semvec/pypi-packages huggingface dataset:
ProtViewer 0.0.6
A web-based tool to visualize activities in proteins
License: MIT
Requires Python: >=3.0
Keywords: python,visualization,protein,activity

# ProtViewer

A tool to view activity pattern in protein structures. Protein structure visualization is only one application of this 
tool. One can visualize arbitrary graphs with some activity patterns with this tool.

## Website

You can use the tool very easily to visualize activities of certain nodes in graphs. The 
[online-viewer](old-shatterhand.github.io/ProtViewer) can be used to visualize activity of nodes in a graph.
One example is the binding prediction of some model for protein-ligand interactions. The model can output
scores defining how much influence a certain node had on the prediction if or if not a certain protein binds to a 
target or not.

## Generating Activity Files

You can easily generate the input files for the online viewer yourself be following the structure described in the "Activity File Structure" section below.

### Package Installation

Otherwise, you can install the python package to generate the files using pip
``````shell
pip install protviewer
``````
and also updating is very easy. Just type
``````shell
pip install --upgrade protviewer
``````

### Package Usage

To use the package and generate the activities for a certain protein, just call
``````python
from viewer import view

view(pdb_file, output_dir, activities, distances)
``````
This will generate the json-file inside the `output_dir` as `[pdb_file].json`. You can then directly upload this
output file to the [web service](old-shatterhand.github.io/ProtViewer) and investigate what your model guided to the 
decision if a model binds or not.

## Activity File Structure
The json-file you input to the [online-viewer](old-shatterhand.github.io/ProtViewer) has to have the following structure
``````json
{
  "nodes": [
    "AA_1": {
      "x": ...,
      "y": ...,
      "z": ...,
      "activity": ...,
      "distance": ...,
    }, ...
  ],
  "edges": {
    "start": [
      0, 2, 1, 5, 3, ...
    ],
    "end": [
      2, 1, 5, 3, 6, ...
    ]
  }
}
``````
polymedia 0.2.1
A polyglot hypermedia library for python ReSTful services
License: MIT

# WSTL-PY

A python package to make implementing [Web Service Transition Language (WSTL)](http://rwcbook.github.io/wstl-spec/) in projects. 

## Package Development

I am developing this package as part of work on the [Open Distributed Information Service (ODIS)](https://github.com/michalporeba/odis/). 
Hopefully, it will be useful beyond this project, but I am not ready to make any promises just yet. 
At the moment it should be considered an experimental work.

## Related Work 

There is also the [ALPS-PY](https://pypi.org/project/alps-py) developed for the same reason, 
which helps with [Application-Level Profile Semantics (ALPS)](http://alps.io/) implementations. 

## Feedback 

Any feedback will be welcomed. Create an issue, or start a discussion on 
the [ODIS repo](https://github.com/michalporeba/odis/)

&nbsp;
# Usage 

At the moment it is possible to create a valid WSTL message from code: 

```python
wstl = Wstl()
wstl.add_action(...)
wstl.add_data_item(...)

print(wstl.to_data())
```

Behind the scenes it can resolve action names to full action descriptions. 

&nbsp;
# Plans

[ ] Integration with [ALPS-PY](https://pypi.org/project/alps-py) project