├── LICENSE ├── README.md ├── clean_build.sh ├── dist ├── pDeepXL-1.2.0-py3-none-any.whl └── pDeepXL-1.2.0.tar.gz ├── pDeepXL.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── entry_points.txt ├── requires.txt └── top_level.txt ├── pDeepXL ├── __init__.py ├── configs │ ├── aa.ini │ ├── config.ini │ └── element.ini ├── console_wapper.py ├── examples │ ├── cleavable │ │ ├── data │ │ │ └── clv_dataset.txt │ │ ├── predict_results │ │ │ ├── clv_predicted_res.txt │ │ │ ├── clv_spectra_library.msp │ │ │ └── imgs │ │ │ │ ├── B180703_03_Lumos_FO_IN_130_MycoDSSO_SCX14_hSAX_f19_rep1.17581.17581.5.0.dta.png │ │ │ │ ├── B180705_39_Lumos_FO_IN_130_MycoDSSO_SCX14_hSAX_f26t27_rep2.28568.28568.3.0.dta.png │ │ │ │ ├── B180706_31_Lumos_FO_IN_130_MycoDSSO_SCX15_hSAX_f23_rep1.18555.18555.4.0.dta.png │ │ │ │ ├── B180723_03_Lumos_FO_IN_130_MycoDSSO_SCX14_hSAX_f7t8_rep2.4813.4813.3.0.dta.png │ │ │ │ ├── B180816_04_Lumos_LS_IN_130_MycoDSSO_SCX16_hSAX_f3t6_rep1.20325.20325.5.0.dta.png │ │ │ │ ├── HEK293_FAIMS_40_55_70_Fr2.44804.44804.4.0.dta.png │ │ │ │ ├── HEK293_FAIMS_506075_Fr2_BioRep2.36106.36106.4.0.dta.png │ │ │ │ ├── HEK293_FAIMS_50_60_75_Fr5.31575.31575.4.0.dta.png │ │ │ │ ├── HEK293_FAIMS_60_70_80_Fr2.32448.32448.3.0.dta.png │ │ │ │ ├── HEK293_noFAIMS_Fr3_BioRep2.41208.41208.5.0.dta.png │ │ │ │ ├── R1_B1.20482.20482.4.0.dta.png │ │ │ │ ├── R1_B2.24489.24489.5.0.dta.png │ │ │ │ ├── R1_B6.9410.9410.3.0.dta.png │ │ │ │ ├── R1_B8.10325.10325.4.0.dta.png │ │ │ │ └── R3_A11.31514.31514.4.0.dta.png │ │ └── predicted_clv_spectrum.png │ ├── examples.zip │ └── non_cleavable │ │ ├── data │ │ └── non_clv_dataset.txt │ │ ├── predict_results │ │ ├── imgs │ │ │ ├── A_Linden_231018_251018_ymitos_glud0-glyd4_10.41750.41750.4.0.dta.png │ │ │ ├── AspN-Trypsin-2-2-1.7532.7532.3.0.dta.png │ │ │ ├── C_Lee_011216_ymitos_WT_Gly_BS3_XL_12_R2.57721.57721.4.0.dta.png │ │ │ ├── C_Lee_090916_ymitos_BS3_XL_B13_C1_13_Rep1.14188.14188.3.0.dta.png │ │ │ ├── C_Lee_300117_ymitos_Glu_BS3_XL_12_R1.20669.20669.3.0.dta.png │ │ │ ├── GluC-Trypsin-2-1.13172.13172.4.0.dta.png │ │ │ ├── HEK293_DSS_FAIMS_405060_Fr1.36531.36531.4.0.dta.png │ │ │ ├── HEK293_DSS_FAIMS_4055_Fr3.40215.40215.5.0.dta.png │ │ │ ├── HEK293_DSS_FAIMS_5060_Fr4.29122.29122.4.0.dta.png │ │ │ ├── I_Parfentev_A_Linden_260617_180717_ymitos_WTGly_A13b.30949.30949.3.0.dta.png │ │ │ ├── ecoli_enri0228_E_bin5_7ul.11740.11740.4.0.dta.png │ │ │ ├── ecoli_enri0228_E_bin5_7ul_re.19880.19880.5.0.dta.png │ │ │ ├── ecoli_enri0302_E_bin6_7ul_re.8379.8379.3.0.dta.png │ │ │ ├── ecoli_enri0302_E_bin7_7ul.14600.14600.4.0.dta.png │ │ │ └── ecoli_enri0302_E_bin8_7ul_re.5306.5306.3.0.dta.png │ │ ├── non_clv_predicted_res.txt │ │ └── non_clv_spectra_library.blib │ │ └── predicted_non_clv_spectrum.png ├── featurer.py ├── mass_util.py ├── model.py ├── plot.py ├── predict.py ├── pt │ ├── clv_model.pt │ └── non_clv_model.pt └── utils.py ├── setup.py └── tests ├── __init__.py ├── test_predict_batch.py └── 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