├── .gitignore ├── HISTORY.rst ├── LICENSE ├── PHANTOMDRAGON.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── entry_points.txt ├── not-zip-safe ├── requires.txt └── top_level.txt ├── README.md ├── data ├── Descriptors │ ├── CatS │ │ ├── gc4FEset.csv │ │ └── gc4scoreset.csv │ ├── DXGB.csv │ ├── ECFPs.csv │ ├── EC_numbers │ │ ├── PDBbind_core_set_GRADE_class1.csv │ │ ├── PDBbind_core_set_GRADE_class2.csv │ │ ├── PDBbind_core_set_GRADE_class3.csv │ │ ├── PDBbind_core_set_GRADE_class4.csv │ │ ├── PDBbind_core_set_GRADE_class5.csv │ │ ├── PDBbind_core_set_GRADE_class6.csv │ │ ├── PDBbind_core_set_GRADE_class7.csv │ │ ├── PDBbind_core_set_X-GRADE_class1.csv │ │ ├── PDBbind_core_set_X-GRADE_class2.csv │ │ ├── PDBbind_core_set_X-GRADE_class3.csv │ │ ├── PDBbind_core_set_X-GRADE_class4.csv │ │ ├── PDBbind_core_set_X-GRADE_class5.csv │ │ ├── PDBbind_core_set_X-GRADE_class6.csv │ │ ├── PDBbind_core_set_X-GRADE_class7.csv │ │ ├── PDBbind_general_set_GRADE_class1.csv │ │ ├── PDBbind_general_set_GRADE_class2.csv │ │ ├── PDBbind_general_set_GRADE_class3.csv │ │ ├── PDBbind_general_set_GRADE_class4.csv │ │ ├── PDBbind_general_set_GRADE_class5.csv │ │ ├── PDBbind_general_set_GRADE_class6.csv │ │ ├── PDBbind_general_set_GRADE_class7.csv │ │ ├── PDBbind_general_set_X-GRADE_class1.csv │ │ ├── PDBbind_general_set_X-GRADE_class2.csv │ │ ├── PDBbind_general_set_X-GRADE_class3.csv │ │ ├── PDBbind_general_set_X-GRADE_class4.csv │ │ ├── PDBbind_general_set_X-GRADE_class5.csv │ │ ├── PDBbind_general_set_X-GRADE_class6.csv │ │ └── PDBbind_general_set_X-GRADE_class7.csv │ ├── PDBbind_core_set_GRADE.csv │ ├── PDBbind_core_set_X-GRADE.csv │ ├── PDBbind_general_set_GRADE.csv │ ├── PDBbind_general_set_X-GRADE.csv │ ├── PDBbind_refined_set_GRADE.csv │ ├── PDBbind_refined_set_X-GRADE.csv │ ├── PL-REX │ │ ├── 001-CA2 │ │ │ ├── GRADE.csv │ │ │ ├── GRADE_charged.csv │ │ │ ├── X-GRADE.csv │ │ │ └── X-GRADE_charged.csv │ │ ├── 002-HIV-PR │ │ │ ├── GRADE.csv │ │ │ ├── GRADE_charged.csv │ │ │ ├── X-GRADE.csv │ │ │ └── X-GRADE_charged.csv │ │ ├── 003-CK2 │ │ │ ├── GRADE.csv │ │ │ ├── GRADE_charged.csv │ │ │ ├── X-GRADE.csv │ │ │ └── X-GRADE_charged.csv │ │ ├── 004-AR │ │ │ ├── GRADE.csv │ │ │ ├── GRADE_charged.csv │ │ │ ├── X-GRADE.csv │ │ │ └── X-GRADE_charged.csv │ │ ├── 005-Cath-D │ │ │ ├── GRADE.csv │ │ │ ├── GRADE_charged.csv │ │ │ ├── X-GRADE.csv │ │ │ └── X-GRADE_charged.csv │ │ ├── 006-BACE1-D3R │ │ │ ├── GRADE.csv │ │ │ ├── GRADE_charged.csv │ │ │ ├── X-GRADE.csv │ │ │ └── X-GRADE_charged.csv │ │ ├── 007-JAK1 │ │ │ ├── GRADE.csv │ │ │ ├── GRADE_charged.csv │ │ │ ├── X-GRADE.csv │ │ │ └── X-GRADE_charged.csv │ │ ├── 008-Trypsin │ │ │ ├── GRADE.csv │ │ │ ├── GRADE_charged.csv │ │ │ ├── X-GRADE.csv │ │ │ └── X-GRADE_charged.csv │ │ ├── 009-CDK2 │ │ │ ├── GRADE.csv │ │ │ ├── GRADE_charged.csv │ │ │ ├── X-GRADE.csv │ │ │ └── X-GRADE_charged.csv │ │ └── 010-MMP12 │ │ │ ├── GRADE.csv │ │ │ ├── GRADE_charged.csv │ │ │ ├── X-GRADE.csv │ │ │ └── X-GRADE_charged.csv │ ├── PLEC.zip │ └── PLEC_sets.zip └── exp_data │ ├── CatS │ ├── gc4FEset.sdf │ └── gc4scoreset.sdf │ ├── CoreSet.dat │ ├── EC_numbers │ ├── 1_x_x_x.csv │ ├── 2_x_x_x.csv │ ├── 3_x_x_x.csv │ ├── 4_x_x_x.csv │ ├── 5_x_x_x.csv │ ├── 6_x_x_x.csv │ ├── 7_x_x_x.csv │ ├── core_set_class1.csv │ ├── core_set_class2.csv │ ├── core_set_class3.csv │ ├── core_set_class4.csv │ ├── core_set_class5.csv │ ├── core_set_class6.csv │ ├── core_set_class7.csv │ ├── ec_numbers_all.csv │ ├── general_set_class1.csv │ ├── general_set_class2.csv │ ├── general_set_class3.csv │ ├── general_set_class4.csv │ ├── general_set_class5.csv │ ├── general_set_class6.csv │ └── general_set_class7.csv │ ├── INDEX_general_PL_data.2020 │ ├── INDEX_refined_data.2020 │ ├── PDBbind_complete_general_set_exp.xlsx │ ├── PDBbind_core_set_all.csv │ ├── PDBbind_core_set_kd.csv │ ├── PDBbind_core_set_ki.csv │ ├── PDBbind_general_set_all.csv │ ├── PDBbind_general_set_kd.csv │ ├── PDBbind_general_set_ki.csv │ ├── PDBbind_refined_set_all.csv │ ├── PDBbind_refined_set_kd.csv │ ├── PDBbind_refined_set_ki.csv │ └── PL-REX │ ├── 001-CA2 │ └── experimental_dG.csv │ ├── 002-HIV-PR │ └── experimental_dG.csv │ ├── 003-CK2 │ └── experimental_dG.csv │ ├── 004-AR │ └── experimental_dG.csv │ ├── 005-Cath-D │ └── experimental_dG.csv │ ├── 006-BACE1-D3R │ └── experimental_dG.csv │ ├── 007-JAK1 │ └── experimental_dG.csv │ ├── 008-Trypsin │ └── experimental_dG.csv │ ├── 009-CDK2 │ └── experimental_dG.csv │ └── 010-MMP12 │ └── experimental_dG.csv ├── docs ├── Makefile ├── authors.rst ├── conf.py ├── contributing.rst ├── history.rst ├── index.rst ├── installation.rst ├── make.bat ├── readme.rst └── usage.rst ├── models └── 0_read.txt ├── phantomdragon ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-39.pyc │ ├── functions.cpython-39.pyc │ └── phantomdragon.cpython-39.pyc ├── functions.py ├── phantomdragon.py └── run_phantomdragon.py ├── plots └── 0_read.txt ├── results ├── PL-REX_results_charged.csv ├── 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