atomsubset {ChemmineR} | 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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### See Also

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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)

[Package ChemmineR version 3.40.0 Index]