| # DeepMASS2 | |
| DeepMASS2 is a cross-platform GUI software tool, which enables deep-learning based metabolite annotation | |
| via semantic similarity analysis of mass spectral language. This approach enables the prediction | |
| of structurally related metabolites for the unknown compounds. By considering the chemical space, these | |
| structurally related metabolites provide valuable information about the potential location of the unknown | |
| metabolites and assist in ranking candidates obtained from molecular structure databases. | |
| ## Installation | |
| Please follow the following installation steps: | |
| 1. Install [Anaconda](https://www.anaconda.com/) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html) | |
| 2. Create a new conda environment and activate: | |
| conda create -n deepmass python=3.8.13 | |
| conda activate deepmass | |
| 3. Clone the repository and enter: | |
| git clone https://github.com/hcji/DeepMASS2_GUI.git | |
| cd DeepMASS2_GUI | |
| 4. Install dependency (note, for *MacOS* some dependency may install with conda manually): | |
| pip install -r requirements.txt | |
| 5. Download the [dependent data](https://github.com/hcji/DeepMASS2_GUI/releases/tag/v0.99.0). | |
| 1) put the following files into *data* folder: | |
| DeepMassStructureDB-v1.0.csv | |
| references_index_negative_spec2vec.bin | |
| references_index_positive_spec2vec.bin | |
| references_spectrums_negative.pickle | |
| references_spectrums_positive.pickle | |
| 2) put the following files into *model* folder: | |
| Ms2Vec_allGNPSnegative.hdf5 | |
| Ms2Vec_allGNPSnegative.hdf5.syn1neg.npy | |
| Ms2Vec_allGNPSnegative.hdf5.wv.vectors.npy | |
| Ms2Vec_allGNPSpositive.hdf5 | |
| Ms2Vec_allGNPSpositive.hdf5.syn1neg.npy | |
| Ms2Vec_allGNPSpositive.hdf5.wv.vectors.npy | |
| 6. Run DeepMASS | |
| python DeepMASS2.py | |
| ## Release | |
| * [Version 0.99.0](https://github.com/hcji/DeepMASS2_GUI/releases/tag/v0.99.0) | |
| ## Documentation | |
| For the details on how to use DeepMASS, please check [Ducomentation](https://github.com/hcji/DeepMASS2_GUI/blob/main/document/documentation.md). | |
| ## Citation | |
| In preparation | |
| ## Contact | |
| Ji Hongchao | |
| E-mail: ji.hongchao@foxmail.com | |
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| WeChat public account: Chemocoder | |
| <img align="center" src="https://github.com/hcji/hcji/blob/main/img/qrcode.jpg" width="20%"/> | |