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>](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/docs/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]