Package schrodinger :: Package trajectory :: Module cmsstructure :: Class CmsStructure
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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 object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods [hide private]

Inherited from structure.Structure: read

Class Variables [hide private]

Inherited from structure.Structure (private): _doc

Properties [hide private]
  charge
charges of individual atoms in the structure
  mass
Mass of individual atoms in this structure
  total_mass
Mass of all atoms in this structure

Inherited from structure.Structure: atom_total, formal_charge, manage_handle, manual_update, mol_total, property, residue, title, total_weight

Inherited from object: __class__

Method Details [hide private]

__init__(self, full_ct, comp_ffsts, manage_handle=True, error_handler=None)
(Constructor)

 

Create a CmsStructure from full_ct and a list of component FFStructure instances ('comp_ffsts').

Overrides: object.__init__

__copy__(self)

 

Allows the structure to be copied by copy.copy.

Overrides: structure.Structure.__copy__

Property Details [hide private]

charge

charges of individual atoms in the structure

Get Method:
_getCharge(self)

mass

Mass of individual atoms in this structure

Get Method:
_getMass(self)

total_mass

Mass of all atoms in this structure

Get Method:
_getTotalMass(self)