pyemma.coordinates.save_traj¶
-
pyemma.coordinates.
save_traj
(traj_inp, indexes, outfile, top=None, stride=1, chunksize=1000, image_molecules=False, verbose=True)¶ Saves a sequence of frames as a single trajectory.
Extracts the specified sequence of time/trajectory indexes from traj_inp and saves it to one single molecular dynamics trajectory file. The output format will be determined by the outfile name.
Parameters: - traj_inp –
traj_inp can be of two types.
1. a python list of strings containing the filenames associated with the indices inindexes
. With this type of input, atopfile
is mandatory.2. a
pyemma.coordinates.data.feature_reader.FeatureReader()
object containing the filename list intraj_inp.trajfiles
. Please usepyemma.coordinates.source()
to construct it. With this type of input, the inputtopfile
will be ignored. andtraj_inp.topfile
will be used instead - indexes (ndarray(T, 2) or list of ndarray(T_i, 2)) – A (T x 2) array for writing a trajectory of T time steps. Each row contains two indexes (i, t), where i is the index of the trajectory from the input and t is the index of the time step within the trajectory. If a list of index arrays is given, these will be simply concatenated, i.e. they will be written subsequently in the same trajectory file.
- outfile (str.) – The name of the output file. Its extension will determine the file type written. Example: “out.dcd” If set to None, the trajectory object is returned to memory
- top (str, mdtraj.Trajectory, or mdtraj.Topology) – The topology needed to read the files in the list
traj_inp
. Iftraj_inp
is not a list, this parameter is ignored. - stride (integer, default is 1) – This parameter informs
save_traj()
about the stride used inindexes
. Typically,indexes
contains frame-indexes that match exactly the frames of the files contained intraj_inp.trajfiles
. However, in certain situations, that might not be the case. Examples are cases in which a stride value != 1 was used when reading/featurizing/transforming/discretizing the files contained intraj_inp.trajfiles
. - chunksize (int. Default 1000.) – The chunksize for reading input trajectory files. If
traj_inp
is apyemma.coordinates.data.feature_reader.FeatureReader()
object, this input variable will be ignored andtraj_inp.chunksize
will be used instead. - image_molecules (boolean, default is False) – If set to true,
save_traj
will call the method traj.image_molecules and try to correct for broken molecules accross periodic boundary conditions. (http://mdtraj.org/1.7.2/api/generated/mdtraj.Trajectory.html#mdtraj.Trajectory.image_molecules) - verbose (boolean, default is True) – Inform about created filenames
Returns: traj – Will only return this object if
outfile
is NoneReturn type: mdtraj.Trajectory
object- traj_inp –