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DeepRank / deeprank

This repository has been integrated in https://github.com/DeepRank/deeprank2
Apache License 2.0
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Cannot Generate Database #209

Open talk2sohail opened 4 years ago

talk2sohail commented 4 years ago

Describe the bug While the installation process was perfectly fine, testing the successful installation involved running several files as mentioned in the website or in README.md file. While creating the database ( running the test_generate.py ) It is showing some ValueError: Residue numbering not identical in ref and decoy and hence the database cannot be created.

Environment: Google colab ( hosted runtime )

CunliangGeng commented 4 years ago

Thanks for trying our package! Could you try to install DeepRank from the "development" branch with pip install -e .? This branch has the latest code that has solved the issues you mentioned.

We're going to merge the updates to mater branch and release a new version soon.

talk2sohail commented 4 years ago

Thank you very much for speedy reply! I was able to generate the Dataset for testing the installation part. However my need to is to run the model as a whole. It would be too much to ask from you if you could please draw on your experience and mention the correct steps to run and train the model as the documentation seems a bit hard to follow.

Your response is highly solicited.

DarioMarzella commented 4 years ago

Hello talk2sohail, thank you for your feedback and sorry for the late answer.

The documentation is getting updated in the "doc_DM" branch. If you clone it, you will be able to find all the documentation HTML files under docs/_build/html/. Could you please have a look at this documentation and see if the procedure seems clearer to you? More specifically, you should use the DeepLearning Tutorial (docs/_build/html/tutorial_deeplearning.html ). Let me know if it is clearer to you, so we can improve it.