├── .coveragerc ├── .github ├── ISSUE_TEMPLATE │ ├── bug-report.md │ └── feature_request.md ├── dependabot.yml └── workflows │ └── build_test.yml ├── .gitignore ├── CHANGELOG.md ├── CODE_OF_CONDUCT.rst ├── CONTRIBUTING.rst ├── LICENSE ├── MANIFEST.in ├── NOTICE ├── README.md ├── deeprank ├── __init__.py ├── __version__.py ├── config │ ├── __init__.py │ ├── chemicals.py │ └── logger_settings.py ├── features │ ├── AtomicFeature.py │ ├── BSA.py │ ├── FeatureClass.py │ ├── FullPSSM.py │ ├── PSSM │ │ ├── ..PSSM │ │ ├── 1AK4.PSSM │ │ ├── 1ATN.PSSM │ │ ├── 1AVX.PSSM │ │ ├── 1AY7.PSSM │ │ ├── 1B6C.PSSM │ │ ├── 1BKD.PSSM │ │ ├── 1BUH.PSSM │ │ ├── 1BVN.PSSM │ │ ├── 1CGI.PSSM │ │ ├── 1CLV.PSSM │ │ ├── 1D6R.PSSM │ │ ├── 1DFJ.PSSM │ │ ├── 1E6E.PSSM │ │ ├── 1E96.PSSM │ │ ├── 1EAW.PSSM │ │ ├── 1EFN.PSSM │ │ ├── 1EWY.PSSM │ │ ├── 1F34.PSSM │ │ ├── 1F6M.PSSM │ │ ├── 1FC2.PSSM │ │ ├── 1FFW.PSSM │ │ ├── 1FLE.PSSM │ │ ├── 1FQ1.PSSM │ │ ├── 1FQJ.PSSM │ │ ├── 1GCQ.PSSM │ │ ├── 1GHQ.PSSM │ │ ├── 1GL1.PSSM │ │ ├── 1GLA.PSSM │ │ ├── 1GPW.PSSM │ │ ├── 1GRN.PSSM │ │ ├── 1GXD.PSSM │ │ ├── 1H1V.PSSM │ │ ├── 1H9D.PSSM │ │ ├── 1HE1.PSSM │ │ ├── 1HE8.PSSM │ │ ├── 1I2M.PSSM │ │ ├── 1IBR.PSSM │ │ ├── 1IRA.PSSM │ │ ├── 1J2J.PSSM │ │ ├── 1JK9.PSSM │ │ ├── 1JTG.PSSM │ │ ├── 1KAC.PSSM │ │ ├── 1KTZ.PSSM │ │ ├── 1KXP.PSSM │ │ ├── 1LFD.PSSM │ │ ├── 1M10.PSSM │ │ ├── 1MAH.PSSM │ │ ├── 1MQ8.PSSM │ │ ├── 1NW9.PSSM │ │ ├── 1OC0.PSSM │ │ ├── 1OPH.PSSM │ │ ├── 1OYV.PSSM │ │ ├── 1PPE.PSSM │ │ ├── 1PVH.PSSM │ │ ├── 1PXV.PSSM │ │ ├── 1QA9.PSSM │ │ ├── 1R0R.PSSM │ │ ├── 1R6Q.PSSM │ │ ├── 1R8S.PSSM │ │ ├── 1S1Q.PSSM │ │ ├── 1SBB.PSSM │ │ ├── 1SYX.PSSM │ │ ├── 1T6B.PSSM │ │ ├── 1TMQ.PSSM │ │ ├── 1UDI.PSSM │ │ ├── 1US7.PSSM │ │ ├── 1WQ1.PSSM │ │ ├── 1XD3.PSSM │ │ ├── 1XQS.PSSM │ │ ├── 1Y64.PSSM │ │ ├── 1YVB.PSSM │ │ ├── 1Z0K.PSSM │ │ ├── 1Z5Y.PSSM │ │ ├── 1ZHH.PSSM │ │ ├── 1ZHI.PSSM │ │ ├── 1ZLI.PSSM │ │ ├── 1ZM4.PSSM │ │ ├── 2A5T.PSSM │ │ ├── 2A9K.PSSM │ │ ├── 2ABZ.PSSM │ │ ├── 2AJF.PSSM │ │ ├── 2AYO.PSSM │ │ ├── 2B42.PSSM │ │ ├── 2BTF.PSSM │ │ ├── 2C0L.PSSM │ │ ├── 2CFH.PSSM │ │ ├── 2FJU.PSSM │ │ ├── 2G77.PSSM │ │ ├── 2H7V.PSSM │ │ ├── 2HLE.PSSM │ │ ├── 2HQS.PSSM │ │ ├── 2HRK.PSSM │ │ ├── 2I9B.PSSM │ │ ├── 2IDO.PSSM │ │ ├── 2J0T.PSSM │ │ ├── 2J7P.PSSM │ │ ├── 2NZ8.PSSM │ │ ├── 2O3B.PSSM │ │ ├── 2O8V.PSSM │ │ ├── 2OOB.PSSM │ │ ├── 2OT3.PSSM │ │ ├── 2OUL.PSSM │ │ ├── 2OZA.PSSM │ │ ├── 2PCC.PSSM │ │ ├── 2SIC.PSSM │ │ ├── 2SNI.PSSM │ │ ├── 2UUY.PSSM │ │ ├── 2VDB.PSSM │ │ ├── 2Z0E.PSSM │ │ ├── 3CPH.PSSM │ │ ├── 3D5S.PSSM │ │ ├── 3SGQ.PSSM │ │ ├── 4CPA.PSSM │ │ ├── 7CEI.PSSM │ │ └── reformat_pssm.py │ ├── PSSM_IC.py │ ├── PSSM_IC │ │ ├── 1AK4.PSSM_IC │ │ ├── 1ATN.PSSM_IC │ │ ├── 1AVX.PSSM_IC │ │ ├── 1AY7.PSSM_IC │ │ ├── 1B6C.PSSM_IC │ │ ├── 1BKD.PSSM_IC │ │ ├── 1BUH.PSSM_IC │ │ ├── 1BVN.PSSM_IC │ │ ├── 1CGI.PSSM_IC │ │ ├── 1CLV.PSSM_IC │ │ ├── 1D6R.PSSM_IC │ │ ├── 1DFJ.PSSM_IC │ │ ├── 1E6E.PSSM_IC │ │ ├── 1E96.PSSM_IC │ │ ├── 1EAW.PSSM_IC │ │ ├── 1EFN.PSSM_IC │ │ ├── 1EWY.PSSM_IC │ │ ├── 1F34.PSSM_IC │ │ ├── 1F6M.PSSM_IC │ │ ├── 1FC2.PSSM_IC │ │ ├── 1FFW.PSSM_IC │ │ ├── 1FLE.PSSM_IC │ │ ├── 1FQ1.PSSM_IC │ │ ├── 1FQJ.PSSM_IC │ │ ├── 1GCQ.PSSM_IC │ │ ├── 1GHQ.PSSM_IC │ │ ├── 1GL1.PSSM_IC │ │ ├── 1GLA.PSSM_IC │ │ ├── 1GPW.PSSM_IC │ │ ├── 1GRN.PSSM_IC │ │ ├── 1GXD.PSSM_IC │ │ ├── 1H1V.PSSM_IC │ │ ├── 1H9D.PSSM_IC │ │ ├── 1HE1.PSSM_IC │ │ ├── 1HE8.PSSM_IC │ │ ├── 1I2M.PSSM_IC │ │ ├── 1IBR.PSSM_IC │ │ ├── 1IRA.PSSM_IC │ │ ├── 1J2J.PSSM_IC │ │ ├── 1JK9.PSSM_IC │ │ ├── 1JTG.PSSM_IC │ │ ├── 1KAC.PSSM_IC │ │ ├── 1KTZ.PSSM_IC │ │ ├── 1KXP.PSSM_IC │ │ ├── 1LFD.PSSM_IC │ │ ├── 1M10.PSSM_IC │ │ ├── 1MAH.PSSM_IC │ │ ├── 1MQ8.PSSM_IC │ │ ├── 1NW9.PSSM_IC │ │ ├── 1OC0.PSSM_IC │ │ ├── 1OPH.PSSM_IC │ │ ├── 1OYV.PSSM_IC │ │ ├── 1PPE.PSSM_IC │ │ ├── 1PVH.PSSM_IC │ │ ├── 1PXV.PSSM_IC │ │ ├── 1QA9.PSSM_IC │ │ ├── 1R0R.PSSM_IC │ │ ├── 1R6Q.PSSM_IC │ │ ├── 1R8S.PSSM_IC │ │ ├── 1S1Q.PSSM_IC │ │ ├── 1SBB.PSSM_IC │ │ ├── 1SYX.PSSM_IC │ │ ├── 1T6B.PSSM_IC │ │ ├── 1TMQ.PSSM_IC │ │ ├── 1UDI.PSSM_IC │ │ ├── 1US7.PSSM_IC │ │ ├── 1WQ1.PSSM_IC │ │ ├── 1XD3.PSSM_IC │ │ ├── 1XQS.PSSM_IC │ │ ├── 1Y64.PSSM_IC │ │ ├── 1YVB.PSSM_IC │ │ ├── 1Z0K.PSSM_IC │ │ ├── 1Z5Y.PSSM_IC │ │ ├── 1ZHH.PSSM_IC │ │ ├── 1ZHI.PSSM_IC │ │ ├── 1ZLI.PSSM_IC │ │ ├── 1ZM4.PSSM_IC │ │ ├── 2A5T.PSSM_IC │ │ ├── 2A9K.PSSM_IC │ │ ├── 2ABZ.PSSM_IC │ │ ├── 2AJF.PSSM_IC │ │ ├── 2AYO.PSSM_IC │ │ ├── 2B42.PSSM_IC │ │ ├── 2BTF.PSSM_IC │ │ ├── 2C0L.PSSM_IC │ │ ├── 2CFH.PSSM_IC │ │ ├── 2FJU.PSSM_IC │ │ ├── 2G77.PSSM_IC │ │ ├── 2H7V.PSSM_IC │ │ ├── 2HLE.PSSM_IC │ │ ├── 2HQS.PSSM_IC │ │ ├── 2HRK.PSSM_IC │ │ ├── 2I9B.PSSM_IC │ │ ├── 2IDO.PSSM_IC │ │ ├── 2J0T.PSSM_IC │ │ ├── 2J7P.PSSM_IC │ │ ├── 2NZ8.PSSM_IC │ │ ├── 2O3B.PSSM_IC │ │ ├── 2O8V.PSSM_IC │ │ ├── 2OOB.PSSM_IC │ │ ├── 2OT3.PSSM_IC │ │ ├── 2OUL.PSSM_IC │ │ ├── 2OZA.PSSM_IC │ │ ├── 2PCC.PSSM_IC │ │ ├── 2SIC.PSSM_IC │ │ ├── 2SNI.PSSM_IC │ │ ├── 2UUY.PSSM_IC │ │ ├── 2VDB.PSSM_IC │ │ ├── 2Z0E.PSSM_IC │ │ ├── 3CPH.PSSM_IC │ │ ├── 3D5S.PSSM_IC │ │ ├── 3SGQ.PSSM_IC │ │ ├── 4CPA.PSSM_IC │ │ ├── 7CEI.PSSM_IC │ │ └── extract_ic.py │ ├── PSSM_NEW │ │ ├── 1ACB.A.pdb.pssm │ │ ├── 1ACB.B.pdb.pssm │ │ ├── 1AK4.A.pdb.pssm │ │ ├── 1AK4.B.pdb.pssm │ │ ├── 1ATN.A.pdb.pssm │ │ ├── 1ATN.B.pdb.pssm │ │ ├── 1AVX.A.pdb.pssm │ │ ├── 1AVX.B.pdb.pssm │ │ ├── 1AY7.A.pdb.pssm │ │ ├── 1AY7.B.pdb.pssm │ │ ├── 1B6C.A.pdb.pssm │ │ ├── 1B6C.B.pdb.pssm │ │ ├── 1BKD.A.pdb.pssm │ │ ├── 1BKD.B.pdb.pssm │ │ ├── 1BUH.A.pdb.pssm │ │ ├── 1BUH.B.pdb.pssm │ │ ├── 1BVN.A.pdb.pssm │ │ ├── 1BVN.B.pdb.pssm │ │ ├── 1CGI.A.pdb.pssm │ │ ├── 1CGI.B.pdb.pssm │ │ ├── 1CLV.A.pdb.pssm │ │ ├── 1CLV.B.pdb.pssm │ │ ├── 1D6R.A.pdb.pssm │ │ ├── 1D6R.B.pdb.pssm │ │ ├── 1DFJ.A.pdb.pssm │ │ ├── 1DFJ.B.pdb.pssm │ │ ├── 1E6E.A.pdb.pssm │ │ ├── 1E6E.B.pdb.pssm │ │ ├── 1E96.A.pdb.pssm │ │ ├── 1E96.B.pdb.pssm │ │ ├── 1EAW.A.pdb.pssm │ │ ├── 1EAW.B.pdb.pssm │ │ ├── 1EFN.A.pdb.pssm │ │ ├── 1EFN.B.pdb.pssm │ │ ├── 1EWY.A.pdb.pssm │ │ ├── 1EWY.B.pdb.pssm │ │ ├── 1F34.A.pdb.pssm │ │ ├── 1F34.B.pdb.pssm │ │ ├── 1F6M.A.pdb.pssm │ │ ├── 1F6M.B.pdb.pssm │ │ ├── 1FC2.A.pdb.pssm │ │ ├── 1FC2.B.pdb.pssm │ │ ├── 1FFW.A.pdb.pssm │ │ ├── 1FFW.B.pdb.pssm │ │ ├── 1FLE.A.pdb.pssm │ │ ├── 1FLE.B.pdb.pssm │ │ ├── 1FQ1.A.pdb.pssm │ │ ├── 1FQ1.B.pdb.pssm │ │ ├── 1FQJ.A.pdb.pssm │ │ ├── 1FQJ.B.pdb.pssm │ │ ├── 1GCQ.A.pdb.pssm │ │ ├── 1GCQ.B.pdb.pssm │ │ ├── 1GHQ.A.pdb.pssm │ │ ├── 1GHQ.B.pdb.pssm │ │ ├── 1GL1.A.pdb.pssm │ │ ├── 1GL1.B.pdb.pssm │ │ ├── 1GLA.A.pdb.pssm │ │ ├── 1GLA.B.pdb.pssm │ │ ├── 1GPW.A.pdb.pssm │ │ ├── 1GPW.B.pdb.pssm │ │ ├── 1GRN.A.pdb.pssm │ │ ├── 1GRN.B.pdb.pssm │ │ ├── 1GXD.A.pdb.pssm │ │ ├── 1GXD.B.pdb.pssm │ │ ├── 1H1V.A.pdb.pssm │ │ ├── 1H1V.B.pdb.pssm │ │ ├── 1H9D.A.pdb.pssm │ │ ├── 1H9D.B.pdb.pssm │ │ ├── 1HE1.A.pdb.pssm │ │ ├── 1HE1.B.pdb.pssm │ │ ├── 1HE8.A.pdb.pssm │ │ ├── 1HE8.B.pdb.pssm │ │ ├── 1I2M.A.pdb.pssm │ │ ├── 1I2M.B.pdb.pssm │ │ ├── 1IBR.A.pdb.pssm │ │ ├── 1IBR.B.pdb.pssm │ │ ├── 1IRA.A.pdb.pssm │ │ ├── 1IRA.B.pdb.pssm │ │ ├── 1J2J.A.pdb.pssm │ │ ├── 1J2J.B.pdb.pssm │ │ ├── 1JIW.A.pdb.pssm │ │ ├── 1JIW.B.pdb.pssm │ │ ├── 1JK9.A.pdb.pssm │ │ ├── 1JK9.B.pdb.pssm │ │ ├── 1JTD.A.pdb.pssm │ │ ├── 1JTD.B.pdb.pssm │ │ ├── 1JTG.A.pdb.pssm │ │ ├── 1JTG.B.pdb.pssm │ │ ├── 1KAC.A.pdb.pssm │ │ ├── 1KAC.B.pdb.pssm │ │ ├── 1KTZ.A.pdb.pssm │ │ ├── 1KTZ.B.pdb.pssm │ │ ├── 1KXP.A.pdb.pssm │ │ ├── 1KXP.B.pdb.pssm │ │ ├── 1KXQ.A.pdb.pssm │ │ ├── 1KXQ.B.pdb.pssm │ │ ├── 1LFD.A.pdb.pssm │ │ ├── 1LFD.B.pdb.pssm │ │ ├── 1M10.A.pdb.pssm │ │ ├── 1M10.B.pdb.pssm │ │ ├── 1MAH.A.pdb.pssm │ │ ├── 1MAH.B.pdb.pssm │ │ ├── 1MQ8.A.pdb.pssm │ │ ├── 1MQ8.B.pdb.pssm │ │ ├── 1NW9.A.pdb.pssm │ │ ├── 1NW9.B.pdb.pssm │ │ ├── 1OC0.A.pdb.pssm │ │ ├── 1OC0.B.pdb.pssm │ │ ├── 1OPH.A.pdb.pssm │ │ ├── 1OPH.B.pdb.pssm │ │ ├── 1OYV.A.pdb.pssm │ │ ├── 1OYV.B.pdb.pssm │ │ ├── 1PPE.A.pdb.pssm │ │ ├── 1PPE.B.pdb.pssm │ │ ├── 1PVH.A.pdb.pssm │ │ ├── 1PVH.B.pdb.pssm │ │ ├── 1PXV.A.pdb.pssm │ │ ├── 1PXV.B.pdb.pssm │ │ ├── 1QA9.A.pdb.pssm │ │ ├── 1QA9.B.pdb.pssm │ │ ├── 1R0R.A.pdb.pssm │ │ ├── 1R0R.B.pdb.pssm │ │ ├── 1R6Q.A.pdb.pssm │ │ ├── 1R6Q.B.pdb.pssm │ │ ├── 1R8S.A.pdb.pssm │ │ ├── 1R8S.B.pdb.pssm │ │ ├── 1RKE.A.pdb.pssm │ │ ├── 1RKE.B.pdb.pssm │ │ ├── 1S1Q.A.pdb.pssm │ │ ├── 1S1Q.B.pdb.pssm │ │ ├── 1SBB.A.pdb.pssm │ │ ├── 1SBB.B.pdb.pssm │ │ ├── 1SYX.A.pdb.pssm │ │ ├── 1SYX.B.pdb.pssm │ │ ├── 1T6B.A.pdb.pssm │ │ ├── 1T6B.B.pdb.pssm │ │ ├── 1TMQ.A.pdb.pssm │ │ ├── 1TMQ.B.pdb.pssm │ │ ├── 1US7.A.pdb.pssm │ │ ├── 1US7.B.pdb.pssm │ │ ├── 1WQ1.A.pdb.pssm │ │ ├── 1WQ1.B.pdb.pssm │ │ ├── 1XD3.A.pdb.pssm │ │ ├── 1XD3.B.pdb.pssm │ │ ├── 1XQS.A.pdb.pssm │ │ ├── 1XQS.B.pdb.pssm │ │ ├── 1Y64.A.pdb.pssm │ │ ├── 1Y64.B.pdb.pssm │ │ ├── 1YVB.A.pdb.pssm │ │ ├── 1YVB.B.pdb.pssm │ │ ├── 1Z0K.A.pdb.pssm │ │ ├── 1Z0K.B.pdb.pssm │ │ ├── 1Z5Y.A.pdb.pssm │ │ ├── 1Z5Y.B.pdb.pssm │ │ ├── 1ZHH.A.pdb.pssm │ │ ├── 1ZHH.B.pdb.pssm │ │ ├── 1ZHI.A.pdb.pssm │ │ ├── 1ZHI.B.pdb.pssm │ │ ├── 1ZLI.A.pdb.pssm │ │ ├── 1ZLI.B.pdb.pssm │ │ ├── 1ZM4.A.pdb.pssm │ │ ├── 1ZM4.B.pdb.pssm │ │ ├── 2A1A.A.pdb.pssm │ │ ├── 2A1A.B.pdb.pssm │ │ ├── 2A5T.A.pdb.pssm │ │ ├── 2A5T.B.pdb.pssm │ │ ├── 2A9K.A.pdb.pssm │ │ ├── 2A9K.B.pdb.pssm │ │ ├── 2ABZ.A.pdb.pssm │ │ ├── 2ABZ.B.pdb.pssm │ │ ├── 2AJF.A.pdb.pssm │ │ ├── 2AJF.B.pdb.pssm │ │ ├── 2AYO.A.pdb.pssm │ │ ├── 2AYO.B.pdb.pssm │ │ ├── 2B42.A.pdb.pssm │ │ ├── 2B42.B.pdb.pssm │ │ ├── 2BTF.A.pdb.pssm │ │ ├── 2BTF.B.pdb.pssm │ │ ├── 2C0L.A.pdb.pssm │ │ ├── 2C0L.B.pdb.pssm │ │ ├── 2CFH.A.pdb.pssm │ │ ├── 2CFH.B.pdb.pssm │ │ ├── 2FJU.A.pdb.pssm │ │ ├── 2FJU.B.pdb.pssm │ │ ├── 2G77.A.pdb.pssm │ │ ├── 2G77.B.pdb.pssm │ │ ├── 2GAF.A.pdb.pssm │ │ ├── 2GAF.B.pdb.pssm │ │ ├── 2GTP.A.pdb.pssm │ │ ├── 2GTP.B.pdb.pssm │ │ ├── 2H7V.A.pdb.pssm │ │ ├── 2H7V.B.pdb.pssm │ │ ├── 2HLE.A.pdb.pssm │ │ ├── 2HLE.B.pdb.pssm │ │ ├── 2HQS.A.pdb.pssm │ │ ├── 2HQS.B.pdb.pssm │ │ ├── 2HRK.A.pdb.pssm │ │ ├── 2HRK.B.pdb.pssm │ │ ├── 2I25.A.pdb.pssm │ │ ├── 2I25.B.pdb.pssm │ │ ├── 2I9B.A.pdb.pssm │ │ ├── 2I9B.B.pdb.pssm │ │ ├── 2IDO.A.pdb.pssm │ │ ├── 2IDO.B.pdb.pssm │ │ ├── 2J0T.A.pdb.pssm │ │ ├── 2J0T.B.pdb.pssm │ │ ├── 2J7P.A.pdb.pssm │ │ ├── 2J7P.B.pdb.pssm │ │ ├── 2NZ8.A.pdb.pssm │ │ ├── 2NZ8.B.pdb.pssm │ │ ├── 2O3B.A.pdb.pssm │ │ ├── 2O3B.B.pdb.pssm │ │ ├── 2O8V.A.pdb.pssm │ │ ├── 2O8V.B.pdb.pssm │ │ ├── 2OOB.A.pdb.pssm │ │ ├── 2OOB.B.pdb.pssm │ │ ├── 2OT3.A.pdb.pssm │ │ ├── 2OT3.B.pdb.pssm │ │ ├── 2OUL.A.pdb.pssm │ │ ├── 2OUL.B.pdb.pssm │ │ ├── 2OZA.A.pdb.pssm │ │ ├── 2OZA.B.pdb.pssm │ │ ├── 2PCC.A.pdb.pssm │ │ ├── 2PCC.B.pdb.pssm │ │ ├── 2SIC.A.pdb.pssm │ │ ├── 2SIC.B.pdb.pssm │ │ ├── 2SNI.A.pdb.pssm │ │ ├── 2SNI.B.pdb.pssm │ │ ├── 2VDB.A.pdb.pssm │ │ ├── 2VDB.B.pdb.pssm │ │ ├── 2X9A.A.pdb.pssm │ │ ├── 2X9A.B.pdb.pssm │ │ ├── 2YVJ.A.pdb.pssm │ │ ├── 2YVJ.B.pdb.pssm │ │ ├── 2Z0E.A.pdb.pssm │ │ ├── 2Z0E.B.pdb.pssm │ │ ├── 3A4S.A.pdb.pssm │ │ ├── 3A4S.B.pdb.pssm │ │ ├── 3AAD.A.pdb.pssm │ │ ├── 3AAD.B.pdb.pssm │ │ ├── 3BIW.A.pdb.pssm │ │ ├── 3BIW.B.pdb.pssm │ │ ├── 3BX7.A.pdb.pssm │ │ ├── 3BX7.B.pdb.pssm │ │ ├── 3CPH.A.pdb.pssm │ │ ├── 3CPH.B.pdb.pssm │ │ ├── 3D5S.A.pdb.pssm │ │ ├── 3D5S.B.pdb.pssm │ │ ├── 3DAW.A.pdb.pssm │ │ ├── 3DAW.B.pdb.pssm │ │ ├── 3F1P.A.pdb.pssm │ │ ├── 3F1P.B.pdb.pssm │ │ ├── 3FN1.A.pdb.pssm │ │ ├── 3FN1.B.pdb.pssm │ │ ├── 3H2V.A.pdb.pssm │ │ ├── 3H2V.B.pdb.pssm │ │ ├── 3K75.A.pdb.pssm │ │ ├── 3K75.B.pdb.pssm │ │ ├── 3PC8.A.pdb.pssm │ │ ├── 3PC8.B.pdb.pssm │ │ ├── 3S9D.A.pdb.pssm │ │ ├── 3S9D.B.pdb.pssm │ │ ├── 3SGQ.A.pdb.pssm │ │ ├── 3SGQ.B.pdb.pssm │ │ ├── 3VLB.A.pdb.pssm │ │ ├── 3VLB.B.pdb.pssm │ │ ├── 4CPA.A.pdb.pssm │ │ ├── 4CPA.B.pdb.pssm │ │ ├── 4FZA.A.pdb.pssm │ │ ├── 4FZA.B.pdb.pssm │ │ ├── 4H03.A.pdb.pssm │ │ ├── 4H03.B.pdb.pssm │ │ ├── 4IZ7.A.pdb.pssm │ │ ├── 4IZ7.B.pdb.pssm │ │ ├── 4M76.A.pdb.pssm │ │ ├── 4M76.B.pdb.pssm │ │ ├── 7CEI.A.pdb.pssm │ │ └── 7CEI.B.pdb.pssm │ ├── ResidueDensity.py │ ├── __init__.py │ └── forcefield │ │ ├── patch.top │ │ ├── protein-allhdg5-4_new.param │ │ └── protein-allhdg5-4_new.top ├── generate │ ├── DataGenerator.py │ ├── GridTools.py │ ├── NormalizeData.py │ ├── __init__.py │ └── kernel_map.c ├── learn │ ├── DataSet.py │ ├── NeuralNet.py │ ├── __init__.py │ ├── classMetrics.py │ ├── metaqnn.py │ ├── model2d.py │ ├── model3d.py │ ├── modelGenerator.py │ └── rankingMetrics.py ├── targets │ ├── __init__.py │ ├── binary_class.py │ ├── capri_class.py │ ├── dockQ.py │ └── rmsd_fnat.py ├── tools │ ├── __init__.py │ ├── sasa.py │ └── sparse.py └── utils │ ├── add_binaryClass.py │ ├── boxplot.R │ ├── cal_hitrate_successrate.py │ ├── clean_all │ ├── cleandata.py │ ├── get_h5subset.py │ ├── hitrate_plot.R │ ├── launch.py │ ├── logger_helper.py │ ├── merge_h5.py │ ├── plot_utils.py │ ├── run_slurmFLs.py │ ├── successrate_plot.R │ └── visualize3Ddata.py ├── developer_guideline.md ├── docs ├── Documentation.rst ├── Makefile ├── conf.py ├── deeprank.features.rst ├── deeprank.generate.rst ├── deeprank.learn.rst ├── deeprank.targets.rst ├── deeprank.tools.rst ├── index.rst ├── make.bat ├── tutorial.rst ├── tutorial1_installing.rst ├── tutorial2_dataGeneration.rst ├── tutorial3_learning.rst └── tutorial4_advanced.rst ├── example ├── README.md ├── alignH5.py ├── caseIDs.txt ├── generate_dataset_alignPDB.py ├── generate_dataset_noalign.py ├── kfold_train-balance_nofilt.slurm ├── learn.py ├── learn_batch.py ├── learn_batch_new.py ├── model_250619.py ├── model_280619.py └── train_001_smallNN_Kfold_balance_nofilt.py ├── makefile ├── paper_pretrained_models ├── 3DeepFace │ ├── arch_001_02.py │ ├── best_model.pt │ └── test.py ├── README.md └── docking_models_scoring │ ├── best_train_model.pt │ ├── model_280619.py │ └── test.py ├── pics ├── class_prediction.png ├── deeprank.png ├── deeprank_pic.png ├── docq.png └── interface.jpeg ├── scripts ├── clean_all ├── cleandata.py ├── launch.py └── simple_generate.py ├── setup.cfg ├── setup.py └── test ├── 1AK4 ├── atomic_features │ ├── 1AK4_100w.pdb │ ├── ref_1AK4_100w.dat │ └── test_1AK4_100w.dat ├── decoys │ ├── 1AK4_cm-it0_745.pdb │ ├── 1AK4_cm-itw_238w.pdb │ ├── 1AK4_ranair-it0_5257.pdb │ ├── 1AK4_ti5-itw_212w.pdb │ └── 1AK4_ti5-itw_312w.pdb ├── haddock_data │ ├── 1AK4.Fnat │ ├── 1AK4.irmsd │ └── 1AK4.lrmsd ├── native │ └── 1AK4.pdb ├── pssm │ └── 1AK4.PSSM └── pssm_new │ ├── 1AK4.C.pssm │ ├── 1AK4.D.pssm │ ├── 1AK4_cm-it0_745.C.pssm │ ├── 1AK4_cm-it0_745.D.pssm │ ├── 1AK4_cm-itw_238w.C.pssm │ ├── 1AK4_cm-itw_238w.D.pssm │ ├── 1AK4_ranair-it0_5257.C.pssm │ ├── 1AK4_ranair-it0_5257.D.pssm │ ├── 1AK4_ti5-itw_212w.C.pssm │ ├── 1AK4_ti5-itw_212w.D.pssm │ ├── 1AK4_ti5-itw_312w.C.pssm │ └── 1AK4_ti5-itw_312w.D.pssm ├── 2OUL ├── atomic_features │ └── test_2OUL_1.dat ├── decoys │ ├── 2OUL_1.pdb │ ├── 2OUL_10.pdb │ ├── 2OUL_2.pdb │ ├── 2OUL_3.pdb │ ├── 2OUL_4.pdb │ ├── 2OUL_5.pdb │ ├── 2OUL_6.pdb │ ├── 2OUL_7.pdb │ ├── 2OUL_8.pdb │ └── 2OUL_9.pdb ├── native │ └── 2OUL.pdb └── test.py ├── hitrate_successrate ├── scores_raw.tsv └── success_hitrate_ANS.tsv ├── test_atomic_features.py ├── test_generate.py ├── test_generate_cuda.py ├── 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