Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of https://github.com/choderalab/espaloma

https://github.com/choderalab/espaloma - Version 0.3.2 - Support Latest DGL Version

Note

This release updates espaloma to support the newest version (1.1.2) of DGL. There are no API breaking changes or updates to the espaloma model. We have attached espaloma-0.3.2.pt to this release for convince, but this model is identical to espaloma-0.3.1.pt. espaloma-latest.pt is also the same as espaloma-0.3.1.pt. Please see https://github.com/choderalab/espaloma/releases/tag/0.3.1 for more information about the espaloma 0.3.x family of models.

What's Changed

  • Support latest (1.1.2) DGL version

Bug fixes, packaging, and documentation updates

  • Installation Guide Update by @mikemhenry in https://github.com/choderalab/espaloma/pull/175
  • Add docker and apptainer image building on demand by @mikemhenry in https://github.com/choderalab/espaloma/pull/176
  • Update to new dgl version (1.1.1) by @mikemhenry in https://github.com/choderalab/espaloma/pull/179
  • Add Instructions on loading local model by @ijpulidos in https://github.com/choderalab/espaloma/pull/183
  • Test & Update to newest DGL Version (1.1.2) by @mikemhenry in https://github.com/choderalab/espaloma/pull/186
  • Update readme and docs for version 0.3.2 @mikemhenry in https://github.com/choderalab/espaloma/pull/188

Full Changelog: https://github.com/choderalab/espaloma/compare/0.3.1...0.3.2

- Python
Published by mikemhenry over 2 years ago

https://github.com/choderalab/espaloma - Version 0.3.1

What's Changed

  • Fix CI -- updated by @ijpulidos in https://github.com/choderalab/espaloma/pull/152
  • Support newer versions of OpenFF Toolkit by @mattwthompson in https://github.com/choderalab/espaloma/pull/155
  • Support for modern openff-toolkit versions (>=0.11) by @ijpulidos in https://github.com/choderalab/espaloma/pull/153
  • Support different improper torsion multiplicity by @kntkb in https://github.com/choderalab/espaloma/pull/157
  • Update default reference force field when creating a system from graph (fix #160) by @kntkb in https://github.com/choderalab/espaloma/pull/161
  • Add comments to why some of the input features were commented out by @kntkb in https://github.com/choderalab/espaloma/pull/163
  • Improved deployment testing with different charge-method options by @ijpulidos in https://github.com/choderalab/espaloma/pull/164
  • Changed default charge method to nn by @madilynpaul in https://github.com/choderalab/espaloma/pull/142
  • Fix loading molecules serialized with older openff-toolkit versions (<=0.11) by @ijpulidos in https://github.com/choderalab/espaloma/pull/166
  • Use rtd for docs by @mikemhenry in https://github.com/choderalab/espaloma/pull/167
  • Speed up and improve CI and update readme by @mikemhenry in https://github.com/choderalab/espaloma/pull/169
  • First pass at model fetch by @mikemhenry in https://github.com/choderalab/espaloma/pull/172
  • Use dgl.to_homogeneous instead of the old deprecated name by @ijpulidos in https://github.com/choderalab/espaloma/pull/173

New Contributors

  • @ijpulidos made their first contribution in https://github.com/choderalab/espaloma/pull/152
  • @mattwthompson made their first contribution in https://github.com/choderalab/espaloma/pull/155
  • @madilynpaul made their first contribution in https://github.com/choderalab/espaloma/pull/142

Full Changelog: https://github.com/choderalab/espaloma/compare/0.3.0...0.3.1

Model updates

  • Note that espaloma-0.3.0.pt is also deployed which is compatible with espaloma-0.3.1.pt. espaloma-0.3.0.pt was renamed to espaloma-0.3.1.ptto maintain consistency with the release version.
  • espaloma-0.3.1.pt (espaloma-0.3.0.pt) is a new espaloma model (see notes_for_espaloma-0.3.1.pdf for more details) with the improved features:
    • Trained with curated quantum chemical dataset covering small molecules, peptides, and nucleic acids, containing over 15,000 unique molecules and 1M conformations
    • Improved training strategy that uses both energies and forces, as well as L2 regularization to proper and improper torsion force constants to reduce the model complexity and variance
    • Restrict improper torsion multiplicity to n=1,2

Notes

  • espaloma-0.3.1.pt (espaloma-0.3.0.pt) was trained and created using a dev version (commit: 4c6155b) of v0.3.1 release based on openff-toolkit 0.10.6
    • A manuscript describing the complete fitting process and assessment is forthcoming
    • Please warn that v0.3.0 is no longer compatible with v0.3.1, and espaloma-0.3.1.pt is not supported by v0.3.0

- Python
Published by kntkb almost 3 years ago

https://github.com/choderalab/espaloma - Version 0.3.0

What's Changed

  • Get rid of large storage by @yuanqing-wang in https://github.com/choderalab/espaloma/pull/133
  • Fix nonbonded force subtraction by @kntkb in https://github.com/choderalab/espaloma/pull/134, https://github.com/choderalab/espaloma/pull/140
  • Exclude resonance variant input features by @yuanqing-wang in https://github.com/choderalab/espaloma/pull/148

Full Changelog: https://github.com/choderalab/espaloma/compare/0.2.4...0.3.0

Model Update

  • espaloma_0.3.0rc1.pt is deployed as a release candidate for espaloma0.3.0 (see `notesfor_espaloma-0.3.0rc1.pdf` for more details).
  • Please note that notes_for_espaloma-0.3.0rc1.pdf are temporal and manuscript describing the complete fitting process and assessment is forthcoming.
  • Please warn that espaloma_0.3.0 is no longer compatible with the 0.2.x models, and vice versa.

- Python
Published by kntkb about 3 years ago

https://github.com/choderalab/espaloma - Version 0.2.4

What's Changed

  • Formal charge fix by @jthorton in https://github.com/choderalab/espaloma/pull/122
  • Subtract nonbonded by @kntkb in https://github.com/choderalab/espaloma/pull/124
  • Fix readme link to docs by @mikemhenry in https://github.com/choderalab/espaloma/pull/117
  • Fix docstring for JanossyPoolingNonbonded class. by @kaminow in https://github.com/choderalab/espaloma/pull/102
  • Pin to older toolkit + fix CI by @mikemhenry in https://github.com/choderalab/espaloma/pull/129
  • fix yaml syntax issue by @mikemhenry in https://github.com/choderalab/espaloma/pull/132

New Contributors

  • @jthorton made their first contribution in https://github.com/choderalab/espaloma/pull/122
  • @kntkb made their first contribution in https://github.com/choderalab/espaloma/pull/124

Full Changelog: https://github.com/choderalab/espaloma/compare/0.2.3...0.2.4

- Python
Published by mikemhenry over 3 years ago

https://github.com/choderalab/espaloma - Version 0.2.3

Fixed the index casting bug caught by new version of DGL.

- Python
Published by yuanqing-wang almost 4 years ago

https://github.com/choderalab/espaloma - Version 0.2.2

Used Smirnoff-style 3-termed improper torsion in stead of 6-termed. (https://github.com/choderalab/espaloma/pull/105)

This version is concurrent with: https://arxiv.org/abs/2010.01196v3

- Python
Published by yuanqing-wang about 4 years ago

https://github.com/choderalab/espaloma - Version 0.2.1

Erased global DGL import to make package compatible with Conda-forge.

- Python
Published by yuanqing-wang over 4 years ago

https://github.com/choderalab/espaloma - Version 0.2.0

Code base for https://arxiv.org/abs/2010.01196 v2.

- Python
Published by yuanqing-wang over 4 years ago

https://github.com/choderalab/espaloma - Code base for preprint arXiv:2010.01196 v1

This release is responsible for generating the results for https://arxiv.org/abs/2010.01196.

- Python
Published by yuanqing-wang over 5 years ago