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Participants
Trevor Gokey - also taking offline notes, may with to consolidate
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Get feedback from CS about how torsion drive submission works and how it can be made easier
Discussion topics
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Item | Presenter | Notes | ||||
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TorsionDrive inputs | CS |
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Indicies | CS | Indices may not line up between fragmenter input (parent molecule) and fragment output (fragment molecule) Checking done by taking fragment, checking indices against parent molecule, and re-generating mapping by canonical cmiles mapping MCSC (maximum substructure matching? something like that; it’s in OE) can be used as a check for when CS is not around for direct input fragments know parent smiles, which is not reliably sufficient for re-constructing fragments TG: Need not just the information, but scripts that are used to generate | ||||
Charges | CS | CS: Right now, charges are done by summing up formal charges. Something about multiplicity | ||||
Job index <--> atom indices in torsion | CS | We have job index, which stores indices of atoms in torsion being driven. This could be used as a backwards double-check if both are given | ||||
Bug from last week | TG: How to re-create the process of finding the most recent bug? CS: Compared indices of fragment and parent molecule | |||||
Wishlist | TG: What do you wish you had? CS: What I’d want is a dict that maps indices between parent and fragment molecule TG: Agree, have the provenance but that does not include this information JH: Do we want fragmenter to return this dictionary? CS: Yes JH: When you’re doing a drive, but without fragments, how do you pick dihedral indices? CS: I’ve never done that work, LPW and group have some rules about picking dihedrals. One way is in-house LPW scripts, another is using OE to select all rotatable bonds | |||||
Pulling data | CS: Would be nice to visualize torsion drives. You get the energy, but hard to do science without being about to visualize the drive. JH: Can do now with | |||||
Another request | CS: Would be really nice if you could get a MM torsion drive with torsion parameters set to 0. TG: Would need to be during submission. Would require
May tie in to functionality currently in ForceBalance |
CS dropped off call here
Item | Presenter | Notes |
|---|---|---|
QCSubmit | TG: Seems like QCSubmit does a lot of work with downloading/gathering QCA data, how does it work? JH: Wanted data for each type of collection (OptimizationCollectionResult, TorsionDriveCollectionResult). Shows example notebook of making one of these classes, downloading metadata in about a second. Locally these classes look about the same as their QCA counterparts; have the same results in them, etc. TG: How is data downloaded? JH: (more or less describes what TG did last summer but with a different list of things downloaded in each molecule) JH/TG: Could allow options to pick what (torsions, hessians, etc.) are actually downloaded TG: Would be nice to be able to combine datasets. Did this previously with a tree structure that uses iterators to interact with data JH: Data are collapsed here by default, although keeps initial db id so could be de-collapsed. Generally agreement TG+JH to work together on building something to better store/search through QC data TG: Notes that a lot of QCSubmit classes are pretty similar to QCFractal classes in structure. Any particular features that motivated this? JH: Not necessarily, but wanted to keep it feeling similar to QCFractal |
Action items
- Find a way to save the parent-fragment index map Joshua Horton raised a PR
- Joshua Horton pretty torsion drive visualizer (goes in QCPortal or QCFractal)
- Trevor Gokey use info from CS to improve torsiondrive submission process
- Joshua Horton will merge the big QCSubmit PR and raise some issues on GitHub about fixes and other features to be implemented