Format Interconversions

The sdf2smiles and smiles2sdf functions provide format interconversion between SMILES strings (Simplified Molecular Input Line Entry Specification) and SDFset containers.

Convert an SDFset container to a SMILES character string:

 data(sdfsample);
 sdfset <- sdfsample[1] 
 smiles <- sdf2smiles(sdfset) 
 smiles 

Convert a SMILES character string to an SDFset container:

 sdf <- smiles2sdf("CC(=O)OC1=CC=CC=C1C(=O)O")
 view(sdf) 

When the ChemineOB package is installed these conversions are performed with the OpenBabel Open Source Chemistry Toolbox. Otherwise the functions will fall back to using the ChemMine Tools web service for this operation. The latter will require internet connectivity and is limited to only the first compound given. ChemmineOB provides access to the compound format conversion functions of OpenBabel. Currently, over 160 formats are supported by OpenBabel. The functions convertFormat and convertFormatFile can be used to convert files or strings between any two formats supported by OpenBabel. For example, to convert a SMILES string to an SDF string, one can use the convertFormat function.

 sdfStr <- convertFormat("SMI","SDF","CC(=O)OC1=CC=CC=C1C(=O)O_name") 

This will return the given compound as an SDF formatted string. 2D coordinates are also computed and included in the resulting SDF string.

To convert a file with compounds encoded in one format to another format, the convertFormatFile function can be used instead.

 convertFormatFile("SMI","SDF","test.smiles","test.sdf") 

To see the whole list of file formats supported by OpenBabel, one can run from the command-line “obabel -L formats”.