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.)

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.)

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.