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``mdconvert`` (``mdconvert-mdtraj``)
=============
``mdconvert`` is a command-line script installed with MDTraj to convert
molecular dynamics trajectories between formats. The DCD, XTC, TRR,
NetCDF, and HDF5 formats are supported (.xtc, .nc, .trr, .h5,
.pdb, .dcd). ``mdconvert`` is memory-efficient, and processes
trajectories in a chunked, streaming fashion. It is capable of converting
trajectory files which cannot be fully loaded into memory. It can also
concatenate trajectories, convert only a subset of the atoms in a trajectory
(i.e. strip solvent molecules), and down-sample trajectories by extract only a
subset of the frames.
On Debian systems ``mdconvert`` has been renamed to ``mdconvert-mdtraj``.
After installing the library, it should be in your ``$PATH``. You can check
this from the command line with this command. ::
$ which mdconvert-mdtraj
Here's the ``mdconvert`` (``mdconvert-mdtraj``) help text. ::
$ mdconvert-mdtraj -h
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,
NetCDF, and HDF5 formats are supported (.xtc, .nc, .trr, .h5,
.pdb, .dcd)
positional arguments:
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
required arguments:
-o OUTPUT, --output OUTPUT
path to the save the output. the output format will
chosen based on the file extension (.xtc, .nc, .trr,
.h5, .pdb, .dcd)
optional arguments:
-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 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 as a PDB file. If
you're converting *to* .h5, the topology will be
stored inside the h5 file.
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