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Info

List of infrastructure aims and tasks for 2020. Last updated on Sept 24, 2020.

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Priority

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colourRed
titlehigh
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titleMEDIUM
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titleLOW

Effort

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titlehigh
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titleMEDIUM
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titleLOW

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titleNot started
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titlePROTOTYPE
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Roadmap

Infrastructure tasks

Priority

Effort

Blocking science?

Infrastructure Dependencies

Start date

End/Due date

Status

Driver

Architecture / General infrastructure

Package namespace reorganization

Status
colourGreen
titleLow

Likely not migrating toolkit and forcefields repo until toolkit 1.0, but new packages should follow the openff namespace convention

Status
colourYellow
titleIN PROGRESS

Matt Thompson

95%+ core package uptime and deployment

(OpenFF TK, s99F, OpenFFs)

Status
colourRed
titleHigh

Status
colourRed
titleHigh

Will be made easier by conda-forge migration once OpenMM gets moved over

Ongoing

Status
colourYellow
titleIN PROGRESS

John Chodera Jeffrey Wagner Matt Thompson David Dotson

Monitoring dashboard, Nightly builds, deployment tests, error severity/triage policy

Status
colourYellow
titlemedium

Nightly builds will be easier after conda-forge migration

April 2020

Status
colourYellow
titleIN PROGRESS

Jaime Rodríguez-Guerra Matt Thompson David Dotson

Automated QC mol submission

Status
colourRed
titleHigh

No, but slowing some things/diverting effort from elsewhere.

Chemper package creation

Migration of CMILES and Fragmenter functionality into OFFTK

May 2020

Status
colourYellow
titleIN PROGRESS
Status
colourBlue
titlePROTOTYPE

Joshua Horton David Dotson

Automate finding FF discrepancies and submitting torsion drives – find more molecules that have underexplored parameters, eats large molecule datasets and compared OpenFF to ANI energies, and flags most discrepant for QM calculation. Emphasize plugin architecture so other people can easily add new criteria. Relevant slack discussion.

Status
colourYellow
titlemedium

David Dotson Trevor Gokey General “reproducible computation” records and data infrastructure

/wiki/spaces/DATA/pages/613089308

Status
colourRed
titleHigh

Interoperable molecule class

Simon Boothroyd Joshua Horton

Bayesian infrastructure: ML frameworks

Bayesian Fitting

Analytically Differentiable System Object

Status
colourRed
titleBLOCKED

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

Status
colourYellow
titleMEDIUM

Hard to spec without VirtualSite Handler implementation

Bespoke Torsion Parametrization package

Won’t be open source until fragmenter is refactored to be OE-free

Chemper conda-forge mir

CMILES conda-forge migration

QC submission infrastructure

Status
colourYellow
titleIN PROGRESS
Status
colourBlue
titlePROTOTYPE

Joshua Horton

Python System object (repo)

Status
colourRed
titleHigh

Analytical parameter gradient-based fitting, possibly other ML or Bayesian optimization routines

(Optional) spec from MolSSI interoperable molecule workgroup

OpenFF-core refactor

March 2020

Status
colourYellow
titleIN PROGRESS
Status
colourBlue
titlePROTOTYPE

Matt Thompson

CLI tool infrastructure

Status
colourRed
titleHIGH

June 2020

Status
colourYellow
titleIN PROGRESS
Status
colourBlue
titlePROTOTYPE

Matt Thompson Jeffrey Wagner

Remove smirnoff_hack.py / Implement CachingToolkitWrappers

Status
colourYellow
titleMEDIUM

Refactor Fragmenter / remove OE dependence / Base off OpenFF Molecule

Status
colourRed
titleHigh

Graph-based charges/WBOs

David Dotson John Chodera Matt Thompson

OpenMM conda-forge migration

Status
colourRed
titleHigh

Late 2019

Status
colourYellow
titleIN PROGRESS

Jaime Rodríguez-Guerra Peter Eastman; Anthony Scopatz (contracted)l John Chodera Jeffrey Wagner Levi Naden

OpenFF Toolkit and general org repo conda-forge migration

Status
colourRed
titleHigh

OpenMM conda-forge migration

Status
colourRed
titleBLOCKED

Toolkit

Virtual Site ParameterHandler

Status
colourYellow
titleMEDIUM

Off-site charge fitting

Likely to be reworked in the long-term to better work with the System object

March 2020

Status
colourYellow
titleIN PROGRESS

Trevor Gokey

WBO Bond ParameterHandler

Status
colourRed
titleHIGH

Matt Thompson David Dotson

AMBER-derived SMIRNOFF-format FF

Status
colourRed
titleHIGH

Biopolymer fitting

March 2020

Status
colourYellow
titleIN PROGRESS

David Cerutti (Unlicensed) Jeffrey Wagner

Polarizability ParameterHandler

Status
colourGreen
titleLOW

Polarizable fitting

A deep dive into toolkit parametrization differences (Josh Fass SMIRKS differences) / Automate complaining about cases where incoming molecule/chemistry is bad/misformatted

Status
colourRed
titleHigh

Spinoff (Potentially Shirts lab undergrad?)

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

Status
colourYellow
titleMEDIUM

Status
colourYellow
titleIN PROGRESS

Matt Thompson Simon Boothroyd Jeffrey Wagner

Implement friendly default behavior, with option for custom validation logic when loading large datasets/high-volume pipelines. Consider making moleculefixer for common data problems.

Status
colourYellow
titleMEDIUM

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

Status
colourRed
titleHigh

Aromaticity refactor

Stereochemistry refactor

Protonation state enumeration

Status
colourGreen
titleLOW

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)

Status
colourBlue
titlePROTOTYPE
Status
colourRed
titleBLOCKED

Joshua Horton building on work of Chaya Stern (Deactivated)

RDKit stereochemistry and tautomer enumeration

Status
colourRed
titleHigh

Jeffrey Wagner

Interoperable molecule/stereochemistry/aromaticity refactor

Status
colourYellow
titleMEDIUM

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)

Status
colourRed
titleHigh
, but can be after protein FF port

Biopolymer fitting

Dec 31 2020

Jeffrey Wagner

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

Status
colourRed
titleHigh
, but can be after protein FF port

Biopolymer fitting

Should discuss design with OpenEye

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

Status
colourRed
titleHigh
, but can be after protein FF port

Biopolymer charge fitting

Yuanqing Wang (Deactivated) Josh Fass (Unlicensed)

CMAP torsions in OFFTK/SMIRNOFF spec

Status
colourGreen
titleLOW

CMAP fitting

Fitting

Migrate FF optimization to ML framework

Status
colourRed
titleHIGH

Automate fitting infrastructure, remove OE dependencies

Status
colourRed
titleHIGH

QC Submission infrastructure (for QCMol-->graph mol conversion)

Jeffrey Wagner Hyesu Jang

PE parallelization (Fractalization? Key-value store in cloud? F@H? etc)

Status
colourRed
titleHIGH

MolSSI packaging Fractal separately from QCFractal

David Dotson John Chodera Simon Boothroyd

Benchmarking

H-G benchmarking

Status
colourYellow
titleMedium

 

 

 

P-L benchmarking /wiki/spaces/EVAL/pages/62095389 (repo)

Status
colourYellow
titleMedium

 

 

Mid 2019?

 

Status
colourYellow
titleIN PROGRESS

David Hahn

Property estimator mixed FF tests (mix AMBER and SMIRNOFF system components)

Status
colourGreen
titleLOW

This may not be necessary.

Automated benchmarking + dashboard

May include geometry tools (MM minimization, conformer generation, torsion scanning, conformer scoring)

Status
colourRed
titleHIGH

(Optional) Reliable QCMol → OFFMol conversion/CMILES deviation checks

???

Status
colourYellow
titleIN PROGRESS

Dashboard: Jaime Rodríguez-Guerra David Dotson John Chodera Trevor Gokey

Documentation / Community / Training

Docs cleanup and Binder-izing all examples

Status
colourYellow
titleMedium

Status
colourYellow
titleIN PROGRESS

Matt Thompson (binder)

Developers guide + true community contributions/branch OE license issue resolution

Status
colourRed
titleHIGH

Dev docs will be a living document

Status
colourYellow
titleIN PROGRESS

Training a 50% QCA developer

Status
colourYellow
titleMedium

April 2020

Status
colourYellow
titleIN PROGRESS

David Dotson

Compute hosting for bespoke workflow on Hypernet Labs' Galileo Platform

Status
colourYellow
titleMedium

Bespoke workflow prototype

Status
colourYellow
titleIN PROGRESS

Joshua Horton Jeffrey Wagner

CHARMM-GUI integration

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

Status
colourRed
titleBLOCKED

Pele-OpenFF Integration (meeting notes)

External

Status
colourYellow
titleIN PROGRESS

Marti Municoy; Victor Guallar; Jeffrey Wagner David Mobley

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