Fig. 1
From: Adding hydrogen atoms to molecular models via fragment superimposition
Hydrogen addition algorithm in a nutshell. This figure displays how hydrogen atoms are added to toluene (target) from information about benzene and isobutylene (reference). A The reference molecules are split into fragments. The central atom is shown in blue, connected heavy atoms in gray and hydrogen atoms in white. The opaque fragments are added to the fragment library, the transparent ones are ignored due to being duplicates. B The target molecule is split into fragments. The central atom is shown in red and connected heavy atoms in gray. C For each target fragment the matching library fragment is superimposed. The central atom for both fragments are positioned in the coordinate origin, the library fragment is rotated to achieve congruence and the library fragment is translated to the original position of the target fragment. The resulting coordinates of the hydrogen atom(s) (encircled) are taken. D The obtained hydrogen positions from the previous step are adopted for the target molecule