README.md
setup.py
ensembler/__init__.py
ensembler/cli.py
ensembler/core.py
ensembler/initproject.py
ensembler/modeling.py
ensembler/packaging.py
ensembler/param_parsers.py
ensembler/pdb.py
ensembler/refinement.py
ensembler/targetexplorer.py
ensembler/uniprot.py
ensembler/utils.py
ensembler/validation.py
ensembler/version.py
ensembler.egg-info/PKG-INFO
ensembler.egg-info/SOURCES.txt
ensembler.egg-info/dependency_links.txt
ensembler.egg-info/entry_points.txt
ensembler.egg-info/top_level.txt
ensembler/attic/amber.py
ensembler/attic/gmx.py
ensembler/cli_commands/__init__.py
ensembler/cli_commands/align.py
ensembler/cli_commands/build_models.py
ensembler/cli_commands/cluster.py
ensembler/cli_commands/gather_targets.py
ensembler/cli_commands/gather_templates.py
ensembler/cli_commands/general.py
ensembler/cli_commands/init.py
ensembler/cli_commands/loopmodel.py
ensembler/cli_commands/mktraj.py
ensembler/cli_commands/package_models.py
ensembler/cli_commands/quickmodel.py
ensembler/cli_commands/refine_explicit.py
ensembler/cli_commands/refine_implicit.py
ensembler/cli_commands/renumber_residues.py
ensembler/cli_commands/solvate.py
ensembler/cli_commands/testrun_pipeline.py
ensembler/cli_commands/validate.py
ensembler/resources/template-manual-overrides.yaml
ensembler/tests/__init__.py
ensembler/tests/integrationtest_utils.py
ensembler/tests/test_core.py
ensembler/tests/test_gather_templates.py
ensembler/tests/test_initproject.py
ensembler/tests/test_loopmodel.py
ensembler/tests/test_modeling.py
ensembler/tests/test_packaging.py
ensembler/tests/test_param_parsers.py
ensembler/tests/test_project_metadata.py
ensembler/tests/test_refinement.py
ensembler/tests/test_tools.py
ensembler/tests/test_validation.py
ensembler/tests/utils.py
ensembler/tests/example_project/manual-overrides.yaml
ensembler/tests/example_project/meta0.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/build_models-meta0.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/cluster_models-meta0.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/determine_nwaters-meta0.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/nwaters-list.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/nwaters-max.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/nwaters-use.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/refine_explicit_md-meta0.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/refine_explicit_md-meta1.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/refine_implicit_md-meta0.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/sequence-identities.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/solvate_models-meta0.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/unique-models.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/alignment.pir
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-energies.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-integrator.xml.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-log.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-refined.pdb.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-state.xml.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-system.xml.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/implicit-energies.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/implicit-log.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/implicit-refined.pdb.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/model.pdb
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/model.pdb.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/modeling-log.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/nwaters.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/restraints.rsr.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/sequence-identity.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/unique_by_clustering
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/alignment.pir
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-energies.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-integrator.xml.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-log.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-refined.pdb.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-state.xml.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-system.xml.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/implicit-energies.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/implicit-log.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/implicit-refined.pdb.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/model.pdb
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/model.pdb.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/modeling-log.yaml
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/nwaters.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/restraints.rsr.gz
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/sequence-identity.txt
ensembler/tests/example_project/models/EGFR_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/unique_by_clustering
ensembler/tests/example_project/models/KC1D_HUMAN_D0/build_models-meta0.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/cluster_models-meta0.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/determine_nwaters-meta0.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/nwaters-list.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/nwaters-max.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/nwaters-use.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/refine_explicit_md-meta0.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/refine_implicit_md-meta0.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/sequence-identities.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/solvate_models-meta0.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/unique-models.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/alignment.pir
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-energies.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-integrator.xml.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-log.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-refined.pdb.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-state.xml.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/explicit-system.xml.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/implicit-energies.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/implicit-log.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/implicit-refined.pdb.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/model.pdb
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/model.pdb.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/modeling-log.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/nwaters.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/restraints.rsr.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/sequence-identity.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4HNF_A/unique_by_clustering
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/alignment.pir
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-energies.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-integrator.xml.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-log.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-refined.pdb.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-state.xml.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/explicit-system.xml.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/implicit-energies.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/implicit-log.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/implicit-refined.pdb.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/model.pdb
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/model.pdb.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/modeling-log.yaml
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/nwaters.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/restraints.rsr.gz
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/sequence-identity.txt
ensembler/tests/example_project/models/KC1D_HUMAN_D0/KC1D_HUMAN_D0_4KB8_D/unique_by_clustering
ensembler/tests/example_project/structures/pdb/4AF3.pdb.gz
ensembler/tests/example_project/structures/sifts/4AF3.xml.gz
ensembler/tests/example_project/targets/meta0.yaml
ensembler/tests/example_project/targets/targets.fa
ensembler/tests/example_project/templates/meta0.yaml
ensembler/tests/example_project/templates/templates-full-seq.fa
ensembler/tests/example_project/templates/templates-resolved-seq.fa
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4HNF_A-loopmodel-log.yaml
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4HNF_A-loopmodel-score.sc
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4HNF_A-pdbfixed.fasta
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4HNF_A-pdbfixed.pdb
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4HNF_A.loop
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4HNF_A.pdb
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4KB8_D-loopmodel-log.yaml
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4KB8_D-loopmodel-score.sc
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4KB8_D-pdbfixed.fasta
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4KB8_D-pdbfixed.pdb
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4KB8_D.loop
ensembler/tests/example_project/templates/structures-modeled-loops/KC1D_HUMAN_D0_4KB8_D.pdb
ensembler/tests/example_project/templates/structures-resolved/KC1D_HUMAN_D0_3UZP_A.pdb
ensembler/tests/example_project/templates/structures-resolved/KC1D_HUMAN_D0_4HNF_A.pdb
ensembler/tests/example_project/templates/structures-resolved/KC1D_HUMAN_D0_4KB8_D.pdb
ensembler/tests/resources/3HLL.pdb.gz
ensembler/tests/resources/4CFE.pdb.gz
ensembler/tests/resources/ABL1_HUMAN_D0_2E2B_B.pdb.gz
ensembler/tests/resources/KC1D_HUMAN_D0_3UYS_D.pdb.gz
ensembler/tests/resources/KC1D_HUMAN_D0_4KB8_D.pdb.gz
ensembler/tests/resources/mock_template-alignment.pir
ensembler/tests/resources/mock_template.pdb
ensembler/tests/resources/uniprot-CK1-kinases.xml
ensembler/tools/__init__.py
ensembler/tools/inspect.py
ensembler/tools/mktraj.py
ensembler/tools/quick_model.py
ensembler/tools/rendering.py
ensembler/tools/renumber_residues.py