Code

These are scripts that I have written as part of various projects. I include them here for any one to use. Feel free to reach out if you have any questions.

Nearest Neighbor DNA Annealing Calculation Script: Enthalpy and Entropy Contributions

Summary. An in-house python script based on the work of SantaLucia et al. Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability (1995). The script calculates a more accurate annealing temperature that accounts for entropic stacking effects of neighboring nucleotides, self-annealing, and initiation energy. The script can be run from the command line with the only input being the sequence of interest.

Quantum Mechanic (QM) Supercomputing Cluster SLURM Script

A SLURM script that has been rigorously optimized to run Gaussian on the Fulton Supercomputing Cluster. If you are outside of Brigham Young University and want to adapt it to a different cluster, you may need to make minor system specific adjustments. The input.sh script contains information on the QM job and the submit.sh script is an optimization protocol.

Convert Between Raw Nuclear Magnetic Microscopy Data to CCPNMR Data

An in-house Python script that takes in a raw proton list, peak list, and a protein sequence and converts it to a file type readable by CCPNMR which can then be manipulated and assigned.