validSDF {ChemmineR} | R Documentation

## Validity check of SDFset

### Description

Performs validity check of SDFs stored in `SDFset` objects. Currently, the function tests whether the atom block and the bond block in each `SDF` component of an `SDFset` have at least `Nabcol` and `Nbbcol` columns (default is 3 for both). In additions, it tests for the presence of NA values in the atom and bond blocks. The function returns a logical vector with `TRUE` values for valid compounds and `FALSE` values for invalid ones.

### Usage

    validSDF(x, Nabcol = 3, Nbbcol = 3, logic = "&", checkNA=TRUE)

### Arguments

`x` | `x` object of class `SDFset`
`Nabcol` | minimum number of columns in atom block
`Nbbcol` | minimum number of columns in bond block
`logic` | logical connection (& or |) among Nabcol and Nbbcol cutoffs
`checkNA` | checks for NA values in atom and bond blocks

### Details

The function is important to remove invalid compounds from `SDFset` containers.

### Value

`logical` vector of length `x` with `TRUE` for valid compounds and `FALSE` for invalid compounds.

### Author(s)

Thomas Girke

### References

...

### See Also

Functions: `read.SDFset`

### Examples

    ## SDFset instance
    data(sdfsample)
    sdfset <- sdfsample

    ## Detect and remove invalid SDFs in SDFset.
    valid <- validSDF(sdfset)
    which(!valid) # Returns index for invalid SDFs
    sdfset <- sdfset[valid] # Returns only valid SDFs.

[Package ChemmineR version 3.32.1 Index]