semvec/pypi-packages huggingface dataset:
ramachandran 0.0.2
Generating Ramachandran plot and statistics.
Requires Python: >=3.8

# Ramachandran

Ramachandran plot visualizes energetically allowed regions for backbone torsion (dihedral) angles ψ against φ of amino acid residues in protein structure. This Python package provides the implementations from scratch to crawling PDB/PDBx files from RCSB PDB Bank, parsing PDB/PDBx files for extracting geometric information, computing the torsion angles of residues from atom coordinates and the Ramachandran favorable regions from the reference PDB/PDBx files selected, and creating Ramachandran plots for user-provided PDB/PDBx files.

## Dependencies

* Python 3.8+
* Numpy 1.20.1+
* Scipy 1.6.0+
* Matplotlib 3.3.4+

## Usages

It is recommended to use Docker container to run the program.

### Build Docker Image

```
$ docker build -f docker/ramachandran.Dockerfile --no-cache --tag=ramachandran:0.0.1 .
```

### Run Docker Container

```
$ docker run -it --rm --gpus device=0 -v $(pwd):/mnt ramachandran:0.0.1
```

### Install

```
$ pip install ramachandran
```

### Create Ramachandran Plots

```
$ ramachandran-plot --help
usage: ramachandran-plot [-h] --file-path FILE_PATH
                         [--save-dir-path SAVE_DIR_PATH]
                         [--protein-name PROTEIN_NAME]

Ramachandran Plot Tool. Plots for GLY, PRO, pre-PRO, and Other residues will
be created.

optional arguments:
  -h, --help            show this help message and exit
  --file-path FILE_PATH
                        PDB/PDBx file path. (default: None)
  --save-dir-path SAVE_DIR_PATH
                        Directory path for saving the Ramachandran plots for
                        the PDB/PDBx file. (default: .)
  --protein-name PROTEIN_NAME
                        Protein name. (default: None)
```

## Demo

```
$ ramachandran_plot --file-path 1AXC.cif --save-dir-path 1AXC --protein-name 1AXC
```

|              General             |              GLY             |              PRO             |             Pre-PRO             |
|:--------------------------------:|:----------------------------:|:----------------------------:|:-------------------------------:|
| ![1AXC](./demo/1AXC/general.svg) | ![1AXC](./demo/1AXC/gly.svg) | ![1AXC](./demo/1AXC/pro.svg) | ![1AXC](./demo/1AXC/prepro.svg) |

## TODO

- [ ] Filter homologous proteins for computing the Ramachandran statistics, since too many homologous protein structures will bias the statistics.
- [ ] Add the [original hard-coded Ramachandran favorable region](https://pubmed.ncbi.nlm.nih.gov/4882249/).

## References

* [Ramachandran Plot](https://en.wikipedia.org/wiki/Ramachandran_plot)
* [PyRAMA](https://github.com/gerdos/PyRAMA)
DFL168A 1.0.0
The python module for OBD2/J1939/J1708 Interpreter IC: DFL168A from Dafulai Electronics Inc.
Requires Python: >=3.6

# DFL168A Python Module

Simply import DFL168A module and use function to get motor data.  Don't need to know OBD2 and J1939/J1708/J1587 protocol, don't need to read DFL168A data sheet, just need to know DFL168A pinout, so easily get vehicle parameters values in real time.

You can get User Manual from
http://www.dafulaielectronics.com/DFL168A_python.pdf 

## Getting Started

Please go to http://www.dafulaielectronics.com/DFL168A_python.pdf and read "How to use Library?" section


### Prerequisites

Python version should be 3.6 or higher. You should install pyserial version 3.5 or higher 

```
pip install pyserial
```
If it does not work, you can try command below:
```
py -m pip install pyserial

```
### Installing

You just use command below

```
pip install DFL168A
```

or 

```
py -m pip install DFL168A
```


## Running the tests

There are lots of example in examples folder.

Please download examples folder from 

https://github.com/Dafulai/DFL168A_python/examples

You just modify your serial port Name to your actual Serial port such as "COM1" (or "/dev/ttyS0" ) instead of default "COM4". You can run it directly.



## Authors

* **Jack Xia** 


## License

This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details