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

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

_verify(self)

_getCharge(self)

_getMass(self)

_getTotalMass(self)

_getTrajectoryDirectory(self)

_updateCms(self, frame)

find_trajectory_directory(self, base_directory=None)
Locate the trajectory directory.

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__, __getstate__, __int__, __ne__, __repr__, __setstate__, addAtom, addAtoms, addBond, addBonds, adjust, append, applyStyle, areBound, atom, bond, chain, closeBlockIfNecessary, copy, deleteAtoms, deleteBond, extend, extract, findResidue, find_rings, get3dStructure, getAtomIndices, getBond, getChainAtoms, getMoleculeAtoms, getMovingAtoms, getResidueAtoms, getXYZ, has3dCoords, 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__

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

trajectory_directory
Directory location of correspondingDesmond simulation trajectory

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, matched_virtuals=`set([])`)
(Constructor)

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

Overrides: object.__init__

find_trajectory_directory(self, base_directory=None)

Locate the trajectory directory. This directory name should be stored directly in a structure property, but the method allows for backwards- compatibility with a trajectory index file.

Parameters:

base_directory (str) - path to look for trajectory file

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)

trajectory_directory

Directory location of correspondingDesmond simulation trajectory

Get Method:: _getTrajectoryDirectory(self)

Class CmsStructure

__init__(self, full_ct, comp_ffsts, manage_handle=True, error_handler=None, matched_virtuals=set([])) (Constructor)

find_trajectory_directory(self, base_directory=None)

__copy__(self)

charge

mass

total_mass

trajectory_directory

init(self, full_ct, comp_ffsts, manage_handle=True, error_handler=None, matched_virtuals=`set([])`)
(Constructor)

copy(self)