François- I've been writing code for a couple of toolkits (rdk, schrodinger, and canvas), and my personal opinion is that mol2 format should be avoided when possible.
In mol2, as far as I can tell, formal charges and valence (and Kekulé form) depend on a scheme of atom types that is large but not exhaustive. Every time a tool reads or writes a mol2 file, it is guessing about the user's intent and guessing what atom types are available to the rest of the user's workflow. These problems are compounded for molecules with implicit hydrogens: negative charges and implicit hydrogens seem difficult to distinguish in a mol2 file. It also does not have official ways to represent elements that are not included in the standard type system (like silver or manganese), but many toolkits have local extensions to cover these elements. Some people use mol2 because it has per-atom properties, but so do .cif and .mae. I'm not speaking for Schrödinger, but this *is* what I tell our internal developers. dan nealschneider | senior staff developer *he/him/his* [image: Schrödinger, Inc.] <https://schrodinger.com/> On Thu, Jun 16, 2022 at 7:42 AM Greg Landrum <greg.land...@gmail.com> wrote: > Hi Francois, > > Yes, I would recommend SDF, the V3000 version if possible. The xyz format > is problematic because it doesn’t have bonds. There is still a way to kind > of work with that together with SMILES or sdf though: > > https://mattermodeling.stackexchange.com/questions/7234/how-to-input-3d-coordinates-from-xyz-file-and-connectivity-from-smiles-in-rdkit > > As for mol2: the RDKit has some support, but only for the corina version > of mol2. I would avoid that format if at all possible > > > -greg > > On Thu, 16 Jun 2022 at 13:58, Francois Berenger <mli...@ligand.eu> wrote: > >> Hi all, >> >> I assume it's ".sdf". >> >> But, do we have good support for ".xyz" also? >> >> In addition, what about RDKit's support of ".mol2" these days? >> >> Regards, >> F. >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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