Options - react CLI

General options:

 -h, --help this help message[-s, --reverse](#src-1803411-options-reactcli-cmdreverse) 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](#src-1803411-options-reactcli-cmdcache) cache search/plugin results[-l, --single](#src-1803411-options-reactcli-cmdsingle) process unambiguous reactions only

 (with each reactant having a single

 active reaction site)[-n, --no-rules <type>](#src-1803411-options-reactcli-cmdrules) 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>](#src-1803411-options-reactcli-cmdstandardize) standardize reactants according to

 configuration[-T, --standardize-products <file/string>](#src-1803411-options-reactcli-cmdstandardize) standardize products according to

 configuration[-m, --mode <mode>](#src-1803411-options-reactcli-cmdmode) processing mode,

 valid modes are:

 comb for combinatorial,

 seq for sequential

 (default: seq)[-X, --ratio <ratio>](reactor_ratio-react-cli.md) 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>](#src-1803411-options-reactcli-cmdreaction) reaction name[-i, --reaction-id <id>](#src-1803411-options-reactcli-cmdreaction) reaction ID[-I, --reaction-id-tag <id-tag>](#src-1803411-options-reactcli-cmdreaction) RDF/MRV tag storing the reaction ID[-R, --reactant-id-tag <id-tag(s)>](#src-1803411-options-reactcli-cmdcid) 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)>](#src-1803411-options-reactcli-cmdcid) SDF/MRV tag storing the product IDs

 a comma-separated list of tags

 if it differs for each product[-G, --generate-id](#src-1803411-options-reactcli-cmdgenerateid) 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

 Pattern:

 "<propertyName>=[<text>*#{<moleculeID>.<propertyID>}]*<text>*"

 Where:

 propertyName - the name of the property in the output file

 text - may contain anything except "/display/lts-mercury/reactor_options-react-cli.md#{" 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>](#src-1803411-options-reactcli-cmdreaction) reaction file or SMARTS string

 optionally with reaction rules[-A, --skip-reaction-mapping-check](#src-1803411-options-reactcli-cmdskipreactionmapping) skip reaction mapping check

 (default: check reaction mapping)[-g, --ignore-error](#src-1803411-options-reactcli-cmderror) continue with next molecule on error

Output options:[-f, --format <format>](#src-1803411-options-reactcli-cmdformat) output file format (default: smiles)[-o, --output <filepath>](#src-1803411-options-reactcli-cmdoutput) output file (default: standard output)[-p, --pieces <pieces>](#src-1803411-options-reactcli-cmdpieces) number of product lists to be returned

 (default: all)[-w, --allow-duplicates](#src-1803411-options-reactcli-cmdunique) allow product list duplicates for

 efficiency (default: no duplicates)[-t, --type <output-type>](#src-1803411-options-reactcli-cmdtype) 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>](#src-1803411-options-reactcli-cmdmapresult) 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,...>](#src-1803411-options-reactcli-cmdextract) 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](#src-1803411-options-reactcli-cmdremove) 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]