Dead links

[mbackenkoehler]

As per the CI, the following links do not work. The 403 are rejections which can probably be added to the skips like doi.org. The 404 either moved or are gone. These need to be fixed manually.

• [404] _static/images/apple-icon-152x152.png

external_dependencies.html

• [404] http://rasbt.github.io/biopandas/

external_tutorials_collections.html

• [404] https://en.gdch.de/network-structures/divisions/computers-in-chemistry-cic.html #342
• [404] https://psychiatrie-psychotherapie.charite.de/metas/person/person/address_detail/ritter-7/

talktorials/T004_compound_similarity.html

• [403] http://pubs.acs.org/doi/abs/10.1021/jm401411z

talktorials/T005_compound_clustering.html

• [404] talktorials/images/butina_full.pdf

talktorials/T011_query_online_api_webservices.html

• [404] talktorials/data/_tmp/video.mp4
• [0] https://2.python-requests.org/en/master/user/quickstart/
• [0] https://2.python-requests.org/en/master/user/authentication/

talktorials/T012_query_klifs.html

• [403] https://www.science.org/doi/10.1126/science.1075762

talktorials/T013_query_pubchem.html

• [0] http://www.icoa.fr/pkidb/
• https://www.icoa.fr/pkidb/index.html

talktorials/T015_protein_ligand_docking.html

• [403] https://www.schrodinger.com/training/videos/small-molecule-drug-discovery/introduction-drugs-drug-targets-and-molecular
• [403] https://www.schrodinger.com/training/videos/small-molecule-drug-discovery/protein-ligand-docking
• [404] http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
• [404] http://vina.scripps.edu/manual.html

talktorials/T022_ligand_based_screening_neural_network.html

• [403] https://machinelearningmastery.com/rectified-linear-activation-function-for-deep-learning-neural-networks/
• [403] https://machinelearningmastery.com/loss-and-loss-functions-for-training-deep-learning-neural-networks/
• [403] https://machinelearningmastery.com/adam-optimization-algorithm-for-deep-learning/
• [410] https://xzz201920.medium.com/activation-functions-linear-non-linear-in-deep-learning-relu-sigmoid-softmax-swish-leaky-relu-a6333be712ea

talktorials/T021_one_hot_encoding.html

• [403] https://machinelearningmastery.com/how-to-one-hot-encode-sequence-data-in-python/
• [0] https://www.machinecurve.com/index.php/2020/02/07/what-is-padding-in-a-neural-network/

talktorials/T009_compound_ensemble_pharmacophores.html

• [403] http://pubs.acs.org/doi/pdf/10.1021/ci049885e

talktorials/T012_query_klifs.html

• [403] https://science.sciencemag.org/content/298/5600/1912
• [403] https://www.science.org/doi/10.1126/science.1075762

talktorials/T018_automated_cadd_pipeline.html

• [404] http://rasbt.github.io/biopandas/
• [404] http://vina.scripps.edu/manual.html

talktorials/T020_md_analysis.html

• [404] https://www.mdanalysis.org/docs/documentation_pages/analysis/hbond_analysis.html

[mbackenkoehler]

@hamzaibrahim21 You can tick off the links you worked through here.

[hamzaibrahim21]

All links should be fixed except for the first error " [404] _static/images/apple-icon-152x152.png" ba8a4c8. Should I add an "apple-icon-152x152.png", because there is no such an image in mentioned directory, or just ignore the error?

[mbackenkoehler]

@hamzaibrahim21 That's great! Thanks! Yes, please add the appli-icon one. It should be safe to ignore.

[mbackenkoehler]

@hamzaibrahim21 Somehow a few new ones popped up for me. You can run the checks locally, following the job in the gh workflow.

Also, for local files you can check in docs/_build.html if everything built correctly. T005 is missing the butina figure, for example.

[hamzaibrahim21]

@mbackenkoehler All broken links are fixed by now 38709b2, please let me know if other links popped up again.