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.

 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