CLI Reference

disvis

Documentation for the disvis script.

disvis --help

usage: disvis [-h] [--version] [-a <float>] [-vs <float>] [-ir <float>]
              [-cv <float>] [-iv <float>] [-d <dir>] [-p <int>] [-g] [-np]
              [-is <file>] [-ic <int>] [-oa] [--delimiter <str>] [--no-report]
              receptor ligand restraints

positional arguments:
  receptor              PDB-file containing fixed chain.
  ligand                PDB-file containing scanning chain.
  restraints            File containing the distance restraints

options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -a, --angle <float>   Rotational sampling density in degrees. Default is 15
                        degrees.
  -vs, --voxelspacing <float>
                        Voxel spacing of search grid in angstrom. Default is
                        1A.
  -ir, --interaction-radius <float>
                        Radius of the interaction space for each atom in
                        angstrom. Atoms are thus considered interacting if the
                        distance is larger than the vdW radius and shorther
                        than or equal to vdW + interaction_radius. Default is
                        3A.
  -cv, --max-clash <float>
                        Maximum allowed volume of clashes. Increasing this
                        number results in more allowed complexes. Default is
                        200 A^3.
  -iv, --min-interaction <float>
                        Minimal required interaction volume for a conformation
                        to be considered a complex. Increasing this number
                        results in a stricter counting of complexes. Default
                        is 300 A^3.
  -d, --directory <dir>
                        Directory where results are written to. Default is
                        current directory.
  -p, --nproc <int>     Number of processors used during search.
  -g, --gpu             Use GPU-acceleration for search. If not available the
                        CPU-version will be used with the given number of
                        processors.
  -np, --no-progress    Do not print the progress of the search.
  -is, --interaction-selection <file>
                        File containing residue number for which interactions
                        will be counted. The first line holds the receptor
                        residue, and the second line the ligand residue
                        numbers.
  -ic, --interaction-restraints-cutoff <int>
                        Number of minimal consistent restraints for which an
                        interaction or occupancy analysis will be performed.
                        Default is number of restraints minus 1.
  -oa, --occupancy-analysis
                        Perform an occupancy analysis, ultimately providing a
                        volume where each grid point represents the normalized
                        probability of that spot being occupied by the ligand.
  --delimiter <str>     Delimiter of the columns in the .out files, e.g. ','
                        or '\t', with a header line. Default is fixed width.
  --no-report           Do not write report.html and state.mvsj (the results
                        with a Mol* view of the accessible interaction space).