biochemHH 0.0.2

Biochemistry & molecular biology helper tools

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:

• Studying of an underinvestigated protein (module Homolog)
• 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 CMD (Win+R → type cmd → Enter).
• Run the following commands
  (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 named temporary.py.
• Paste the code below into temporary.py and set your working directory (wd)
  (no Chinese characters allowed).

from pathlib import Path
import shutil, importlib.resources as ir, biochemHH

wd = r'C:\Users\ees26\Desktop\playground3'  # replace the path with your working directory

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)

• Right-click → Run temporary.py. This creates an example_script subfolder
  in your working directory, containing example scripts and playground.py.

Step 4. Open playground.py and an example script 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

• Set the same working directory in playground.py as in step 3.
  All input/output files will be read/written in this folder.
• Copy a code block from the example and paste it into playground.py.
• Modify variable values to your own data.
• Right-click → Run playground.py.

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

Suggested:

• Do not modify the example scripts. Work only in the playground.py.
• For beginners, start with these examples:
  • examples_Cloning_(batch-mode).py
  • examples_Protein_analyses.py
• Run scripts in the PyCharm console (supports unlimited line length).
  Terminal may truncate GBparser output due to line limits.
• If you are new to Python, always copy example code blocks completely,
  including the # { ... # } lines, to avoid indentation errors.

Warning:

• Files in the working directory may be overwritten.
  To avoid data loss, copy the input files into the working directory
  and move the output files elsewhere after completion.