LOOS
v2.3.2

Functions  
def  averageStructure (traj) 
Python version of averageStructure (using loos.pyloos.Trajectorylike objects) The subset defined in the trajectory controls what is averaged over. More...  
def  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. More...  
def  svd (traj) 
Returns a tuple containing the SVD result for a trajectory, along with the average structure. More...  
PyLOOS functions applicable to ensembles (trajectories or trajectorylike collections)
def loos.pyloos.ensembles.averageStructure  (  traj  ) 
Python version of averageStructure (using loos.pyloos.Trajectorylike 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)
Definition at line 14 of file ensembles.py.
def 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)
Definition at line 35 of file ensembles.py.
def loos.pyloos.ensembles.svd  (  traj  ) 
Returns a tuple containing the SVD result for a trajectory, along with the average structure.
The tuple is, (leftsingularvectors, singularvalues, rightsingularvectors, 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 Calphas
Returns a tuple containing SVD results along with the average structure for a trajectory >>> (L,S,V,avg) = loos.pyloos.svd(traj)
Definition at line 66 of file ensembles.py.