If the command line parameters --reactant-id-tag and --product-id-tag are specified, then an ID is generated and stored for each product in the specified SDF/MRV data field. If only one of them is specified, then both reactant and product IDs are set to this value. If each reactant/product has its ID in a different tag, then specify them in a comma-separated list in the reactant/product order of the reaction. It is necessary to specify the reaction ID as well, either directly in the --reaction-id parameter, or else in form of a RDF/MRV data field of the reaction file where the field name is given in the --reaction-id-tag parameter.

The --generate-id command line option helps in generating the product ID. If the --generate-id parameter is specified and --reactant-id-tag parameter is omitted, then the reactant ID is generated from the filename or reactant string. If the --product-id-tag is omitted while --generate-id is specified, then the product ID is written to SDF property field named Synthesis Code. Synthesis Code and Name property fields are used to read the reaction ID from if both of the --reaction-id and --reaction-id-tag parameters are omitted.