create_reagent_library.py Command Help

Command: $SCHRODINGER/run create_reagent_library.py

usage: create_reagent_library.py <input_file> [-all|-name <name>] [options]

Create a reagent library for combinatorial synthesis from a SMARTS search.

positional arguments:
  input_file            Structure input file (.csv, .smi, .sdf[gz], or
                        .mae[gz]).

options:
  -h, --help            show this help message and exit
  -install              Install output files.
  -dest DEST            Installation directory (default:
                        /Users/bozhang/.schrodinger/reagents).
  -dest_reagent_classes DEST_REAGENT_CLASSES
                        Reagent_classes file to update (default:
                        /Users/bozhang/.schrodinger/reagent_classes.json).
  -all                  Create files for all known reagent classes.
  -prefix PREFIX        Prefix to add to reagent class names when using -all
  -suffix SUFFIX        Suffix to add to reagent class names when using -all
  -name NAME            Name of reagent class.
  -smarts SMARTS [SMARTS ...]
                        SMARTS patterns to use. Only used with -name. If
                        omitted, the SMARTS pattern from the reagent classes
                        file will be used, unless -smarts_from is used.
  -smarts_from SMARTS_FROM [SMARTS_FROM ...]
                        Use SMARTS patterns from named reagent classes.
  -single_match         only retain structures that match the SMARTS pattern
                        once.
  -id_property ID_PROPERTY
                        Name of property to use to identify reagents (default:
                        s_m_title).
  -reagent_classes_file REAGENT_CLASSES_FILE
                        JSON reagent classes file to use instead of the
                        default file from the data directory.
  -properties PROPERTIES
                        Comma-separated list of properties to store in output
                        file. Special values "all" and "none" may also be used
                        (default: none).
  -pfx                  write output files in .pfx format
  -add                  Add structures to existing output file.
  -no_dedup             Don't exclude duplicate structures (by canonical
                        SMILES).
  -desalt               Desalt reactants.
  -neutralize           Neutralize reactants.

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.