Hi Hao, As a long-time file format geek. I feel the need to jump into this one.
1. mol2 I'm not a fan of using mol2. AFAIK, there is no definitive documentation for the atom typing rules or the aromaticity model. 2. sdf The RDKit has had a facility for storing atom properties in an SDF since 2019.03.1. This is documented in the "Atom Properties and SDF files" section in the RDKit Book. If I remember correctly, OEChem adopted the same scheme. 3. pqr I don't have much experience with this one, but it appears to be derived from the pdb format. As with #4, I don't think the pdb format is appropriate for small molecules. 4. pdbqt No, just no. I really wish the Autodock developers would get rid of pdbqt once and for all. Why would anyone use a small molecule file format that throws away bond order information? Ok, rant complete, I feel better now. These are my views, your mileage may vary. Pat On Wed, Oct 27, 2021 at 4:18 PM Hao <shenha...@gmail.com> wrote: > Hi! > > I was wondering if anyone has worked with file formats that keep track of > partial charges that easily interface with rdkit / other programs. I did a > little bit of searching and found several ways including 1. mol2 2. sdf > storing partial charges as a list in the data field 3. pqr 4. pdbqt. > > Obviously there are pros and cons to all but I was wondering if there has > been a system that has worked particularly well for you. The main things I > am looking for in descending order of importance are 1. ease of storage 2. > interfacing with rdkit (this could be through file conversions with other > software) 3. visualization > > Thanks, > Hao > _______________________________________________ > 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
