Oh! I didn't realize atom properties were so cleanly integrated into sdfs. This is great - I will try things out and hopefully it works smoothly. Thanks a lot!
On Wed, Oct 27, 2021 at 8:53 PM Patrick Walters <wpwalt...@gmail.com> wrote: > 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 >> >
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