AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
apps/pilot/jadolfbr/copy_top_each_strategy.py
apps/pilot/jadolfbr/glycan_basic_LCM_protocol.py
apps/pilot/jadolfbr/nnk_scorefxn.py
apps/public/antibody_benchmark_utils/RunRosettaBenchmarksMPI.py
apps/public/antibody_benchmark_utils/bm-RAbD_Jade.py
apps/public/antibody_benchmark_utils/bm-calculate_graft_closure_rabd.py
apps/public/antibody_benchmark_utils/bm-calculate_plot_mc_acceptance_rabd.py
apps/public/antibody_benchmark_utils/bm-calculate_recoveries_and_risk_ratios.py
apps/public/antibody_benchmark_utils/bm-output_all_clusters.py
apps/public/antibody_benchmark_utils/bm-plot_features.py
apps/public/antibody_benchmark_utils/bm-run_rabd_benchmarks.py
apps/public/antibody_utils/RAbD_Jade.py
apps/public/antibody_utils/convert_IMGT_to_fasta.py
apps/public/antibody_utils/create_features_json.py
apps/public/antibody_utils/generate_rabd_features_dbs.py
apps/public/antibody_utils/match_antibody_structures.py
apps/public/antibody_utils/order_ab_chains.py
apps/public/antibody_utils/split_antibody_components.py
apps/public/general/canceljobs.py
apps/public/general/convert_fig.py
apps/public/general/genscript_to_fasta.py
apps/public/general/get_seq.py
apps/public/general/rename_designs.py
apps/public/pdb_utils/place_TERs.py
apps/public/pdb_utils/strip_ANISOU.py
apps/public/pdb_utils/strip_ter.py
apps/public/pyrosetta/build_loop_pyrosetta.py
apps/public/pyrosetta/find_my_glycans.py
apps/public/pyrosetta/find_my_residues.py
apps/public/pyrosetta/get_mutation_energy.py
apps/public/rosetta/RunRosettaDBMode.py
apps/public/rosetta/RunRosettaMPI.py
apps/public/rosetta/check_missing_rosetta_nstruct.py
apps/public/rosetta/create_score_json_from_scored_decoys.py
apps/public/rosetta/insert_natives_table_into_features_db.py
apps/public/rosetta/score_analysis.py
bio_jade.egg-info/PKG-INFO
bio_jade.egg-info/SOURCES.txt
bio_jade.egg-info/dependency_links.txt
bio_jade.egg-info/not-zip-safe
bio_jade.egg-info/requires.txt
bio_jade.egg-info/top_level.txt
docs/Makefile
docs/authors.rst
docs/conf.py
docs/contributing.rst
docs/history.rst
docs/index.rst
docs/installation.rst
docs/jade.rst
docs/make.bat
docs/modules.rst
docs/readme.rst
docs/usage.rst
docs/_build/html/_static/ajax-loader.gif
docs/_build/html/_static/comment-bright.png
docs/_build/html/_static/comment-close.png
docs/_build/html/_static/comment.png
docs/_build/html/_static/down-pressed.png
docs/_build/html/_static/down.png
docs/_build/html/_static/file.png
docs/_build/html/_static/minus.png
docs/_build/html/_static/plus.png
docs/_build/html/_static/up-pressed.png
docs/_build/html/_static/up.png
docs/api/jade.RAbD.AnalyzeAntibodyDesigns.rst
docs/api/jade.RAbD.rst
docs/api/jade.RAbD.window_main.AnalysisFrame.rst
docs/api/jade.RAbD.window_main.CompareStrategiesFrame.rst
docs/api/jade.RAbD.window_main.FeaturesFrame.rst
docs/api/jade.RAbD.window_main.menu.rst
docs/api/jade.RAbD.window_main.rst
docs/api/jade.RAbD.window_modules.FilterSettingsWindow.rst
docs/api/jade.RAbD.window_modules.rst
docs/api/jade.RAbD_BM.AnalysisInfo.rst
docs/api/jade.RAbD_BM.AnalyzeRecovery.rst
docs/api/jade.RAbD_BM.RunBenchmarksRAbD.rst
docs/api/jade.RAbD_BM.benchmark_plotting.rst
docs/api/jade.RAbD_BM.recovery_rr_tools.rst
docs/api/jade.RAbD_BM.rst
docs/api/jade.RAbD_BM.tools.rst
docs/api/jade.RAbD_BM.tools_ab_db.rst
docs/api/jade.RAbD_BM.tools_features_db.rst
docs/api/jade.antibody.CDRClusterer.rst
docs/api/jade.antibody.ClusterData.rst
docs/api/jade.antibody.ab_db.rst
docs/api/jade.antibody.cdr_data.CDRData.rst
docs/api/jade.antibody.cdr_data.CDRDataTypes.rst
docs/api/jade.antibody.cdr_data.rst
docs/api/jade.antibody.decoy_data.DecoyData.rst
docs/api/jade.antibody.decoy_data.DecoyDataTypes.rst
docs/api/jade.antibody.decoy_data.rst
docs/api/jade.antibody.outliers.rst
docs/api/jade.antibody.rst
docs/api/jade.antibody.split_structure.rst
docs/api/jade.antibody.util.rst
docs/api/jade.basic.RestypeDefinitions.rst
docs/api/jade.basic.TKinter.ImageFrame.rst
docs/api/jade.basic.TKinter.Listbox.rst
docs/api/jade.basic.TKinter.rst
docs/api/jade.basic.filters.DataFilter.rst
docs/api/jade.basic.filters.DataFilters.rst
docs/api/jade.basic.filters.FilterSettings.rst
docs/api/jade.basic.filters.rst
docs/api/jade.basic.general.rst
docs/api/jade.basic.numeric.rst
docs/api/jade.basic.pandas.PandasDataFrame.rst
docs/api/jade.basic.pandas.rst
docs/api/jade.basic.pandas.stats.rst
docs/api/jade.basic.path.rst
docs/api/jade.basic.plotting.MakeFigure.rst
docs/api/jade.basic.plotting.correlations.rst
docs/api/jade.basic.plotting.error_bars.rst
docs/api/jade.basic.plotting.rst
docs/api/jade.basic.rst
docs/api/jade.basic.sequence.ClustalRunner.rst
docs/api/jade.basic.sequence.PDBConsensusInfo.rst
docs/api/jade.basic.sequence.SequenceInfo.rst
docs/api/jade.basic.sequence.SequenceResults.rst
docs/api/jade.basic.sequence.SequenceStats.rst
docs/api/jade.basic.sequence.fasta.rst
docs/api/jade.basic.sequence.rst
docs/api/jade.basic.sql.StatementCreator.rst
docs/api/jade.basic.sql.rst
docs/api/jade.basic.structure.BasicPose.rst
docs/api/jade.basic.structure.BioPose.rst
docs/api/jade.basic.structure.SQLPose.rst
docs/api/jade.basic.structure.Structure.rst
docs/api/jade.basic.structure.rst
docs/api/jade.basic.structure.util.rst
docs/api/jade.basic.threading.JobDistributor.rst
docs/api/jade.basic.threading.Threader.rst
docs/api/jade.basic.threading.rst
docs/api/jade.clustering.CaliburRunner.rst
docs/api/jade.clustering.rst
docs/api/jade.machine_learning.rst
docs/api/jade.machine_learning.util.rst
docs/api/jade.nnk.NNKAbMaturation.rst
docs/api/jade.nnk.NNKEnrichments.rst
docs/api/jade.nnk.rst
docs/api/jade.pymol_jade.PyMolScriptWriter.rst
docs/api/jade.pymol_jade.rst
docs/api/jade.rosetta_jade.BenchmarkInfo.rst
docs/api/jade.rosetta_jade.FeaturesJsonCreator.rst
docs/api/jade.rosetta_jade.Region.rst
docs/api/jade.rosetta_jade.RunRosetta.rst
docs/api/jade.rosetta_jade.RunRosettaBenchmarks.rst
docs/api/jade.rosetta_jade.ScoreFiles.rst
docs/api/jade.rosetta_jade.SetupRosettaOptionsBenchmark.rst
docs/api/jade.rosetta_jade.SetupRosettaOptionsGeneral.rst
docs/api/jade.rosetta_jade.alignment.rst
docs/api/jade.rosetta_jade.features.rst
docs/api/jade.rosetta_jade.flag_util.rst
docs/api/jade.rosetta_jade.monte_carlo_analysis.AnalyzeMCAcceptance.rst
docs/api/jade.rosetta_jade.monte_carlo_analysis.CycleData.rst
docs/api/jade.rosetta_jade.monte_carlo_analysis.MCData.rst
docs/api/jade.rosetta_jade.monte_carlo_analysis.rst
docs/api/jade.rosetta_jade.rst
docs/api/jade.rosetta_jade.score_util.rst
docs/api/jade.rosetta_jade.structure_editing.rst
docs/api/jade.rst
docs/api/jade.utility.rst
docs/api/jade.utility.string_util.rst
docs/api/modules.rst
docs/apps_pilot_api/apps.pilot.jadolfbr.rst
docs/apps_pilot_api/apps.pilot.rst
docs/apps_pilot_api/modules.rst
docs/apps_public_api/apps.public.antibody_benchmark_utils.rst
docs/apps_public_api/apps.public.antibody_utils.rst
docs/apps_public_api/apps.public.general.rst
docs/apps_public_api/apps.public.pdb_utils.rst
docs/apps_public_api/apps.public.pyrosetta.rst
docs/apps_public_api/apps.public.rosetta.rst
docs/apps_public_api/apps.public.rst
docs/apps_public_api/modules.rst
jade/RAbD/AnalyzeAntibodyDesigns.py
jade/RAbD/__init__.py
jade/RAbD/window_main/AnalysisFrame.py
jade/RAbD/window_main/CompareStrategiesFrame.py
jade/RAbD/window_main/FeaturesFrame.py
jade/RAbD/window_main/__init__.py
jade/RAbD/window_main/menu.py
jade/RAbD/window_modules/FilterSettingsWindow.py
jade/RAbD/window_modules/__init__.py
jade/RAbD_BM/AnalysisInfo.py
jade/RAbD_BM/AnalyzeRecovery.py
jade/RAbD_BM/RunBenchmarksRAbD.py
jade/RAbD_BM/__init__.py
jade/RAbD_BM/benchmark_plotting.py
jade/RAbD_BM/recovery_rr_tools.py
jade/RAbD_BM/tools.py
jade/RAbD_BM/tools_ab_db.py
jade/RAbD_BM/tools_features_db.py
jade/antibody/CDRClusterer.py
jade/antibody/ClusterData.py
jade/antibody/__init__.py
jade/antibody/ab_db.py
jade/antibody/outliers.py
jade/antibody/split_structure.py
jade/antibody/util.py
jade/antibody/cdr_data/CDRData.py
jade/antibody/cdr_data/CDRDataTypes.py
jade/antibody/cdr_data/__init__.py
jade/antibody/decoy_data/DecoyData.py
jade/antibody/decoy_data/DecoyDataTypes.py
jade/antibody/decoy_data/__init__.py
jade/basic/RestypeDefinitions.py
jade/basic/__init__.py
jade/basic/general.py
jade/basic/numeric.py
jade/basic/path.py
jade/basic/TKinter/ImageFrame.py
jade/basic/TKinter/Listbox.py
jade/basic/TKinter/__init__.py
jade/basic/filters/DataFilter.py
jade/basic/filters/DataFilters.py
jade/basic/filters/FilterSettings.py
jade/basic/filters/__init__.py
jade/basic/pandas/PandasDataFrame.py
jade/basic/pandas/__init__.py
jade/basic/pandas/stats.py
jade/basic/plotting/MakeFigure.py
jade/basic/plotting/__init__.py
jade/basic/plotting/correlations.py
jade/basic/plotting/error_bars.py
jade/basic/sequence/ClustalRunner.py
jade/basic/sequence/PDBConsensusInfo.py
jade/basic/sequence/SequenceInfo.py
jade/basic/sequence/SequenceResults.py
jade/basic/sequence/SequenceStats.py
jade/basic/sequence/__init__.py
jade/basic/sequence/fasta.py
jade/basic/sql/StatementCreator.py
jade/basic/sql/__init__.py
jade/basic/structure/BasicPose.py
jade/basic/structure/BioPose.py
jade/basic/structure/SQLPose.py
jade/basic/structure/Structure.py
jade/basic/structure/__init__.py
jade/basic/structure/util.py
jade/basic/threading/JobDistributor.py
jade/basic/threading/Threader.py
jade/basic/threading/__init__.py
jade/clustering/CaliburRunner.py
jade/clustering/__init__.py
jade/machine_learning/__init__.py
jade/machine_learning/util.py
jade/nnk/NNKAbMaturation.py
jade/nnk/NNKEnrichments.py
jade/nnk/NNKIndex.py
jade/nnk/NNKScoreFunction.py
jade/nnk/__init__.py
jade/pymol_jade/PyMolScriptWriter.py
jade/pymol_jade/__init__.py
jade/pymol_jade/pymol_extensions.py
jade/rosetta_jade/BenchmarkInfo.py
jade/rosetta_jade/FeaturesJsonCreator.py
jade/rosetta_jade/Region.py
jade/rosetta_jade/RunRosetta.py
jade/rosetta_jade/RunRosettaBenchmarks.py
jade/rosetta_jade/ScoreFiles.py
jade/rosetta_jade/SetupRosettaOptionsBenchmark.py
jade/rosetta_jade/SetupRosettaOptionsGeneral.py
jade/rosetta_jade/__init__.py
jade/rosetta_jade/alignment.py
jade/rosetta_jade/features.py
jade/rosetta_jade/flag_util.py
jade/rosetta_jade/score_util.py
jade/rosetta_jade/monte_carlo_analysis/AnalyzeMCAcceptance.py
jade/rosetta_jade/monte_carlo_analysis/CycleData.py
jade/rosetta_jade/monte_carlo_analysis/MCData.py
jade/rosetta_jade/monte_carlo_analysis/__init__.py
jade/rosetta_jade/structure_editing/__init__.py
jade/rosetta_jade/structure_editing/loop_building.py
jade/utility/__init__.py
jade/utility/string_util.py
tests/9_mer_linear_glycan_test_0001.pdb
tests/__init__.py
tests/test_path.py
tests/inputs/2j88.pdb
tests/inputs/json_test.json