atomsubset: Subset SDF/SDFset Objects by Atom Index to Obtain...

In ChemmineR: Cheminformatics Toolkit for R

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

...

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)

Example output

An instance of "SDF"

<<header>>
                            Molecule_Name 
                                 "650001" 
                                   Source 
                 "  -OEChem-07071010512D" 
                                  Comment 
                                       "" 
                              Counts_Line 
" 18 12  0     0  0  0  0  0  0999 V2000" 

<<atomblock>>
          C1     C2  C3  C5  C6  C7  C8  C9 C10 C11 C12 C13 C14 C15 C16
O_1   7.0468 0.0839   0   0   0   0   0   0   0   0   0   0   0   0   0
O_2  12.2708 1.0492   0   0   0   0   0   0   0   0   0   0   0   0   0
...      ...    ... ... ... ... ... ... ... ... ... ... ... ... ... ...
C_17  8.7788 0.0839   0   0   0   0   0   0   0   0   0   0   0   0   0
C_18  9.6448 1.5839   0   0   0   0   0   0   0   0   0   0   0   0   0

<<bondblock>>
     C1  C2  C3  C4  C5  C6  C7
1     1  16   2   0   0   0   0
2     6  10   1   0   0   0   0
... ... ... ... ... ... ... ...
11   14  15   1   0   0   0   0
12   16  17   1   0   0   0   0

<<datablock>> (0 data items)
character(0)
An instance of "SDFset" with 2 molecules

ChemmineR documentation built on Feb. 28, 2021, 2:02 a.m.