Options - react CLI

General options:
-h, --help this help message-s, --reverse reverse reaction
-z, --transform transform mode:
creates 1-reactant 1-product
reaction to process all reaction
centers at the same time
(deprecated, use Standardizer)-u, --use-cache cache search/plugin results-l, --single process unambiguous reactions only
(with each reactant having a single
active reaction site)-n, --no-rules <type> ignore reaction rules,
depending on type:
r - ignore reactivity rule
s - ignore selectivity rule
t - ignore selectivity tolerance
rs - ignore both reactivity and
selectivity rules
rt - ignore reactivity rule and
selectivity tolerance-S, --standardize <file/string> standardize reactants according to
configuration-T, --standardize-products <file/string> standardize products according to
configuration-m, --mode <mode> processing mode,
valid modes are:
comb for combinatorial,
seq for sequential
(default: seq)-X, --ratio <ratio> ratio of the reactants (e.g. 1:4:4)
--list-reaction-names <filename>
list reaction names
--test-examples <filename> test reaction examples

Input options:-N, --reaction-name <name> reaction name-i, --reaction-id <id> reaction ID-I, --reaction-id-tag <id-tag> RDF/MRV tag storing the reaction ID-R, --reactant-id-tag <id-tag(s)> SDF/MRV tag storing the reactant IDs
a comma-separated list of tags
if it differs for each reactant-P, --product-id-tag <id-tag(s)> SDF/MRV tag storing the product IDs
a comma-separated list of tags
if it differs for each product-G, --generate-id generate ID
--copy-reactant-properties copy reactant properties to output:
ID->R1ID,LOGP->R1LOGP;ID->R2ID... is the
comma-separated list of property names,
semicolon separates reactants;
use # to copy all properties
--generate-properties creates pattern-based properties on output

propertyName - the name of the property in the output file
text - may contain anything except "#{" and ..
moleculeID - a text that has a numeric postfix optionally:
Non-numeric postfix - property of the reaction itself
Numeric postfix - index of a reactant (indexing starts from 1)
propertyID - a property of the input molecule
Examples of pattern:
"logP=logP values of reactants: 1st:#{r1.LOGP}, 2nd:#{r2.LOGP}"
"id=#{Reaction.ID}(#{mol1.ID}, #{mol2.ID}, #{mol3.ID})"
"corp_ID=#{R.ID}(#{R1.corp_ID}, #{R2.corp_ID}, #{R3.corp_ID})" -r, --reaction <filepath/string> reaction file or SMARTS string
optionally with reaction rules-A, --skip-reaction-mapping-check skip reaction mapping check
(default: check reaction mapping)-g, --ignore-error continue with next molecule on error

Output options:-f, --format <format> output file format (default: smiles)-o, --output <filepath> output file (default: standard output)-p, --pieces <pieces> number of product lists to be returned
(default: all)-w, --allow-duplicates allow product list duplicates for
efficiency (default: no duplicates)-t, --type <output-type> output type
(not available in transform mode):
product for product array output,
reaction for reaction molecule output,
fused for fused reaction molecule output
(default: product)-M, --map-result <mapping-style> output reaction mapping style:
changing for ChemAxon style
(map all changing atoms)
matching for Daylight style
(map all matching atoms)
complete for complete mapping
(map all atoms)
(default: none)-x, --extract <i1,i2,...> return only the specified products:
i1,i2,... is the comma-separated
list of 1-based product indexes
according to reaction equation-k, --remove-duplicate-refs remove duplicate product references
within product lists
--show-unsuccessful-reactions show unsuccessful reactions
(reactions which do not result products)
-v, --verbose verbose output with time results
--log <filepath> write log messages to file
default: write log to system error
--loglevel <level> sets the log level
levels: [severe|warning|info|off]