prody catdcd

Usage

Running prody catdcd -h displays:

usage: prody catdcd [-h] [--quiet] [--examples] [-s SEL] [-o FILE] [-n]
                    [--psf PSF] [--pdb PDB] [--first INT] [--last INT]
                    [--stride INT] [--align SEL]
                    dcd [dcd ...]

positional arguments:
  dcd                   DCD filename(s) (all must have same number of atoms)

optional arguments:
  -h, --help            show this help message and exit
  --quiet               suppress info messages to stderr
  --examples            show usage examples and exit
  -s SEL, --select SEL  atom selection (default: all)
  -o FILE, --output FILE
                        output filename (default: trajectory.dcd)
  -n, --num             print the number of frames in each file and exit
  --psf PSF             PSF filename (must have same number of atoms as DCDs)
  --pdb PDB             PDB filename (must have same number of atoms as DCDs)
  --first INT           index of the first output frame, default: 0
  --last INT            index of the last output frame, default: -1
  --stride INT          number of steps between output frames, default: 1
  --align SEL           atom selection for aligning frames, a PSF or PDB file
                        must be provided, if a PDB is provided frames will be
                        superposed onto PDB coordinates

Examples

Running prody catdcd --examples displays:

Concatenate two DCD files and output all atmos:

  $ prody catdcd mdm2.dcd mdm2sim2.dcd

Concatenate two DCD files and output backbone atoms:

  $ prody catdcd mdm2.dcd mdm2sim2.dcd --pdb mdm2.pdb -s bb