Add warning and option for adding explicit hydrogens about xtb

[awvwgk]

In case of PDB or molfile/SDF input this is useful, since a kind of meta-information about hydrogen atoms is present in the file format (e.g. for a PDB file it is extremely unlikely to encounter a valid input without any hydrogen atoms). For molfile/SDF input it is more difficult, any assumption on the topology or valency of an atom without performing a calculation is out-of-scope for xtb. The hydrogen atom query field can be used to determine if explicit hydrogen atoms are missing and to reject input, but it is not required to be present if no explicit hydrogen atoms are given. A more sophisticated scheme would use the formal charges, topology information and bond orders to check for missing hydrogen atoms, which in my opinion is actually the responsibility of the provider.

For Turbomole coordinates and xyz input this check has to be performed by the provider of the input geometry, xtb should not perform any checks for topology or valency here.

[sozenoid]

Related to this topic, xtb will refuse to process a molecule supplied in an .pdb format without any hydrogen even when the molecule is valid. An example is hexafluorobenzene which xtb will accept as .sdf format but reject as .pdb. I think adding a warning in an absence of hydrogens is fine but rejecting the input seems a bit too conservative.

• xtb version 6.3.3 (5b13467) compiled by 'ehlert@majestix' on 2020-09-17

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[ERROR] Program stopped due to fatal error
-2- reading geometry input 'testmol2.pdb' failed
-1- io_reader_readMolecule: You get no calculation today, please add hydrogen atoms first
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