bonds: Bonds, charges and missing hydrogens

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Bonds, charges and missing hydrogens

Description

Returns information about bonds, charges and missing hydrogens in SDF and SDFset objects.

Usage

bonds(x, type = "bonds")

Arguments

x	SDF or SDFset containers
type	If type="bonds" (default), a data.frame is returned with columns: atom (atom labels), Nbondcount (observed bond count), Nbondrule (bond count according to position in periodic table) and charge (charge of each atom). If type="charge", all charged atoms are returned and if type="addNH", the number of missing hydrogens are returned for each molecule.

Details

It is used by many other functions (e.g. MW, MF, atomcount, atomcuntMA and plot) to correct for missing hydrogens that are often not specified in SD files.

Value

If x is of class SDF, then a single data.frame or vector is returned. If x is of class SDFset, then a list of data.frames or vecotors is returned that has the same length and order as x.

Author(s)

Thomas Girke

References

...

See Also

Functions: conMA

Class: SDF and SDFset

Examples

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

## Returns data frames with bonds and charges 
bonds(sdfset[1:2], type="bonds")

## Returns charged atoms in each molecule
bonds(sdfset[1:2], type="charge")

## Returns the number of missing hydrogens in each molecule
bonds(sdfset[1:2], type="addNH")

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