smiles2sdf: Convert SMILES ('character') to 'SDFset'

In ChemmineR: Cheminformatics Toolkit for R

Description

Accepts a named vector or SMIset of SMILES (Simplified Molecular Input Line Entry Specification) strings and returns its equivalent as an SDFset container.

This function runs in two modes. If ChemmineOB is available then it will use OpenBabel to convert all the given smiles into an SDFset with 2D coordinates. Otherwise the compound is submitted to the ChemMine Tools web service for conversion with the Open Babel Open Source Chemistry Toolbox. In this case only the first element will be used since this is a very slow operation.

Usage

	smiles2sdf(smiles)

Arguments

smiles

A named vector of SMILES strings. The names will be used to name the SDF objects.

Value

SDFset

for details see ?"SDFset-class"

Author(s)

Tyler Backman, Kevin Horan

References

Chemmine web service: http://chemmine.ucr.edu

Open Babel: http://openbabel.org

SMILES Format: http://en.wikipedia.org/wiki/Chemical_file_format#SMILES

Examples

## Not run: 
## convert to sdf
data(smisample)
(sdf <- smiles2sdf(smisample[1:4]))

## End(Not run)

Example output

An instance of "SDFset" with 4 molecules

ChemmineR documentation built on Feb. 28, 2021, 2:02 a.m.