mdconvert-mdtraj - use mdtraj to convert molecular dynamics
trajectories between formats
usage: mdconvert-mdtraj [-h] -o OUTPUT [-c CHUNK] [-f] [-s
STRIDE] [-i INDEX]
- [-a ATOM_INDICES] [-t TOPOLOGY] input [input ...]
Convert molecular dynamics trajectories between formats. The DCD,
XTC, TRR, PDB, binpos, NetCDF, binpos, LH5, and HDF5 formats are supported
(.dcd, .xtc, .trr, .binpos, .nc, .netcdf, .h5, .lh5, .pdb)
- input
- path to one or more trajectory files. Multiple trajectories, if supplied,
will be concatenated together in the output file in the order supplied.
all of the trajectories should be in the same format. the format will be
detected based on the file extension
- -o OUTPUT, --output
OUTPUT
- path to the save the output. the output format will chosen based on the
file extension (.dcd, .xtc, .trr, .binpos, .nc, .netcdf, .h5, .lh5,
.pdb)
- -h, --help
- show this help message and exit
- -c CHUNK, --chunk
CHUNK
- number of frames to read in at once. this determines the memory
requirements of this code. default=1000
- -f, --force
- force overwrite if output already exsits
- -s STRIDE, --stride
STRIDE
- load only every stride-th frame from the input file(s), to subsample.
- -i INDEX, --index
INDEX
- load a *specific* set of frames. flexible, but inefficient for a large
trajectory. specify your selection using (pythonic) "slice
notation" e.g. '-i N' to load the the Nth frame, '-i -1' will
load the last frame, '-i N:M to load frames N to M, etc. see
http://bit.ly/143kloq for details on the notation
- -a ATOM_INDICES,
--atom_indices ATOM_INDICES
- load only specific atoms from the input file(s). provide a path to file
containing a space, tab or newline separated list of the (zero-based)
integer indices corresponding to the atoms you wish to keep.
- -t TOPOLOGY,
--topology TOPOLOGY
- path to a PDB/prmtop file. this will be used to parse the topology of the
system. it's optional, but useful. if specified, it enables you to output
the coordinates of your dcd/xtc/trr/netcdf/binpos as a PDB file. If you're
converting *to* .h5, the topology will be stored inside the h5 file.