List of infrastructure tasks for 2022. Each task should be linked to its Confluence or GitHub page with more information. See also Science Roadmap 2021 .
Labels
Category | Labels |
|---|---|
Priority | HIGH | MEDIUM | LOW |
Effort | HIGH | MEDIUM | LOW |
Status | NOT STARTED | IN PROGRESS | PROTOTYPE | COMPLETED | BLOCKED | |
Roadmap
Infrastructure tasks | Priority | Effort | Blocking science? | Infrastructure Dependencies | Start date | End/Due date | Status | Driver |
|---|---|---|---|---|---|---|---|---|
Architecture / General infrastructure | ||||||||
95%+ core package uptime and deployment (OpenFF TK, s99F, OpenFFs) | HIGH | HIGH | Ongoing | COMPLETED | ||||
Add | HIGH | |||||||
| MEDIUM | |||||||
Refresh , consolidate, and prune OpenFF toolkit examples | MEDIUM | |||||||
SQM AM1 optimization connectivity change handling | MEDIUM | |||||||
| HIGH | |||||||
Streamline | MEDIUM | |||||||
| LOW | |||||||
Refactor | Unresolved – Don’t know timeline for adoption – Bring up in leadership/gov board meeting. Infra team will look into completeness of tests/reference values to estimate refactor cost | |||||||
Accept, reject, or request specific feedback for SMIRNOFF spec proposals within 4 weeks of submission | HIGH | |||||||
Automated upstream RC tests | MEDIUM | IN PROGRESS | ||||||
“Did I break something else?” tests against | MEDIUM | |||||||
QCA Standards v3 implementation | HIGH | new qca hire? | ||||||
MEDIUM | ||||||||
QCA 2D torsiondrive support (may just need to verify that this works) | HIGH | |||||||
HIGH | ||||||||
LOW (may increase if found to be blocking) | ||||||||
HIGH | Interoperable molecule class | |||||||
Bayesian infrastructure: ML frameworks | Bayesian Fitting | Analytically Differentiable System Object | BLOCKED | |||||
Off-site charges (support for conversion to other packages) | MEDIUM |
| June 2021 | IN PROGRESS | ||||
Define and maintain specific goals for Bespokefit deployability/stability (succeeds on 95% of minidrugbank? In under some set number CPU-hours? Regression test suite incorporated into CI) | HIGH | |||||||
Local torsiondrive executor (default qc, ANI, and XTB - a more formalized version of this command line command in | MEDIUM | |||||||
Interchange: Have ForceField.create_openmm_system either be deprecated or wrap Interchange call | MEDIUM | GBSA suport in Interchange Plugin support in Interchange, and a few months of lead time for scientists who need to port parameterhandler plugins | ||||||
Interchange: System combination | MEDIUM | PROTOTYPE | ||||||
Interchange: AMBER export | HIGH | Biopolymer topologies SMIRNOFF updates | IN PROGRESS | |||||
Interchange: GROMACS export | HIGH | Biopolymer topologies SMIRNOFF updates | PROTOTYPE | |||||
Interchange: OpenMM export | HIGH | PROTOTYPE | ||||||
Intercharge: LAMMPS export | LOW | SMIRNOFF updates | ||||||
Interchange: ParmEd export | MEDIUM | Biopolymer topologies SMIRNOFF updates | PROTOTYPE (not to be advertised for production use) | |||||
Interchange: AMBER import | MEDIUM | Biopolymer topologies | IN PROGRESS | |||||
Interchange: GROMACS import | LOW | Biopolymer topologies | IN PROGRESS | |||||
Interchange: OpenMM import | LOW | Biopolymer topologies | PROTOTYPE | |||||
Interchange: ParmEd import | MEDIUM | Biopolymer topologies | PROTOTYPE (not to be advertised for production use) | |||||
Interchange: Track parameter provenance on import (ie, hold a single value for shared GAFF parameters) | LOW | Biopolymer topologies | ||||||
Interchange: Interfacing with ML-based fitting | Blocked by lack of specification / needs to be broken into more discrete deliverables | BLOCKED | ||||||
Interchange: “Book” documentation/user’s guide | MEDIUM | IN PROGRESS PROTOTYPE | ||||||
HIGH | June 2020 | IN PROGRESS PROTOTYPE | ||||||
Remove | MEDIUM | |||||||
HIGH | PROTOTYPE IN PROGRESS | |||||||
Toolkit | ||||||||
HIGH | Biopolymer fitting | March 2020 | PROTOTYPE | |||||
Polarizability ParameterHandler | LOW | Polarizable fitting | ||||||
(Follow up with Jeffry Setiadi Michael Gilson to understand long term plans and infrastructure needs) | PROTOTYPE | |||||||
WBOs for improper torsions | Waiting on research results to assign priority | |||||||
A deep dive into toolkit parametrization differences (Josh Fass SMIRKS differences) / Automate complaining about cases where incoming molecule/chemistry is bad/misformatted | HIGH | IN PROGRESS | ||||||
Refactor/make our own Exception hierarchy, implement some problems as catch-able warnings. | MEDIUM | IN PROGRESS | ||||||
Implement friendly default behavior when loading large molecule datasets/high-volume pipelines, with option for custom validation logic. Consider making moleculefixer for common data problems. | MEDIUM | |||||||
openforcefield-core/pydantic refactor (possibly driving a SMIRNOFF spec update) | HIGH | Aromaticity refactor Stereochemistry refactor | ||||||
Remove OpenFF-Toolkit’s hard dependency on OpenMM (migrate to pint/openff-units) (patch) | MEDIUM | Sep 2021 | 0.11.0 release | IN PROGRESS | ||||
LOW | RDKit doesn’t have helpful protonation state enumeration; need to publicize and see if community wants to contribute there https://github.com/openforcefield/openforcefield/issues/526 Could use EPIK from schrodinger suite? Example in OpenMolTools | Mar 2020 | July 2020 (incomplete) | PROTOTYPEBLOCKED | ||||
Interoperable molecule/stereochemistry/aromaticity refactor | MEDIUM | Need to decide on desired behavior for how stereochemistry and aromaticity is handled. Also need to decide on which molecule formats should be losslessly round-trippable. | ||||||
Biopolymer infrastructure (SMARTS typing optimization) | HIGH | Biopolymer fitting | Dec 31 2020 | IN PROGRESSPROTOTYPE | ||||
Biopolymer infrastructure (infra improvement/Topology refactor/automated polymer unit recognition) | HIGH | Biopolymer fitting | Should discuss design with OpenEye | IN PROGRESS | ||||
Biopolymer infrastructure (graph charges and/or other scalable solution) | HIGH | Biopolymer charge fitting | ||||||
CMAP torsions in OFFTK/SMIRNOFF spec | LOW | CMAP fitting | ||||||
Fitting | ||||||||
Migrate FF optimization to ML framework | HIGH | |||||||
QM-MM / iPolQ solvent calcs on QCA | MEDIUM Needs research cycle: Could another QC program offer performant continuum solvent model and be compatible with QCF? | (Maybe: Way to generate solvent configuration in QCA? Or is this cheap enough to do outside QCA?) | Chapin Cavender Maybe @new-qca-hire Trevor Gokey Jeffrey Wagner | |||||
Single-point QM-MM of a subset of packed/folded protein on QCA | LOW | Need to decide on a QC program and ensure feature support/QCA compatibility) | ||||||
Benchmarking | ||||||||
MEDIUM |
|
|
| |||||
MEDIUM |
|
| Mid 2019? |
| IN PROGRESS PROTOTYPE | |||
Protein Xtal/NMR observable based benchmarking and fitting (chemical shift/scalar couplings/RDCs/kirkwood-buff integrals/etc) (specific effort to be directed by Chapin Cavender) | HIGH | |||||||
PL Benchmarking on Folding@Home (aligning with architecture from | HIGH | |||||||
Automated benchmarking + dashboard May include geometry tools (MM minimization, conformer generation, torsion scanning, conformer scoring) | HIGH | (Optional) Reliable QCMol → OFFMol conversion/CMILES deviation checks | ??? | IN PROGRESS | Dashboard: Jaime Rodríguez-Guerra (Deactivated) David Dotson John Chodera Trevor Gokey | |||
Documentation / Community / Training | ||||||||
Reference energies data package (curation write-up) | MEDIUM | MEDIUM | SMIRNOFF updates | Sep 2021 | IN PROGRESS | |||
CHARMM-GUI integration / validation | LOW | A way to create CHARMM residue template files (ParmEd Issue #1103) | ||||||