Combine and filter NAGL2 Optimization Datasets Part 1 + Part 2 #416
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ers, despite me limiting it to 5
QCSubmit Validation Report
QC Specification Report
QCSubmit version information(click to expand)
|
ntBre
approved these changes
Dec 9, 2024
There was a problem hiding this comment.
Thanks for doing this, Lexie! I was working on something similar last week but by combining the dataset.json.bz2 files directly. This is a little more complicated but has the obvious benefit of being able to filter the records, so I think this looks good. Also glad to see the hashes check! Hopefully QCArchive will detect this as complete right after submission.
Lifecycle - QCSubmit Submission Report : SUCCESS
Response from public QCArchive: QCSubmit version information(click to expand)
|
Current status - Error CyclingConsider manually moving this. |
Lifecycle - Error Cycling Report
All errored tasks will be restarted.
|
| specification | COMPLETE | RUNNING | WAITING | ERROR | CANCELLED | INVALID | DELETED |
|---|---|---|---|---|---|---|---|
| default | 128281 | 0 | 0 | 0 | 0 | 0 | 0 |
OptimizationRecord Error Tracebacks:
Tracebacks (click to expand)
QCSubmit version information(click to expand)
| version | |
|---|---|
| openff.qcsubmit | 0.54.0 |
| openff.toolkit | 0.16.6 |
| basis_set_exchange | 0.10 |
| qcelemental | 0.28.0 |
| rdkit | 2024.09.3 |
Current status - Archived/CompleteConsider manually moving this. |
Lifecycle - Archived/Complete
Dataset Complete! |
Lifecycle - Error Cycling Report
All errored tasks will be restarted.
|
| specification | COMPLETE | RUNNING | WAITING | ERROR | CANCELLED | INVALID | DELETED |
|---|---|---|---|---|---|---|---|
| default | 128281 | 0 | 0 | 0 | 0 | 0 | 0 |
OptimizationRecord Error Tracebacks:
Tracebacks (click to expand)
QCSubmit version information(click to expand)
| version | |
|---|---|
| openff.qcsubmit | 0.54.0 |
| openff.toolkit | 0.16.6 |
| basis_set_exchange | 0.10 |
| qcelemental | 0.28.0 |
| rdkit | 2024.09.3 |
Current status - Archived/CompleteConsider manually moving this. |
Lifecycle - Archived/Complete
Dataset Complete! |
Lifecycle - Error Cycling Report
All errored tasks will be restarted.
|
| specification | COMPLETE | RUNNING | WAITING | ERROR | CANCELLED | INVALID | DELETED |
|---|---|---|---|---|---|---|---|
| default | 128281 | 0 | 0 | 0 | 0 | 0 | 0 |
OptimizationRecord Error Tracebacks:
Tracebacks (click to expand)
QCSubmit version information(click to expand)
| version | |
|---|---|
| openff.qcsubmit | 0.54.0 |
| openff.toolkit | 0.16.6 |
| basis_set_exchange | 0.10 |
| qcelemental | 0.28.0 |
| rdkit | 2024.09.3 |
Current status - Archived/CompleteConsider manually moving this. |
Lifecycle - Archived/Complete
Dataset Complete! |
openff-dangerbot
added
scientific-review
end-of-life
and removed
scientific-review
labels
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
I have combined the NAGL part 1 and part 2 datasets, and filtered out problematic records (crashes, geometric rearrangements, and stereochemistry). We may want to filter for Conformer RMSD, but I thought we would save that for the single point dataset creation if we do want to do it, let me know what you think.
To combine the two optimization datasets and have QCA recognize they had already been computed, I had to add the initial molecule to the dataset, not the optimized one. It should then recognize the hash and skip the computation, and I confirmed that the hashes were the same between the separate and combined datasets.
Also, I called it
v4.0, but I'm not sure if it should be calledv4.1since it has been filtered? It would be the first version of the combined dataset, which is why I pickedv4.0, but I'm not sure how this fits into the naming convention. Happy to change it.It was non-trivial to combine these two datasets into one, partly due to it being an optimization dataset, and partly because of the large size of the dataset, so I am even more in favor of @ntBre's suggestion of tagging individual records than I was before.
New Submission Checklist
README.mddescribing the dataset see here for examplesdataset*.json; may feature a compression extension, such as.bz2README.md