AtomMapping script incorrectly assings hydrogens #54
Description
In some cases, atomMapping script creates incorrect mappings, which are not consistent with molecular topology. This happens, since molecule is created from pdb without CONECT entries, thus, bonds are guessed from topology. In some cases (complex molecular geometry + poorly minimized molecule from molecular generation soft) this can lead to hydrogen that is bonded to one atom to be closer to the other atom. Generating molecule from pdb thus, will assign this hydrogen to the wrong heavy atom and will create wrong topology, if hydrogens are mapped.
I propose a simple solution, by optionally allowing to read CONECT entries from pdb file. I will make a PR soon.