rcdk (version 3.4.7.2)

get.smiles: Get the SMILES for 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

A Java object of class IAtomContainer

flavor

Customizations for SMILES generation. See smiles.flavors

smigen

An instance of SmilesGenerator, which can be useful if you are generating SMILES for a large number of molecules

Value

An R character object containing the SMILES

See Also

smiles.flavors, parse.smiles

Examples

# NOT RUN {
m <- parse.smiles('C1C=CCC1N(C)c1ccccc1')[[1]]
get.smiles(m)
get.smiles(m, smiles.flavors(c('Generic','UseAromaticSymbols')))
# }