This is the implement of the paper Deep Representation Learning for Electron Ionization Mass Spectra Retrieval
Authors: Shibo Liu, Xuan Zhang, Anlei Jiao, Shiwei Sun, Longyang Dian*, Xuefeng Cui*
Contact: liuburger@qq.com
The suggested python version is 3.11.5 and the cuda version is 12.1
Clone this repository by:
git clone https://github.com/xfcui/EI-MS2VEC.git
Create virtual environment and install packages:
cd EI-MS2VEC
chmod +x run_setup.sh
bash ./run_setup.sh
Get expanded in-silico library from: https://zenodo.org/records/13968329, and then put the lib under 'EI-MS2VEC/data/mine/'
You need to get the NIST17 (https://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:nist17) mainlib and replib by yourself, and follow the explore_nist17.ipynb to process the raw data to get test set (put it under 'EI-MS2VEC/data/mine/').
The metadata of test set (https://github.com/Qiong-Yang/FastEI/blob/main/data/NEIMS_test_11499molecules.csv) is supplied by FastEI and the extra test set (https://github.com/Qiong-Yang/FastEI/tree/main/data/extra_test_set) is supplied too.
conda activate eims2vec
nohup python -Bu test.py >test.out