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Generate flag for customizing SMILES generation.

Source: R/smiles.R
smiles.flavors.Rd

The CDK supports a variety of customizations for SMILES generation including the use of lower case symbols for aromatic compounds to the use of the ChemAxon CxSmiles format. Each 'flavor' is represented by an integer and multiple customizations are bitwise OR'ed. This method accepts the names of one or more customizations and returns the bitwise OR of them. See CDK documentation for the list of flavors and what they mean.

Usage

smiles.flavors(flavors = c("Generic"))

Arguments

flavors

A character vector of flavors. The default is Generic (output non-canonical SMILES without stereochemistry, atomic masses). Possible values are

  • Absolute

  • AtomAtomMap

  • AtomicMass

  • AtomicMassStrict

  • Canonical

  • Cx2dCoordinates

  • Cx3dCoordinates

  • CxAtomLabel

  • CxAtomValue

  • CxCoordinates

  • CxFragmentGroup

  • CxMulticenter

  • CxPolymer

  • CxRadical

  • CxSmiles

  • CxSmilesWithCoords

  • Default

  • Generic

  • InChILabelling

  • Isomeric

  • Stereo

  • StereoCisTrans

  • StereoExTetrahedral

  • StereoTetrahedral

  • Unique

  • UniversalSmiles

  • UseAromaticSymbols

Value

A numeric representing the bitwise `OR`` of the specified flavors

References

CDK documentation

See also

get.smiles

Author

Rajarshi Guha rajarshi.guha@gmail.com

Examples

m <- parse.smiles('C1C=CCC1N(C)c1ccccc1')[[1]]
get.smiles(m)
#> [1] "C1C=CCC1N(C)C2=CC=CC=C2"
get.smiles(m, smiles.flavors(c('Generic','UseAromaticSymbols')))
#> [1] "C1C=CCC1N(C)c2ccccc2"

m <- parse.smiles("OS(=O)(=O)c1ccc(cc1)C(CC)CC |Sg:n:13:m:ht,Sg:n:11:n:ht|")[[1]]
get.smiles(m,flavor = smiles.flavors(c("CxSmiles")))
#> [1] "OS(=O)(=O)C1=CC=C(C=C1)C(CC)CC |Sg:n:11:n:ht,Sg:n:13:m:ht|"
get.smiles(m,flavor = smiles.flavors(c("CxSmiles","UseAromaticSymbols")))
#> [1] "OS(=O)(=O)c1ccc(cc1)C(CC)CC |Sg:n:11:n:ht,Sg:n:13:m:ht|"