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2DUV Machine Learning Protocol Code

<p>Simulation data and code of ML protocol for 2DUV spectra of proteins.</p> <p>Any researchers who interested in protein spectroscopy can use our ML protocol online service:&nbsp;<a href="http://www.dcaiku.com:13000">http://www.dcaiku.com:13000</a></p> <p>For the machine learning protocol source code written&nbsp;in&nbsp;Python&nbsp;and Bash&nbsp;language which including:</p> <ul> <li>2duv_simulation folder <ul> <li>2DUV folder <ul> <li>0_parse_traj.py:&nbsp;Parse the MD trajectory in pdb format.</li> <li>1_bench_genH.sh: PBS script for generating the excition Hamiltonian,and E/M dipoles.</li> <li>1_cal_Hamil.py:&nbsp; Python script for submitting a large number of PBS script at once.</li> <li>2_extract_struc.py:&nbsp; Extract&nbsp; mode information&nbsp;of secondary structure segments&nbsp;from pdb file.</li> <li>3_extract_Hamil.py: Extract Hamiltonian, E/M dipoles information of&nbsp;secondary structure segments.</li> <li>4_cal_spectra.py: Python script for calculate the 2DUV spectra.</li> <li>4_run_calspectra.py:&nbsp; Python script for submitting a large number of PBS script&nbsp; for calculating 2DUV spectra at once.</li> <li>4_sub_calspectra.pbs:&nbsp;PBS script for runing python script of calculating 2DUV spectra.</li> <li>inputs folder: Spectron main input files.</li> </ul> </li> <li>GramacsFile: Gromacs main input files.</li> </ul> </li> <li>web-api folder: Source code of&nbsp;&nbsp;our ML protocol online service.</li> </ul>