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[WIP] Protein Mutations #618

Merged
merged 49 commits into from
Mar 18, 2020
Merged

[WIP] Protein Mutations #618

merged 49 commits into from
Mar 18, 2020

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dominicrufa
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make ring closure work

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seems that checks are failing due to openmoltools issues

dominicrufa
dominicrufa commented Jan 29, 2020
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dominicrufa
dominicrufa commented Jan 29, 2020
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jchodera commented Mar 5, 2020

trying to fix topology_proposal with monumental failure

@dominicrufa : Anything I can help with? Happy to find time for a quick call or slack chat!

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dominicrufa commented Mar 5, 2020 •
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@dominicrufa : Anything I can help with? Happy to find time for a quick call or slack chat!

I'm being melodramatic. didn't even break as many tests as i thought. there is an irritating problem with the atom map expressions where using the oechem.OEExprOpts_IntType causes faulty atom mappings, though, but i'll look at it in the morning. Thanks!

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jchodera approved these changes Mar 17, 2020
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OK, looks good! Left some minor comments!

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This was referenced Mar 17, 2020
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@hannahbrucemacdonald
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Can we look more at the implicitSolvent situation? It's called in a bunch of different examples and tests, sometimes set to None, and sometimes set to 'implicitSolvent' : app.OBC2

For now, I'm adding a comment wherever I see it that it's not supported yet anyway, but I don't see the harm of it being set to None here. I'll add an issue to the tracker #654. If the tests pass, I'm going to merge and cut a release.

@hannahbrucemacdonald hannahbrucemacdonald merged commit 6e5c193 into master Mar 18, 2020
@jchodera jchodera deleted the new_ring_closing branch March 18, 2020 21:02
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Can we look more at the implicitSolvent situation? It's called in a bunch of different examples and tests, sometimes set to None, and sometimes set to 'implicitSolvent' : app.OBC2

I'll prioritize fixing this!

For now, I'm adding a comment wherever I see it that it's not supported yet anyway, but I don't see the harm of it being set to None here. I'll add an issue to the tracker #654. If the tests pass, I'm going to merge and cut a release.

Sounds fine!

@jchodera jchodera mentioned this pull request May 17, 2021
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@jchodera jchodera jchodera approved these changes

@zhang-ivy zhang-ivy Awaiting requested review from zhang-ivy

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@dominicrufa @jchodera @hannahbrucemacdonald