Command Line Usage

Metabolizer command string contains the following elements: 

   metabolize [<input files>] [<options>]

Input

Most molecular file formats are accepted ( Marvin Documents (MRV), MDL molfile, SDfile, RXNfile, RDfile, SMILES, etc.).

The input is either specified in input file(s), or else in input string(s), usually in SMILES format.

Output

Metabolizer writes output molecules in the format specified by the -f option (the default format is 'smiles'). If the -o is omitted, results are written to the standard output.

Options

Metabolizer's command line help

Main parameters are required ("input file names")
Usage:  [options] input file names
  Options:
    -ce, --exclude-condition
       metabolites fulfilling this Chemical Terms expression are ignored
    -x, --exhaustive
       exhaustive enumeration method producing minor metabolites as well
       Default: false
    -lf, --fast_mode-limit
       when not in exhaustive mode, metabolites below this relative formation,
       are ignored, value 0.1 means 10% of the highest rate from the same parent
       compound
       Default: 0.1
    -from, --from-substrate
       enumeration starts with the substrate having this identifier
    -lg, --generation-limit
       maximum number of generations
       Default: 1
    -g, --global
       return metabolites sorted by global accumulation order (likelihood)
       Default: false
    -ga, --global-accummulation-limit
       The minimum global accumulation of the metabolites to return, zero or
       negative value means no filtering
       Default: -1.0
    -gn, --global-number-limit
       the maximum number of global metabolites to return, zero means all
       Default: 0
    -h, --help
       prints this help message
       Default: false
    -l, --likely
       metabolites with higher global accumulation are considered likely
       Default: 0.1
    -m, --multi
       multiple substrates outputs to multiple files
       Default: false
    -o, --output
       output file name, or directory name in case of multiple substrates
    -f, --output-format
       output file format
       Default: smiles:T*
    -t, --output-type
       output type, molecule for metabolite output, reaction for
       biotransformation output
       Default: molecule
    -lp, --population-limit
       maximum number of metabolites, when reached further generations are not
       enumerated
       Default: 0
    -rid, --reaction-id-field
       the name of the field containing the unique reaction identifier
       Default: Synthesis Code
    -r, --reactions
       biotransformation library file name, ChemAxon's human phase one library
       is used if not specified
    -s, --scale
       the sensitivity of calculations for rank difference
       Default: 7
    -sid, --substrate-id-field
       the name of the field containing the unique substrate identifier
       Default: Synthesis Code
    -ct, --termination-condition
       metabolites fulfilling this Chemical Terms expression are not enumerated
       further
    -to, --to-substrate
       enumeration stops after the substrate having this identifier
    -u, --unlikely
       metabolites with lower global accumulation value are considered unlikely
       Default: 0.001
    -v, --verbose
       verbose mode printing detailed log and time results on the console
       Default: false

Examples

Enumerate the direct human metabolites of toluene
metabolize Cc1ccccc1 -x

Fast enumerate three generations of metabolites of toluene calculating global indicators and sorted by likelihood
metabolize Cc1ccccc1 -lg 3 -g

Enumerate three generations of metabolites of the substrate in a molfile exhaustively to an SDfile sorted by likelihood and displaying progress information
metabolize in.mol -x -g 3 -g -f sdf -o out.sdf -v