├── .gitignore ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.html ├── README.md ├── _config.yml ├── dependencies.txt ├── docs ├── LogoPDBcopy22.png ├── example_2vyr.png ├── example_AF_O15151.png ├── pdbmapper_methods.png └── pdbmapper_methods_old.png ├── example ├── 1-makestructuraldb │ ├── human_proteome_blastdb │ │ ├── human_proteome_uniprot.phr │ │ ├── human_proteome_uniprot.pin │ │ └── human_proteome_uniprot.psq │ ├── input_pdbs.txt │ ├── pdbs │ │ ├── 2vyr-assembly1.cif │ │ ├── 2vyr-assembly1.cif.gz │ │ ├── 5mnj-assembly1.cif │ │ ├── 5mnj-assembly1.cif.gz │ │ ├── 6yr7-assembly1.cif │ │ ├── 6yr7-assembly1.cif.gz │ │ ├── 7jt9-assembly1.cif │ │ ├── 7jt9-assembly1.cif.gz │ │ ├── AF-O15151-F1-model_v4.pdb │ │ └── AF-P09769-F1-model_v4.pdb │ ├── run_makestructuredb.sh │ └── structural_db │ │ ├── makestructuraldb.report │ │ ├── pdb_chainseqs │ │ └── PDB_prot_nuc_lig_db.txt │ │ └── structuralDB │ │ ├── sp|O15151|MDM4_HUMAN.txt.gz │ │ ├── sp|P09769|FGR_HUMAN.txt.gz │ │ ├── sp|P0CG47|UBB_HUMAN.txt.gz │ │ ├── sp|P0CG48|UBC_HUMAN.txt.gz │ │ ├── sp|P31947|1433S_HUMAN.txt.gz │ │ ├── sp|P61077|UB2D3_HUMAN.txt.gz │ │ ├── sp|P62837|UB2D2_HUMAN.txt.gz │ │ ├── sp|P62979|RS27A_HUMAN.txt.gz │ │ ├── sp|P62987|RL40_HUMAN.txt.gz │ │ ├── sp|Q00987|MDM2_HUMAN.txt.gz │ │ └── tr|A0A2R8Y422|A0A2R8Y422_HUMAN.txt.gz ├── 2-makevariantsdb │ ├── DBs │ │ ├── makevariantsdb.log │ │ ├── makevariantsdb.report │ │ └── varDB │ │ │ ├── ENST00000367182.vep │ │ │ ├── ENST00000374005.vep │ │ │ └── variants.index │ ├── run_makevariantsdb.sh │ └── variants.vep ├── 3-mapper │ ├── 3dmapper_results │ │ ├── 3dmapper.log │ │ ├── 3dmapper.report │ │ ├── csv │ │ │ ├── InterfacePositions_pident20.0_isoform_all_consequence_all.csv │ │ │ ├── NoncodingPositions_pident20.0_isoform_all_consequence_all.csv │ │ │ └── StructurePositions_pident20.0_isoform_all_consequence_all.csv │ │ ├── hdf5 │ │ │ ├── InterfacePositions │ │ │ │ └── InterfacePositions_pident20.0_isoform_all_consequence_all_sp|O15151|MDM4_HUMAN.hdf5 │ │ │ ├── NoncodingPositions │ │ │ │ ├── NoncodingPositions_pident20.0_isoform_all_consequence_all_sp|O15151|MDM4_HUMAN.hdf5 │ │ │ │ └── NoncodingPositions_pident20.0_isoform_all_consequence_all_sp|P09769|FGR_HUMAN.hdf5 │ │ │ └── StructurePositions │ │ │ │ ├── StructurePositions_pident20.0_isoform_all_consequence_all_sp|O15151|MDM4_HUMAN.hdf5 │ │ │ │ └── StructurePositions_pident20.0_isoform_all_consequence_all_sp|P09769|FGR_HUMAN.hdf5 │ │ └── setID_pident20.0_isoform_all_consequence_all.txt │ ├── dict_geneprot_GRCh38_uniprot.txt │ └── run_mapper.sh ├── 4-makevisualization │ ├── chimerax_scripts │ │ ├── 2vyr-assembly1.cif_struct_int.cxc │ │ ├── 5mnj-assembly1.cif_struct_int.cxc │ │ ├── 7jt9-assembly1.cif_struct_int.cxc │ │ ├── AF-O15151-F1-model_v4.pdb_struct_int.cxc │ │ ├── AF-P09769-F1-model_v4.pdb_struct_int.cxc │ │ ├── makevisualization.log │ │ └── makevisualization.report │ ├── list_pdbs.txt │ └── run_makevisualization.sh └── run_test.sh ├── makechimera ├── __init__.py ├── __main__.py ├── helpers.py ├── logger.py ├── makechimera.py ├── parsers.py └── templates.py ├── makeinterfacedb ├── __init__.py ├── __main__.py ├── decorator.py ├── input_isfile.py ├── logger.py ├── makeinterfacedb.py ├── parse_argv.py ├── rscripts │ ├── PDB_pairwise_interaction.R │ ├── PDB_pairwise_interatom_dist.R │ ├── biolip_list.txt │ ├── calc_interatom_dist.R │ ├── extract_pdb_chain_seqs.R │ ├── filter_blast_output.R │ ├── map_interfaces.R │ ├── new_mapped_interfaces.R │ ├── predict_PDB_interfaces_main.R │ ├── readPDB.R │ └── read_Blast.R └── run_subprocess.py ├── makevariantsdb ├── __init__.py ├── __main__.py ├── add_header.py ├── create_var_index.py ├── decorator.py ├── detect_vcf_format.py ├── input_isfile.py ├── logger.py ├── maf2vep.py ├── makevariantsdb.py ├── parse_argv.py ├── run_subprocess.py ├── run_vep.py ├── split.py └── vcf2vep.py ├── mapper ├── __init__.py ├── __main__.py ├── data │ ├── 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