The function bonds returns information about the number of bonds, charges and missing hydrogens in SDF and SDFset objects. 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.

 bonds(sdfset[[1]], type="bonds")[1:4,]
##   atom Nbondcount Nbondrule charge
## 1    O          2         2      0
## 2    O          2         2      0
## 3    O          2         2      0
## 4    O          2         2      0
 bonds(sdfset[1:2], type="charge")
## $CMP1
## NULL
## 
## $CMP2
## NULL
 bonds(sdfset[1:2], type="addNH") 
## CMP1 CMP2 
##    0    0