Biskit :: Dock :: ComplexEvolving :: ComplexEvolving :: Class ComplexEvolving

Class ComplexEvolving

Complex that keeps track of its previous versions. The object behaves like a normal Biskit.Dock.Complex but encapsulates a Biskit.Dock.ComplexList with older versions/conformations of this Complex.

com[0] gives the very first version, com[1] the second, etc.
com[-1] gives the current version (but as normal Complex, not ComplexEvolving).
e.g. com[0, 'fnac'] gives the according info value of the first version
e.g. com['fnac'] gives the current info value (as for Dock.Complex)

Instance Methods

[hide private]

__init__(self, rec_model, lig_model, com_0=None, ligMatrix=None, info={})
Create a new ComplexEvolving from a previous Complex or ComplexEvolving and a new set of receptor, ligand conformation and transformation.

str version(self)
Version of class.

__iter__()
for k in self

__len__(self)
length of self

Dock.Complex getComplex(self, i, copy=0)
Return one version as Complex.

dict __getitem__(self, k)
Get a Complex OR a info key value for a Complex specified Complex OR info dic value.

PDBModel __syncModel(self, new_model, old_model)
Connect new rec or lig model to old one, to minimize storage.

sortHistory(self)
Sort by date

ComplexList toList(self)
Returns all historic complexes plus current one as Complex

[Complex] toSimpleList(self)
Returns all historic complexes plus current one as Complex

Complex toComplex(self, copy=0)
Copy of latest version as a normal Complex.

[any] valuesOf(self, infoKey, default=None)
Get info values from all versions of this complex (oldest first).

Inherited from Complex.Complex: __contains__, __delitem__, __getstate__, __setitem__, __setstate__, atomContacts, compareAtoms, compress, conservationScore, contPairScore, contactResDistribution, contactResPairs, contactTypeDistribution, contactsDiff, contactsOverlap, contactsShared, equalAtoms, extractLigandMatrix, foldXEnergy, fractionNativeContacts, fractionNativeSurface, get, getInfo, has_key, interfaceArea, keys, lig, ligMatrix, loadResContacts, model, prosa2003Energy, rec, resContacts, resPairCounts, rmsInterface, rmsLig, rtTuple2matrix, setLigMatrix, slim, take, values, writeComplex, writeLigand, writeReceptor

Method Details

[hide private]

init(self, rec_model, lig_model, com_0=None, ligMatrix=None, info={})
(Constructor)

source code

Create a new ComplexEvolving from a previous Complex or ComplexEvolving and a new set of receptor, ligand conformation and transformation.

Parameters:

rec_model (PDBModel) - PDBModel/PCRModel, receptor conformation
lig_model (PDBModel) - PDBModel/PCRModel, ligand conformation
com_0 (Complex OR ComplexEvolving) - Complex /ComplexEvolving, previous version(s) of this com
ligMatrix (4x4 array) - transformation matrix of ligand versus receptor
info (dict) - {'info_key': value, ..}, additional infos

Overrides: Complex.Complex.__init__

version(self)

source code

Version of class.

Returns: str: version of class

Overrides: Complex.Complex.version

iter()

source code

for k in self

len(self)
(Length operator)

source code

length of self

getComplex(self, i, copy=0)

source code

Return one version as Complex. -1 returns a copy of the latest version. By default the info dictionary remains connected but other fields don't. I.e. replacing rec_model in the copy does not affect the original complex.

Parameters:

i (int) - index in complex history, -1 returns toComplex()
copy (1|0) - copy info dictionary in case of i==-1 (changes in c.getComplex( -1 ).info will not appear in c.info [0]

Returns: Dock.Complex: complex

getitem(self, k)
(Indexing operator)

source code

Get a Complex OR a info key value for a Complex specified Complex OR info dic value.

Parameters:

k (any OR Complex) - tuple OR int OR str

Returns: dict: C.info[ key ]

Overrides: Complex.Complex.__getitem__

__syncModel(self, new_model, old_model)

source code

Connect new rec or lig model to old one, to minimize storage.

Parameters:

new_model (PDBModel) - PDBModel / PCRModel
old_model (PDBModel) - PDBModel / PCRModel

Returns: PDBModel: PDBModel / PCRModel, new model that only keeps changes relative to old, the old model becomes the source of the new, if possible

sortHistory(self)

source code

Sort by date

toList(self)

source code

Returns: ComplexList: all historic complexes plus current one as Complex

toSimpleList(self)

source code

Returns: [Complex]: all historic complexes plus current one as Complex

toComplex(self, copy=0)

source code

Copy of latest version as a normal Complex.

Parameters:

copy (1|0) - also disconnect info dict (default: 0)

Returns: Complex: Complex

valuesOf(self, infoKey, default=None)

source code

Get info values from all versions of this complex (oldest first).

Parameters:

infoKey (str) - info dic key
default (any) - default value, if key is not present

Returns: [any]: list of values

Class ComplexEvolving

__init__(self, rec_model, lig_model, com_0=None, ligMatrix=None, info={}) (Constructor)

version(self)

__iter__()

__len__(self) (Length operator)

getComplex(self, i, copy=0)

__getitem__(self, k) (Indexing operator)

__syncModel(self, new_model, old_model)

sortHistory(self)

toList(self)

toSimpleList(self)

toComplex(self, copy=0)

valuesOf(self, infoKey, default=None)

init(self, rec_model, lig_model, com_0=None, ligMatrix=None, info={})
(Constructor)

iter()

len(self)
(Length operator)

getitem(self, k)
(Indexing operator)