Package schrodinger :: Package application :: Package desmond :: Module ffiostructure :: Class FFIOStructure
[hide private]
[frames] | no frames]

Class FFIOStructure

structure.Structure --+
                      |
                     FFIOStructure

Class to create python interface to force field data. This is just a wrapper around the mmffio/mmfepio functionality. I/O happens through the underlying libraries. mmffio/mmfepio handles are created on demand when ffio/fepio blocks are accesssed.

Instance Methods [hide private]
 
__init__(self, handle, manage_handle=True, error_handler=None)
Parent class would take care of basic CT data.
 
_hasBlock(self, block_name)
 
_createFFIOBlock(self)
 
_createFEPIOBlock(self)
 
hasFfio(self)
 
hasFepio(self)
 
__copy__(self)
Allows the structure to be copied by copy.copy
 
copy(self)
Returns a copy of the structure.
 
write(self, filename, format=None)
Write the cms structure to a file, overwriting any previous content.
 
append(self, filename, format=None)
Append the structure to the file.
 
__del__(self)
Delete the underlying mmffio, mmfepio handles

Inherited from structure.Structure: __eq__, __getstate__, __int__, __ne__, __repr__, __setstate__, addAtom, addAtoms, addBond, addBonds, adjust, applyStyle, areBound, closeBlockIfNecessary, deleteAtoms, deleteBond, extend, extract, findResidue, find_rings, getBond, getChainAtoms, getMoleculeAtoms, getMovingAtoms, getResidueAtoms, getXYZ, inRing, isEquivalent, measure, merge, putToM2ioFile, retype, setXYZ, update, writeToString

Static Methods [hide private]

Inherited from structure.Structure: read

Class Variables [hide private]
  ffio = CreateWhenNeeded(_createFFIOBlock, "ffio")
  fepio = CreateWhenNeeded(_createFEPIOBlock, "fepio")

Inherited from structure.Structure: atom, atom_total, bond, chain, formal_charge, manage_handle, manual_update, mol_total, molecule, property, residue, ring, title, total_weight

Inherited from structure.Structure (private): _doc, _proxy

Method Details [hide private]

__init__(self, handle, manage_handle=True, error_handler=None)
(Constructor)

 

Parent class would take care of basic CT data.

Overrides: structure.Structure.__init__

__copy__(self)

 

Allows the structure to be copied by copy.copy

Overrides: structure.Structure.__copy__

copy(self)

 

Returns a copy of the structure.

Overrides: structure.Structure.copy

write(self, filename, format=None)

 

Write the cms 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. Only cms format is supported as of know, if other types are choosen, basic CT information would be written, which is taken care by the parent class.

Overrides: structure.Structure.write

append(self, filename, format=None)

 

Append the structure to the file. Format is determined from the file suffix if None is specified, otherwise an explicit value of maestro, sd, pdb, or smiles can be used. Only cms format is supported as of know, if other types are choosen, basic CT information would be written, which is taken care by the parent class.

Parameters:
  • format - By default, the file format is determined from the filename suffix, but this can be specified explicitly. Supported option values are one of the PDB, MOL2, SD, MAESTRO, SMILES, SMILESCSV module-level constants.
Overrides: structure.Structure.append