├── LICENSE ├── PDBminer ├── PDBminer.py ├── PDBminer2coverage.py ├── PDBminer2network.py └── __init__.py ├── README.md ├── REPRODUCE_PAPER ├── TIMING │ ├── 1core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── 2core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── 3core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── 4core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── 5core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── 6core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── time.csv │ └── time.py ├── TP53_CASESTUDY │ ├── input_file.csv │ ├── log.txt │ ├── readme.txt │ └── results │ │ └── P04637 │ │ ├── P04637_all.json │ │ ├── all_coverage_plot.pdf │ │ └── all_network.pdf └── readme.txt ├── examples ├── command_line │ ├── do.sh │ ├── input_file.csv │ ├── log.txt │ └── results │ │ └── P22307 │ │ ├── P22307_all.json │ │ ├── all_coverage_plot_chunk_0.pdf │ │ ├── all_coverage_plot_chunk_1.pdf │ │ └── all_network.pdf ├── csv_output │ ├── do.sh │ ├── input_file.csv │ ├── log.txt │ └── results │ │ ├── O15520 │ │ ├── O15520_all.csv │ │ ├── all_coverage_plot.pdf │ │ └── all_network.pdf │ │ └── O75385 │ │ ├── O75385_all.csv │ │ ├── all_coverage_plot_chunk_0.pdf │ │ ├── all_coverage_plot_chunk_1.pdf │ │ ├── all_coverage_plot_chunk_2.pdf │ │ └── all_network.pdf ├── different_clusters │ ├── do.sh │ ├── input_file_clusters.csv │ ├── log.txt │ └── results │ │ └── P22307 │ │ ├── P22307_all.json │ │ ├── P22307_cluster_1.json │ │ ├── P22307_cluster_2.json │ │ ├── P22307_filtered.json │ │ ├── all_coverage_plot_chunk_0.pdf │ │ ├── all_coverage_plot_chunk_1.pdf │ │ ├── all_network.pdf │ │ ├── filtered_coverage_plot_cluster_1_chunk_0.pdf │ │ ├── filtered_coverage_plot_cluster_1_chunk_1.pdf │ │ ├── filtered_coverage_plot_cluster_2_chunk_0.pdf │ │ ├── filtered_coverage_plot_cluster_2_chunk_1.pdf │ │ └── filtered_network.pdf └── input_file │ ├── do.sh │ ├── input_file.csv │ ├── log.txt │ └── results │ ├── P0A7Y7 │ ├── P0A7Y7_all.json │ ├── P0A7Y7_cluster_1.json │ ├── P0A7Y7_filtered.json │ ├── all_coverage_plot.pdf │ └── filtered_coverage_plot_cluster_1.pdf │ └── P11532 │ ├── P11532_all.json │ ├── P11532_cluster_1.json │ ├── P11532_filtered.json │ ├── all_coverage_plot_chunk_0.pdf │ ├── all_coverage_plot_chunk_1.pdf │ ├── all_coverage_plot_chunk_2.pdf │ ├── all_coverage_plot_chunk_3.pdf │ ├── all_coverage_plot_chunk_4.pdf │ ├── all_coverage_plot_chunk_5.pdf │ ├── all_coverage_plot_chunk_6.pdf │ ├── all_coverage_plot_chunk_7.pdf │ ├── all_network.pdf │ ├── filtered_coverage_plot_cluster_1_chunk_0.pdf │ ├── filtered_coverage_plot_cluster_1_chunk_1.pdf │ ├── filtered_coverage_plot_cluster_1_chunk_2.pdf │ ├── filtered_coverage_plot_cluster_1_chunk_3.pdf │ ├── filtered_coverage_plot_cluster_1_chunk_4.pdf │ ├── filtered_coverage_plot_cluster_1_chunk_5.pdf │ ├── filtered_coverage_plot_cluster_1_chunk_6.pdf │ └── filtered_coverage_plot_cluster_1_chunk_7.pdf ├── schema.json └── setup.py /PDBminer/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/PDBminer/464adacc5c978a305c2a0599e5f141eed3eb63ec/PDBminer/__init__.py -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/1core/input_file.csv: -------------------------------------------------------------------------------- 1 | hugo_name,uniprot,uniprot_isoform,mutations,cluster_id 2 | FAK1,Q05397,1,NA,NA 3 | FKBP1A,P62942,1,NA,NA 4 | MZF1,P28698,1,NA,NA 5 | ULK1,O75385,1,NA,NA 6 | MHL1,P40692,1,NA,NA 7 | MAP1LC3B,Q9GZQ8,1,NA,NA 8 | ARID3A,Q99856,1,NA,NA 9 | BCL2,P10415,1,NA,NA 10 | PPIA,P62937,1,NA,NA 11 | BCL2L1,Q07817,1,NA,NA 12 | TRAP1,Q12931,1,NA,NA 13 | CPA2,P48052,1,NA,NA 14 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/1core/log.txt: -------------------------------------------------------------------------------- 1 | 2023-10-06 08:50:22,488 - INFO - PDBminer is starting 2 | 2023-10-06 08:50:22,488 - INFO - input file mode is choosen and input file has been identified. 3 | 2023-10-06 08:50:22,496 - INFO - Pipeline is starting 4 | 2023-10-06 09:03:06,921 - INFO - total runtime: 0:12:44.432206 5 | 2023-10-06 09:03:06,921 - INFO - PDBminer has finished. 6 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/1core/results/P28698/P28698_all.json: -------------------------------------------------------------------------------- 1 | {"hugo_name":{"0":"MZF1","1":"MZF1"},"uniprot_id":{"0":"P28698","1":"P28698"},"uniprot_isoform":{"0":1,"1":1},"structure_id":{"0":"AF-P28698-F1-model_v4","1":"2FI2"},"deposition_date":{"0":"2022-06-01","1":"2005-12-27"},"experimental_method":{"0":"PREDICTED","1":"SOLUTION 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-------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/2core/input_file.csv: -------------------------------------------------------------------------------- 1 | hugo_name,uniprot,uniprot_isoform,mutations,cluster_id 2 | FAK1,Q05397,1,NA,NA 3 | FKBP1A,P62942,1,NA,NA 4 | MZF1,P28698,1,NA,NA 5 | ULK1,O75385,1,NA,NA 6 | MHL1,P40692,1,NA,NA 7 | MAP1LC3B,Q9GZQ8,1,NA,NA 8 | ARID3A,Q99856,1,NA,NA 9 | BCL2,P10415,1,NA,NA 10 | PPIA,P62937,1,NA,NA 11 | BCL2L1,Q07817,1,NA,NA 12 | TRAP1,Q12931,1,NA,NA 13 | CPA2,P48052,1,NA,NA 14 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/2core/log.txt: -------------------------------------------------------------------------------- 1 | 2023-10-06 08:50:32,339 - INFO - PDBminer is starting 2 | 2023-10-06 08:50:32,339 - INFO - input file mode is choosen and input file has been identified. 3 | 2023-10-06 08:50:32,347 - INFO - Pipeline is starting 4 | 2023-10-06 08:58:51,882 - INFO - total runtime: 0:08:19.542430 5 | 2023-10-06 08:58:51,882 - INFO - PDBminer has finished. 6 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/2core/results/P28698/P28698_all.json: -------------------------------------------------------------------------------- 1 | {"hugo_name":{"0":"MZF1","1":"MZF1"},"uniprot_id":{"0":"P28698","1":"P28698"},"uniprot_isoform":{"0":1,"1":1},"structure_id":{"0":"AF-P28698-F1-model_v4","1":"2FI2"},"deposition_date":{"0":"2022-06-01","1":"2005-12-27"},"experimental_method":{"0":"PREDICTED","1":"SOLUTION 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-------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/3core/input_file.csv: -------------------------------------------------------------------------------- 1 | hugo_name,uniprot,uniprot_isoform,mutations,cluster_id 2 | FAK1,Q05397,1,NA,NA 3 | FKBP1A,P62942,1,NA,NA 4 | MZF1,P28698,1,NA,NA 5 | ULK1,O75385,1,NA,NA 6 | MHL1,P40692,1,NA,NA 7 | MAP1LC3B,Q9GZQ8,1,NA,NA 8 | ARID3A,Q99856,1,NA,NA 9 | BCL2,P10415,1,NA,NA 10 | PPIA,P62937,1,NA,NA 11 | BCL2L1,Q07817,1,NA,NA 12 | TRAP1,Q12931,1,NA,NA 13 | CPA2,P48052,1,NA,NA 14 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/3core/log.txt: -------------------------------------------------------------------------------- 1 | 2023-10-06 08:50:47,610 - INFO - PDBminer is starting 2 | 2023-10-06 08:50:47,610 - INFO - input file mode is choosen and input file has been identified. 3 | 2023-10-06 08:50:47,618 - INFO - Pipeline is starting 4 | 2023-10-06 08:56:04,635 - INFO - total runtime: 0:05:17.024713 5 | 2023-10-06 08:56:04,635 - INFO - PDBminer has finished. 6 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/3core/results/P28698/P28698_all.json: -------------------------------------------------------------------------------- 1 | {"hugo_name":{"0":"MZF1","1":"MZF1"},"uniprot_id":{"0":"P28698","1":"P28698"},"uniprot_isoform":{"0":1,"1":1},"structure_id":{"0":"AF-P28698-F1-model_v4","1":"2FI2"},"deposition_date":{"0":"2022-06-01","1":"2005-12-27"},"experimental_method":{"0":"PREDICTED","1":"SOLUTION 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-------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/4core/input_file.csv: -------------------------------------------------------------------------------- 1 | hugo_name,uniprot,uniprot_isoform,mutations,cluster_id 2 | FAK1,Q05397,1,NA,NA 3 | FKBP1A,P62942,1,NA,NA 4 | MZF1,P28698,1,NA,NA 5 | ULK1,O75385,1,NA,NA 6 | MHL1,P40692,1,NA,NA 7 | MAP1LC3B,Q9GZQ8,1,NA,NA 8 | ARID3A,Q99856,1,NA,NA 9 | BCL2,P10415,1,NA,NA 10 | PPIA,P62937,1,NA,NA 11 | BCL2L1,Q07817,1,NA,NA 12 | TRAP1,Q12931,1,NA,NA 13 | CPA2,P48052,1,NA,NA 14 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/4core/log.txt: -------------------------------------------------------------------------------- 1 | 2023-10-06 08:58:38,762 - INFO - PDBminer is starting 2 | 2023-10-06 08:58:38,762 - INFO - input file mode is choosen and input file has been identified. 3 | 2023-10-06 08:58:38,770 - INFO - Pipeline is starting 4 | 2023-10-06 09:03:14,796 - INFO - total runtime: 0:04:36.033670 5 | 2023-10-06 09:03:14,796 - INFO - PDBminer has finished. 6 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/4core/results/P28698/P28698_all.json: -------------------------------------------------------------------------------- 1 | {"hugo_name":{"0":"MZF1","1":"MZF1"},"uniprot_id":{"0":"P28698","1":"P28698"},"uniprot_isoform":{"0":1,"1":1},"structure_id":{"0":"AF-P28698-F1-model_v4","1":"2FI2"},"deposition_date":{"0":"2022-06-01","1":"2005-12-27"},"experimental_method":{"0":"PREDICTED","1":"SOLUTION 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-------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/5core/input_file.csv: -------------------------------------------------------------------------------- 1 | hugo_name,uniprot,uniprot_isoform,mutations,cluster_id 2 | FAK1,Q05397,1,NA,NA 3 | FKBP1A,P62942,1,NA,NA 4 | MZF1,P28698,1,NA,NA 5 | ULK1,O75385,1,NA,NA 6 | MHL1,P40692,1,NA,NA 7 | MAP1LC3B,Q9GZQ8,1,NA,NA 8 | ARID3A,Q99856,1,NA,NA 9 | BCL2,P10415,1,NA,NA 10 | PPIA,P62937,1,NA,NA 11 | BCL2L1,Q07817,1,NA,NA 12 | TRAP1,Q12931,1,NA,NA 13 | CPA2,P48052,1,NA,NA 14 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/5core/log.txt: -------------------------------------------------------------------------------- 1 | 2023-10-06 08:59:40,825 - INFO - PDBminer is starting 2 | 2023-10-06 08:59:40,825 - INFO - input file mode is choosen and input file has been identified. 3 | 2023-10-06 08:59:40,833 - INFO - Pipeline is starting 4 | 2023-10-06 09:03:49,054 - INFO - total runtime: 0:04:08.229123 5 | 2023-10-06 09:03:49,054 - INFO - PDBminer has finished. 6 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/5core/results/P28698/P28698_all.json: -------------------------------------------------------------------------------- 1 | {"hugo_name":{"0":"MZF1","1":"MZF1"},"uniprot_id":{"0":"P28698","1":"P28698"},"uniprot_isoform":{"0":1,"1":1},"structure_id":{"0":"AF-P28698-F1-model_v4","1":"2FI2"},"deposition_date":{"0":"2022-06-01","1":"2005-12-27"},"experimental_method":{"0":"PREDICTED","1":"SOLUTION 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-------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/6core/input_file.csv: -------------------------------------------------------------------------------- 1 | hugo_name,uniprot,uniprot_isoform,mutations,cluster_id 2 | FAK1,Q05397,1,NA,NA 3 | FKBP1A,P62942,1,NA,NA 4 | MZF1,P28698,1,NA,NA 5 | ULK1,O75385,1,NA,NA 6 | MHL1,P40692,1,NA,NA 7 | MAP1LC3B,Q9GZQ8,1,NA,NA 8 | ARID3A,Q99856,1,NA,NA 9 | BCL2,P10415,1,NA,NA 10 | PPIA,P62937,1,NA,NA 11 | BCL2L1,Q07817,1,NA,NA 12 | TRAP1,Q12931,1,NA,NA 13 | CPA2,P48052,1,NA,NA 14 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/6core/log.txt: -------------------------------------------------------------------------------- 1 | 2023-10-06 09:10:07,892 - INFO - PDBminer is starting 2 | 2023-10-06 09:10:07,892 - INFO - input file mode is choosen and input file has been identified. 3 | 2023-10-06 09:10:07,900 - INFO - Pipeline is starting 4 | 2023-10-06 09:14:14,150 - INFO - total runtime: 0:04:06.257695 5 | 2023-10-06 09:14:14,150 - INFO - PDBminer has finished. 6 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/6core/results/P28698/P28698_all.json: -------------------------------------------------------------------------------- 1 | {"hugo_name":{"0":"MZF1","1":"MZF1"},"uniprot_id":{"0":"P28698","1":"P28698"},"uniprot_isoform":{"0":1,"1":1},"structure_id":{"0":"AF-P28698-F1-model_v4","1":"2FI2"},"deposition_date":{"0":"2022-06-01","1":"2005-12-27"},"experimental_method":{"0":"PREDICTED","1":"SOLUTION 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-------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/time.csv: -------------------------------------------------------------------------------- 1 | ,cores,total,per_pdb 2 | 1core,1core,0 days 00:12:44.432206,0 days 00:00:01.643940 3 | 2core,2core,0 days 00:08:19.542430,0 days 00:00:01.074285 4 | 3core,3core,0 days 00:05:17.024713,0 days 00:00:00.681774 5 | 4core,4core,0 days 00:04:36.033670,0 days 00:00:00.593621 6 | 5core,5core,0 days 00:04:08.229123,0 days 00:00:00.533826 7 | 6core,6core,0 days 00:04:06.257695,0 days 00:00:00.529586 8 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TIMING/time.py: -------------------------------------------------------------------------------- 1 | import pandas as pd 2 | import numpy as np 3 | import datetime 4 | 5 | def get_n(uni_list): 6 | n = [] 7 | for uniprot in uni_list: 8 | df_pdbminer = pd.read_json(f"1core/results/{uniprot}/{uniprot}_all.json") 9 | n.append(len(df_pdbminer)) 10 | n = sum(n) 11 | return n 12 | 13 | uni_list = ["Q05397", "P62942", "P28698", 14 | "O75385", "P40692", "Q9GZQ8", 15 | "Q99856", "P10415", "P62937", 16 | "Q07817", "Q12931", "P48052"] 17 | 18 | total_n = get_n(uni_list) 19 | 20 | df = pd.DataFrame(columns=['cores', 'total', "per_pdb"]) 21 | 22 | directory_list = ["1core", "2core", "3core", "4core", "5core","6core"] 23 | 24 | def read_core_runs(df, directory_list, n): 25 | for directory in directory_list: 26 | with open(f"{directory}/log.txt", "r") as f: 27 | lines = f.readlines() 28 | t = lines[-2][:-1].split(": ")[-1] 29 | (h, m, s) = t.split(':') 30 | st = datetime.timedelta(hours=int(h), minutes=int(m), seconds=float(s)) 31 | per_structure = st/n 32 | list_of_values = [directory, st, per_structure] 33 | df.loc[directory] = np.array(list_of_values, dtype="object") 34 | return df 35 | 36 | df1 = read_core_runs(df, directory_list, total_n) 37 | 38 | df1.to_csv("time.csv") 39 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TP53_CASESTUDY/input_file.csv: -------------------------------------------------------------------------------- 1 | ,hugo_name,uniprot,uniprot_isoform,mutations,cluster_id 2 | 0,TP53,P04637,1,NA,NA 3 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TP53_CASESTUDY/log.txt: -------------------------------------------------------------------------------- 1 | 2023-10-05 13:31:06,075 - INFO - PDBminer is starting 2 | 2023-10-05 13:31:06,080 - INFO - input file created based on hugo name and uniprot id, file name: input_file.csv 3 | 2023-10-05 13:31:06,080 - INFO - Pipeline is starting 4 | 2023-10-05 13:31:11,834 - WARNING - Uniprot returned 260 structures. NOTICE that structures deposited in the PDB within 8 weeks may not be included in this list, P04637. 5 | 2023-10-05 13:41:57,695 - INFO - total runtime: 0:10:51.619906 6 | 2023-10-05 13:41:57,695 - INFO - PDBminer has finished. 7 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TP53_CASESTUDY/readme.txt: -------------------------------------------------------------------------------- 1 | #activate environment 2 | ../../PDBminer -g TP53 -u P04637 -n 1 3 | ../../PDBminer2coverage 4 | ../../PDBminer2network -i input_file.csv -u P04637 -c '#1F968BFF' -p '#238A8DFF' -s '#B8DE29FF' -t '#39568CFF' 5 | 6 | 7 | -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TP53_CASESTUDY/results/P04637/all_coverage_plot.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/PDBminer/464adacc5c978a305c2a0599e5f141eed3eb63ec/REPRODUCE_PAPER/TP53_CASESTUDY/results/P04637/all_coverage_plot.pdf -------------------------------------------------------------------------------- /REPRODUCE_PAPER/TP53_CASESTUDY/results/P04637/all_network.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/PDBminer/464adacc5c978a305c2a0599e5f141eed3eb63ec/REPRODUCE_PAPER/TP53_CASESTUDY/results/P04637/all_network.pdf -------------------------------------------------------------------------------- /REPRODUCE_PAPER/readme.txt: -------------------------------------------------------------------------------- 1 | These two directories contain readme files to recreate the runtime and TP53 casestudy of the PDBminer application note. 2 | -------------------------------------------------------------------------------- /examples/command_line/do.sh: -------------------------------------------------------------------------------- 1 | PDBminer -u P22307 2 | PDBminer2coverage 3 | PDBminer2network 4 | 5 | -------------------------------------------------------------------------------- /examples/command_line/input_file.csv: -------------------------------------------------------------------------------- 1 | ,hugo_name,uniprot,uniprot_isoform,mutations,cluster_id 2 | 0,NA,P22307,1,NA,NA 3 | -------------------------------------------------------------------------------- /examples/command_line/log.txt: -------------------------------------------------------------------------------- 1 | 2025-01-15 13:15:53,099 - INFO - PDBminer is starting 2 | 2025-01-15 13:15:53,592 - WARNING - No Uniprot record in this id, no Hugo Name could be retrived with UniProt for ['P22307']. Gene name assigned NA. 3 | 2025-01-15 13:15:53,642 - INFO - input file created based on hugo name and uniprot id, file name: input_file.csv 4 | 2025-01-15 13:15:53,642 - INFO - Pipeline is starting 5 | 2025-01-15 13:16:03,960 - INFO - total runtime: 0:00:10.860971 6 | 2025-01-15 13:16:03,961 - INFO - PDBminer has finished. 7 | -------------------------------------------------------------------------------- /examples/command_line/results/P22307/P22307_all.json: -------------------------------------------------------------------------------- 1 | {"hugo_name":{"0":null,"1":null,"2":null},"uniprot_id":{"0":"P22307","1":"P22307","2":"P22307"},"uniprot_isoform":{"0":1,"1":1,"2":1},"structure_id":{"0":"AF-P22307-F1-model_v4","1":"2C0L","2":"1QND"},"deposition_date":{"0":"2022-06-01","1":"2005-09-05","2":"1999-10-14"},"experimental_method":{"0":"PREDICTED","1":"X-RAY DIFFRACTION","2":"SOLUTION NMR"},"resolution":{"0":"NA","1":2.3,"2":null},"r_free":{"0":"NA","1":0.256,"2":"NA"},"PDBREDOdb":{"0":"NO","1":"YES","2":"NO"},"PDBREDOdb_rfree":{"0":"NA","1":0.2747,"2":"NA"},"complex_protein":{"0":"NA","1":"protein complex","2":"NA"},"complex_protein_details":{"0":"NA","1":["PEX5_HUMAN, P50542, chain_A;SCP2_HUMAN, P22307, chain_B"],"2":"NA"},"complex_nucleotide":{"0":"NA","1":"NA","2":"NA"},"complex_nucleotide_details":{"0":"NA","1":"NA","2":"NA"},"complex_ligand":{"0":"NA","1":"NA","2":"NA"},"complex_ligand_details":{"0":"NA","1":"NA","2":"NA"},"chains":{"0":"A","1":"B","2":"A"},"coverage":{"0":{"A":"[(10, 412);(430, 539)]"},"1":{"B":"[(426, 547)]"},"2":{"A":"[(425, 547)]"}},"mutations_in_pdb":{"0":"NA","1":"NA","2":"NA"},"b_factor":{"0":{"A":[42.03,43.5,46.86,48.96,59.83,55.67,50.1,58.23,65.16,77.8,86.84,96.32,98.22,98.85,98.92,98.95,98.81,98.83,98.95,98.77,98.87,98.25,97.67,97.89,96.3,95.53,94.66,89.03,83.75,72.46,72.36,76.5,90.59,95.66,97.37,98.07,97.12,97.59,98.42,98.34,98.34,98.77,98.77,98.65,98.78,98.87,98.64,98.54,98.57,98.06,97.25,96.57,97.29,98.23,97.73,97.97,98.71,98.67,98.82,98.92,98.94,98.93,98.91,98.76,98.0,95.72,95.44,97.86,98.43,98.5,98.72,98.72,98.71,98.62,98.28,98.53,97.54,92.15,90.86,96.05,96.08,97.29,97.83,97.85,98.63,98.84,98.85,98.88,98.91,98.89,98.71,98.54,97.32,98.18,98.73,98.87,98.86,98.93,98.95,98.96,98.96,98.93,98.91,98.91,98.83,98.69,98.69,98.71,97.93,97.25,97.03,97.8,98.45,98.57,98.82,98.95,98.94,98.97,98.95,98.9,98.73,98.02,96.38,94.93,91.58,88.98,87.27,83.97,86.62,83.15,84.41,86.35,90.82,92.22,95.52,96.0,96.74,95.28,96.12,95.56,95.56,96.79,96.87,95.79,96.58,96.07,94.7,95.79,95.62,95.05,94.9,94.38,93.64,93.29,92.95,93.2,93.06,94.66,95.7,96.66,97.59,97.69,98.3,98.33,98.36,98.63,98.66,98.25,98.42,98.76,98.7,98.08,98.26,98.57,98.33,98.7,98.69,98.35,98.61,98.84,98.85,98.81,98.88,98.89,98.69,98.75,98.83,98.85,98.78,98.67,98.79,98.64,98.56,97.17,98.65,98.22,98.46,98.42,97.52,97.9,98.15,98.12,97.08,98.43,98.59,98.49,98.53,98.6,98.68,98.22,98.23,98.26,97.9,97.9,97.06,97.49,96.08,97.86,98.49,98.62,97.92,98.57,98.77,98.27,97.3,96.66,96.24,97.14,97.26,97.82,98.66,98.92,98.96,98.97,98.94,98.94,98.85,98.69,98.3,97.97,98.55,98.63,97.18,97.04,96.74,96.77,97.55,97.96,95.47,95.68,98.63,98.91,98.86,98.91,98.58,98.71,98.89,98.86,98.89,98.75,98.73,98.33,98.12,98.17,97.75,97.28,97.54,97.06,97.06,96.66,97.93,98.2,98.55,98.42,98.31,98.47,98.57,98.79,98.77,98.82,98.89,98.85,98.86,98.92,98.92,98.81,98.85,98.86,98.84,98.51,97.52,97.78,98.22,98.64,98.71,98.62,98.36,98.57,98.82,98.74,98.92,98.97,98.98,98.9,98.88,98.75,97.63,98.65,98.83,98.82,98.85,98.88,98.91,98.88,98.91,98.92,98.86,98.87,98.91,98.75,98.84,98.71,98.53,98.42,98.42,98.63,98.67,98.54,98.67,98.78,98.77,98.59,98.47,98.32,98.7,98.77,98.75,98.24,96.6,97.72,97.94,98.8,98.88,98.94,98.91,98.91,98.85,98.75,98.76,98.82,98.76,98.48,97.93,97.73,98.41,98.08,98.2,98.58,98.83,98.88,98.92,98.96,98.95,98.96,98.97,98.93,98.95,98.95,98.9,98.77,98.77,98.66,97.91,97.21,97.31,98.0,96.56,97.98,98.64,98.64,98.6,96.7,94.23,98.1,98.33,98.81,98.96,98.95,98.97,98.94,98.92,98.75,98.28,97.29,95.12,95.63,98.78,98.93,98.96,98.96,98.97,98.95,98.93,98.7,98.47,97.98,97.37,91.26,87.96,82.6,74.93,70.82,58.49,57.03,53.22,40.12,35.94,36.48,36.17,29.17,28.2,27.8,24.4,30.17,31.1,41.86,50.08,55.46,60.32,77.48,88.51,88.81,89.84,89.57,87.08,89.75,92.98,88.58,87.87,89.17,91.72,86.93,87.7,89.54,88.09,87.51,88.75,87.64,90.04,90.1,89.28,90.11,88.51,87.32,90.09,90.52,93.2,93.95,94.66,94.83,94.78,94.82,94.42,94.23,92.01,87.9,81.15,82.86,85.43,88.96,91.57,91.68,93.19,94.2,94.9,94.39,93.81,92.82,91.77,88.8,89.97,89.38,91.6,92.78,93.27,90.71,88.43,83.5,81.78,80.1,85.45,88.59,92.29,93.97,93.6,94.05,93.16,95.3,94.95,95.45,94.02,91.47,93.06,92.8,89.21,87.99,88.95,86.6,81.28,82.67,84.88,85.47,87.11,84.5,83.79,86.17,87.91,87.47,87.74,90.2,89.46,90.75,91.77,93.55,91.9,92.06,90.58,86.87,82.83,82.09,84.03,82.55,80.5,81.46,74.5,74.69,75.48,71.08,71.45,60.25,51.88,36.87,36.7,35.9,34.68,29.62,33.41]},"1":{"B":[61.32,59.19,55.15,51.52,44.11,36.48,34.31,28.89,24.75,27.04,26.57,28.3,29.66,29.99,33.41,37.08,38.18,39.5,38.45,43.17,47.55,47.91,47.01,48.34,49.86,49.9,50.39,52.53,52.99,48.97,45.53,42.42,38.59,36.18,35.76,36.45,38.45,38.39,40.13,41.27,37.51,34.17,32.2,33.08,34.28,38.83,36.23,35.86,33.92,31.61,33.52,33.72,34.27,38.41,38.35,39.98,44.01,43.6,43.8,43.28,43.37,43.18,47.67,49.88,49.84,49.33,49.48,46.25,41.84,37.24,35.43,34.17,31.9,33.67,30.11,28.46,31.12,33.63,36.21,33.35,32.28,30.3,29.59,34.01,39.39,46.97,50.28,44.47,40.98,37.86,33.42,31.92,31.32,30.53,32.35,31.36,32.94,30.98,31.98,33.33,34.44,36.35,36.78,35.66,34.86,33.02,33.3,36.08,39.64,41.18,40.84,38.76,36.39,38.73,39.68,40.95,35.38,33.04,32.72,23.94,19.8,19.26]},"2":{"A":[0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0]}},"warnings":{"0":"NA","1":"NA","2":"NA"}} -------------------------------------------------------------------------------- /examples/command_line/results/P22307/all_coverage_plot_chunk_0.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/PDBminer/464adacc5c978a305c2a0599e5f141eed3eb63ec/examples/command_line/results/P22307/all_coverage_plot_chunk_0.pdf -------------------------------------------------------------------------------- /examples/command_line/results/P22307/all_coverage_plot_chunk_1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/PDBminer/464adacc5c978a305c2a0599e5f141eed3eb63ec/examples/command_line/results/P22307/all_coverage_plot_chunk_1.pdf -------------------------------------------------------------------------------- /examples/command_line/results/P22307/all_network.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/PDBminer/464adacc5c978a305c2a0599e5f141eed3eb63ec/examples/command_line/results/P22307/all_network.pdf -------------------------------------------------------------------------------- /examples/csv_output/do.sh: -------------------------------------------------------------------------------- 1 | PDBminer -i input_file.csv -f csv 2 | PDBminer2coverage 3 | PDBminer2network 4 | -------------------------------------------------------------------------------- /examples/csv_output/input_file.csv: -------------------------------------------------------------------------------- 1 | hugo_name,uniprot,uniprot_isoform,mutations,cluster_id 2 | FGF10,O15520,1,NA,NA 3 | ULK1,O75385,1,NA,NA 4 | -------------------------------------------------------------------------------- /examples/csv_output/log.txt: -------------------------------------------------------------------------------- 1 | 2023-10-05 13:28:13,052 - INFO - PDBminer is starting 2 | 2023-10-05 13:28:13,052 - INFO - input file mode is choosen and input file has been identified. 3 | 2023-10-05 13:28:13,061 - INFO - Pipeline is starting 4 | 2023-10-05 13:28:34,578 - INFO - total runtime: 0:00:21.526100 5 | 2023-10-05 13:28:34,579 - INFO - PDBminer has finished. 6 | -------------------------------------------------------------------------------- /examples/csv_output/results/O15520/O15520_all.csv: -------------------------------------------------------------------------------- 1 | structure_rank,hugo_name,uniprot_id,uniprot_isoform,structure_id,deposition_date,experimental_method,resolution,r_free,PDBREDOdb,PDBREDOdb_rfree,complex_protein,complex_protein_details,complex_nucleotide,complex_nucleotide_details,complex_ligand,complex_ligand_details,chains,coverage,mutations_in_pdb,b_factor,warnings 2 | 0,FGF10,O15520,1,AF-O15520-F1-model_v4,2022-06-01,PREDICTED,NA,NA,NO,NA,NA,NA,NA,NA,NA,NA,A,"{'A': '[(67, 207)]'}",NA,"{'A': [46.61, 46.32, 34.52, 62.1, 49.28, 59.14, 58.05, 58.8, 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36.67, 38.55, 38.4 , 28.77, 26.53, 27.1 , 29.47, 33.25, 9 | 36.08, 39.65, 42.08, 47.14, 50.71, 51.27, 52.06, 54.65, 50.35, 10 | 46.8 , 43.95, 46.29, 53.48, 52.62, 53. , 56.41, 55.2 , 51.17, 11 | 47.66, 52.32, 52.34, 50.47, 51.63, 49.25, 48.23, 48.37, 49.2 , 12 | 47.37, 42.59, 41.23, 39.47, 37.02, 31.13, 26.47, 30.64, 31.22, 13 | 27.99, 26.05, 27.35, 26.52, 28.91, 31.31, 34.67, 38.74, 43.6 , 14 | 53.57, 55.18, 58.53, 63.08, 64.84, 58.96, 53.7 , 48.29, 44.17, 15 | 36.53, 35.74, 40.77, 45.59, 54.06, 56.72, 59.59, 57.84, 53.72, 16 | 49.42, 45.32, 46.45, 48.71, 49.01, 47.5 , 44.01, 43.62, 42.31, 17 | 41.3 , 43.15, 44.06, 45.81, 42.76, 36.71, 35.48, 36.69, 40.55, 18 | 44.92, 46.61, 52.24, 59.66])}",NA 19 | -------------------------------------------------------------------------------- /examples/csv_output/results/O15520/all_coverage_plot.pdf: -------------------------------------------------------------------------------- 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/examples/csv_output/results/O75385/all_coverage_plot_chunk_1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/PDBminer/464adacc5c978a305c2a0599e5f141eed3eb63ec/examples/csv_output/results/O75385/all_coverage_plot_chunk_1.pdf -------------------------------------------------------------------------------- /examples/csv_output/results/O75385/all_coverage_plot_chunk_2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ELELAB/PDBminer/464adacc5c978a305c2a0599e5f141eed3eb63ec/examples/csv_output/results/O75385/all_coverage_plot_chunk_2.pdf -------------------------------------------------------------------------------- /examples/csv_output/results/O75385/all_network.pdf: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | 2023-10-05 13:28:33,161 - INFO - PDBminer is starting 2 | 2023-10-05 13:28:33,161 - INFO - input file mode is choosen and input file has been identified. 3 | 2023-10-05 13:28:33,168 - INFO - Pipeline is starting 4 | 2023-10-05 13:28:42,811 - INFO - total runtime: 0:00:09.649699 5 | 2023-10-05 13:28:42,811 - INFO - PDBminer has finished. 6 | -------------------------------------------------------------------------------- /examples/different_clusters/results/P22307/P22307_all.json: -------------------------------------------------------------------------------- 1 | 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-------------------------------------------------------------------------------- 1 | hugo_name,uniprot,uniprot_isoform,mutations,cluster_id 2 | RNH,P0A7Y7,1,D134N,1 3 | DMD,P11532,1,K18N,1 4 | -------------------------------------------------------------------------------- /examples/input_file/log.txt: -------------------------------------------------------------------------------- 1 | 2023-10-05 13:28:52,526 - INFO - PDBminer is starting 2 | 2023-10-05 13:28:52,526 - INFO - input file mode is choosen and input file has been identified. 3 | 2023-10-05 13:28:52,535 - INFO - Pipeline is starting 4 | 2023-10-05 13:28:53,327 - WARNING - Uniprot did not return any structures for P0A7Y7 5 | 2023-10-05 13:28:54,507 - WARNING - The Alphafold Database returned an error for the request of P11532. 6 | 2023-10-05 13:28:54,507 - WARNING - AlphaFold database returned an error for P11532. This may indicate that there are no structure for P11532 in the Alphafold Database. 7 | 2023-10-05 13:29:00,338 - INFO - total runtime: 0:00:07.811826 8 | 2023-10-05 13:29:00,338 - INFO - PDBminer has finished. 9 | -------------------------------------------------------------------------------- /examples/input_file/results/P0A7Y7/P0A7Y7_all.json: -------------------------------------------------------------------------------- 1 | {"hugo_name":{"0":"RNH"},"uniprot_id":{"0":"P0A7Y7"},"uniprot_isoform":{"0":1},"structure_id":{"0":"AF-P0A7Y7-F1-model_v4"},"deposition_date":{"0":"2022-06-01"},"experimental_method":{"0":"PREDICTED"},"resolution":{"0":"NA"},"r_free":{"0":"NA"},"PDBREDOdb":{"0":"NO"},"PDBREDOdb_rfree":{"0":"NA"},"complex_protein":{"0":"NA"},"complex_protein_details":{"0":"NA"},"complex_nucleotide":{"0":"NA"},"complex_nucleotide_details":{"0":"NA"},"complex_ligand":{"0":"NA"},"complex_ligand_details":{"0":"NA"},"chains":{"0":"A"},"coverage":{"0":{"A":"[(1, 123);(126, 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-------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup, find_packages 2 | 3 | setup( 4 | name="PDBminer", 5 | version="1.0.0", 6 | description="Tool for mining PDB data", 7 | long_description=open("README.md").read(), 8 | long_description_content_type="text/markdown", 9 | author="Kristine Degn", 10 | author_email="krde@dtu.com", 11 | url="https://github.com/ELELAB/PDBminer", 12 | packages=find_packages(), 13 | include_package_data=True, 14 | python_requires=">=3.6", 15 | install_requires=[ 16 | "biopython==1.83", 17 | "matplotlib==3.8.3", 18 | "networkx==3.2.1", 19 | "numpy==1.26.4", 20 | "pandas==2.2.1", 21 | "PyYAML==6.0.1", 22 | "requests==2.31.0", 23 | "seaborn==0.13.2", 24 | ], 25 | entry_points={ 26 | "console_scripts": [ 27 | "PDBminer=PDBminer.PDBminer:main", 28 | "PDBminer2coverage=PDBminer.PDBminer2coverage:main", 29 | "PDBminer2network=PDBminer.PDBminer2network:main", 30 | ], 31 | }, 32 | ) 33 | --------------------------------------------------------------------------------