readme

.gitignore

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 # Data
 example/
-temp/*.png
+temp/
 *.mgf
 *.msp
 *.npy

ReadMe.md

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+# DeepMASS2
+
+DeepMASS2 is a cross-platform GUI software tool, which enables deep-learning based metabolite annotation
+ via semantic similarity analysis of mass spectral language (DeepMASS). 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:
+
+    pip install -r requirements.txt
+
+5. Run DeepMASS
+
+    python DeepMASS2.py
+
+
+## Release
+
+In preparation
+
+## Documentation
+
+In preparation
+
+## Citation
+
+In preparation
+
+
+## Contact
+
+Ji Hongchao   
+E-mail: [email protected]    
+<div itemscope itemtype="https://schema.org/Person"><a itemprop="sameAs" content="https://orcid.org/0000-0002-7364-0741" href="https://orcid.org/0000-0002-7364-0741" target="orcid.widget" rel="me noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon">https://orcid.org/0000-0002-7364-0741</a></div>
+
+WeChat public account: Chemocoder    
+<img align="center" src="https://github.com/hcji/hcji/blob/main/img/qrcode.jpg" width="20%"/>

requirements.txt

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+adjustText==0.7.3
+gensim==4.2.0
+matchms==0.17.0
+matplotlib==3.5.3
+molmass==2021.6.18
+ms2deepscore==0.2.3
+networkx==2.8.6
+numba==0.56.2
+numpy==1.23.3
+pandas==1.4.4
+pyinstaller==5.5
+rdkit-pypi
+scikit-learn==1.1.3
+scikit-opt==0.6.6
+scipy==1.9.3
+seaborn==0.12.1
+spec2vec==0.6.0
+tqdm==4.64.1
+PyQt5==5.15.7
+hnswlib==0.6.2
+JPype1==1.4.1
+beautifulsoup4==4.11.1