List of infrastructure tasks for 2020. |
Category | Labels |
---|---|
Priority | | | |
Effort | | | |
Status | | | |
Infrastructure tasks | Priority | Effort | Blocking science? | Infrastructure Dependencies | Start date | End date | Status | Driver |
Architecture / General infrastructure | ||||||||
Package namespace reorganization |
| |||||||
Nightly build framework and decision matrix |
| Jaime Rodríguez-Guerra (Deactivated) Matt Thompson David Dotson | ||||||
Automated QC mol submission |
| No, but slowing some things/diverting effort from elsewhere. | Chemper package creation Migration of CMILES and Fragmenter functionality into OFFTK |
| ||||
General “reproducible computation” records and data infrastructure → How to store datasets? Github, tarballs, images, etc? |
| |||||||
Bayesian infrastructure: ML frameworks | Bayesian Fitting | Analytically Differentiable System Object | ||||||
Off-site charges (support for conversion to other packages) |
| |||||||
Python System object |
| Analytical parameter gradient-based fitting | (Optional) spec from MolSSI interoperable molecule workgroup (Optional) OpenFF-core refactor | |||||
Remove |
| |||||||
Chemper and CMILES conda-forge packaging | ||||||||
Toolkit | ||||||||
Virtual Site ParameterHandler | Off-site charge fitting |
| ||||||
WBO Torsion ParameterHandler | WBO torsion parameter fitting |
| ||||||
Charge Increment ParameterHandler | BCC refitting |
| ||||||
AMBER-derived SMIRNOFF-format library charges and torsions | Biopolymer fitting | |||||||
Polarizability ParameterHandler | Polarizable fitting | |||||||
Charged SDF I/O |
|
| ||||||
A deep dive into toolkit parameterization differences → Josh Fass SMIRKS differences |
| |||||||
Refactor/make our own Exception hierarchy |
| |||||||
openforcefield-core/pydantic refactor (possibly driving a SMIRNOFF spec update) |
| |||||||
Tools for molecule submission: Fragmentation, tautomer enumeration, protonation state enumeration | 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 |
| Joshua Horton building on work of Chaya Stern (Deactivated) | |||||
Interoperable molecule/Stereochemistry refactor |
| |||||||
Biopolymer infrastructure (SMARTS typing optimization and infra improvement) | , but can be after protein FF port | Biopolymer fitting | ||||||
Biopolymer infrastructure (graph charges and/or other scalable solution) | , 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 |
| |||||||
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) |
| |||||||
Automate fitting infrastructure, remove OE dependencies |
| QC Submission infrastructure | ||||||
pAPRika - PE integration and production-readiness | H-G fitting |
| ||||||
PE parallelization (Fractalization?) |
| MolSSI packaging Fractal separately from QCFractal | ||||||
Benchmarking | ||||||||
H-G benchmarking |
|
|
| |||||
P-L benchmarking |
|
|
|
|
| |||
Property estimator mixed FF tests (mix AMBER and SMIRNOFF system components) | This may not be necessary. | |||||||
Automated benchmarking + dashboard May include geometry tools (MM minimization, conformer generation, torsion scanning, conformer scoring) |
| (Optional) Reliable QCMol → OFFMol conversion/CMILES deviation checks |
| Dashboard: Jaime Rodríguez-Guerra (Deactivated) David Dotson John Chodera | ||||
Documentation / Community / Training | ||||||||
Docs cleanup and binder-izing all OFFTK examples |
| |||||||
Developers guide + true community contributions/branch OE license issue resolution |
| |||||||
Training a 50% QCA developer |
|