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)

sanitize_for_viparr(self)
Viparr's custom mae file reader does not play well with certain characters like \[ and \] (square brackets).

get_fep_cts(self)
find ref and mut cts by fep_fragname property

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

get_lambda_atom_indices(self, l)
Returns: list of int (for atoms), list of list of int (for virtual sites)

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)

fix_filenames(self, cms_fname=None, trj_fname=None)

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, get3dStructure, getAtomIndices, getBond, getChainAtoms, getMoleculeAtoms, getMovingAtoms, getResidueAtoms, getXYZ, has3dCoords, inRing, isEquivalent, measure, merge, molecule, putToM2ioFile, retype, ring, setXYZ, update, writeToString

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

PROP_CMS = 's_m_original_cms_file'

PROP_TRJ = 's_chorus_trajectory_file'

Inherited from structure.Structure (private): _doc

Properties

[hide private]

Inherited from structure.Structure: atom_total, formal_charge, 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__

sanitize_for_viparr(self)

Viparr's custom mae file reader does not play well with certain characters like \[ and \] (square brackets). This is also true when the these characters are 'escaped'. Thus this method sanitizes offensive property names and their values by replacing them with forward slashes. This method checks if the CT properties are okay for viparr.

get_lambda_atom_indices(self, l)

Parameters:

l - lambda value, 0 or 1

Returns:

list of int (for atoms), list of list of int (for virtual sites)

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)

sanitize_for_viparr(self)

get_lambda_atom_indices(self, l)

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)