Bond matrices provide an efficient data structure for many basic
computations on small molecules. The function conMA
creates this data structure from SDF and
SDFset objects. The resulting bond matrix contains the
atom labels in the row/column titles and the bond types in the data
part. The labels are defined as follows: 0 is no connection, 1 is a
single bond, 2 is a double bond and 3 is a triple bond.
conMA(sdfset[1:2],
exclude=c("H")) # Create bond matrix for first two molecules in sdfset
conMA(sdfset[[1]], exclude=c("H")) # Return bond matrix for first molecule
plot(sdfset[1], atomnum = TRUE, noHbonds=FALSE , no_print_atoms = "", atomcex=0.8) # Plot its structure with atom numbering
rowSums(conMA(sdfset[[1]], exclude=c("H"))) # Return number of non-H bonds for each atom