loos.pyloos.alignment Namespace Reference

Functions
	iterativeAlignment (ensemble, threshold=1e-8, maxiter=1000)
	Iteratively align a loos.pyloos.Trajectory object (or a list of AtomicGroups)
	iterativeAlignTrajectory (model, traj, threshold=1e-8, maxiter=1000, **kwargs)

Detailed Description

PyLOOS interface to the LOOS iterative alignment routines

Function Documentation

iterativeAlignment()

loos.pyloos.alignment.iterativeAlignment	(		ensemble,
			threshold = 1e-8,
			maxiter = 1000 )

Iteratively align a loos.pyloos.Trajectory object (or a list of AtomicGroups)

Iteratively align a loos.pyloos.Trajectory object (or a list of AtomicGroups).
Returns the transformations needed to perform the alignment.  Note that it does
not currently transform what's passed into it.

Args

  ensemble: loos.pyloos.Trajectory, or list of AtomicGroups
  threshold (opt): change in average less than this ends alignment
  maxiter(opt): maximum number of iterations allowed


Returns

  (list-of-xforms, final-rmsd, number-of-iterations)


Examples

  model = loos.createSystem('foo.pdb')
  traj = loos.pyloos.Trajectory('foo.dcd', model, subset = 'name == "CA"')
  (xforms, rmsd, iters) = loos.pyloos.iterativeAlignment(traj)

  ensemble = [frame.copy() for frame in traj]
  (xforms, rmsd, iters) = loos.pyloos.iterativeAlignment(ensemble)

iterativeAlignTrajectory()

loos.pyloos.alignment.iterativeAlignTrajectory	(		model,
			traj,
			threshold = 1e-8,
			maxiter = 1000,
		**	kwargs )

Interface to the standard LOOS iterative alignment routines.
Returns the transformations needed to perform the alignment.  Note that it does
not currently transform what's passed into it.

Args

  model: AtomicGroup (subset of trajectory model) to use for aligning
  traj: trajectory to align
  threshold (opt): change in avg less than this ends alignment
  maxiter (opt): max number of iterations allowed
  framelist (opt): a python list (or loos.UIntVector) of frame indices
      from the trajectory to use


Returns

  (list-of-xforms, final-rmsd, number-of-iterations)


Examples

  model = loos.createSystem('foo.pdb')
  traj = loos.createTrajectory('foo.dcd', model)
  subset = loos.selectAtoms(model, 'backbone')

  (xforms, rmsd, iters) = loos.pyloos.iterativeAlignTrajectory(subset, traj)