Page Comparison

Architecture / General infrastructure

95%+ core package uptime and deployment

(OpenFF TK, s99F, OpenFFs)

Ongoing

John Chodera Jeffrey Wagner Matt Thompson David Dotson

Add openff-qcsubmit openff-evaluator, bespokefit to core packages

openff-qcsubmit and bespokefit users guide

Josh Mitchell

Refresh , consolidate, and prune OpenFF toolkit examples

Josh Mitchell

SQM AM1 optimization connectivity change handling

Jeffrey Wagner Connor Davel

openff-benchmark refactor (make components be Python-first and more modular to enable more flexible workflows)

Jeffrey Wagner

Streamline ForceBalance CI and pre-release testing

ForceBalance developers guide

Refactor espaloma for production use or implement in OFF Toolkit

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

Jeffrey Wagner David Mobley John Chodera Simon Boothroyd

Automated upstream RC tests

Matt Thompson

“Did I break something else?” tests against master/main branches of OpenFF packages

Matt Thompson Jeffrey Wagner

QCA Standards v3 implementation

new qca hire?

QCA in-server, policy-based error cycling

QCA 2D torsiondrive support (may just need to verify that this works)

Psi4 to conda-forge

QCA chained operations

/wiki/spaces/DATA/pages/613089308

Interoperable molecule class

Simon Boothroyd Joshua Horton

Bayesian infrastructure: ML frameworks

Bayesian Fitting

Analytically Differentiable System Object

Off-site charges (support for conversion to other packages)

Hard to spec without VirtualSite Handler implementation

June 2021

Matt Thompson

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)

Jeffrey Wagner Matt Thompson Joshua Horton

Local torsiondrive executor (default qc, ANI, and XTB - a more formalized version of this command line command in openff-benchmark)

David Dotson

Interchange: Have ForceField.create_openmm_system either be deprecated or wrap Interchange call

GBSA suport in Interchange

Plugin support in Interchange, and a few months of lead time for scientists who need to port parameterhandler plugins

Jeffrey Wagner Matt Thompson

Interchange: System combination

Matt Thompson

Interchange: AMBER export

Biopolymer topologies

SMIRNOFF updates

Matt Thompson

Interchange: GROMACS export

Biopolymer topologies

SMIRNOFF updates

Matt Thompson

Interchange: OpenMM export

Matt Thompson

Intercharge: LAMMPS export

SMIRNOFF updates

Matt Thompson

Interchange: ParmEd export

Biopolymer topologies

SMIRNOFF updates

Matt Thompson

Interchange: AMBER import

Biopolymer topologies

Matt Thompson

Interchange: GROMACS import

Biopolymer topologies

Matt Thompson

Interchange: OpenMM import

Biopolymer topologies

Matt Thompson

Interchange: ParmEd import

Biopolymer topologies

Matt Thompson

Interchange: Track parameter provenance on import (ie, hold a single value for shared GAFF parameters)

Biopolymer topologies

Matt Thompson

Interchange: Interfacing with ML-based fitting

Blocked by lack of specification / needs to be broken into more discrete deliverables

Matt Thompson

Interchange: “Book” documentation/user’s guide

Josh MitchellMatt Thompson

CLI tool infrastructure

June 2020

Matt Thompson Jeffrey Wagner

Remove smirnoff_hack.py

Jeffrey Wagner

Implement CachingToolkitWrappers

Jeffrey Wagner Connor Davel

Toolkit

AMBER-derived SMIRNOFF-format FF

Biopolymer fitting

March 2020

Jeffrey Wagner Chapin Cavender

Polarizability ParameterHandler

Polarizable fitting

Custom GBSA handler

(Follow up with Jeffry Setiadi Michael Gilson to understand long term plans and infrastructure needs)

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

Connor Davel Jeffrey Wagner

Refactor/make our own Exception hierarchy, implement some problems as catch-able warnings.

Matt Thompson Simon Boothroyd Jeffrey Wagner

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.

openforcefield-core/pydantic refactor (possibly driving a SMIRNOFF spec update)

Aromaticity refactor

Stereochemistry refactor

Remove OpenFF-Toolkit’s hard dependency on OpenMM (migrate to pint/openff-units) (patch)

Sep 2021

0.11.0 release

Matt Thompson

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

Could use EPIK from schrodinger suite? Example in OpenMolTools

Mar 2020

July 2020 (incomplete)

Interoperable molecule/stereochemistry/aromaticity refactor

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.

Jeffrey Wagner

Biopolymer infrastructure (SMARTS typing optimization)

Biopolymer fitting

Dec 31 2020

Jeffrey Wagner Connor Davel

Biopolymer infrastructure (infra improvement/Topology refactor/automated polymer unit recognition)

Biopolymer fitting

Should discuss design with OpenEye

Jeffrey Wagner Iván Pulido

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

Biopolymer charge fitting

CMAP torsions in OFFTK/SMIRNOFF spec

CMAP fitting

Fitting

Migrate FF optimization to ML framework

QM-MM / iPolQ solvent calcs on QCA

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

Need to decide on a QC program and ensure feature support/QCA compatibility)

Benchmarking

H-G calculations in OpenFF-Evaluator

Jeffry Setiadi

/wiki/spaces/EVAL/pages/62095389 (repo)

Mid 2019?

David HahnDavid Dotson

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)

Chapin Cavender Jeffrey Wagner

PL Benchmarking on Folding@Home (aligning with architecture from bespokefit where possible/appropriate)

David Dotson

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 Trevor Gokey

Documentation / Community / Training

Reference energies data package (curation write-up)

SMIRNOFF updates

Sep 2021

Matt Thompson

CHARMM-GUI integration / validation

A way to create CHARMM residue template files (ParmEd Issue #1103)