Driver

Approver

Contributors

Stakeholder

Joshua Horton

Jeffrey Wagner

Chaya Stern (Deactivated)

David Mobley

Status

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

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)

Type /trello to add a card or board to this page or /jira to include a Jira issue, chart, or project.

Milestones and deadlines

Plot out milestones and deadlines using the table below. Put each milestone on its own row, @mention milestone owners, and type /date to quickly add deadlines.

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

Reference materials

Add links to relevant research and any other key documents