Change order of 3D-check and hydrogen check; modify hydrogen check

[cisert]

Change order of 3D-check and hydrogen check; modify hydrogen check

[josejimenezluna]

Good first point.

About the second, should we respect if the user has already assigned hydrogens to a mol, even if they don't correspond with OBabel's choice? Sounds a bit too aggressive to me.

[cisert]

Hm, depends. I think the case where only some of the hydrogens are explicit but others are not would likely give strange results, since all the molecules in the training set had all their hydrogens added. Although that would lie in the user's responsibility, if they decide to explicitly set addh=False.

[cisert]

I'd make addh=True by default though - it doesn't change anything if hydrogens are present, and if they are not we add them. If someone disabled that and get's strange results, that's on them.

[josejimenezluna]

Fixed with 1472e38