atomcount: Molecular property functions

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Molecular property functions

Description

Functions to compute molecular properties: weight, formula, atom frequencies, etc.

Usage

atomcount(x, addH = FALSE, ...)

atomcountMA(x, ...)

MW(x, mw=atomprop, ...)

MF(x, ...)

Arguments

x	object of class SDFset or SDF
mw	data.frame with atomic weights; imported by default with data(atomprop); supports custom data sets
addH	'addH = TRUE' should be passed on to any of these function to add hydrogens that are often not specified in SD files
...	Arguments to be passed to/from other methods.

Details

...

Value

named vector	MW and MF
list	atomcount
matrix	atomcountMA

Author(s)

Thomas Girke

References

Standard atomic weights (2005) from: http://iupac.org/publications/pac/78/11/2051/

See Also

Functions: datablock, datablocktag

Examples

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

## Compute properties; to consider missing hydrogens, set 'addH = TRUE'
MW(sdfset[1:4], addH = FALSE)
MF(sdfset[1:4], addH = FALSE)
atomcount(sdfset[1:4], addH = FALSE)
propma <- atomcountMA(sdfset[1:4], addH = FALSE)
boxplot(propma, main="Atom Frequency")

## Example for injecting a custom matrix/data frame into the data block of an
## SDFset and then writing it to an SD file
props <- data.frame(MF=MF(sdfset), MW=MW(sdfset), atomcountMA(sdfset))
datablock(sdfset) <- props
view(sdfset[1:4])
# write.SDF(sdfset[1:4], file="sub.sdf", sig=TRUE, cid=TRUE)

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