Extending and updating curation sets.

[chrisiacovella]

Description

This will add new datasets into model forge, including full spice 1.1.4, preliminary spice 2, ani2x, and the test dataset.

Notes:

• Currently, the spice openff code only pulls the pubchem datapoints from qcarchive; the full dataset will be included in the updated code. As part of this, the hdf5 file will get an additional optional source attribute for dataset, to allow for future filtering (as mentioned in #65). This file will also write out forces, rather than gradients, again as mentioned in #65.
• As we have been started to discuss in #72 , we do not necessarily need formation energies within the datasets. The linear regression scheme, or using a dictionary of values can be done in the dataset pre-processing.

Todos

Notable points that this PR has either accomplished or will accomplish.

• [x] Ani2x
• [x] ANi2x tests
• [x] spice 2
• [x] spice 2 tests
• [x] full spice 1.1.4
• [x] Add unit tests for new datasets
• [x] updated wiki with dataset/hdf5 format description.
• [x] upon discussion, add field that reports total molecule charge (needed for spice that allow for non-neutral molecules).

Status

• [x] Ready to go

[codecov-commenter]

Codecov Report

Merging #74 (41f6653) into main (342c5ed) will increase coverage by 8.90%. The diff coverage is 94.14%.

Additional details and impacted files

[chrisiacovella]

The wiki has been updated with a lot of examples and discussion about the hdf5 file format and underlying "data" datastructure passed to the hdf5 file.

https://github.com/choderalab/modelforge/wiki/Dataset-and-curation

[chrisiacovella]

I still need to implement the test data set. I had to rerun some calculations.

[chrisiacovella]

There appears to be another change in the naming scheme in one of the datasets (Processing SPICE DES370K Single Points Dataset); I need to add in some regex searching to identify this different naming convention and skip all the sorting by conformers ids.