piper.py Command Help

Command: $SCHRODINGER/run -FROM psp piper.py

usage: 

$SCHRODINGER/run -FROM psp piper.py -receptor <receptor pdb> -receptor_chains <chain ids for receptor> -ligand <ligand pdb> -ligand_chains <chain ids for ligands> [<other options>]

Use -h option for full description of options.

options:
  -h, --help            show this help message and exit
  -receptor RECEPTOR    The receptor protein used in docking (.pdb file). If
                        running in antibody mode this is the antibody.
  -receptor_chains RECEPTOR_CHAINS
                        Comma-separated list of chains to use in the receptor.
                        Do not use spaces, use an underscore (_) for a blank
                        chain name.
  -ligand LIGAND        The ligand protein used in docking (.pdb file). If
                        running in antibody mode this is the antigen. Not used
                        for Multimer/symmetry calculations.
  -ligand_chains LIGAND_CHAINS
                        Comma-separated list of chains to use in the ligand.
                        Do not use spaces, use an underscore (_) for a blank
                        chain name. Not used for Multimer/symmetry
                        calculations.
  -use_nonstandard_residue USE_NONSTANDARD_RESIDUE
                        Whether or not to use nonstandard residues in the
                        docking calculation. The default is no.
  -s {C2,C3}            Run docking in C2 (dimer) or C3 (trimer) mode.
  -antibody             Run in antibody mode.
  -nomask_cdr           In antibody mode, do not mask the CDR region
  -rotations ROTATIONS  Number of rotation matrices to use from rotation file.
                        Default is 70000
  -poses POSES          Number of poses to return. Default is 30.
  -constraints_file CONSTRAINTS_FILE
                        The file name that contains the definitions for each
                        attraction/repulsion defined. This is a JSON formatted
                        file and should be an array of objects. Each object is
                        required to have the keywords "asl", "constraint_type"
                        and "protein_type", and can optionally have the
                        keyword "attraction".
  -constraints_file_example
                        Print an example constraints file.
  -atom_prm ATOM_PRM    Path to atom parameters file
  -rot_prm ROT_PRM      Path to rotations parameter file
  -coeffs_prm COEFFS_PRM
                        Path to coefficients parameter file
  -protein_interaction_analysis PROTEIN_INTERACTION_ANALYSIS
                        Whether to include protein interaction analysis in
                        output yes or no (default)
  -score_in_place SCORE_IN_PLACE
                        Whether to score the input structure in addition to
                        docked poses. yes or no (default)
  -refinement_protocol {minimize,vacuum_minimize,interface,none}
                        Refinement protocol to run after the docking is
                        complete. Options: none, interface (default),
                        vacuum_minimize, or minimize
  -raw                  Store ALL piper poses for each cluster in pose-viewer
                        format. This setting will override the refinement
                        option and set it to none.
  -no_wam               If set, WAM property will not be written to output
                        structure
  -v                    show program's version number and exit
  -jobname JOBNAME, -JOBNAME JOBNAME, -j JOBNAME
                        Set the base name of outputs
  -OMPI OMPI, -ompi OMPI
                        Run job using using this number of processors

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
  -WAIT                 Do not return a prompt until the job completes.
  -D, -DEBUG            Show details of Job Control operation.
  -NOJOBID              Run the job directly, without Job Control layer.

Standard Options:
  -NOLAUNCH             Set up subjob inputs, but don't run the jobs.