Molecules from Simon | CD – I’m unable to reproduce connectivity changes from Simon’s report. This is probably due to the code I sent him initially. When I try to run these using the new (rdkit-based) ways of finding connectivity changes, I don’t see the connectivity changes. I suspect that the root cause of the cases he found are due to OE automatically adding protons. JW – If the cases here are due to an OE molecule interpretation error, then this probably isn’t relevant for our look into proton migration. Could you clarify what we’re looking to do with this step? CD – We start with an sqm.in file containing coordinates but no bonds. Then we end up with a sqm.out file with coordinates but no bonds. Then we can use various AmberTools to turn that into a sdf or mol2 file. I’ve had trouble getting either of those into RDKit. So I tried using OpenEye to read them and that’s where I hit this problem. JW – Could we move forward with this just using RDKit to guess the final connectivity? CD – That’s looked OK in my experimentation, so I think that would be fine.
CD – I’d like to send a new script to Simon and have him re-run it.  CD – I’m a bit concerned overall because SB only found 9 cases in a set of about 50k. (General) – We could incorporate protomer enumeration into the molecule-loading routine: protomers = mol.enumerate_protomers() OM – Could get you set up on Summit eventually, or on a Shirts lab workstation sooner. (General) – CD will work on testing the new connectivity rearrangement workflow on a Shirts lab workstation. Once that’s tested+running CD will send the updated script to SB, though SB will be on vacation for a week.
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