Page Comparison

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

Joshua Horton David Dotson

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

Matt Thompson

Remove smirnoff_hack.py / Implement CachingToolkitWrappers

Chemper and CMILES conda-forge packaging

Matt Thompson

Toolkit

Virtual Site ParameterHandler

Off-site charge fitting

Trevor Gokey

WBO Torsion ParameterHandler

WBO torsion parameter fitting

David Dotson Jeffrey Wagner

Charge Increment ParameterHandler

BCC refitting

Jeffrey Wagner

AMBER-derived SMIRNOFF-format library charges and torsions

Biopolymer fitting

David Cerutti (Deactivated) Jeffrey Wagner

Polarizability ParameterHandler

Polarizable fitting

Charged SDF I/O

Jeffrey Wagner

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)

Biopolymer fitting

Biopolymer infrastructure (graph charges and/or other scalable solution)

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

Jeffry Setiadi David Dotson

PE parallelization (Fractalization?)

MolSSI packaging Fractal separately from QCFractal

Benchmarking

H-G benchmarking

P-L benchmarking

David Hahn

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

David Dotson