dps trjconv

Select, transform, and convert a DROPPS trajectory.

Synopsis and options

usage: dps trjconv [-h] -s FILE -f FILE [-n FILE] [-sel EXPR] -o FILE [-b START_TIME]
                   [-e END_TIME] [-dt DELTA_TIME] [-tu {fs,ps,ns,us,ms,s}]
                   [-pbc {none,whole,atom,res,mol,nojump}] [--center {none,geometry,mass,dense}]
                   [--center-select EXPR] [--center-axis {x,y,z,xyz}] [-dpt DENSE_PHASE_THRESHOLD]
                   [--density-bin-width DENSITY_BIN_WIDTH]
                   [-fit {none,translation,transxy,rot+trans,rotxy+transxy,progressive}]
                   [--fit-select EXPR] [--fit-reference {tpr,first}]
                   [--fit-weighting {mass,uniform}] [-trans DX DY DZ] [-shift DX DY DZ]
                   [-ndec PRECISION] [-sep] [--zero-pad ZERO_PAD] [--conect]

Select, transform, and convert a DROPPS trajectory.

Input:
  -s FILE, --run-input FILE
                        Input DROPPS run file (.tpr) containing topology and coordinates.
                        (required)
  -f FILE, --input FILE
                        Input trajectory or structure file (.xtc or .pdb). (required)
  -n FILE, --index FILE
                        Optional index file (.ndx) defining additional atom groups. (default:
                        None)
  -sel EXPR, --select EXPR
                        DROPPS selection expression for atoms to write; when omitted, prompt
                        interactively. (default: None)
  --center-select EXPR  Selection used for centering; defaults to the output selection.
  --fit-select EXPR     Selection used for fitting; defaults to the output selection.

Output:
  -o FILE, --output FILE
                        Output trajectory or structure file (.xtc or .pdb). (required)

Parameters:
  -h, --help            Show this help message and exit.
  -b START_TIME, --start-time START_TIME
                        First trajectory time to write. (default: None)
  -e END_TIME, --end-time END_TIME
                        Last trajectory time to write; set equal to -b to select the nearest saved
                        frame. (default: None)
  -dt DELTA_TIME, --delta-time DELTA_TIME
                        Time interval between output frames, using nearest saved frames. (default:
                        None)
  -tu {fs,ps,ns,us,ms,s}, --time-unit {fs,ps,ns,us,ms,s}
                        Unit used by -b, -e, and -dt. (default: ns)
  -pbc {none,whole,atom,res,mol,nojump}, --pbc {none,whole,atom,res,mol,nojump}
                        Periodic-boundary treatment: whole reconstructs bonded molecules; atom
                        packs atoms; res/mol pack residue or whole-molecule centers; nojump
                        removes temporal box jumps. (default: none)
  --center {none,geometry,mass,dense}
                        Center the selected group geometrically, by mass, or as a dense slab.
                        (default: none)
  --center-axis {x,y,z,xyz}
                        Axes to center; defaults to xyz for geometry/mass and z for dense
                        centering.
  -dpt DENSE_PHASE_THRESHOLD, --dense-phase-threshold DENSE_PHASE_THRESHOLD
                        Dense bins must exceed this fraction of the maximum mass density.
                        (default: 0.5)
  --density-bin-width DENSITY_BIN_WIDTH
                        Dense-phase histogram bin width in nm. (default: 0.05)
  -fit {none,translation,transxy,rot+trans,rotxy+transxy,progressive}, --fit {none,translation,transxy,rot+trans,rotxy+transxy,progressive}
                        Fit coordinates to the TPR or first processed frame. (default: none)
  --fit-reference {tpr,first}
                        Reference coordinates for ordinary or progressive fitting. (default: tpr)
  --fit-weighting {mass,uniform}
                        Weights used to determine fit centers and rotations. (default: mass)
  -trans DX DY DZ, --translate DX DY DZ
                        Final constant Cartesian translation vector in nm. (default: None)
  -shift DX DY DZ, --shift DX DY DZ
                        Additional translation in nm multiplied by the input frame index.
                        (default: None)
  -ndec PRECISION, --precision PRECISION
                        Number of decimal places used for XTC output precision. (default: 3)
  -sep, --separate      Write each selected frame to a separate numbered PDB file. (default:
                        False)
  --zero-pad ZERO_PAD   Number of digits in filenames created by --separate. (default: 6)
  --conect              Add reindexed topology bonds as CONECT records to PDB output. (default:
                        False)

Frame selection is time-based. Set -b and -e to the same value to write the saved frame nearest that time. Transform order is: make whole/no-jump, center, pack into the box, fit, translate.

Examples:
  dps trjconv -s run.tpr -f run.xtc -o frame.pdb -b 100 -e 100 -sel 'group 0'

Note

This page is generated from the DROPPS 1.0 argument parser. Run dps trjconv -h in the installed environment for the same reference at the command line.