PenguineMol3D is an open source Python3 package, which utilizes OpenGL python binding (https://pyopengl.sourceforge.net) for rendering of small compounds' 3D models.
Basic installation
Project page on PyPI: https://pypi.org/project/PenguinMol3D/
- pip install PenguinMol3D
Manual installation
- Create root directory
- Clone the repository to root directory
- Move setup.py from the repository to root directory
- Open terminal and set current working directory to root directory
- pip install .
Dependencies
- numpy
- rdkit
- PyOpenGL
- PyOpenGL_accelerate
- glfw
- Pillow
NOTE: Although dependencies are installed with package, on Windows OS Microsoft C++ 14 Build Tools are required to install PyOpenGL_accelerate
To check if package was installed correctly after installation enter:
Windows OS:
- python -m PenguinMol3D.glfw_surface_example
- python -m PenguinMol3D.glfw_screenshot_example
- python -m PenguinMol3D.glfw_transformations_example
Linux OS:
- python3 -m PenguinMol3D.glfw_surface_example
- python3 -m PenguinMol3D.glfw_screenshot_example
- python3 -m PenguinMol3D.glfw_transformations_example
Main folder also contains script, which can be used for small molecule visualization with predefined scene, to run it enter:
Windows OS:
- python -m PenguinMol3D.display_molecule molecule_name.sdf
Linux OS:
- python3 -m PenguinMol3D.display_molecule molecule_name.sdf
Initially, the RDKit Mol object is created from data in a file (e.g, MOL\SDF, MOL2 format) provided by user; the Mol object is further passed as an argument to the Mol3D class constructor, which generates a 3D model based on atom coordinates of the Mol object conformer. During the initialization stage (before running an event loop) user has to setup a scene by creating MolecularScene object and adding all necessary components like molecule and light sources as it is demonstrated in examples. As a drawing surface for rendering can be used any surface compatible with OpenGL; particularly, provided by such GUI libaries as GLFW (used in examples), PyGame, PyQt, PySide, wxPython, Tkinter + Togl widget, etc.
