hitting a lot of “Unknown error” cases; may try option (c) and see if this produces different results
these do appear to reduce in number after each error cycling, so not easy to reproduce in a single case
DD: if there are any persistent error cases after several rounds of error cycling, please share (if you can) the input molecule and we can take it to the psi4 devs to get a better solution in place (at least better error messaging)
JW: worked on deployment last week; making conda package (automation), implementing single-file installer (automation)
tricky bug in RDKit; seen references by Greg Landrum
in validation, when a mol passes other checks, later on the mol will get written and read in SDF
there are cases where there is not full fidelity in write/read; we do this as part of our validation for this reason; write to a StringIO object to avoid hammering filesystem
there are some cases that roundtripping StringIO fails, but to a file does not. Is consistently reproducible for a given molecule that fails; not clear what about these molecules is causing this
so, switched to using filesystem writes instead of StringIO to avoid the issue for now; will pursue (later) creating an RDKit issue with an example
also found a mangling of the atom indices from QM output
QM export is the first place we see it
have ideas on where the problem is; will investigate and report back findings
working to make parameter coverage output (step 3) be the input for optimizations (step 4)
have two places where we use arbitrary RMS cutoffs
minimum allowable RMS between generated conformers (step 2): 1.0A
propose changing to 1.5A
deduplication for input conformers (step 1): 0.1A
propose changing to 1.0A
the proposed changes would reduce the number of conformers in a dataset, speeding up the QM stage of the benchmark globally
the existing choices give more conformers, and differences between them are perhaps not meaningful at the level of our forcefield
[decision] change input conformer deduplication cutoff from 0.1 to 1.0A heavy-atom RMS; change conformer generation cutoff from 1.0A to 1.5A heavy-atom RMS
Jeff will make this change as a PR; David H. will give it a go to see how many molecules come through from his testing dataset
need to make sure we don’t end up with e.g. over 50% of molecules with only one conformer
JH: had a go at the burn-in set; will use to investigate issues with Jeff
played around with psi4 versions; resolved
we should follow up with Ben and ask about psi4 release schedule plans
DD:
need to create group codes for each partner
BASF : BSF
VRTX : VTX
XTALPI : XTP
BMS : BMS
MERCK : MRK
BOEHRINGER-INGELHEIM : BRI
ROCHE : RCH
GENENTECH : GNT
BAYER : BYR
JANSSEN : JNS
working
Burn-in
David D.
DD: how do we poke partners to get feedback?
JW: we’ll run out of bandwidth if we resort to DMs; best to keep it on the channels
resort to DM threads with all of us on it if needed, but only if asked
DD: will draft a “poke” message for #benchmarks-partners, send to JW,JH,DH as draft
DD: will prepare a spreadsheet of all partners, with status indicators like “burn-in complete”, “started production run”, “choice of optimization approach”, “variation notes”
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