List of infrastructure tasks for 2020.
Labels
Category | Labels |
|---|---|
Priority | HIGH | MEDIUM | LOW |
Effort | HIGH | MEDIUM | LOW |
Status | NOT STARTED | IN PROGRESS | COMPLETED |
Roadmap
Infrastructure tasks | Priority | Effort | Blocking science? | Infrastructure Dependencies | Start date | End date | Status | Driver |
Architecture / General infrastructure | ||||||||
Package namespace reorganization | LOW | |||||||
Nightly build framework and decision matrix | MEDIUM | IN PROGRESS | Jaime Rodríguez-Guerra (Deactivated) Matt Thompson David Dotson | |||||
Automated QC mol submission | HIGH | No, but slowing some things/diverting effort from elsewhere. | Chemper package creation Migration of CMILES and Fragmenter functionality into OFFTK | IN PROGRESS | ||||
General “reproducible computation” records and data infrastructure → How to store datasets? Github, tarballs, images, etc? | HIGH | |||||||
Bayesian infrastructure: ML frameworks | Bayesian Fitting | Analytically Differentiable System Object | ||||||
Off-site charges (support for conversion to other packages) | MEDIUM | |||||||
Python System object | HIGH | Analytical parameter gradient-based fitting | (Optional) spec from MolSSI interoperable molecule workgroup (Optional) OpenFF-core refactor | IN PROGRESS | ||||
Remove | HIGH | |||||||
Chemper and CMILES conda-forge packaging | MEDIUM | IN PROGRESS | ||||||
Toolkit | ||||||||
Virtual Site ParameterHandler | MEDIUM | Off-site charge fitting | IN PROGRESS | |||||
WBO Torsion ParameterHandler | HIGH | WBO torsion parameter fitting | COMPLETED | |||||
Charge Increment ParameterHandler | HIGH | BCC refitting | COMPLETED | |||||
AMBER-derived SMIRNOFF-format library charges and torsions | HIGH | Biopolymer fitting | IN PROGRESS | |||||
Polarizability ParameterHandler | LOW | Polarizable fitting | ||||||
Charged SDF I/O | HIGH | COMPLETED | ||||||
A deep dive into toolkit parameterization differences → Josh Fass SMIRKS differences | HIGH | |||||||
Refactor/make our own Exception hierarchy | MEDIUM | |||||||
openforcefield-core/pydantic refactor (possibly driving a SMIRNOFF spec update) | HIGH | |||||||
Tools for molecule submission: Fragmentation, tautomer enumeration, protonation state enumeration | HIGH | 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 | IN PROGRESS | Joshua Horton building on work of Chaya Stern (Deactivated) | ||||
Interoperable molecule/Stereochemistry refactor | MEDIUM | |||||||
Biopolymer infrastructure (SMARTS typing optimization and infra improvement) | HIGH, but can be after protein FF port | Biopolymer fitting | ||||||
Biopolymer infrastructure (graph charges and/or other scalable solution) | HIGH, but can be after protein FF port | Biopolymer charge fitting | ||||||
Polymer infrastructure (topological residue detetion, etc) | Nonstandard AA fitting | |||||||
CMAP torsions in OFFTK/SMIRNOFF spec | CMAP fitting | |||||||
Fitting | ||||||||
More efficient ways to simultaneously co-optimize valence and nonbonded parameters | LOW | |||||||
Efficient energy calc during optimization based on tracking parameters being changed, and only recomputing energy terms that changed (PE may already have this? LPW + SB can touch base) | LOW | |||||||
Automate fitting infrastructure, remove OE dependencies | HIGH | QC Submission infrastructure | ||||||
pAPRika - PE integration and production-readiness | H-G fitting | IN PROGRESS | ||||||
PE parallelization (Fractalization?) | HIGH | MolSSI packaging Fractal separately from QCFractal | ||||||
Benchmarking | ||||||||
H-G benchmarking | MEDIUM |
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P-L benchmarking | MEDIUM |
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| IN PROGRESS | ||
Property estimator mixed FF tests (mix AMBER and SMIRNOFF system components) | LOW | This may not be necessary. | ||||||
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 | ||||
Documentation / Community / Training | ||||||||
Docs cleanup and binder-izing all OFFTK examples | MEDIUM | |||||||
Developers guide + true community contributions/branch OE license issue resolution | HIGH | |||||||
Training a 50% QCA developer | MEDIUM | IN PROGRESS | ||||||