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DeepRank
This repository has been integrated in https://github.com/DeepRank/deeprank2
Hi, thanks for the great work! I want to use deeprank to indentify the native pose from its decoys generated by ZDock. How can i use deeprank to get the...
**Describe the bug** DeepRank output format is not user friendly **Environment:** Not relevant **To Reproduce** See any example from https://github.com/DeepRank/deeprank/tree/master/paper_pretrained_models **Expected Results** The output of the network is an HDF5...
- [ ] add CITATION.cff - [ ] add reference (https://www.nature.com/articles/s41467-021-27396-0)
The class `DataSet` argument `grid_shape` is removed in PR #242 and use `grid_info` instead. The `grid_shape` related part should be updated in - [ ] README - [ ] documentation
**Describe the bug** While creating the database ( the data were generated by antibody complex ) It is showing some ValueError: Residue Center not found and the decoys were removed....
Energy of desolvation currently working in this branch (complete issue: [#issue68](https://github.com/DeepRank/deeprank/issues/68)). The organization of ```deeprank/features/Edesolv.py``` though might not be great, so I would appreciate comments on that (if needed).
**Describe the bug** DataGenerator crashes when no "pssm_source" is provided **Environment:** - OS system:Linux **To Reproduce** Steps/commands to reproduce the behaviour: 1. Create a DataGenerator object, do not specify "pssm_souce"...
Hi Alex, Currently deeprank implemented Eelec, Evdw, and BSA. But we did not implement desolvation energy in deeprank yet. Do you think we should implement it? Could you please point...
**Describe the problem** The data_set definition in "Tutorial: Deep Learning" is obsolete, not up-to-date with the data_set definition present in `test/test_learn.py`. **Environment:** - OS system: Linux **To Reproduce** Steps/commands to...
Advanced tutorial for creating your own features and targets presents some typos and it's not really clear. Especially, it's not clear how the feature/target should be shaped to be correctly...