rcdk: smiles.flavors – R documentation

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smiles.flavors

Generate flag for customizing SMILES generation.

Description

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

Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

References

CDK documentation

Examples

m <- parse.smiles('C1C=CCC1N(C)c1ccccc1')[[1]]
get.smiles(m)
get.smiles(m, smiles.flavors(c('Generic','UseAromaticSymbols')))

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")))
get.smiles(m,flavor = smiles.flavors(c("CxSmiles","UseAromaticSymbols")))

rcdk

Interface to the 'CDK' Libraries

v3.5.0

LGPL

Authors

Rajarshi Guha [aut, cph], Zachary Charlop-Powers [cre], Emma Schymanski [ctb]

Initial release

2020-03-06