├── .gitattributes ├── README.md ├── example ├── 1_generateSeeds │ ├── genSeeds.params │ └── run_generateSeeds.sh ├── 2_findOverlaps │ ├── run_findoverlaps_array.sh │ └── run_findoverlaps_singlenode.sh ├── 3_buildSeedGraph │ └── run_buildSeedGraph.sh ├── 4_samplePaths │ └── run_samplepaths.sh ├── 5_buildPeptideRMSDMatrix │ ├── 1_makePeptideBin │ │ └── run_buildPeptideRMSDMatrix_1.sh │ ├── 2_computeRMSD │ │ └── run_buildPeptideRMSDMatrix_2.sh │ └── 3_buildMatrix │ │ └── run_buildPeptideRMSDMatrix_3.sh ├── 6_scoreStructures │ └── run_scoreStructures.sh ├── 7_dTERMenSequenceDesign │ └── run_dTERMenSequenceDesign.sh ├── 8_rosettaRelax │ └── run_rosettaRelax.sh ├── 9_rosettaFPDRefine │ ├── refine_flags │ ├── run_FPDRefine.sh │ └── submit_FPDRefine.sh └── input_files │ ├── 1LB6_A__.pdb │ ├── dTERMen.configfile │ ├── multichainDB.configfile │ └── singlechainDB.configfile ├── helperprograms ├── FASSTDBProperties.cpp ├── addToBin.cpp ├── compareBackbones.cpp ├── getStructureFromBin.cpp ├── peptideWindowDistance.cpp ├── sampleSequencesMCMC.cpp ├── searchFragment.cpp ├── seedStatistics.cpp └── writeStructureResidueProperties.cpp ├── inc ├── .DS_Store ├── benchmarkutilities.h ├── clustertree.h ├── clusterutils.h ├── coverage.h ├── fileutilities.h ├── findfuseable.h ├── findpaths.h ├── fragments.h ├── freesasaext.h ├── kmedoids.tpp ├── mstsystem_exts.h ├── overlaps.h ├── overlaps.tpp ├── params.h ├── pathsampler.h ├── ranklist.h ├── secondarystructure.h ├── seedgraph.h ├── seedscore.h ├── structure_iter.h ├── termextension.h ├── utilities.h └── vdwRadii.h ├── license.md ├── makefile ├── programs ├── buildClusterTree.cpp ├── buildGreedyClusters.cpp ├── buildPeptideRMSDMatrix.cpp ├── buildSeedGraph.cpp ├── countContacts.cpp ├── coverageBenchmark.cpp ├── coverageInterfaceFragments.cpp ├── exportSeeds.cpp ├── findOverlaps.cpp ├── generateSeeds.cpp ├── samplePaths.cpp ├── scoreProteinBindingHotspots.cpp ├── scoreStructures.cpp └── seedCentroidDistanceDistribution.cpp ├── scripts ├── dTERMenScoreSequences.py ├── formatCoveringSeeds.py └── load_seeds.py ├── src ├── benchmarkutilities.cpp ├── clustertree.cpp ├── clusterutils.cpp ├── coverage.cpp ├── fileutilities.cpp ├── findfuseable.cpp ├── findpaths.cpp ├── fragments.cpp ├── freesasaext.cpp ├── overlaps.cpp ├── params.cpp ├── pathsampler.cpp ├── python.cpp ├── secondarystructure.cpp ├── seedgraph.cpp ├── seedscore.cpp ├── structure_iter.cpp ├── termextension.cpp ├── utilities.cpp └── vdwRadii.cpp ├── testfiles ├── 1LB5.pdb ├── 1LB5_apo.pdb └── 1LB5_peptide.pdb └── tests ├── defaultConstructor.cpp ├── nullModelCentroidDistance.cpp ├── testClusterTree.cpp ├── testConFind.cpp ├── testFASSTPerformance.cpp ├── testFreedom.cpp ├── testFuseFragments.cpp ├── testOverlapPerformance.cpp ├── testRandom.cpp ├── testSecStructure.cpp └── testStructuresBinaryFile.cpp /.gitattributes: -------------------------------------------------------------------------------- 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