groups: Enumeration of Functional Groups and Atom Neighbors
In girke-lab/ChemmineR-git-svn-bridge: Cheminformatics Toolkit for R

Description Usage Arguments Details Value Author(s) References See Also Examples

Returns frequency information of functional groups in molecules provided as SDF or SDFset objects. Alternatively, the function can return for each atom its atom/bond neighbor information.

1	groups(x, groups = "fctgroup", type = "countMA")

`x`	`SDF` or `SDFset` containers
`groups`	if `groups="fctgroup"`, frequencies of functional groups are returned; if `groups="neighbors"`, atom/bond neighbor information is returned.
`type`	if `type="all"`, then the complete neighbor information is generated for each atom in a molecule; if `type="count"`, the neighbors are enumerated in a list and if `type="countMA"`, then the counts of atom neighbors or functional groups are returned in a frequency matrix.

At this point this function is in an experimental stage.

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Thomas Girke

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## Instances of SDFset class
data(sdfsample)
sdfset <- sdfsample

## Enumerate functional groups
groups(sdfset[1:20], groups="fctgroup", type="countMA") 

## Report atom/bond neighbors
groups(sdfset[1:4], groups="neighbors", type="countMA")
groups(sdfset[1:4], groups="neighbors", type="count")
groups(sdfset[1:4], groups="neighbors", type="all")