x.name

__getitem__(...)
x.__getitem__(y) <==> x[y]

__getslice__(...)
x.__getslice__(i, j) <==> x[i:j]                                Use of negative indices is not supported.

__reduce__(...)

__repr__(...)
x.__repr__() <==> repr(x)

__setattr__(...)
x.__setattr__('name', value) <==> x.name = value

__setstate__(...)

__str__(...)
x.__str__() <==> str(x)

Data and other attributes inherited from exceptions.BaseException:

__dict__ = <dictproxy object at 0xee2c20>

args = <attribute 'args' of 'exceptions.BaseException' objects>

message = <member 'message' of 'exceptions.BaseException' objects>
exception message

Functions

testC2(sel1, sel2, rmsdTol=0.01, transTol=0.01, rotTol=0.10000000000000001)
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)

Functions
		testC2(sel1, sel2, rmsdTol=0.01, transTol=0.01, rotTol=0.10000000000000001) 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)