Objective
We aim to automate the filtering and submission of molecules to public and local qcarchive instances.
Due date
01 May 2020
Key outcomes
Automate the preparation of optimisation and torsiondrive datasets from input lists of molecules.
Status
Problem Statement QCSubmit
Github link macrolink https://github.com/openforcefield/qcsubmit
Currently submitting molecules to the public QCArchive has involved the use of scripts hosted at this github repo
Github link macrolink https://github.com/openforcefield/qca-dataset-submission
. 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
Github link macrolink https://github.com/openforcefield/openforcefield/issues/516#issuecomment-588987644
.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:
Not in scope:
Timeline
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Milestones and deadlines
Reference materials
Decisions and Problems Description
Github link
Status
Blocking
1 Draft 1 spec for the python API
Github link macrolink https://github.com/openforcefield/openforcefield/issues/516
Statuscolour Yellow title In progress
Statuscolour Green title Not blocking
2 Report which toolkit was used.
Github link macrolink https://github.com/openforcefield/qcsubmit/issues/1
Statuscolour Yellow title in progress
Statuscolour Green title not blocking
All OFFTK methods will use OpenEye for consistency until we implement a way to retrieve which backend toolkit performed the requested function.