README.md

Codes

Ths folder contains the scripts and executables to run the spectra prediction workflow. The templates used by the scripts which are used to generate the folder structure are located in the templates folder.

Spectra generation steps

Handling input files for molecular optimization in the HPC

 ~/codes/write_dirs_files_for_gamess_qcxms.sh   

It submits the following command:

python codes/write_dirs_files_for_gamess_qcxms.py --sdf_filename data/RECETOX_GC-EI-MS_20201028.sdf   --params_filename codes/all_parameters.in --project_dirname /storage/du-cesnet/home/wrojasv/VO_metacentrum-tape_tape-archive/QC_SPECTRA_EI_RECETOX

Submitting jobs for molecular optimization

 ~/codes/submit_gamess_opt_jobs.sh   ~/codes/all_parameters.in

Extracting optimized molecules for spectra simulation

python codes/extract_coords_into_inp_xyz.py --sdf_filename data/RECETOX_GC-EI-MS_20201028.sdf   --params_filename codes/all_parameters.in --project_dirname /storage/du-cesnet/home/wrojasv/VO_metacentrum-tape_tape-archive/QC_SPECTRA_EI_RECETOX

Handling batch jobs for spectra simulations

 ~/codes/submit_qcxms_batch_jobs.sh   ~/codes/all_parameters.in

Collecting simulated spectra in MSP format

 ~/codes/get_full_results.sh   ~/codes/all_parameters.in

Additional tools

Print resume of completed molecular spectra simulation and delete unnecessary files

 ~/codes/explore_qcxms_batch_jobs.sh   ~/codes/all_parameters.in