QCSubmit
Driver | Approver | Contributors | Stakeholder |
|---|---|---|---|
@Joshua Horton |
| @David Mobley @Jeffrey Wagner @John Chodera |
|
Objective | We aim to automate the filtering and submission of molecules to public and local qcarchive instances. |
Due date | May 1, 2020 |
Key outcomes | Automate the preparation of optimisation and torsiondrive datasets from input lists of molecules. |
Status | Started |
Problem Statement
QCSubmit
Currently submitting molecules to the public QCArchive has involved the use of scripts hosted at this github repo . While this method seems to be stable we aim to expand its capabilities while automating the procedure, this will be particularly helpful in the case of the bespoke workflow, but will also impact on the generation of datasets for general force field fitting.
Scope
Must have:
A workflow, the process to filter and prepare the molecules should be easy to configure and control given a large number of settings available. This should be controllable through the API, settings files and a CLI. Spec for how we imagine this to look can be found here .
state enumeration stereoisomers/tautomers
fragmentation
cmiles identifiers on all submissions
WBO on all submissions
filtering based on simple molecule properties (element type size/weight)
Be easy to serialise to file
A convenient way to collect the results as well
Nice to have:
Ability to ensure that calculations can be reused where possible
Not in scope:
Timeline
Milestones and deadlines
Milestone | Owner | Deadline | Status |
|---|---|---|---|
Draft 1 of QCSubmit | @Joshua Horton |
| STARTED |
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Reference materials
Decisions and Problems
Description | Github link | Status | Blocking | |
|---|---|---|---|---|
| 1 | Draft 1 spec for the python API |
| In progress | Not blocking |
| 2 | Report which toolkit was used. |
| in progress | not blocking |
- All OFFTK methods will use OpenEye for consistency until we implement a way to retrieve which backend toolkit performed the requested function.