Machine learning protocol code

<p>README.md</p> <p>This project &quot;A Machine Learning Protocol for Predicting Protein Infrared Spectra&quot; was supported by Prof. Shaul Mukamel(the University of California, Irvine), Prof. Jonathan D. Hirst(University of Nottingham),and Prof.Jun Jiang(University of Science and Technology of China).</p> <p>Simulation data and code of ML protocl for IR spectra of proteins.</p> <p>Any researchers who interested in protein spectroscopy can use our ML protcol online service:&nbsp;<a href="http://dcaiku.com:12880/platform/first">http://dcaiku.com:12880/platform/first</a></p> <p>For the machine learning protocol source code written&nbsp;in&nbsp;Python&nbsp;and Bash&nbsp;language which including:</p> <p>1.1.py: Split the protein into individual peptide bonds and dipeptides.</p> <p>1.2.py: Calculate the center of mass for each each peptide bond and dipeptide.</p> <p>1.3.sh: Convert the pdb format file to xyz format</p> <p>2.py: Extracte the Coulomb Matrix (CM) descriptors of peptide bond and dipeptide..</p> <p>3.py: Predict the vibrational frequency and vibrational transition dipole moment of each peptide bond from trained NMA Neural Networks (NN) model.</p> <p>4.py: Predict the neighboring coupling of each dipeptide from trained GLDP NN model.</p> <p>5.sh: Generate the input file for SPECTRON program to calculate the IR spectra of proteins.</p> <p>6.py: Construct the model Hamiltonian for amide I vibrations in a protein based on vibration exciton model theory.</p> <p>IR.sh: Diagonalize the Hamilton matrix calculate the IR spectra by using the SPECTRON.</p> <p>&nbsp;</p>