LOOS  v2.3.2
loos.pyloos.alignment Namespace Reference

Functions

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

Detailed Description

PyLOOS interface to the LOOS iterative alignment routines

Function Documentation

def 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)

Definition at line 12 of file alignment.py.

def 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)

Definition at line 48 of file alignment.py.