rcdk (version 3.4.7.1)

parse.smiles: Parse a Vector of SMILES Strings

Description

This function parses a vector of SMILES strings to generate a list of IAtomContainer objects. Note that the resultant molecule will not have any 2D or 3D coordinates.

Note that the molecules obtained from this method will not have any aromaticity perception, atom typing or isotopic configuration done on them. This is in contrast to the load.molecules method. Thus, you should perform these steps manually on the molecules.

Usage

parse.smiles(smiles, kekulise=TRUE)

Arguments

smiles

A SMILES string

kekulise

If set to FALSE disables electron checking and allows for parsing of incorrect SMILES. If a SMILES does not parse by default, try setting this to FALSE - though the resultant molecule may not have consistent bonding. As an example, c4ccc2c(cc1=Nc3ncccc3(Cn12))c4 will not be parsed by default because it is missing a nitrogen. With this argument set to FALSE it will parse succesfully, but this is a hack to handle an incorrect SMILES

Value

A list of jobjRefs to their corresponding CDK IAtomContainer objects. If a SMILES string could not be parsed, NA is returned instead.

See Also

load.molecules, get.smiles, get.smiles.parser, view.molecule.2d, do.aromaticity, do.typing, do.isotopes

Examples

# NOT RUN {
smiles <- c('CCC', 'c1ccccc1', 'C(C)(C=O)C(CCNC)C1CC1C(=O)')
mol <- parse.smiles(smiles[1])
mols <- parse.smiles(smiles)
# }