ligfilter Command Help

Command: $SCHRODINGER/utilities/ligfilter

usage: ligfilter [-v] [-h] [-remove] [-any] [-values]
                            [-f CRITERIA_FILE] [-n NOMATCH_FILE]
                            [-e CONDITIONS] [-asl ASL_STRINGS]
                            [-asl_file ASL_FILE] [-max_atoms MAX_ATOMS]
                            [-addprops] [-add_descriptors] [-addprop ADDPROP]
                            [-noout] [-o OUTPUT_FILE] [-doc] [-descriptors]
                            [-j JOBNAME] [-NJOBS NJOBS] [-HOST <hostname>]
                            [-WAIT] [-LOCAL] [-NOLOCAL] [-NOJOBID]
                            input_file

Ligfilter Script

This script filteres a ligand file based on specified criteria.

Copyright Schrodinger, LLC.  All Rights Reserved.

positional arguments:
  input_file            Input structure file

options:
  -v, -version          Show the program's version and exit.
  -h, -help             Show this help message and exit.
  -remove, -invert      Invert criteria
  -any                  Structure will pass if it matches any criteria (by
                        default it must match all criteria.
  -values               Print criteria values for each processed structure to
                        stdout.
  -f CRITERIA_FILE      Criteria file
  -n NOMATCH_FILE       Output file for the non-matching structures (optional)
  -e CONDITIONS         one or more conditions
  -asl ASL_STRINGS      one or more ASL strings
  -asl_file ASL_FILE    ASL file
  -max_atoms MAX_ATOMS  max atoms
  -addprops             For each filter criteria, add a property to each
                        output structure listing the result (or count) for
                        each criteria. Added properties will be in format
                        "i/r_ligfilter_<Criteria-name>". For example,
                        filtering by criteria -e "Num_rings > 2" will add a
                        property i_ligfilter_Num_rings to each output
                        structure. To add all descriptors, use
                        -add_descriptors option.
  -add_descriptors      For each output structure, add a property for each
                        criteria that LigFilter is able to calculate. Like
                        -addprops, but includes all supported properties.
                        Example usage: ligfilter                        input.mae -o output.mae -add_descriptors
  -addprop ADDPROP      Instead of filtering structures, add the specified
                        boolean property to each structure. Example usage:
                        -addprop b_user_Matched.
  -noout                Do not write output
  -o OUTPUT_FILE        Output file for the matching structures (optional)
  -doc                  Print out the LigFilter documentation
  -descriptors          Print out the descriptors
  -j JOBNAME
  -NJOBS NJOBS          Number of jobs to split the calculation into. Default
                        is 1.

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
  -WAIT                 Do not return a prompt until the job completes.
  -LOCAL                Do not use a temporary directory for job files. Keep
                        files in the current directory.
  -NOLOCAL              Use a temporary directory for job files.
  -NOJOBID              Run the job directly, without Job Control layer.