Package schrodinger :: Package application :: Package desmond :: Module cms :: Class Cms

Class Cms

         object --+    
                  |    
structure.Structure --+
                      |
                     Cms

Instance Methods

[hide private]

__init__(self, file=None, string=None)
Initialize an object with an existing MMCT handle.

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

_synchronize_fsys_ct(self)

ffio_refresh(self)
`atom_index' starts from 1.

gid_refresh(self)

gid(self, atom_index)
`atom_index' is the index of the atom in the 'full_system' CT.

site(self, atom_index)
`atom_index' starts from 1.

model_system_type(self)

get_fragname(self)

select_atom(self, asl)

select_atom_comp(self, asl)
Returns a list of lists.

get_restrain(self)

_ct_set_restrain(self, ct, ct_restrain)
`ct_restrain' must be a list of `Restrain' objects.

set_restrain(self, restrain_list)
`restrain_list' must be a list.

clear_restrain(self)
Deletes all existing restraints.

get_atom_group(self)

set_atom_group(self, atom_group)

merge_atom_group(self, atom_group)

set_atom_group_from_asl(self, asl, group_name, group_index)

merge_atom_group_from_asl(self, asl, group_name, group_index)

delete_atom_group(self, group_name)

delete_all_atom_group(self, exception=[])

get_vdw(self)
Returns the Vdw parameters for all atoms.

get_constraint(self)

get_num_constraint(self)

get_degrees_of_freedom(self)

write(self, fname)
Write the structure to a file, overwriting any previous content.

write_to_string(self)

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, 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]

ATOMGROUP_PREFIX = 'i_ffio_grp_'

MODEL_SYSTEM_TYPE = ['standard model system', 'model system fo...

META_ASL = {'heavy_atom': 'not atom.elem H', 'solute': 'atom.s...

Inherited from structure.Structure (private): _doc

Properties

[hide private]

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, file=None, string=None)
(Constructor)

Initialize an object with an existing MMCT handle. The only way to get an existing handle in this module at the moment is by using the StructureReader class or the static read method below.

By default, the MMCT resources will be managed by the object. To keep these from being cleaned upon object deletion, set manage_handle=False.

Overrides: object.__init__

copy(self)

Allows the structure to be copied by copy.copy

Overrides: structure.Structure.__copy__

select_atom_comp(self, asl)

Returns a list of lists. Each list element contains a list of atom indices of the corresponding component CT.

set_restrain(self, restrain_list)

`restrain_list' must be a list. Each element must be a list of `Restrain' objects.

get_vdw(self)

Returns the Vdw parameters for all atoms. The returned object is a list. Each element of the returned list is a Vdw object for the corresponding atom.

write(self, fname)

Write the structure to a file, overwriting any previous content. Format is determined from the file suffix if None is specified, otherwise an explicit value of maestro, sd, pdb, or smiles can be used.

Overrides: structure.Structure.write

Class Variable Details

[hide private]

MODEL_SYSTEM_TYPE

Value:

['standard model system',
 'model system for mutation FEP',
 'model system for total free energy FEP']

META_ASL

Value:

{'heavy_atom': 'not atom.elem H',
 'solute': 'atom.s_ffio_ct_type \'solute\'',
 'solute_heavy_atom': 'atom.s_ffio_ct_type \'solute\'  and not atom.el
em H',
 'solvent': 'atom.s_ffio_ct_type \'solvent\'',
 'solvent_heavy_atom': 'atom.s_ffio_ct_type \'solvent\' and not atom.e
lem H'}

Class Cms

__init__(self, file=None, string=None) (Constructor)

__copy__(self)

select_atom_comp(self, asl)

set_restrain(self, restrain_list)

get_vdw(self)

write(self, fname)

MODEL_SYSTEM_TYPE

META_ASL

init(self, file=None, string=None)
(Constructor)

copy(self)