loos.pyloos.ensembles Namespace Reference

Functions
	averageStructure (traj)
	Python version of averageStructure (using loos.pyloos.Trajectory-like objects) The subset defined in the trajectory controls what is averaged over.
	extractCoords (traj)
	Returns the coordinates for an entire trajectory as an MxN numpy matrix where M is 3*natoms and N is the length of the trajectory.
	svd (traj)
	Returns a tuple containing the SVD result for a trajectory, along with the average structure.

Detailed Description

PyLOOS functions applicable to ensembles (trajectories or trajectory-like collections)

Function Documentation

averageStructure()

loos.pyloos.ensembles.averageStructure

(

traj

)

Python version of averageStructure (using loos.pyloos.Trajectory-like objects) The subset defined in the trajectory controls what is averaged over.

The trajectory may actually be a VirtualTrajectory or an AlignedVirtualTrajectory.

Returns the average structure for a trajectory.
>>> avg = loos.pyloos.averageStructure(traj)

extractCoords()

loos.pyloos.ensembles.extractCoords

(

traj

)

Returns the coordinates for an entire trajectory as an MxN numpy matrix where M is 3*natoms and N is the length of the trajectory.

The subset in the trajectory controls what is extracted. The trajectory may actually be a VirtualTrajectory or an AlignedVirtualTrajectory.

Extracts coords from a trajectory as a NumPy matrix
>>> A = loos.pyloos.extractCoords(traj)

svd()

loos.pyloos.ensembles.svd

(

traj

)

Returns a tuple containing the SVD result for a trajectory, along with the average structure.

The tuple is, (left-singular-vectors, singular-values, right-singular-vectors, average)

The subset set in the trajectory controls what is used for the SVD. The trajectory may be a VirtualTrajectory or an AlignedVirtualTrajectory. The following example computes an SVD using backbone atoms for a trajectory that has been iteratively aligned using C-alphas

traj = loos.pyloos.Trajectory('foo.dcd', model, subset = 'backbone')
aligned = loos.pyloos.AlignedVirtualTrajectory(traj, alignwith = 'name == "CA"')
(L,S,V,avg) = loos.pyloos.svd(aligned)

Returns a tuple containing SVD results along with the average structure for a trajectory
>>> (L,S,V,avg) = loos.pyloos.svd(traj)