Add explicit_hydrogen parameter

[padix-key]

This parameter in interface.rdkit.to_mol() defines whether hydrogen should be explicitly or implicitly included in the created Mol

[codspeed-hq]

CodSpeed Performance Report

Merging #741 will not alter performance

_{Comparing padix-key:rdkit (167c31a) with main (2624c37)}

Summary

✅ 59 untouched benchmarks

[Croydon-Brixton]

In the base case where explicity_hydrogen=True, what would this mean if I just call to_mol for a typical crystal structure that won't have any hydrogens resolved? Will RDKit infer charges / valences in that case? If so this might lead to broken molecules -- if that were the case, should we check that if explicit hydrogen is true there have to be hydrogens in the structure? (I could see this being sth users will try -- at least I would have tried it :D )

[padix-key]

Charges would also not be inferred automatically before this PR. But I am not sure what this means for valence: As the bond types are also explicitly set I guess RDKit assumes a radical, if explicit_hydrogen=True, but hydrogen atoms are actually missing. Probably, I should test this.

Having a check there sounds like a good idea, especially as I would agree that this could be a common mistake. However, I also think strictly checking for the simple presence of hydrogen atoms might not be sensible enough, as there are valid molecules without hydrogen atoms, although they appear rarely. What do you think about raising a warning as a 'reminder' to the user to check the input?

[padix-key]

I checked the different behaviors when an AtomArray without hydrogen is passed to as_mol() with explicit_hydrogen being False/True:

import biotite.interface.rdkit as rdkit_interface
import biotite.structure.info as info
import rdkit.Chem.AllChem as Chem
import rdkit.Chem.Draw as Draw

atoms = info.residue("C")
atoms = atoms[atoms.element != "H"]

mol = rdkit_interface.to_mol(atoms, explicit_hydrogen=True)
Chem.Compute2DCoords(mol)
Draw.MolToFile(mol, "explicit.png")

mol = rdkit_interface.to_mol(atoms, explicit_hydrogen=False)
Chem.Compute2DCoords(mol)
Draw.MolToFile(mol, "non_explicit.png")

explicit.png:

non_explicit.png:

So rdkit correctly understands that in the latter case it should additional hydrogen atoms to the visualization, as the Mol already contains the hydrogen implicitly.

[padix-key]

I added a warning in case the structure contains no hydrogen atoms. @Croydon-Brixton Could you have a look again?