By default, the program exits when an error occurs during reactant processing. If the command line parameter --ignore-error (-g) is specified, then errors will not stop the processing: the error is written to the console, the erroneous molecule is skipped, and the reactant processing will continue.
Reactant standardization can be specified in the --standardize, while product standardization in the --standardize-products option. The standardization configuration is given either directly in a simple action string or as a configuration XML. Each reactant and each product can be standardized separately using standardizer task groups: group containing the first reactant can be referred as "reactant1", group containing the second reactant as "reactant2", etc.
Reactant standardization configuration can be given also in the STANDARDIZATION RDF/MRV tag of the reaction file. Standardization is optional. (Read Standardizer documentation for more information.)
If the command line parameter --transform is specified, then the original input molecule is modified according to the reaction equation. The reaction equation is fused to form a 1-reactant 1-product reaction. Instead of producing different products for each reaction center, all reaction centers are processed at the same time. Atom coordinates are preserved where possible. This mode is equivalent to a single reaction step in Standardizer. Reaction rules cannot be applied in this case.
If the command line parameter --use-cache is specified then the results of substructure search and plugin calculation are stored for later usage. The --use-cache mode increases efficiency if the rule list contains the same plugin calculation for the same atom/molecule more than once, and/or there are multiple reactants since otherwise processing all combination of the reaction centers would result in substructure search repetitions.