def iterativeAlignment(ensemble, threshold=1e-8, maxiter=1000):
"""
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)
"""
enlist = loos.DoubleVectorMatrix()
for e in ensemble:
enlist.push_back(e.coordsAsVector())
result = loos.iterativeAlignmentPy(enlist, threshold, maxiter)
return(loos.xformVectorToList(result.transforms), result.rmsd, result.iterations)
def iterativeAlignment(ensemble, threshold=1e-8, maxiter=1000):
"""
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)
"""
enlist = loos.DoubleVectorMatrix()
for e in ensemble:
enlist.push_back(e.coordsAsVector())
result = loos.iterativeAlignmentPy(enlist, threshold, maxiter)
return (loos.xformVectorToList(result.transforms), result.rmsd,
result.iterations)
def 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)
"""
# If traj is not a loos.Trajectory, assume it supports the trajectory()
# method to access the underlying loos one
if not isinstance(traj, loos.Trajectory):
traj = traj.trajectory()
# Handle framelist request
if 'framelist' in kwargs:
framelist = kwargs['framelist']
# If it's not a vector<uint>, assume it's iterable
if not isinstance(framelist, loos.UIntVector):
flist = loos.UIntVector(kwargs['framelist'])
else:
flist = framelist
result = loos.iterativeAlignmentPy(model, traj, flist, threshold,
maxiter)
else:
result = loos.iterativeAlignmentPy(model, traj, threshold, maxiter)
return (loos.xformVectorToList(result.transforms), result.rmsd,
result.iterations)
def 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)
"""
# If traj is not a loos.Trajectory, assume it supports the trajectory()
# method to access the underlying loos one
if not isinstance(traj, loos.Trajectory):
traj = traj.trajectory()
# Handle framelist request
if 'framelist' in kwargs:
framelist = kwargs['framelist']
# If it's not a vector<uint>, assume it's iterable
if not isinstance(framelist, loos.UIntVector):
flist = loos.UIntVector(kwargs['framelist'])
else:
flist = framelist
result = loos.iterativeAlignmentPy(model, traj, flist, threshold, maxiter)
else:
result = loos.iterativeAlignmentPy(model, traj, threshold, maxiter)
return(loos.xformVectorToList(result.transforms), result.rmsd, result.iterations)
def _align(self):
"""
Align the frames (called implicitly on iterator or array access)
"""
current_traj = None
current_subset = None
ensemble = []
if self._stale:
self._initFrameList()
if self._reference: # Align to a reference structure
self._xformlist = []
for i in range(len(self._framelist)):
t = self._trajectories[self._trajlist[i]]
if t != current_traj:
current_traj = t
current_subset = loos.selectAtoms(t.model(),
self._alignwith)
t.readFrame(self._framelist[i])
m = current_subset.superposition(self._reference)
x = loos.XForm()
x.load(m)
self._xformlist.append(x)
self._rmsd = 0.0
self._iters = 0
else: # Iterative alignment
ensemble = loos.DoubleVectorMatrix()
for i in range(len(self._framelist)):
t = self._trajectories[self._trajlist[i]]
if t != current_traj:
current_traj = t
current_subset = loos.selectAtoms(t.model(),
self._alignwith)
t.readFrame(self._framelist[i])
ensemble.push_back(current_subset.coordsAsVector())
result = loos.iterativeAlignmentPy(ensemble)
(self._xformlist, self._rmsd,
self._iters) = (loos.xformVectorToList(result.transforms),
result.rmsd, result.iterations)
self._aligned = True
def _align(self):
"""
Align the frames (called implicitly on iterator or array access)
"""
current_traj = None
current_subset = None
ensemble = []
if self._stale:
self._initFrameList()
if self._reference: # Align to a reference structure
self._xformlist = []
for i in range(len(self._framelist)):
t = self._trajectories[self._trajlist[i]]
if t != current_traj:
current_traj = t
current_subset = loos.selectAtoms(t.model(), self._alignwith)
t.readFrame(self._framelist[i])
m = current_subset.superposition(self._reference)
x = loos.XForm()
x.load(m)
self._xformlist.append(x)
self._rmsd = 0.0
self._iters = 0
else: # Iterative alignment
ensemble = loos.DoubleVectorMatrix()
for i in range(len(self._framelist)):
t = self._trajectories[self._trajlist[i]]
if t != current_traj:
current_traj = t
current_subset = loos.selectAtoms(t.model(), self._alignwith)
t.readFrame(self._framelist[i])
ensemble.push_back(current_subset.coordsAsVector())
result = loos.iterativeAlignmentPy(ensemble)
(self._xformlist, self._rmsd, self._iters) = (loos.xformVectorToList(result.transforms), result.rmsd, result.iterations)
self._aligned = True