Review initial MOL2 creation (DockFlow, ScoreFlow, LigFlow)

[diegoenry]

Currently Tripos mol2 it the default input format for both receptor and ligand in DockFlow and ScoreFlow, and for compounds in LigFlow.

RDKit does not write a .mol2 file, sticking to .sdf which is the industry-standard. That's not an issue for most modern software but as far as we want to support VINA and SEED we need properly convert the initial SMILES into MOL2.

Currently we do this conversion using openbabel (arrrg) and looks like it doesn't not follow SYBYL all the time, producing incompatible atoms types such as "S.O2" instead of "S.o2", tiny inconsistencies which may break some parts of the codes.

We found this after frequently finding out PLANTS "Du" (dummy) atoms both for protein and ligand, that could severly compromise the Docking outcome.

Finally if these DUMMY atoms progress into MM/GBSA rescoring or QM parametrization, they'll fail to produce correct parameters.

The latest ChemBase (from CN+DrugBank, July 2018) was based on SDF->MOL2 using OPENBABEL, so once again we may probably need to trash it. We put a quickfix inside Dock/ScoreFlow using antechamber to convert the files.

Finally, for ChemBase we can keep using .sdf and may migrate to amber "database" command.