Metadata-Version: 2.4
Name: biobridge
Version: 0.2.0
Summary: A library for simulating all biology related things, analyzing them and visualizing them.
Author-email: Okerew <okerewgroup@proton.me>
License-Expression: MIT
Project-URL: Documentation, https://github.com/Okerew/biobridge#readme
Project-URL: Issues, https://github.com/Okerew/biobridge/issues
Project-URL: Source, https://github.com/Okerew/biobridge
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: numpy>=1.21.0
Requires-Dist: matplotlib>=3.5.0
Requires-Dist: py3Dmol>=2.0.0
Requires-Dist: opencv-python>=4.5.0
Requires-Dist: mediapipe>=0.8.0
Requires-Dist: scikit-learn>=1.0.0
Requires-Dist: scipy>=1.7.0
Requires-Dist: imageio>=2.9.0
Requires-Dist: scikit-image>=0.18.0
Requires-Dist: networkx>=2.6.0
Requires-Dist: biopython>=1.78.0
Requires-Dist: requests>=2.25.0
Requires-Dist: pyusb>=1.1.0
Requires-Dist: opcua>=0.98.0
Requires-Dist: pyserial>=3.4.0
Requires-Dist: Flask>=2.0.0
Requires-Dist: pandas>=1.3.0
Requires-Dist: okrolearn>=0.2.0
Requires-Dist: pytesseract>=0.3.8
Requires-Dist: pillow>=8.0.0
Requires-Dist: pybind11>=2.10.0

# Biobridge

<img src="biobridge.png" alt="Biobridge Logo">

Biobridge is a Python library for simulating biological processes and systems also analyzing them, visualising them, and interacting with them.

## Installation

Firstly you need to install pyrosetta

Then install biobridge

```sh
pip install biobridge
```

## Usage

To use Biobridge in your project, import it for example:

``` python
from biobridge import *
# Create two proteins
protein1 = Protein("Protein A", "ACDEFGHIKLMNPQRSTVWY")
protein2 = Protein("Protein B", "YVWTSRQPNMLKIHGFEDCA")

# Define bindings for the proteins
protein1.add_binding("Site 1", "High")
protein2.add_binding("Site 3", "Medium")

# Create a cell with specific properties
cell1 = Cell(
    name="Cell X",
    cell_type="Epithelial Cell",
)

organelle = Mitochondrion(0.5, 100)

# Add organelles to the cell
cell1.add_organelle(organelle, quantity=10)
cell1.add_organelle(Organelle("Nucleus", 1), quantity=1)
cell1.add_organelle(Organelle("Ribosome", 100), quantity=100)
cell1.add_chromosome(Chromosome(DNA("ATCG" * 1000), "Chromosome 1"))

# Print cell details
print("Cell X Description:")
print(cell1)
```

## The notable functions are:

```python
from biobridge import *

Cell()
DNA()
RNA()
Protein()
Chromosome()
Environment()
Tissue()
System()
ImageAnalyzer()
Orchestrator()
Virus()
Infection()
SQLDNAEncoder()
SurgicalSimulator()
```

To see more examples how to use biobridge see the test files, biobridge works well with jupyter notebooks.

You can setup a config for biobridge to do this download the create_config.py file.

If you want to use something else than vscode you can use my <a href="https://github.com/Okerew/biobridge_editor">editor</a> built for this library.
