fromOldAdjacencyList: reduce code duplication
fromOldAdjacencyList: reduce code duplication

There was a whole block for if atom.isHydrogen() and another for
if it's not, but they only differed by the value of two constants
(the maximum number of lone pairs and the charge)

chatelak/RMG-Py,nyee/RMG-Py,pierrelb/RMG-Py,enochd/RMG-Py,enochd/RMG-Py,nickvandewiele/RMG-Py,comocheng/RMG-Py,nickvandewiele/RMG-Py,pierrelb/RMG-Py,comocheng/RMG-Py,nyee/RMG-Py,chatelak/RMG-Py