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