openff-nagl-models - Version 0.4.1

What's Changed

• Bump actions/checkout from 4 to 5 by @dependabot[bot] in https://github.com/openforcefield/openff-nagl-models/pull/67
• Work around case where absolute path as PosixPath is passed to get_model by @j-wags in https://github.com/openforcefield/openff-nagl-models/pull/71

Full Changelog: https://github.com/openforcefield/openff-nagl-models/compare/v0.4.0...v0.4.1

- Python
Published by mattwthompson 8 months ago

openff-nagl-models - Version 0.4.0

This release does not contain any new models, instead it just contains new functionality to fetch models from Zenodo DOIs, verify their file hashes, and cache fetched models locally.

What's Changed

• Minor fixes to CI by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/32
• Fix some docs naming typos by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/33
• Add zenodo badge by @mattwthompson in https://github.com/openforcefield/openff-nagl-models/pull/35
• Bump mamba-org/setup-micromamba from 1 to 2 by @dependabot[bot] in https://github.com/openforcefield/openff-nagl-models/pull/36
• Drop macos-12 from actions by @mattwthompson in https://github.com/openforcefield/openff-nagl-models/pull/38
• Fix test name by @mattwthompson in https://github.com/openforcefield/openff-nagl-models/pull/50
• Do not use old pkg_resources in test by @mattwthompson in https://github.com/openforcefield/openff-nagl-models/pull/46
• Try fixing docs builds by @mattwthompson in https://github.com/openforcefield/openff-nagl-models/pull/48
• Use stdlib importlib instead of backports by @mattwthompson in https://github.com/openforcefield/openff-nagl-models/pull/51
• Move more tooling over to pyproject.toml by @mattwthompson in https://github.com/openforcefield/openff-nagl-models/pull/53
• Fix version metadata by @mattwthompson in https://github.com/openforcefield/openff-nagl-models/pull/56
• Dynamically load models from GitHub release assets and cache by @mattwthompson in https://github.com/openforcefield/openff-nagl-models/pull/44
• Drop testing on Python 3.10 by @mattwthompson in https://github.com/openforcefield/openff-nagl-models/pull/54
• Implement fetching by doi and custom hashes by @j-wags in https://github.com/openforcefield/openff-nagl-models/pull/61
• Temporarily stop cron workflow by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/66
• Broken navigation links by @Yoshanuikabundi in https://github.com/openforcefield/openff-nagl-models/pull/63
• Add names to docs by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/65
• Remove fetching from GitHub release assets by @j-wags in https://github.com/openforcefield/openff-nagl-models/pull/62

New Contributors

• @mattwthompson made their first contribution in https://github.com/openforcefield/openff-nagl-models/pull/35
• @dependabot[bot] made their first contribution in https://github.com/openforcefield/openff-nagl-models/pull/36
• @j-wags made their first contribution in https://github.com/openforcefield/openff-nagl-models/pull/61
• @Yoshanuikabundi made their first contribution in https://github.com/openforcefield/openff-nagl-models/pull/63

Full Changelog: https://github.com/openforcefield/openff-nagl-models/compare/v0.3.0...v0.4.0

- Python
Published by j-wags 9 months ago

openff-nagl-models - Version 0.3.0

This release includes the "openff-gnn-am1bcc-0.1.0-rc.3.pt" model. This model can only be loaded with GNNModel.load with NAGL 0.4.x.

This model inherits from openff-gnn-am1bcc-0.1.0-rc.2.pt, and contains a lookup table comprising pre-computed charges for molecules with 3 heavy atoms or fewer. The provenance of each molecule charge is provided in each entry.

The model is applicable to molecules with: - elements C, O, H, N, S, F, Br, Cl, I, P - atoms with between 1 and 6 bonds

It is not trained on molecules with the following bond patterns: - [#15:1]#[*:2] - [#15:1]-[#53:2] - [#15:1]:[*:2] - [#15:1]=[!#6&!#7&!#8&!#16:2] - [#16:1]#[*:2] - [#16:1]-[#35,#53:2] - [#16:1]=[!#15&!#6&!#7&!#8:2] - [#17:1]#,:,=[*:2] - [#17:1]-[!#15&!#16!#6&!#7&!#8:2] - [#1:1]#,:,=[*:2] - [#1:1]-[#1:2] - [#35:1]#,:,=[*:2] - [#35:1]-[!#15&!#6&!#7&!#8:2] - [#53:1]#,:,=[*:2] - [#53:1]-[!#53&!#6&!#7&!#8:2] - [#7:1]#[!#7&!#6:2] - [#8:1]#[*:2] - [#9:1]#,:,=[*:2] - [#9:1]-[!#15&!#16!#6&!#7&!#8:2]

More information can be found in the documentation.

- Python
Published by lilyminium over 1 year ago

openff-nagl-models - Version 0.2.0

This release includes the "openff-gnn-am1bcc-0.1.0-rc.2.pt" model. These models can only be loaded with GNNModel.load with NAGL 0.3.x.

This model inherits from openff-gnn-am1bcc-0.1.0-rc.1.pt, and is further trained to a combination of charge RMSEs, dipole moment, and weighted ESPs as projected by OpenEye ELF10 charges.

The model is applicable to molecules with: - elements C, O, H, N, S, F, Br, Cl, I, P - atoms with between 1 and 6 bonds

It is not trained on molecules with the following bond patterns: - [#15:1]#[*:2] - [#15:1]-[#53:2] - [#15:1]:[*:2] - [#15:1]=[!#6&!#7&!#8&!#16:2] - [#16:1]#[*:2] - [#16:1]-[#35,#53:2] - [#16:1]=[!#15&!#6&!#7&!#8:2] - [#17:1]#,:,=[*:2] - [#17:1]-[!#15&!#16!#6&!#7&!#8:2] - [#1:1]#,:,=[*:2] - [#1:1]-[#1:2] - [#35:1]#,:,=[*:2] - [#35:1]-[!#15&!#6&!#7&!#8:2] - [#53:1]#,:,=[*:2] - [#53:1]-[!#53&!#6&!#7&!#8:2] - [#7:1]#[!#7&!#6:2] - [#8:1]#[*:2] - [#9:1]#,:,=[*:2] - [#9:1]-[!#15&!#16!#6&!#7&!#8:2]

More information can be found in the documentation.

- Python
Published by lilyminium about 2 years ago

openff-nagl-models - Version 0.1.2

This is a minor patch release that moves get_models_by_type to the top level and removes use of the deprecated pkg_resources.

What's Changed

• Try fix deployment by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/15
• add getmodelsby_top to top level import by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/17
• Move on from pkg_resources and use paths everywhere by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/18
• Add and update metadata by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/19
• Add back importlib_resources by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/20
• Remove docs extras by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/22
• Update readme for usage by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/23
• Remove from toml too by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/24
• add importlib_resources to dependencies by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/25

Full Changelog: https://github.com/openforcefield/openff-nagl-models/compare/v0.1.1...v0.1.2

- Python
Published by lilyminium about 2 years ago

openff-nagl-models - Version 0.1.1

This is a minor patch release that adds the function get_models_by_type() that returns models sorted by version.

What's Changed

• Add model to toc by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/11
• Add getlatest_models by @lilyminium in https://github.com/openforcefield/openff-nagl-models/pull/13

Full Changelog: https://github.com/openforcefield/openff-nagl-models/compare/v0.1.0...v0.1.1

- Python
Published by lilyminium over 2 years ago

openff-nagl-models - Version 0.1.0

This release includes the "openff-gnn-am1bcc-0.1.0-rc.1.pt" model. It also upgrades the existing pre-production model to use NAGL 0.3.0 architecture. As such, these models can only be loaded with GNNModel.load with NAGL 0.3.x.

This model is trained to a combination of charge RMSEs, dipole moment, and ESPs as projected by OpenEye ELF10 charges.

The model is applicable to molecules with: - elements C, O, H, N, S, F, Br, Cl, I, P - atoms with between 1 and 6 bonds

It is not trained on molecules with the following bond patterns: - [#15:1]#[*:2] - [#15:1]-[#53:2] - [#15:1]:[*:2] - [#15:1]=[!#6&!#7&!#8&!#16:2] - [#16:1]#[*:2] - [#16:1]-[#35,#53:2] - [#16:1]=[!#15&!#6&!#7&!#8:2] - [#17:1]#,:,=[*:2] - [#17:1]-[!#15&!#16!#6&!#7&!#8:2] - [#1:1]#,:,=[*:2] - [#1:1]-[#1:2] - [#35:1]#,:,=[*:2] - [#35:1]-[!#15&!#6&!#7&!#8:2] - [#53:1]#,:,=[*:2] - [#53:1]-[!#53&!#6&!#7&!#8:2] - [#7:1]#[!#7&!#6:2] - [#8:1]#[*:2] - [#9:1]#,:,=[*:2] - [#9:1]-[!#15&!#16!#6&!#7&!#8:2]

More information can be found in the documentation.

- Python
Published by lilyminium over 2 years ago

openff-nagl-models - Version 0.0.2

This is an initial release with the v0.0.1-alpha.1 pre-production GNN model for assigning AM1-BCC-like partial charges to molecules.

Warning: as this model has not yet passed our validation benchmarks, we do not recommend using this model in real scientific work.

Warning: model included here is currently a serialized dict that must be loaded by GNNModel.load in openff-nagl>=0.2.1. This format and API may change in the future.

- Python
Published by lilyminium about 3 years ago

openff-nagl-models - Version 0.0.1

This is an initial release with the v0.0.1-alpha.1 pre-production GNN model for assigning AM1-BCC-like partial charges to molecules.

Warning: as this model has not yet passed our validation benchmarks, we do not recommend using this model in real scientific work.

Warning: model included here is currently an openff.nagl.GNNModel that can be loaded with torch.load. This format and API may change in the future.

- Python
Published by lilyminium about 3 years ago