2DUV Machine Learning Protocol Code

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.