getMolecule: Create Rcdk molecule from SMILES

In RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Generates a Rcdk molecule object from SMILES code, which is fully typed and usable (in contrast to the built-in parse.smiles).

Usage

getMolecule(smiles)

Arguments

smiles

The SMILES code of the compound.

Details

NOTE: As of today (2012-03-16), Rcdk discards stereochemistry when loading the SMILES code! Therefore, do not trust this function blindly, e.g. don't generate InChI keys from the result. It is, however, useful if you want to compute the mass (or something else) with Rcdk.

Value

A Rcdk IAtomContainer reference.

Author(s)

Michael Stravs

See Also

parse.smiles

Examples

# Lindane:
getMolecule("C1(C(C(C(C(C1Cl)Cl)Cl)Cl)Cl)Cl")
# Benzene:
getMolecule("C1=CC=CC=C1")

RMassBank documentation built on Nov. 8, 2020, 6:06 p.m.