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 cms object

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

_synchronize_fsys_ct(self)

ffio_refresh(self)
'atom_index' starts from 1.

get_fullsys_ct_atom_index_range(self, comp_ct_index)
for a given component CT, return a map of that compontent CT in full_system CT

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__, __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, 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 cms object

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)