canonicalNumbering_OB: Canonical Numbering OB

In ChemmineOB: R interface to a subset of OpenBabel functionalities

Description

Computes a re-arrangement required to transform the atom numbering of the given compound into the canonical atom numbering. This function uses the OBGraphSym and CanonicalLabels classes of Open Babel to compute the re-arrangement.

Usage

canonicalNumbering_OB(obmolRefs)

Arguments

obmolRefs

A list of OBMol references ( of class '_p_OpenBabel__OBMol') representing the compounds.

Value

A list of vectors of index values. Each item in the list corresponds to one of the given compounds. The values of a list item are the re-arrangement of the atoms. For example, if the value in item 1, column 1 is 25, that means that atom number 1 in the original compound should become atom number 25 in the canonical version of that compound.

Author(s)

Kevin Horan

References

http://openbabel.org/api/2.3/canonical_code_algorithm.shtml

See Also

convertFormat to return a new compound in the canonical format.

Examples

## Not run: 
   library(ChemmineR)
   data(sdfsample)
   labels = canonicalNumbering_OB(obmol(sdfsample[[1]]))

## End(Not run)

ChemmineOB documentation built on April 13, 2021, 6:03 p.m.