CANDIY-spectrum
Human analyis of chemical spectra such as Mass Spectra (MS), Infra-Red Specta (FTIR), and Nuclear Magnetic Resonance is both time consuming and potentially inaccurate. This project aims to develop a set of methodologies incorporating these spectra for the prediction of chemical functional groups and structures.
Scraping
Manual Scraping
IR and MS spectra were downloaded from NIST website. https://webbook.nist.gov/chemistry/.
Scraping can be done through replacing the correct CAS number in the placeholder. https://webbook.nist.gov/cgi/cbook.cgi?ID=”insert_cas”&Units=SI and downloading the required spectra.
(Or)
Automatic Scraping
Download all the species name available in NIST from this link https://webbook.nist.gov/chemistry/download/. Change path of cas_list to where the species name file is stored.
python scrap.py --save_dir='./data/' --cas_list='species.txt' --scrap_IR=true --scrap_MS=true --scrap_InChi=true
Prepare dataset
Parse all jdx files of IR and Mass spectra to standardize and store in a csv format. Also, parse inchi.txt to create target csv indicating presence of functional groups
python prepare_load_dataset.py --data_dir='./data/' --cas_list='species.txt'
Train the model
Run Spectra_Train.ipynb to train the model.
