sdf.subset: Subset a SDF and return SDF segements for selected compounds

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Subset a SDF and return SDF segements for selected compounds

Description

'sdf.subset' will take a descriptor database generated by 'cmp.parse' and an array of indices, and return an SDF string consisting of SDFs for compounds corresponding to that list of indices. The returned value is a character string.

Usage

sdf.subset(db, cmps)

Arguments

db	The database generated by 'cmp.parse'
cmps	An array of indecies that correspond to a set of selected compounds from the database

Details

'sdf.subset' depends on information embedded in the descriptor database returned by 'cmp.parse'. It also relies on the availability of the original SDF where the database has been generated from. Basically, when 'cmp.parse' parses the original SDF file, it will store the path of that SDF file as well as offset information for SDF segment in that file. Therefore, if the SDF file has been changed or deleted, 'sdf.subset' cannot function properly.

The result SDF will also have names added to compounds if they are not present in the original SDF.

Value

Return a character string whose content is the concatenation of SDFs for the selected compounds.

See Also

cmp.parse, sdf.visualize

Examples

## Note: this functionality has become obsolete since the introduction of the 
## 'SDFset' and 'apset' S4 classes.

# load sample database from web
# db <- cmp.parse("http://bioweb.ucr.edu/ChemMineV2/static/example_db.sdf")
# select SDF for 1st and 2nd compound in that SDF
# sdf_segments <- sdf.subset(db, c(1, 2))
# now sdf_segments containt the 2 SDFs for those 2 compounds

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