confgenx Command Help

Command: $SCHRODINGER/confgenx

usage: confgenx [-v] [-h] [-profile <string>] [-L <path>] [-n <number>]
                [-m <number>] [-t <number>] [-drop_properties]
                [-drop_problematic] [-S <number>] [-optimize]
                [-force_field <string>] [-dont_vary_nitrogens] [-keep_amides]
                [-j <string>] [-no_cleanup] [-sublocal] [-NJOBS NJOBS]
                [-NSTRUCTS NSTRUCTS] [-DRIVERHOST <hostname>] [-STRICT]
                [-RETRIES RETRIES] [-HOST <hostname>] [-WAIT] [-LOCAL] [-D]
                [-SAVE] [-NOJOBID]
                input_file

positional arguments:
  input_file            File containing input structures in Maestro, Mol2 or
                        SD format (must reside in the current working
                        directory). The input structures are expected to
                        explicitly include all Hydrogen atoms.

options:
  -v, -version          Show the program's version and exit.
  -h, -help             Show this help message and exit.
  -profile <string>     Quality mode: "default" (default) or "basic" (slightly
                        faster processing at the cost of lower conformer
                        quality).
  -L <path>, -library <path>
                        Custom fragment library path. Overrides default
                        location from the application data directory if
                        specified.
  -n <number>, -num_conformers <number>
                        Desired number of conformers. If not specified, the
                        number is determined by the quality mode settings.
                        Small values (less than about 50) may degrade quality
                        significantly and should be avoided: the -m option can
                        be used to reduce the number of conformations instead.
  -m <number>, -max_num_conformers <number>
                        Largest number of conformers to be stored for each
                        input structure. The conformers get ranked and sorted
                        prior to the storage.
  -t <number>, -auto_increase_threshold <number>
                        Threshold number of rotatable bonds for automatic
                        increase of the number of conformers to be generated
                        (Default: 9).
  -drop_properties      Save CT level properties for only the first conformer.
  -drop_problematic     Do not save input molecules for which no conformers
                        were obtained into the output file.
  -S <number>, -stereo <number>
                        Stereochemistry source: 0 - enforce stereochemistry
                        specified via the input CT-level properties; 1
                        (default) - respect the input stereo properties,
                        derive unspecified stereochemistry from the input
                        coordinates; 2 - infer stereochemistry from the input
                        coordinates ignoring the input CT-level properties. In
                        the latter two cases stereochemical CT-level
                        properties are set to reflect the assumed
                        configuration.
  -optimize             Optimize conformer geometry using an OPLS potential
                        (Default: False).
  -force_field <string>
                        OPLS potential to use for the optional geometry
                        optimization: OPLS_2005, S-OPLS, SPFF (Default:
                        OPLS_2005).
  -dont_vary_nitrogens  Do not vary pyramidal Nitrogens (Default: False).
  -keep_amides          Preserve amide bond input configurations. (Default:
                        False).
  -j <string>, -jobname <string>
                        Job name. By default it is derived from the input file
                        name.
  -no_cleanup           Do not clean up after the job is complete.
  -sublocal             Run subjobs in the driver's job directory.

Standard Options:
  -NJOBS NJOBS          Divide the overall job into NJOBS subjobs.
  -NSTRUCTS NSTRUCTS    Divide the overall job into subjobs with no more than
                        NSTRUCTS structures.
  -DRIVERHOST <hostname>
                        Run the driver on the specified host. The subjobs are
                        run on the hosts specified with -HOST.
  -STRICT               Terminate the job if any subjob dies.
  -RETRIES RETRIES      If a subjob fails for any reason, it will be retried
                        RETRIES times. (Default: 2)

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.
  -D, -DEBUG            Show details of Job Control operation.
  -SAVE                 Return zip archive of job directory at job completion.
  -NOJOBID              Run the job directly, without Job Control layer.