PDB-H-H

Scripts for finding C-H···H-C contacts in NMR structures.

Contents

• nmr_finder.py Filters a local installation of the protein data bank to find NMR sructures containing peptide chains with aliphatic residues.
• h2hbond.py Finds all C-H··H-C pairs within 3 angstroms of each other, and extracts data about their distance, angles, and dihedral.
• nmr_files_peptide.pkl List of NMR peptide files in the PDB as of May 2018. Input for h2hbond.py.
• hhcontacts.pkl Raw contact data as a pandas DataFrame
• full_pdb_analysis.ipynb Exploratory analysis of the data.

Requirements

• pyspark: conda install pyspark