Biskit :: Dock :: ComplexTraj :: ComplexTraj :: Class ComplexTraj

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Class ComplexTraj

Multi-copy trajectory of a protein-protein complex. Quite basic.

ComplexTraj keeps the reference PDBModel of the normal Trajectory but, additionally, knows which chains in the reference belong to the receptor and which chains belong to the ligand. It tries to keep the 2 lists of chain indices ( cr and cl ) up-to-date, even if chains are removed or re-ordered.

Appending of atoms/chains (e.g. with concatAtoms) is currently not considered and will most likely leed to additional chains that are ignored by the complex-specific functions.

Instance Methods

__init__(self, traj=None, recChains=[0], n_members=10, rec=None)
Use:

str version(self)
Version of Dock.Complex

EnsembleTraj ligTraj(self)
Returns ligand part of this Trajectory (copy)

EnsembleTraj recTraj(self)
Returns receptor part of this Trajectory (copy)

PDBModel refRec(self)
Returns copy of the receptor part of the reference model

PDBModel refLig(self)
Returns copy of the ligand part of the reference model

refCom(self)
Returns Complex

__getitem__(self, i)

Complex getComplex(self, index)
Use:

replaceContent(self, traj)
Replace content of this trajectory by content of given traj.

{int:int} __translateChainIndices(self, atomIndices, newChainMap)
Translate current chain indices into what they would look like in a PDBModel containing only the given atoms in the given order.

ComplexTraj takeAtoms(self, indices, returnClass=None)
takeAtoms( indices, [returnClass] ) -> ComplexTraj

ComplexTraj concatAtoms(self, recChains, *traj)
Concatenate 2 trajectories of same (frame) length 'horizontally', i.e.

matrix atomContacts(self, index, cutoff=4.5, rec_mask=None, lig_mask=None)
Use:

matrix averageContacts(self, step=10, cutoff=4.5)
Use:

plotContactDensity(self, step=1, cutoff=4.5)
Example.

Method Details

init(self, traj=None, recChains=[0], n_members=10, rec=None)
(Constructor)

Use:

  ComplexTraj( traj, recChains=[0], n_members=10 )

Parameters:

traj (Trajectory) - Trajectory (default: 0)
recChains ([int]) - list of chain indices defining receptor (default: [0])
n_members (int) - number of ensemble members (for multi-copy MD) (default: 10)
rec (PDBModel) - instead of using recChains, autodetect rec chains by comparing traj.ref with the model given as rec (default: None)

version(self)

Version of Dock.Complex

Returns: str: version of class

ligTraj(self)

Returns: EnsembleTraj: ligand part of this Trajectory (copy)

recTraj(self)

Returns: EnsembleTraj: receptor part of this Trajectory (copy)

refRec(self)

Returns: PDBModel: copy of the receptor part of the reference model

refLig(self)

Returns: PDBModel: copy of the ligand part of the reference model

refCom(self)

Returns:: Complex

getitem(self, i)
(Indexing operator)

getComplex(self, index)

Use:

 getComplex( frame_index ) -> Complex

Parameters:

index (int) - frame index

Returns: Complex: Complex

replaceContent(self, traj)

Replace content of this trajectory by content of given traj. No deep-copying, only references are taken.

Parameters:

traj (Trajectory) - Trajectory

Raises:

ComplexTrajError - if given traj is no ComplexTraj.

__translateChainIndices(self, atomIndices, newChainMap)

Translate current chain indices into what they would look like in a PDBModel containing only the given atoms in the given order.

Parameters:

atomIndices ([int]) - indices of atoms
newChainMap ([int]) - chain map [0000011133333..]

Returns: {int:int}: { int:int, .. } map current chain indices to new ones

Raises:

ComplexTrajError - if (parts of) chains are inserted into each other

takeAtoms(self, indices, returnClass=None)

takeAtoms( indices, [returnClass] ) -> ComplexTraj

Parameters:

indices ([int]) - atoms to extract
returnClass (class) - return type (default: current class)

Returns: ComplexTraj: ComplexTraj

Raises:

ComplexTrajError - if (parts of) chains are inserted into each other

concatAtoms(self, recChains, *traj)

Concatenate 2 trajectories of same (frame) length 'horizontally', i.e. for each frame the coordinates of one are appended to the coordinates of the other. The ref model of the new trajectory is a 'semi-deep' copy of this trajectory's model (see Biskit.PDBModel.take() ).:

 concatAtoms( recChains, traj1 [traj2, traj3..]) -> ComplexTraj

Parameters:

recChains ([int]) - chain indices into traj that will be assigned to the receptor; all remaining chains (if any) go to the ligand
traj (Trajectory) - trajectories to concatenate

Returns: ComplexTraj: ComplexTraj

Warning: NOT TESTED!!

atomContacts(self, index, cutoff=4.5, rec_mask=None, lig_mask=None)

Use:

 atomContacts( frame_index ) -> array len_rec x len_lig of 0||1

Parameters:

index ([int]) - frame index
cutoff (float) - contact cutoff in Angstrom (default: 4.5)
rec_mask ([int]) - atom mask
lig_mask ([int]) - atom mask

Returns: matrix: contact matrix

averageContacts(self, step=10, cutoff=4.5)

Use:

 averageContacts( step=1, cutoff=4.5 )

Parameters:

step (int) - take only each |step|th frame (default: 10)
cutoff (float) - distance cutoff in Angstrom (default: 4.5)

Returns: matrix: contact matrix with frequency of each contact in (thinned) traj.

plotContactDensity(self, step=1, cutoff=4.5)

Example. plot histogramm of contact density. Somehing wrong??

Raises:

ComplexTrajError - if gnuplot program is not installed