├── .gitignore ├── .readthedocs.yaml ├── LICENSE.txt ├── PDAnalysis ├── __init__.py ├── deformation.py ├── pdb_parser.py ├── protein.py ├── requirements.txt └── utils.py ├── README.md ├── html └── PDAnalysis │ ├── deformation.html │ ├── index.html │ ├── pdb_parser.html │ ├── protein.html │ └── utils.html ├── main.py ├── setup.py └── test_data ├── BFP ├── 3m24.cif ├── 3m24.npy ├── 3m24.pdb └── 3m24.txt ├── GFP ├── GFP_WT.pdb ├── GFP_WT_ver2.pdb ├── GFP_mutant.pdb ├── MUT_all │ ├── var00500_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb │ ├── var00500_relaxed_rank_002_alphafold2_ptm_model_3_seed_000.pdb │ ├── var00500_relaxed_rank_003_alphafold2_ptm_model_4_seed_001.pdb │ ├── var00500_relaxed_rank_004_alphafold2_ptm_model_4_seed_002.pdb │ ├── var00500_relaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb │ ├── var00500_relaxed_rank_006_alphafold2_ptm_model_4_seed_003.pdb │ ├── var00500_relaxed_rank_007_alphafold2_ptm_model_4_seed_004.pdb │ ├── var00500_relaxed_rank_008_alphafold2_ptm_model_3_seed_002.pdb │ ├── var00500_relaxed_rank_009_alphafold2_ptm_model_3_seed_001.pdb │ ├── var00500_relaxed_rank_010_alphafold2_ptm_model_5_seed_001.pdb │ ├── var00500_relaxed_rank_011_alphafold2_ptm_model_5_seed_004.pdb │ ├── var00500_relaxed_rank_012_alphafold2_ptm_model_3_seed_003.pdb │ ├── var00500_relaxed_rank_013_alphafold2_ptm_model_5_seed_003.pdb │ ├── var00500_relaxed_rank_014_alphafold2_ptm_model_3_seed_004.pdb │ ├── var00500_relaxed_rank_015_alphafold2_ptm_model_5_seed_002.pdb │ ├── var00500_relaxed_rank_016_alphafold2_ptm_model_2_seed_003.pdb │ ├── var00500_relaxed_rank_017_alphafold2_ptm_model_2_seed_000.pdb │ ├── var00500_relaxed_rank_018_alphafold2_ptm_model_2_seed_001.pdb │ ├── var00500_relaxed_rank_019_alphafold2_ptm_model_2_seed_004.pdb │ ├── var00500_relaxed_rank_020_alphafold2_ptm_model_2_seed_002.pdb │ ├── var00500_relaxed_rank_021_alphafold2_ptm_model_1_seed_003.pdb │ ├── var00500_relaxed_rank_022_alphafold2_ptm_model_1_seed_002.pdb │ ├── var00500_relaxed_rank_023_alphafold2_ptm_model_1_seed_000.pdb │ ├── var00500_relaxed_rank_024_alphafold2_ptm_model_1_seed_004.pdb │ └── var00500_relaxed_rank_025_alphafold2_ptm_model_1_seed_001.pdb ├── WT_all │ ├── original_relaxed_rank_001_alphafold2_ptm_model_4_seed_002.pdb │ ├── original_relaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb │ ├── original_relaxed_rank_003_alphafold2_ptm_model_4_seed_003.pdb │ ├── original_relaxed_rank_004_alphafold2_ptm_model_4_seed_001.pdb │ ├── original_relaxed_rank_005_alphafold2_ptm_model_4_seed_004.pdb │ ├── original_relaxed_rank_006_alphafold2_ptm_model_3_seed_000.pdb │ ├── original_relaxed_rank_007_alphafold2_ptm_model_3_seed_001.pdb │ ├── original_relaxed_rank_008_alphafold2_ptm_model_3_seed_002.pdb │ ├── original_relaxed_rank_009_alphafold2_ptm_model_5_seed_003.pdb │ ├── original_relaxed_rank_010_alphafold2_ptm_model_5_seed_000.pdb │ ├── original_relaxed_rank_011_alphafold2_ptm_model_5_seed_004.pdb │ ├── original_relaxed_rank_012_alphafold2_ptm_model_3_seed_004.pdb │ ├── original_relaxed_rank_013_alphafold2_ptm_model_5_seed_001.pdb │ ├── original_relaxed_rank_014_alphafold2_ptm_model_3_seed_003.pdb │ ├── original_relaxed_rank_015_alphafold2_ptm_model_2_seed_001.pdb │ ├── original_relaxed_rank_016_alphafold2_ptm_model_5_seed_002.pdb │ ├── original_relaxed_rank_017_alphafold2_ptm_model_2_seed_004.pdb │ ├── original_relaxed_rank_018_alphafold2_ptm_model_2_seed_002.pdb │ ├── original_relaxed_rank_019_alphafold2_ptm_model_1_seed_004.pdb │ ├── original_relaxed_rank_020_alphafold2_ptm_model_2_seed_000.pdb │ ├── original_relaxed_rank_021_alphafold2_ptm_model_2_seed_003.pdb │ ├── original_relaxed_rank_022_alphafold2_ptm_model_1_seed_001.pdb │ ├── original_relaxed_rank_023_alphafold2_ptm_model_1_seed_000.pdb │ ├── original_relaxed_rank_024_alphafold2_ptm_model_1_seed_002.pdb │ └── original_relaxed_rank_025_alphafold2_ptm_model_1_seed_003.pdb ├── mut_all.txt └── wt_all.txt ├── GuanylateKinase ├── 1s4q.pdb ├── 1znw.pdb ├── 1znx.pdb ├── 1zny.pdb └── 1znz.pdb └── Lysozyme ├── 1b5u.pdb ├── 1gaz.pdb ├── 1rex.pdb ├── AF-P61626-F1-model_v4.pdb ├── AF-P61627-F1-model_v4.pdb ├── AF-P61628-F1-model_v4.pdb ├── AF-P79179-F1-model_v4.pdb ├── AF-P79180-F1-model_v4.pdb └── AF-P79239-F1-model_v4.pdb /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mirabdi/PDAnalysis/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mirabdi/PDAnalysis/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /LICENSE.txt: 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