ch_isosteric_matching_driver Command Help

Command: $SCHRODINGER/utilities/ch_isosteric_matching_driver

Usage: ch_isosteric_matching_driver $SCHRODINGER/utilities/ch_isosteric_matching_driver [<options>] -i <ligand file> -c <cores file> -core_asl <ASL expression defining core atoms>



Description:  Ligand-based core hopping. Initial core is defined by -core_asl
option specifying atoms in ligand input by option -i. shape_screen program is
used to align potential cores onto these atoms.

Options:
  -v, -version          Show the program's version and exit.
  -h, -help             Show this help message and exit.
  -i inputLig, -input inputLig
                        Single input ligand structure file. Must contain atoms
                        specified by -core_asl option. If more than one ligand
                        is supplied, the first will be used. (Required.)
  -c inputCores, -cores inputCores
                        Input file of compounds (mae, sd, or sdf) to use as
                        potential new cores. (Required.)
  -core_asl asl         ASL specifying core atoms in input ligand. e.g.
                        "atom.num 11, 12, 13, 14, 15, 16, 17" (Required.)
  -f, -flex             Treat cores as flexible during shape_screen screening.
                        Default is to treat cores rigidly.
  -xvol <xvolFile>      Apply excluded volumes during the shape_screen search
                        for new cores. Run "shape_screen -h" for a description
                        of approved xvol file types.
  -at ["none","mmod","element","pharm"]
                        Use atom types during shape_screen alignment. Default
                        = element.
  -attachment_weight float
                        Atom weight during shape_screen search for atoms in
                        the core that were attachment bonds in the input
                        ligand. Default = 1.0
  -default_weight float
                        Atom weight during shape_screen search for atoms in
                        the core that were NOT attachment bonds in the input
                        ligand. Default = 0.2
  -a float, -angle float
                        Maximum angle deviation in degrees between two
                        comparison X-Y bonds to make a new bond (default=15.0)
  -d float, -distance float
                        Maximum distance between atoms for bond joining
                        (default = 1.0)
  -core_restrict <property>
                        Restrict core attachment bonds to those with this
                        property defined. The property must be a positive
                        integer on the terminal attachment atom which
                        specifies the other atom number in the attachment
                        bond. Use "-core_restrict i_cgch_from_atom" to use
                        definition from CombiGlide.
  -m, -minimize         Minimize resulting structures
  -j jobname, -jobname jobname
                        Provide job name. If not provided, jobname will be
                        based on the input filename.
  -o output             Output structure file with new cores. If not provided,
                        output filename will be based on the input filename
  -q QUERY_OPTS, -query_options QUERY_OPTS
                        SQL query options for the select query (if using
                        .sqlite file).
  -s minimum_shapesim, -shapesim minimum_shapesim
                        Set the minimum ShapeSim score for potential
                        isosteres.
  -WAIT                 When using Schrodinger job control (the default),
                        don't return from the command-line invocation until
                        the job is complete. Default is to return as soon as
                        the job has been launched by the job-control layer.
  -HOST HOST            Host for execution of job or driver (if there are
                        subjobs). If not specified, then the local host is
                        used. If there are subjobs and no -SUBHOST option is
                        specified, then the subjobs, as well as the driver,
                        are executed on this host. This option must be
                        supplied on the command line, not in an argument file.
  -NOJOBID              Run immediately and locally, without Schrodinger job-
                        control. Cannot be called from the commandline with
                        -HOST, or used when there are subjobs.