OpenFF Bespokefit

Owned by Karmen Condic-Jurkic
Last updated: Feb 04, 2022 by Karmen Condic-Jurkic
2 min read

Driver

Approver

Contributors

Stakeholder

Driver

Approver

Contributors

Stakeholder

@Joshua Horton

@Jeffrey Wagner

@Chaya Stern (Deactivated)

@David Mobley

Status

STARTED

Timeline

The dates on this timeline are not real!

This is a priority-view of the project and how large-scale concepts depend on different technical developments. Basically, it’s just split into

  • “Stuff that’s already done” (before Jan 2020)

  • “Stuff that’s already in progress” (overlaps Jan 30)

  • “Stuff that isn’t in progress but that we plan to complete before Sage” (stuff between Jan 30 and red line)

  • “Stuff that might be completed before Sage, but we don’t expect it to be” (overlaps red line)

  • “Stuff that we won’t consider starting until after Sage” (right of red line)

The “Conceptual” lane provides a high-level view of the functionality we will provide, in priority order. The subsequent lanes describe the discrete features that need to be added (They’ll end up roughly lining up with PRs in the different packages)

Nov2019DecJan2020FebMarAprMayJunJulAugSepOctNovDecSage
Conceptual
QCArchive
Forcebalance
OFFTK
Chemper
Fragmenter

Feature 1

Feature 2

Feature 3

Feature 4

Load the molecule into the OFFTK

Identify degrees of freedom to scan

Optional fragmentation

Design specific SMARTS

Prepare for QCArchive/fractal submission

collect results from archive

Prepare forcebalance targets

Run forcebalance

iOS app

Android app

Archive crawler

Add charge_from_molecules/other OFF opts

Find rotatable bonds

make molecules from QCArchive

QCArchive submission framework

Collecting results from archive

transfer qcarchive data to local targets

Universal canonical ordering

Wrap forcebalance

Integrate fragmenter

Chemper integration/ToolkitWrapper

CMILES integration/ToolkitWrapper

Produce conda package

Switch to rdkit backend

Switch to AmberTools WBO backend

Milestones and deadlines

Milestone

Owner

Deadline

Status

Milestone

Owner

Deadline

Status

Alpha release (hard OE dependence)

Conda installable bespokefit package
Have QCA → FB data flow use SDF
Add option to use Parsley values for torsion as an initial guess, but mention that “we don’t recommend it”
Make alpha user instructions/tutorial
Dependency installation
For ANI backend, make sure to pip install ANI
For QM on linux, install psi4
For QM on mac, have special instructions for installing psi4 into a separate environment, and then spinning up workers using that separate environment
QCA setup
When to use snowflake vs. standalone/persistent QCF server
Instructions
Start with either Merck comp chem protein-ligand complex or one of D Hahn’s systems
Take ligand file, show bespokefit configuration in YAML, call bespokefit from CLI
Explain why we have to select a “base” FF, which will affect the final values of the torsions
Indicate that it’s possible to call from python, but don’t provide an example. Just point users to API docs.
Talk about output shown during execution
Walk through results file (OFFXML)
Show a diff of the Parsley (base FF) torsion values vs final (bespokefit) torsion values – Maybe use label_molecules and grab results for specific torsions?
Explain that this new file will be APPENDED to Parsley, so that the torsions simply override certain values from the base FF
Show how to start a solvated protein-ligand simulation from it (using OpenMMForceFields)

@Joshua Horton @Jeffrey Wagner

 

NOT STARTED

 

 

 

 

 

 

 

 

 

Reference materials