rcdk: get.smiles – R documentation

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get.smiles

Generate a SMILES representation of a molecule.

Description

The function will generate a SMILES representation of an 'IAtomContainer' object. The default parameters of the CDK SMILES generator are used. This can mean that for large ring systems the method may fail. See CDK Javadocs for more information

Usage

get.smiles(molecule, flavor = smiles.flavors(c("Generic")), smigen = NULL)

Arguments

`molecule`	The molecule to query. Should be a 'jobjRef' representing an 'IAtomContainer'
`flavor`	The type of SMILES to generate. See `smiles.flavors`. Default is 'Generic' SMILES
`smigen`	A pre-existing SMILES generator object. By default, a new one is created from the specified flavor

Value

A character string containing the generated SMILES

Author(s)

Rajarshi Guha (rajarshi.guha@gmail.com)

References

SmilesGenerator

Examples

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