├── .gitignore ├── LICENSE ├── README.md ├── data ├── ExternalTestData.csv ├── TestData-pred.csv ├── TestData.csv └── TrainData.csv ├── logo.png ├── model ├── model.h5 ├── model_new.h5 └── new_model.h5 ├── others ├── Attribute Analysis.ipynb ├── CFM-ID4 │ ├── cfmid4_singularity.py │ ├── cfmid4_singularity.sh │ ├── molecules.txt │ └── spectrum.txt ├── Completely random rotations.ipynb ├── Filtering.ipynb ├── GNN-RT │ └── README.md ├── MultidimensionalFiltering │ ├── Example.ipynb │ ├── LipidBlastPredCCS.xlsx │ ├── MListWithPredictedRTs_329.xlsx │ └── Mouse_lung_adduct_negative.xlsx ├── Performance on the test set with large rotations.ipynb ├── RotationMatrix.py ├── UMAP.ipynb ├── UMAPDataset.py ├── Visualization of the 3D conformers using different seeds of ETKDG.ipynb ├── data │ ├── Attribute importance data │ │ ├── Coordinate data │ │ │ ├── 0.csv │ │ │ ├── 1.csv │ │ │ ├── 2.csv │ │ │ ├── 3.csv │ │ │ ├── 4.csv │ │ │ ├── 5.csv │ │ │ ├── 6.csv │ │ │ ├── 7.csv │ │ │ ├── 8.csv │ │ │ └── 9.csv │ │ └── data.csv │ ├── Filtering data │ │ └── data.csv │ ├── UMAP data │ │ ├── Coordinate data │ │ │ ├── T1.mol │ │ │ ├── T10.mol │ │ │ ├── T2.mol │ │ │ ├── T3.mol │ │ │ ├── T4.mol │ │ │ ├── T5.mol │ │ │ ├── T6.mol │ │ │ ├── T7.mol │ │ │ ├── T8.mol │ │ │ └── T9.mol │ │ ├── data-UMAP-EUC-60.npy │ │ ├── data.csv │ │ └── data_molvec.npy │ └── theoretical calculation data │ │ ├── Coordinate data │ │ ├── 0.csv │ │ ├── 1.csv │ │ ├── 2.csv │ │ ├── 3.csv │ │ ├── 4.csv │ │ ├── 5.csv │ │ ├── 6.csv │ │ ├── 7.csv │ │ ├── 8.csv │ │ └── 9.csv │ │ ├── LJ_data.csv │ │ └── data.csv ├── model │ └── model.h5 └── theoretical calculation.ipynb ├── parameter └── parameter.pkl ├── requirements ├── conda │ └── environment.yml └── pip │ └── requirements.txt ├── sigma ├── GraphData.py ├── model.py ├── parameter.py └── sigma.py ├── slurm ├── mp.py ├── multiple_job.sh └── normal_job.sh └── test.ipynb /.gitignore: -------------------------------------------------------------------------------- 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