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Copyright (C) 2017 Honglue Shi honglue_dot_shi_at_duke_dot_edu This database is updated until April 27th 2017 All crystal structures are with resolution <= 3.0 A required package for running MismatchPDB: pandas v 0.18.1 numpy v 1.11.2 json v 2.0.9 written library: common learna_json commontool pull_pdb_all.py is to loop all the PDB file in ./Crystal directory, generate a array text file containing all the PDB id in alphabet order. Please copy this output All_crystal.txt into ./PDBinfo pull_pdb_json.py is to read all the PDB file in ./Crystal directory using DSSR, generate Json file into ./Json generate all the stem, bulge, internal loop, hairpin fragment check_json.py is to check the sanity of the json files in ./Json pdbToPairTable.py is to parse all the json files into a searchable database containing all DNA/RNA base pairs into a searchable database --> Pair_crystal.csv Please copy Pair_crystal.csv into ./PairTable Note that this database has excluded all the multiplets data pull_pair_list.py is to select all the corresponding entry in the searchable database (Pair_crystal.csv) based on category of PDB (cat), crystal structure resolution (reso), base pair name (bp_name) we simply load csv file into a Dataframe using pandas library and use .loc function to select
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A comprehensive PDB database of all DNA/RNA base pairs
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