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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
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| title | Roadmap%20Planner |
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| hash | 2bdc296f1fe3c21fa63ea203d44cc013 |
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Milestones and deadlines
Milestone | Owner | Deadline | Status |
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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 | | |
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Reference materials