PenguinMol3D

PenguinMol3D is an open source Python3 package, which utilizes OpenGL python binding (https://pyopengl.sourceforge.net) for rendering of small compounds' 3D models.

Installation

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

Usage

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.

To check if package was installed correctly after installation enter:

Windows OS:

• python -m PenguinMol3D.glfw_surface_example

Linux OS:

• python3 -m PenguinMol3D.glfw_surface_example

PenguinMol3D currently supports two lighting models: Physically Based Lighting Model (default) and Blinn-Phong Lighting Model. To see examples of this two models enter:

Windows OS:

• python -m PenguinMol3D.glfw_bpr_example
• python -m PenguinMol3D.glfw_pbr_example
• python -m PenguinMol3D.glfw_custom_material_example

Linux OS:

• python3 -m PenguinMol3D.glfw_bpr_example
• python3 -m PenguinMol3D.glfw_pbr_example
• python3 -m PenguinMol3D.glfw_custom_material_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