Shervine Amidi

**Context**. With package repos such as [PyPI](https://packaging.python.org/glossary/#term-Python-Package-Index-PyPI), package installation can be done with a single command. **Setup**. Suppose a user wants to install EnzyNet. **Current behavior**. The user currently needs...

**Context**. Real-time PDB parsing with the BioPython package, e.g. typically: https://github.com/shervinea/enzynet/blob/31d30e0272e0c9425e0c76085761f211b89f8b7c/enzynet/pdb.py#L53 is expensive and bottlenecks the training process if done on the fly. For this reason, we put in place...

This one is self-explanatory. We need to make sure all implemented logic of the package is properly tested.

**Context**. The [`pdb.py`](https://github.com/shervinea/enzynet/blob/31d30e0272e0c9425e0c76085761f211b89f8b7c/enzynet/pdb.py) file encodes extraction-related operations. We need to ensure all extraction operations produce objects that are comparable with each other, as it is the hidden assumption behind the...

**Context**. The [`weights.py`](https://github.com/shervinea/enzynet/blob/31d30e0272e0c9425e0c76085761f211b89f8b7c/enzynet/weights.py) file implements amino-acid weights. These may be useful additional information for training. **Current behavior**. There is no way to query existing weights. Users need to navigate to...

**Context**. At training time, the enzymes' volumes are precomputed with the `check_precomputed()` method, e.g. for the training set: https://github.com/shervinea/enzynet/blob/31d30e0272e0c9425e0c76085761f211b89f8b7c/scripts/architecture/run_enzynet.py#L162 Since enzymes' volumes are independent from each other, this task is...

**Context**. Issue opened based on @w-t-2017's comment https://github.com/shervinea/enzynet/issues/4#issuecomment-824681634. **Background**. This package relies on ever-changing dependencies listed as requirements such as Keras or Tensorflow. It would be useful to know which...