Cation Pi Bond Detection with MDAnalysis for Proteins

A custom class using MDAnalysis to detect cation pi bonds and pi pi bonds for a protein in solvent.

List of Files and Descriptions

• cation_pi_analysis_demo.ipynb : Jupyter notebook which demonstrates the usage of the function 'CationPiBondAnalysis' and 'PiPiBondAnalysis' as defined in cation_pi_analysis.py and pi_pi_analysis.py respectively.
• cation_pi_analysis.py : Python script containing the custom MDAnalysis class 'CationPiBondAnalysis.'
• demo_trajectory/ionized.pdb : Protein data bank file (pdb) containing atom information for protein, water, and ions. See Introduction to Protein Data Bank Format for more details on pdb file format.
• demo_trajectory/ionized.psf : Protein structure file (psf) containing atom and connectivity information for protein, water, and ions See PSF Files for details on psf file format.
• demo_trajectory/trajectory.dcd : Molecular dynamics simulation trajectory of strutre in ionized.pdb.
• mda_cation_pi_env.yml : Conda YAML file (yml) which can be used to generate a conda environment with MDAnalysis and other packages required to run 'cation_pi_analysis_demo.ipynb' and 'cation_pi_analysis.py.' See Creating an environment from an environment.yml file in the conda documentation.
• pi_pi_analysis.py : Python script containing the custom MDAnalysis class 'PiPiBondAnalysis.'

Instructions

1. Create a conda virtual environment with the appropriate packages by following the instructions in Creating an environment from an environment.yml file.
2. Activate the environment and follow step 3 at this link to install the IPython Kernel package.
3. Register the envrionment as a kernel for use in Jupyter Notebook by following step 4 at this link.
4. Open cation_pi_analysis_demo.ipynb using Jupyter Notebook and run the script with your new kernel.

Additional Information

For details regarding distance cutoff and output format of class 'CationPiBondAnalysis,' please see the comments in cation_pi_analysis.py and pi_pi_analysis.py and follow along with instructions in cation_pi_analysis_demo.ipynb.