ChemmineR: Cheminformatics Toolkit for R

atomsubset

R Documentation

Subset SDF/SDFset Objects by Atom Index to Obtain Substructure

Description

Function to obtain a substructure from SDF/SDFset objects by providing a row index for the atom block in an SDF referencing the atoms of interest. The function subsets both the atom and bond block(s) accordingly.

Usage

atomsubset(x, atomrows, type="new", datablock = FALSE)

Arguments

`x`	object of class `SDFset` or `SDF`
`atomrows`	The argument `atomrows` can be assigned a numeric index referencing the atoms in the atom block of `x`. If `x` is of class `SDF`, the index needs to be provided as `vector`. If `x` is of class `SDFset`, the same number of index vectors as molecules stored in `x` need to be passed on in a list with component names identical to the component (molecule) names stored in `x`.
`type`	The argument `type="new"` assigns new atom numbers to a subsetted SDF, while `type="old"` maintains the numbering of the source SDF.
`datablock`	By default the data block(s) in `SDF/SDFset` objects are removed after atom subsetting. The setting `datablock=TRUE` will maintain the data block information in the subsetted result.

Details

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Value

object of class SDF or SDFset

Author(s)

Thomas Girke

References

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Examples

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

## Subset one or more molecules with atom index(es) to obtain substructure(s)
atomsubset(sdfset[[1]], atomrows=1:18) 
indexlist <- list(1:18, 1:12)
names(indexlist) <- cid(sdfset[1:2])
atomsubset(sdfset[1:2], atomrows=indexlist)

girke-lab/ChemmineR documentation built on July 28, 2023, 10:36 a.m.