2023.05.2

This release adds a deep learning edition with 6 new talktorials. An overview is given in the pre-print TeachOpenCADD goes Deep Learning: Open-source Teaching Platform Exploring Molecular DL Applications.

More details below.

What's changed

New talktorials

• T033: Molecular representations by @gerritgr #314
• T034: Recurrent neural networks for molecular property prediction by @azmtag #320
• T035: Graph neural networks for molecular property prediction by @PaulaKramer #287
• T036: E(3)-equivariant graph neural network for molecular property prediction by @joschka-gross #326
• T037: Uncertainty estimation by @mbackenkoehler #286
• T038: Protein ligand interaction prediction by @Old-Shatterhand #290

Fixes

• Updated environment for new notebooks and integrate into CI by @mbackenkoehler
• Additional notebook reviews by @f-sod, @hamzaibrahim21, @verenawolf and @AndreaVolkamer
• Added talktorials on the website @PaulaKramer #384
• T020: Fixed typo by @jaketanderson #383

Notes

• Talktorials T035, T036, and T038 currently require a manual installation of pytorch-geometric
• Some talktorials are ignored in the CI because they may require repeated executions, mainly due to the use of online APIs. #382

New contributors - Thanks!

• @gerritgr
• @azmtag
• @joschka-gross
• @Old-Shatterhand
• @f-sod
• @jaketanderson
• Verena Wolf

2023.05.1

This release

• fixes notebooks that broke since the 2022.09.01 release
• includes an updated environment for all talktorials
• updates the fingerprint generator from RDKit in all talktorials
• includes T008 and T019 in CI again
• cleans up and syncs TeachOpenCADD documentation and README
• updates GHA configs in order to solve undescriptive conda fails

More details are below.

What’s changed

Fixes

Notebooks

• T002: fix deprecated pandas functions by @mbackenkoehler in #331
• T004/T007/T022: Updated fingerprint generator by @hamzaibrahim21 in #361 #348 and @greglandrum in #330
• T008: is working again, since Ligand Expo website is back online
• T011: delete deprecated web scraping for image URL by @dominiquesydow in #322
• T018: fix and update notebook by @Armin-Ariamajd in #350
• T019: template bug fix by @schallerdavid and @mbackenkoehler in #308
• T020: updated deprecated code by @dominiquesydow in #363
• T023: fix deprecated link by @t-kimber in #324
• For all notebooks: update deprecated links by @hamzaibrahim21 in #341
• Remove local directories in outputs by @mbackenkoehler in #353

Environment

• Switch to linkinator by @mbackenkoehler in #335
• Update pytest for new pandas version by @mbackenkoehler in #332
• CI: Update actions/checkout from v2 to v3 and use mambaforge instead of mamba as resolver by @dominiquesydow in #323
• Updated environment: RDKit version 2022.09.1, pandas version 2.0.0

Docs

• Update TeachOpenCADD website (docs) and repo README by @dominiquesydow in #315
• README: Link to new website pages by @dominiquesydow in #317

New Contributors - Thanks!

• @mbackenkoehler
• @hamzaibrahim21
• @PaulaKramer

2022.09.1

This release

• fixes notebooks that broke since the 2022.09.0 release (updating notebook content and the environment)
• extends the TeachOpenCADD documentation (contributor guide including extended PR template)
• supports Linux Python 3.8 & 3.9 and MacOS/Windows Python 3.8
• temporarily has to drop support for T008 and T019 (see section Important notes)

More details below.

Important notes

The following notebooks are not available at the moment:

• T008 in January due to the temporary shutdown of http://ligand-expo.rcsb.org/ - we will revisit T008 in Februray to check if the notebook can run again fully: #303
• T019 until the following bug is fixed: #307

What's Changed

Fixes (notebooks / environment)

• Base branch for CI/env fixes by @dominiquesydow in #296
  • T008/10/15/16/18/20: AttributeError: module 'numpy' has no attribute 'typeDict' by @dominiquesydow in #294
  • T011/12: Remove pinned jsonschema from env by @dominiquesydow in #297
  • T018: Remove nbval check for complex cell output by @dominiquesydow in #304
  • T008: Remove from CI in Jan 2023 by @dominiquesydow in #305
  • T019: Fix atom unit conversion by @dominiquesydow in #306
  • T021/22: Run under global environment by @dominiquesydow in #309

Documentation / README

• Add TeachOpenCADD contribution guide by @dominiquesydow in #274
• Extend PR template (for new talktorials) by @dominiquesydow in #276
• [DOCS] Added Jupyter Notebook tutorial by @Telomelonia in #291
• README: Fix broken anaconda badge/link by @dominiquesydow in #293
• README: Update Zenodo badge by @dominiquesydow in #272
• Docs: Update TeachOpenCADD citations by @dominiquesydow in #295
• Docs: Add more MacOS/M1 install instructions by @dominiquesydow in #301

New Contributors

• @Telomelonia made their first contribution in #291 --- thank you!!

Full Changelog: 2022.09.0...2022.09.1

2022.09.0

Description

This is our Sep 2022 TeachOpenCADD release (2022.09.0). From now on, we will keep at least a biyearly major release cycle 20xx.03.0 and 20xx.09.0.

What's Changed

• FIX: correction description num layers and neurons (hidden_layer_sizes) by @AJK-dev in #249
• README: Add paper links to latest release news by @dominiquesydow in #250
• Docs: Update installing documentation by @dominiquesydow in #253
• Python requirements >= 3.8 by @dominiquesydow in #254
• T008: Use GraphQL for PDB ligand search #248 by @dominiquesydow in #259
• Pin ipywidgets < 8 to solve #262 by @dominiquesydow in #263
• CI: Drop figure size nbval check by @dominiquesydow in #264
• CI: Revert Win Py3.9 back to Py3.8; pin tensorflow<=2.6 by @dominiquesydow in #267
• README: Add TOC-kinase topics to main png by @dominiquesydow in #266

New Contributors

• @AJK-dev made their first contribution in #249

Full Changelog: 2021.12.2...2022.09.0

2021.12.2

Description

Changes added during the LiveCoMS paper revision (kinase similarity edition T023-T028) + some documentation enhancements and CI/bug fixes

What's Changed

Kinase edition updates

• T028 sequence plot svg by @t-kimber in #214
• Identify kinase with the most structures. by @t-kimber in #215
• Add usage scope to notebooks by @dominiquesydow in #219
• T23 fig by @t-kimber in #235
• T028: Heatmap with similarity matrix by @t-kimber in #236
• T028 : Combined measures by @t-kimber in #237
• Base branch for T23-28 revisions by @dominiquesydow in #238
• Kinase similarity demo mode by @dominiquesydow in #239

Documentation updates

• Update README.md by @t-kimber in #202
• Update website (2021 collection + open website disclaimer) by @dominiquesydow in #207
• Update install details with conda-forge channel by @dominiquesydow in #208
• Update installation instructions by @dominiquesydow in #210
• Update citations (NAR, LiveCoMS) by @dominiquesydow in #246

CI and bug fixes

• Fix typos in T016. by @t-kimber in #205
• Fix pandas failure by @schallerdavid in #206
• Fixes for protonation of protein and binding site detection by @corey-taylor in #216
• Pin jinja2 to fix failing docs by @dominiquesydow in #217
• Fix CI failures by @schallerdavid in #222
• Run ci on weekly bases by @schallerdavid in #224
• Test docs every week on monday by @schallerdavid in #225
• Pin rdkit to fix kekulize error by @schallerdavid in #226
• Fix T008 under windows by @schallerdavid in #229
• fix github star link by @schallerdavid in #230
• Fix CI for T025 and T026 by @dominiquesydow in #234
• Fix black-nb in T019 by @t-kimber in #242

New Contributors

• @corey-taylor made their first contribution in #216

Full Changelog: 2021.12.1...2021.12.2

2021.12.1

Add a set of notebooks on kinase similarity #115

• T023 - What is a kinase? #120
• T024 - Kinase similarity: Sequence #117
• T025 - Kinase similarity: Structure (kinome-specific) #121
• T026 - Kinase similarity: Interactions #122
• T027 - Kinase similarity: Ligand profiles #118
• T028 - Kinase similarity: Compare perspectives #123

2021.12.0

This is the next official TeachOpenCADD release 2021.12.0 that contains a lot of new talktorials, a new website, and a new convenient way to install TeachOpenCADD locally via our new conda package.

Note: Some changes were already part of the prior experimental release v1.4.0 but are listed here again and extended as part of this official release.

RELEASE NAMING SCHEME

• We are changing our version naming scheme from v0.0.0 to YYYY.MM.0.
• For TeachOpenCADD maintainers: Increase 0 (+1) for bugs and new features, until you want to cut the next major release with accumulated changes, which will then again be YYYY.MM.0 for the year/month of your release cut.

NEW

• More talktorials: T000 and T011-T022
• Browse our talktorials online on our new TeachOpenCADD website.
• We have a conda package now (mamba install teachopencadd), which allows our users to install all dependencies and copy all notebooks to their own workspace for local interaction with the talktorials.
• Use our new teachopencadd command-line interface (CLI) to access and install the talktorials easily on your machine.
• Set up continuous integration (CI) for Windows/Ubuntu/MacOS:
  • Test all talktorials with nbval (a) to ensure they do not throw errors and (b) to check for selected cells if the output stays the same.
  • Format all talktorials with black-nb.

IMPROVEMENTS

• Refactoring of the previously published talktorials T001-T010 (PEP8 guidelines)
• Update README (TOC figure incl. all 22 topics and references incl. our book chapter).
• Update website installation instructions (use conda package; note that Windows users have to add the defaults channel).
• Add sphinxext-opengraph extension to enable the preview of our website whenever we post the link.
• Update badges (e.g. add conda badge).

v1.4.0

This is an experimental release used to submit teachopencadd to conda-forge.

Note: The upcoming 2021.1 release will be the official release.

NEW

• New talktorials: T000 and T011-T022 (excluding T018)
• New website
• New teachopencadd CLI
• New CI
• New repo structure

IMPROVEMENTS

• Refactoring of the previously published talktorials T001-T010

v1.3.0

ℹ Note: This is the last release of the v1.x series. Future releases will adopt the YYYY.MM versioning scheme (as in 2021.01) and will feature a reworked package structure that will allow us to distribute the project as a conda package. It will also include more content! Track progress on #74.

If for some reason you prefer the old repository structure, this is the last release that will provide the content in that way.

NEW

• Talktorial T11 (preview): use online webservices to create a docking pipeline in the cloud

IMPROVEMENTS

• Simplified dependencies
• NGLView visualization replaces PyMol

FIXES

• #37 was fixed via #38

Thanks to @rhjohnstone, @richardjgowers, @speleo3, @Andy-Wilkinson

v1.2.0

NEW

• Conda yml file is provided to ensure an easy and quick setup of an environment containing all required packages

IMPROVEMENTS

• Use new RDKit function to generate fingerprints (http://rdkit.org/docs/source/rdkit.Chem.rdFingerprintGenerator.html)
• T4: scatter plots added, comparing similarity values based on different fingerprints (Morgan/MACCS) and different similarity measures (Tanimoto/Dice)
• Add and clearify explanatory text

FIXES

• Typos fixed
• Style/formatting inconsistencies removed