conMA: Bond Matrices

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Bond Matrices

Description

Creates a bond matrix from SDF and SDFset objects. The matrix contains the atom labels in the row and column titles and the bond types are given in the data part as follows: 0 is no connection, 1 is a single bond, 2 is a double bond and 3 is a triple bond.

Usage

conMA(x, exclude = "none")

Arguments

x	SDF or SDFset containers
exclude	if exclude="none", then all atoms will be considered in the resulting connection table; if exclude=c("H"), then the H atoms will be excluded. Any number of atom labels to be excluded can be passed on to this argument in form of a character vector.

Details

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Value

If x is of class SDF, then a single bond matrix is returned. If x is of class SDFset, then a list of matrices is returned that has the same length as x.

Author(s)

Thomas Girke

References

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See Also

Functions: bonds

Class: SDF and SDFset

Examples

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

## Create bond matrix for first two molecules in sdfset
conMA(sdfset[1:2], exclude=c("H"))

## Return bond matrix for first molecule and plot its structure with atom numbering
conMA(sdfset[[1]], exclude=c("H"))
plot(sdfset[1], atomnum = TRUE, noHbonds=FALSE , no_print_atoms = "", atomcex=0.8)

## Return number of non-H bonds for each atom 
rowSums(conMA(sdfset[[1]], exclude=c("H")))

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