Generate a SMILES representation of a molecule.

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

References

SmilesGenerator

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"