Metadata-Version: 2.4
Name: biochemHH
Version: 0.0.4
Summary: Biochemistry & molecular biology helper tools
Author: Otter Brown
Author-email: 
License: GPL-2.0-only
Keywords: biochemistry molecular biology bioinformatics
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: matplotlib
Requires-Dist: pandas
Requires-Dist: primer3-py
Requires-Dist: pillow
Requires-Dist: chardet
Dynamic: author
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: keywords
Dynamic: license
Dynamic: license-file
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

# biochemHH

**biochemHH** is a Python package developed for experimental protein engineering. 

It provides tools for:
- **Batch-mode DNA cloning primer design**, prioritizing primer reuse
- **Protein-ligand interaction analysis**
- **Editing and processing of PDB, CIF, and GenBank (GB) files**

It can be used for:
- Preparing PDB inputs for AI protein design tools (**module StructureHH**)
- Analyzing PDB outputs from AI protein design tools (**module StructureHH**)
- Constructing plasmids for experimental protein screening (**module GBparser**)


## Quick Start (Installation & Accessing Example Files)

biochemHH is designed for wet lab scientists who may be new to programming.  
Ready-to-run example code blocks are provided to get started quickly.

**Step 0. Install Python and PyCharm**
  - Download and install the latest versions of Python and PyCharm.

**Step 1. Create a PyCharm project**
  - In PyCharm, go to File → New Project. A new window will open.
  - Change and record your `project location` shown at the top.
  - Keep the default settings (Project venv), then click CREATE.

**Step 2. Install biochemHH in your project environment**
  - Open Command Prompt using the Windows search bar.
  - Run the following commands in Command Prompt.
    (Replace the `path` in the first line with your `project location`.)

```bat
cd "C:\Users\ees26\PycharmProjects\project4"
IF EXIST ".venv\Scripts\activate.bat" (call .\.venv\Scripts\activate.bat
) ELSE IF EXIST "venv\Scripts\activate.bat" (call .\venv\Scripts\activate.bat
) ELSE (echo No virtual environment found & exit /b 1
)
pip install biochemHH
```

**Step 3. Copy example files to your working directory**
  - In your PyCharm project, create a new Python file.
  - Run the following code in Python.
    (Replace the `wd` path in the third line with a `working directory` of your choice.)

```python
from pathlib import Path
import shutil, importlib.resources as ir, biochemHH
wd = r"C:\Users\ees26\Desktop\playground3"

Path(wd).mkdir(exist_ok=True)
with ir.as_file(ir.files(biochemHH)/"example_input") as src:
    shutil.copytree(src, wd, dirs_exist_ok=True) 
with ir.as_file(ir.files(biochemHH)/"example_script") as src:
    shutil.copytree(src, f'{wd}/example_script', dirs_exist_ok=True)
```
  - This step copies the example input files and `Demonstration.pdf` into your `working directory`
    and the example Python scripts into a new subfolder named `example_script`.
 
**Step 4. Open the example Python scripts in PyCharm**
  - Go to File → Open and navigate to the `example_script` folder.
  - Select `playground.py` and one of the `examples_{}.py` files, then click OK.

**Step 5. Working in the playground**
  - Follow the instructions in `playground.py` to set your `working directory`.
    All input/output files will be read/written in this folder.

**Step 6. Optional: download & install PYMOL for protein visualization**

## Recommendations
  - Do not modify the example scripts. Work only in the `playground.py`.
  - For more details, see `Demonstration.pdf` in your `working directory`.
  - Files in the working directory may be overwritten.
    Move the output files elsewhere after completion to avoid data loss.
    
