Command Line Usage

Metabolizer command string contains the following elements:

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


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.


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.


Metabolizer's command line help

Main parameters are required ("input file names")
Usage: [options] input file names
-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
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
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
-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


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