Biskit :: PCRModel :: PCRModel :: Class PCRModel

Class PCRModel

PDBModel with attached Xplor topology (PSF). Creates more problems than it solves...

Instance Methods

__init__(self, fPsf=None, source=None, pdbCode=None, **params)
PDBModel() creates an empty Model to which coordinates (field xyz) and PDB infos (field atoms) have still to be added.

version(self)

str getPsfFile(self)
Returns file name

PDBModel take(self, i, deepcopy=0)
All fields of the result model are shallow copies of this model's fields.

concat(self, *models)
Concatenate atoms, coordinates and profiles.

Inherited from PDBModel.PDBModel: __getstate__, __len__, __setstate__, addChainFromSegid, addChainId, argsort, atom2chainIndices, atom2resIndices, atom2resMask, atomNames, atomProfile, center, centerOfMass, centered, chain2atomIndices, chainBreaks, chainIndex, chainMap, clone, compareAtoms, compareChains, compress, disconnect, equalAtoms, equals, filter, filterIndex, fit, getAtoms, getPdbCode, getXyz, indices, isChanged, isChangedFromDisc, keep, lenAtoms, lenChains, lenResidues, magicFit, mask, maskBB, maskCA, maskCB, maskF, maskH, maskH2O, maskHeavy, maskHetatm, maskProtein, maskSolvent, mass, masses, profile, profile2atomMask, profile2mask, profileChangedFromDisc, profileInfo, remove, removeProfile, removeRes, renumberResidues, res2atomIndices, res2atomMask, res2atomProfile, resEndIndex, resIndex, resList, resMap, resMapOriginal, resModels, resProfile, residusMaximus, returnPdb, rms, saveAs, sequence, setAtomProfile, setAtoms, setPdbCode, setProfileInfo, setResProfile, setSource, setXyz, slim, sort, sourceFile, takeChains, transform, transformation, unsort, update, validSource, writePdb, xplor2amber

Method Details

[hide private]

init(self, fPsf=None, source=None, pdbCode=None, **params)
(Constructor)

source code

PDBModel() creates an empty Model to which coordinates (field xyz) and PDB infos (field atoms) have still to be added.
PDBModel( file_name ) creates a complete model with coordinates and PDB infos taken from file_name (pdb, pdb.gz, pickled PDBModel)
PDBModel( PDBModel ) creates a copy of the given model
PDBModel( PDBModel, noxyz=1 ) creates a copy without coordinates

Parameters:

fPsf (str) - file name of psf
source (str | PDBModel) - file name of pdb OR PDBModel instance
pdbCode (str) - if None, first 4 letters of filename will be used

Overrides: PDBModel.PDBModel.__init__

version(self)

source code

Overrides: PDBModel.PDBModel.version

getPsfFile(self)

source code

Returns: str: file name

take(self, i, deepcopy=0)

source code

All fields of the result model are shallow copies of this model's fields. I.e. removing or reordering of atoms does not affect the original model but changes to entries in the atoms dictionaries would also change the atom dictionaries of this model.

take( atomIndices, [deepcopy=0] ) -> PDBModel / sub-class.

Returns: PDBModel: PDBModel / sub-class

Overrides: PDBModel.PDBModel.take: (inherited documentation)

concat(self, *models)

source code

Concatenate atoms, coordinates and profiles. source and fileName are lost, so are profiles that are not available in all models. model0.concat( model1 [, model2, ..]) -> single PDBModel.

Overrides: PDBModel.PDBModel.concat: (inherited documentation)

Class PCRModel

__init__(self, fPsf=None, source=None, pdbCode=None, **params) (Constructor)

version(self)

getPsfFile(self)

take(self, i, deepcopy=0)

concat(self, *models)

init(self, fPsf=None, source=None, pdbCode=None, **params)
(Constructor)