ChemmineR integrates now a subset of cheminformatics
functionalities implemented in the OpenBabel C++ library (Noel M O’Boyle et al., 2008; Y. Cao et al., 2008). These
utilities can be accessed by installing the
package and the OpenBabel software itself.
will automatically detect the availability of
ChemmineOB and make use of the additional utilities.
The following lists the functions and methods that make use of
OpenBabel. References are included to locate the sections in the manual
where the utility and usage of these functions is described.
Structure format interconversions (see Section Format Inter-Conversions)
smiles2sdf: converts from SMILES to SDF object
sdf2smiles: converts from SDF to SMILES object
convertFormat: converts strings between two formats
convertFormatFile: converts files between two formats. This function can be used to enable ChemmineR to read in any
format supported by Open Babel. For example, if you had an SML file you could do:
propOB: generates several compound properties. See the man page for a current list of properties computed.
fingerprintOB: generates fingerprints for compounds. The fingerprint name can be anything supported by OpenBabel. See the man page
for a current list.
smartsSearchOB: find matches of SMARTS patterns in compounds
exactMassOB: Compute the monoisotopic (exact) mass of a set of compounds
regenerateCoords: Re-compute the 2D coordinates of a compound using Open Babel. This can sometimes
improve the quality of the compounds plot. See also the
regenCoords option of the plot function.
generate3DCoords: Generate 3D coordinates for compounds with only 2D coordinates.
canonicalize: Compute a canonicalized atom numbering. This allows compounds with the same molecular
structure but different atom numberings to be compared properly.
canonicalNumbering: Return a mapping from the original atom numbering to the
canonical atom number.