Package schrodinger :: Package trajectory :: Module cmsstructure :: Class CmsStructure

Class CmsStructure

         object --+    
                  |    
structure.Structure --+
                      |
                     CmsStructure

CmsStructure represents a complete description of Desmond model system, which includes one full ct and several component cts.

Instance Methods

[hide private]

__init__(self, full_ct, comp_ffsts, manage_handle=True, error_handler=None)
Create a CmsStructure from full_ct and a list of component FFStructure instances ('comp_ffsts').

_verify(self)

_getCharge(self)

_getMass(self)

_getTotalMass(self)

_updateCms(self, frame)

writeCms(self, filename, frame=None)
Write out a cms file for a particular frame.

__copy__(self)
Allows the structure to be copied by copy.copy.

Inherited from structure.Structure: __eq__, __int__, __ne__, __repr__, addAtom, addAtoms, addBond, addBonds, adjust, append, applyStyle, areBound, atom, bond, chain, closeBlockIfNecessary, copy, deleteAtoms, deleteBond, extend, extract, findResidue, find_rings, getBond, getChainAtoms, getMoleculeAtoms, getResidueAtoms, getXYZ, inRing, isEquivalent, measure, merge, molecule, putToM2ioFile, retype, ring, setXYZ, update, write, writeToString

Inherited from structure.Structure (private): _createAtomContainer, _createBondContainer, _createProxy, _createStructureChainIterator, _createStructureMoleculeIterator, _createStructureRingIterator, _getAtomTotal, _getFormalCharge, _getManageHandle, _getManualUpdate, _getMolTotal, _getStructureProperty, _getStructureResidueIterator, _getTitle, _getTotalWeight, _proxy, _setManageHandle, _setManualUpdate, _setStructureProperty, _setTitle

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__