EXACT_V1.md
EXACT_V1_MIGRATION.md
LICENSE
MANIFEST.in
MIGRATION_RDPEPPER.md
RDPEPPER_RELEASE_NOTES.md
README.md
THIRD_PARTY_DATA.md
V5_ARTIFACT_CONTRACT.md
V5_REPRODUCIBILITY.md
V7_MAX_COVERAGE_FALLBACK_DESIGN.md
__init__.py
application.py
bond_order_inference.py
build_monomer_library.py
build_rdpepper_release.py
build_sublibraries.py
candidate_assessment.py
chemical_audit.py
derived_monomer_library.csv
derived_monomer_manifest.json
derived_monomer_quarantine.csv
exact_v1.py
max_coverage.py
pipeline.py
pyproject.toml
reconstruction.py
remediation_v3.py
remediation_v5.py
remediation_v6.py
representations.py
result_first.py
run.py
sequence.py
special_residue_library.csv
unified_monomer_library.csv
v5_reproducibility.py
validate_monomer_library.py
./EXACT_V1.md
./EXACT_V1_MIGRATION.md
./MIGRATION_RDPEPPER.md
./RDPEPPER_RELEASE_NOTES.md
./THIRD_PARTY_DATA.md
./V5_ARTIFACT_CONTRACT.md
./V5_REPRODUCIBILITY.md
./V7_MAX_COVERAGE_FALLBACK_DESIGN.md
./__init__.py
./application.py
./bond_order_inference.py
./build_monomer_library.py
./build_rdpepper_release.py
./build_sublibraries.py
./candidate_assessment.py
./chemical_audit.py
./derived_monomer_library.csv
./derived_monomer_manifest.json
./derived_monomer_quarantine.csv
./exact_v1.py
./max_coverage.py
./pipeline.py
./reconstruction.py
./remediation_v3.py
./remediation_v5.py
./remediation_v6.py
./representations.py
./result_first.py
./run.py
./sequence.py
./special_residue_library.csv
./unified_monomer_library.csv
./v5_reproducibility.py
./validate_monomer_library.py
./admet/__init__.py
./admet/predictor.py
./cli/__init__.py
./cli/main.py
./compare/__init__.py
./compare/authoritative_stereo.py
./compare/smiles_compare.py
./core/__init__.py
./core/applicability.py
./core/artifacts.py
./core/cxsmiles_gen.py
./core/cyclic_peptide_graph.py
./core/cyclization.py
./core/data.py
./core/derived_monomers.py
./core/geometry_candidate.py
./core/geometry_complex.py
./core/geometry_inference.py
./core/geometry_params.py
./core/geometry_simple.py
./core/identity_memo.py
./core/local_monomer_inference.py
./core/mmcif_chem_comp.py
./core/mol2_compat.py
./core/mol2_format.py
./core/molecule.py
./core/monomer_admin.py
./core/monomer_resolution.py
./core/native_mmcif_graph.py
./core/overlay_collector.py
./core/pdb_parser.py
./core/pdb_utils.py
./core/rigor.py
./core/special_residues.py
./core/structure_io.py
./data/applicability_manifest.json
./data/v5_evidence_dossier.json
./data/templates/templates_index.json
./data/templates/10_N-C/centroid_001.pdb
./data/templates/10_N-C/centroid_002.pdb
./data/templates/10_N-C/centroid_005.pdb
./data/templates/10_N-C/centroid_006.pdb
./data/templates/10_N-C/centroid_007.pdb
./data/templates/10_N-C/centroid_008.pdb
./data/templates/10_N-C/centroid_009.pdb
./data/templates/10_N-C/centroid_010.pdb
./data/templates/10_N-C/centroid_011.pdb
./data/templates/10_N-C/centroid_015.pdb
./data/templates/10_SC/centroid_001.pdb
./data/templates/10_SC/centroid_002.pdb
./data/templates/10_SC/centroid_003.pdb
./data/templates/10_SC/centroid_004.pdb
./data/templates/10_SC/centroid_005.pdb
./data/templates/10_SC/centroid_006.pdb
./data/templates/10_SC/centroid_007.pdb
./data/templates/10_SC/centroid_008.pdb
./data/templates/10_SC/centroid_009.pdb
./data/templates/10_SC/centroid_011.pdb
./data/templates/10_SC/centroid_012.pdb
./data/templates/10_SC/centroid_013.pdb
./data/templates/10_SC/centroid_014.pdb
./data/templates/10_SC/centroid_015.pdb
./data/templates/10_disulfide/centroid_001.pdb
./data/templates/10_disulfide/centroid_002.pdb
./data/templates/10_disulfide/centroid_003.pdb
./data/templates/10_disulfide/centroid_004.pdb
./data/templates/10_disulfide/centroid_005.pdb
./data/templates/10_disulfide/centroid_006.pdb
./data/templates/10_disulfide/centroid_007.pdb
./data/templates/10_disulfide/centroid_008.pdb
./data/templates/10_disulfide/centroid_009.pdb
./data/templates/10_disulfide/centroid_010.pdb
./data/templates/10_disulfide/centroid_011.pdb
./data/templates/10_disulfide/centroid_012.pdb
./data/templates/10_disulfide/centroid_013.pdb
./data/templates/10_disulfide/centroid_014.pdb
./data/templates/10_disulfide/centroid_015.pdb
./data/templates/10_mixed/centroid_001.pdb
./data/templates/10_none/centroid_001.pdb
./data/templates/10_none/centroid_002.pdb
./data/templates/10_none/centroid_003.pdb
./data/templates/10_none/centroid_004.pdb
./data/templates/10_none/centroid_005.pdb
./data/templates/10_none/centroid_006.pdb
./data/templates/10_none/centroid_007.pdb
./data/templates/10_none/centroid_008.pdb
./data/templates/10_none/centroid_009.pdb
./data/templates/10_none/centroid_010.pdb
./data/templates/10_none/centroid_011.pdb
./data/templates/10_none/centroid_012.pdb
./data/templates/10_none/centroid_013.pdb
./data/templates/10_none/centroid_014.pdb
./data/templates/10_none/centroid_015.pdb
./data/templates/10_none/synthetic_001.pdb
./data/templates/10_none/synthetic_002.pdb
./data/templates/10_none/synthetic_003.pdb
./data/templates/10_none/synthetic_004.pdb
./data/templates/10_none/synthetic_005.pdb
./data/templates/11_N-C/centroid_001.pdb
./data/templates/11_N-C/centroid_004.pdb
./data/templates/11_N-C/centroid_005.pdb
./data/templates/11_N-C/centroid_006.pdb
./data/templates/11_N-C/centroid_008.pdb
./data/templates/11_N-C/centroid_009.pdb
./data/templates/11_N-C/centroid_011.pdb
./data/templates/11_SC/centroid_001.pdb
./data/templates/11_SC/centroid_002.pdb
./data/templates/11_SC/centroid_003.pdb
./data/templates/11_SC/centroid_004.pdb
./data/templates/11_SC/centroid_005.pdb
./data/templates/11_SC/centroid_006.pdb
./data/templates/11_SC/centroid_007.pdb
./data/templates/11_SC/centroid_008.pdb
./data/templates/11_SC/centroid_009.pdb
./data/templates/11_SC/centroid_010.pdb
./data/templates/11_SC/centroid_011.pdb
./data/templates/11_SC/centroid_012.pdb
./data/templates/11_SC/centroid_014.pdb
./data/templates/11_SC/centroid_015.pdb
./data/templates/11_disulfide/centroid_001.pdb
./data/templates/11_disulfide/centroid_002.pdb
./data/templates/11_disulfide/centroid_003.pdb
./data/templates/11_disulfide/centroid_004.pdb
./data/templates/11_disulfide/centroid_005.pdb
./data/templates/11_disulfide/centroid_006.pdb
./data/templates/11_disulfide/centroid_007.pdb
./data/templates/11_disulfide/centroid_008.pdb
./data/templates/11_disulfide/centroid_009.pdb
./data/templates/11_disulfide/centroid_010.pdb
./data/templates/11_disulfide/centroid_011.pdb
./data/templates/11_disulfide/centroid_012.pdb
./data/templates/11_disulfide/centroid_013.pdb
./data/templates/11_disulfide/centroid_014.pdb
./data/templates/11_disulfide/centroid_015.pdb
./data/templates/11_none/centroid_001.pdb
./data/templates/11_none/centroid_002.pdb
./data/templates/11_none/centroid_003.pdb
./data/templates/11_none/centroid_004.pdb
./data/templates/11_none/centroid_005.pdb
./data/templates/11_none/centroid_006.pdb
./data/templates/11_none/centroid_007.pdb
./data/templates/11_none/centroid_008.pdb
./data/templates/11_none/centroid_009.pdb
./data/templates/11_none/centroid_010.pdb
./data/templates/11_none/centroid_011.pdb
./data/templates/11_none/centroid_013.pdb
./data/templates/11_none/centroid_015.pdb
./data/templates/11_none/synthetic_001.pdb
./data/templates/11_none/synthetic_002.pdb
./data/templates/11_none/synthetic_003.pdb
./data/templates/11_none/synthetic_004.pdb
./data/templates/11_none/synthetic_005.pdb
./data/templates/11_none/synthetic_006.pdb
./data/templates/11_none/synthetic_007.pdb
./data/templates/11_none/synthetic_008.pdb
./data/templates/11_none/synthetic_009.pdb
./data/templates/12_N-C/centroid_001.pdb
./data/templates/12_N-C/centroid_002.pdb
./data/templates/12_N-C/centroid_003.pdb
./data/templates/12_N-C/centroid_004.pdb
./data/templates/12_N-C/centroid_005.pdb
./data/templates/12_N-C/centroid_006.pdb
./data/templates/12_N-C/centroid_007.pdb
./data/templates/12_N-C/centroid_009.pdb
./data/templates/12_N-C/centroid_010.pdb
./data/templates/12_N-C/centroid_012.pdb
./data/templates/12_N-C/centroid_014.pdb
./data/templates/12_SC/centroid_001.pdb
./data/templates/12_SC/centroid_003.pdb
./data/templates/12_SC/centroid_004.pdb
./data/templates/12_SC/centroid_005.pdb
./data/templates/12_SC/centroid_006.pdb
./data/templates/12_SC/centroid_007.pdb
./data/templates/12_SC/centroid_008.pdb
./data/templates/12_SC/centroid_009.pdb
./data/templates/12_SC/centroid_010.pdb
./data/templates/12_SC/centroid_011.pdb
./data/templates/12_SC/centroid_012.pdb
./data/templates/12_SC/centroid_013.pdb
./data/templates/12_SC/centroid_015.pdb
./data/templates/12_disulfide/centroid_001.pdb
./data/templates/12_disulfide/centroid_002.pdb
./data/templates/12_disulfide/centroid_003.pdb
./data/templates/12_disulfide/centroid_004.pdb
./data/templates/12_disulfide/centroid_005.pdb
./data/templates/12_disulfide/centroid_006.pdb
./data/templates/12_disulfide/centroid_007.pdb
./data/templates/12_disulfide/centroid_008.pdb
./data/templates/12_disulfide/centroid_009.pdb
./data/templates/12_disulfide/centroid_010.pdb
./data/templates/12_disulfide/centroid_011.pdb
./data/templates/12_disulfide/centroid_012.pdb
./data/templates/12_disulfide/centroid_013.pdb
./data/templates/12_disulfide/centroid_014.pdb
./data/templates/12_disulfide/centroid_015.pdb
./data/templates/12_mixed/centroid_001.pdb
./data/templates/12_none/centroid_002.pdb
./data/templates/12_none/centroid_003.pdb
./data/templates/12_none/centroid_004.pdb
./data/templates/12_none/centroid_005.pdb
./data/templates/12_none/centroid_006.pdb
./data/templates/12_none/centroid_007.pdb
./data/templates/12_none/centroid_008.pdb
./data/templates/12_none/centroid_009.pdb
./data/templates/12_none/centroid_010.pdb
./data/templates/12_none/centroid_011.pdb
./data/templates/12_none/centroid_012.pdb
./data/templates/12_none/centroid_014.pdb
./data/templates/12_none/centroid_015.pdb
./data/templates/12_none/synthetic_001.pdb
./data/templates/12_none/synthetic_002.pdb
./data/templates/13_N-C/centroid_003.pdb
./data/templates/13_N-C/centroid_005.pdb
./data/templates/13_N-C/centroid_007.pdb
./data/templates/13_N-C/centroid_008.pdb
./data/templates/13_N-C/centroid_010.pdb
./data/templates/13_N-C/centroid_011.pdb
./data/templates/13_N-C/centroid_012.pdb
./data/templates/13_N-C/centroid_013.pdb
./data/templates/13_N-C/centroid_014.pdb
./data/templates/13_N-C/centroid_015.pdb
./data/templates/13_SC/centroid_001.pdb
./data/templates/13_SC/centroid_002.pdb
./data/templates/13_SC/centroid_003.pdb
./data/templates/13_SC/centroid_004.pdb
./data/templates/13_SC/centroid_005.pdb
./data/templates/13_SC/centroid_006.pdb
./data/templates/13_SC/centroid_007.pdb
./data/templates/13_SC/centroid_009.pdb
./data/templates/13_SC/centroid_011.pdb
./data/templates/13_SC/centroid_012.pdb
./data/templates/13_SC/centroid_014.pdb
./data/templates/13_SC/centroid_015.pdb
./data/templates/13_disulfide/centroid_001.pdb
./data/templates/13_disulfide/centroid_002.pdb
./data/templates/13_disulfide/centroid_003.pdb
./data/templates/13_disulfide/centroid_004.pdb
./data/templates/13_disulfide/centroid_005.pdb
./data/templates/13_disulfide/centroid_006.pdb
./data/templates/13_disulfide/centroid_007.pdb
./data/templates/13_disulfide/centroid_008.pdb
./data/templates/13_disulfide/centroid_009.pdb
./data/templates/13_disulfide/centroid_010.pdb
./data/templates/13_disulfide/centroid_011.pdb
./data/templates/13_disulfide/centroid_012.pdb
./data/templates/13_disulfide/centroid_013.pdb
./data/templates/13_disulfide/centroid_014.pdb
./data/templates/13_disulfide/centroid_015.pdb
./data/templates/13_mixed/centroid_001.pdb
./data/templates/13_mixed/centroid_002.pdb
./data/templates/13_mixed/centroid_003.pdb
./data/templates/13_none/centroid_001.pdb
./data/templates/13_none/centroid_002.pdb
./data/templates/13_none/centroid_003.pdb
./data/templates/13_none/centroid_004.pdb
./data/templates/13_none/centroid_005.pdb
./data/templates/13_none/centroid_006.pdb
./data/templates/13_none/centroid_007.pdb
./data/templates/13_none/centroid_008.pdb
./data/templates/13_none/centroid_009.pdb
./data/templates/13_none/centroid_010.pdb
./data/templates/13_none/centroid_011.pdb
./data/templates/13_none/centroid_012.pdb
./data/templates/13_none/centroid_013.pdb
./data/templates/13_none/centroid_014.pdb
./data/templates/13_none/centroid_015.pdb
./data/templates/13_none/synthetic_001.pdb
./data/templates/13_none/synthetic_002.pdb
./data/templates/13_none/synthetic_003.pdb
./data/templates/13_none/synthetic_004.pdb
./data/templates/14_N-C/centroid_001.pdb
./data/templates/14_N-C/centroid_002.pdb
./data/templates/14_N-C/centroid_003.pdb
./data/templates/14_N-C/centroid_004.pdb
./data/templates/14_N-C/centroid_005.pdb
./data/templates/14_N-C/centroid_006.pdb
./data/templates/14_N-C/centroid_007.pdb
./data/templates/14_N-C/centroid_008.pdb
./data/templates/14_N-C/centroid_010.pdb
./data/templates/14_N-C/centroid_011.pdb
./data/templates/14_N-C/centroid_012.pdb
./data/templates/14_N-C/centroid_014.pdb
./data/templates/14_N-C/centroid_015.pdb
./data/templates/14_N-C/synthetic_001.pdb
./data/templates/14_N-C/synthetic_002.pdb
./data/templates/14_N-C/synthetic_003.pdb
./data/templates/14_N-C/synthetic_004.pdb
./data/templates/14_SC/centroid_001.pdb
./data/templates/14_SC/centroid_002.pdb
./data/templates/14_SC/centroid_003.pdb
./data/templates/14_SC/centroid_004.pdb
./data/templates/14_SC/centroid_005.pdb
./data/templates/14_SC/centroid_006.pdb
./data/templates/14_SC/centroid_007.pdb
./data/templates/14_SC/centroid_010.pdb
./data/templates/14_SC/centroid_011.pdb
./data/templates/14_SC/centroid_012.pdb
./data/templates/14_SC/centroid_013.pdb
./data/templates/14_SC/centroid_014.pdb
./data/templates/14_SC/centroid_015.pdb
./data/templates/14_disulfide/centroid_001.pdb
./data/templates/14_disulfide/centroid_002.pdb
./data/templates/14_disulfide/centroid_003.pdb
./data/templates/14_disulfide/centroid_004.pdb
./data/templates/14_disulfide/centroid_005.pdb
./data/templates/14_disulfide/centroid_006.pdb
./data/templates/14_disulfide/centroid_007.pdb
./data/templates/14_disulfide/centroid_008.pdb
./data/templates/14_disulfide/centroid_009.pdb
./data/templates/14_disulfide/centroid_010.pdb
./data/templates/14_disulfide/centroid_011.pdb
./data/templates/14_disulfide/centroid_012.pdb
./data/templates/14_disulfide/centroid_013.pdb
./data/templates/14_disulfide/centroid_014.pdb
./data/templates/14_disulfide/centroid_015.pdb
./data/templates/14_mixed/centroid_001.pdb
./data/templates/14_mixed/centroid_002.pdb
./data/templates/14_mixed/centroid_003.pdb
./data/templates/14_none/centroid_001.pdb
./data/templates/14_none/centroid_002.pdb
./data/templates/14_none/centroid_003.pdb
./data/templates/14_none/centroid_004.pdb
./data/templates/14_none/centroid_005.pdb
./data/templates/14_none/centroid_006.pdb
./data/templates/14_none/centroid_007.pdb
./data/templates/14_none/centroid_008.pdb
./data/templates/14_none/centroid_009.pdb
./data/templates/14_none/centroid_010.pdb
./data/templates/14_none/centroid_011.pdb
./data/templates/14_none/centroid_012.pdb
./data/templates/14_none/centroid_013.pdb
./data/templates/14_none/centroid_014.pdb
./data/templates/14_none/centroid_015.pdb
./data/templates/14_none/synthetic_001.pdb
./data/templates/14_none/synthetic_002.pdb
./data/templates/14_none/synthetic_003.pdb
./data/templates/15_N-C/centroid_002.pdb
./data/templates/15_N-C/centroid_003.pdb
./data/templates/15_N-C/centroid_004.pdb
./data/templates/15_N-C/centroid_005.pdb
./data/templates/15_N-C/centroid_006.pdb
./data/templates/15_N-C/centroid_008.pdb
./data/templates/15_N-C/centroid_015.pdb
./data/templates/15_N-C/synthetic_001.pdb
./data/templates/15_N-C/synthetic_002.pdb
./data/templates/15_N-C/synthetic_003.pdb
./data/templates/15_N-C/synthetic_004.pdb
./data/templates/15_N-C/synthetic_005.pdb
./data/templates/15_N-C/synthetic_006.pdb
./data/templates/15_N-C/synthetic_007.pdb
./data/templates/15_N-C/synthetic_008.pdb
./data/templates/15_N-C/synthetic_009.pdb
./data/templates/15_N-C/synthetic_010.pdb
./data/templates/15_N-C/synthetic_011.pdb
./data/templates/15_N-C/synthetic_012.pdb
./data/templates/15_N-C/synthetic_013.pdb
./data/templates/15_N-C/synthetic_014.pdb
./data/templates/15_N-C/synthetic_015.pdb
./data/templates/15_N-C/synthetic_016.pdb
./data/templates/15_N-C/synthetic_017.pdb
./data/templates/15_N-C/synthetic_018.pdb
./data/templates/15_N-C/synthetic_019.pdb
./data/templates/15_N-C/synthetic_020.pdb
./data/templates/15_N-C/synthetic_021.pdb
./data/templates/15_N-C/synthetic_022.pdb
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./data/templates/15_N-C/synthetic_031.pdb
./data/templates/15_N-C/synthetic_032.pdb
./data/templates/15_N-C/synthetic_033.pdb
./data/templates/15_N-C/synthetic_034.pdb
./data/templates/15_N-C/synthetic_035.pdb
./data/templates/15_N-C/synthetic_036.pdb
./data/templates/15_N-C/synthetic_037.pdb
./data/templates/15_N-C/synthetic_038.pdb
./data/templates/15_N-C/synthetic_039.pdb
./data/templates/15_N-C/synthetic_040.pdb
./data/templates/15_N-C/synthetic_041.pdb
./data/templates/15_N-C/synthetic_042.pdb
./data/templates/15_N-C/synthetic_043.pdb
./data/templates/15_N-C/synthetic_044.pdb
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./data/templates/15_N-C/synthetic_057.pdb
./data/templates/15_N-C/synthetic_058.pdb
./data/templates/15_SC/centroid_001.pdb
./data/templates/15_SC/centroid_002.pdb
./data/templates/15_SC/centroid_003.pdb
./data/templates/15_SC/centroid_004.pdb
./data/templates/15_SC/centroid_005.pdb
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./data/templates/15_SC/centroid_011.pdb
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./data/templates/16_N-C/centroid_002.pdb
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./data/templates/4_none/synthetic_001.pdb
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./data/templates/5_N-C/synthetic_001.pdb
./data/templates/5_SC/centroid_002.pdb
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./data/templates/5_disulfide/centroid_001.pdb
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./data/templates/6_N-C/centroid_001.pdb
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./data/templates/6_N-C/centroid_004.pdb
./data/templates/6_N-C/centroid_006.pdb
./data/templates/6_N-C/centroid_011.pdb
./data/templates/6_N-C/centroid_012.pdb
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./data/templates/6_SC/centroid_001.pdb
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./data/templates/6_disulfide/centroid_001.pdb
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./data/templates/7_N-C/centroid_003.pdb
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./data/templates/7_disulfide/centroid_001.pdb
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./data/templates/8_N-C/centroid_003.pdb
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./data/torsion_priors/torsion_definitions.json
./data/torsion_priors/torsion_prior_manifest_runtime.json
./data/torsion_priors/torsion_priors_runtime.json
./docking/__init__.py
./docking/box.py
./docking/build_template_library.py
./docking/build_torsion_priors.py
./docking/compress_template_library.py
./docking/flexibility.py
./docking/ligand_pdbqt.py
./docking/mol2_input.py
./docking/mol2_pdbqt.py
./docking/pdbqt_validation.py
./docking/protonation.py
./docking/receptor_pdbqt.py
./docking/template_library.py
./docking/template_view.py
./docking/torsion_budget.py
./docking/torsion_observations.py
./docking/torsion_prior.py
./docking/vina.py
./docking/vina_wrapper.py
./docking/workflow.py
./export/__init__.py
./export/conformer.py
./export/conformer_ensemble.py
./gui/__init__.py
./gui/__main__.py
./gui/main_window.py
./gui/params_panel.py
./gui/render.py
./gui/workers.py
./libraries/caps.csv
./libraries/core.csv
./libraries/curated_cycpep.csv
./libraries/helm_gpt.csv
./libraries/manifest.json
./libraries/nnaa_diverse.csv
./libraries/special.csv
./paths/__init__.py
./paths/_map_utils.py
./paths/path_a.py
./paths/path_b.py
./paths/path_c.py
./paths/path_f.py
./paths/path_g.py
./paths/path_h.py
./paths/residue_template_factory.py
./schemas/candidate_assessment.schema.json
./schemas/exact_v1.schema.json
./schemas/v5_artifact.schema.json
admet/__init__.py
admet/predictor.py
cli/__init__.py
cli/main.py
compare/__init__.py
compare/authoritative_stereo.py
compare/smiles_compare.py
core/__init__.py
core/applicability.py
core/artifacts.py
core/cxsmiles_gen.py
core/cyclic_peptide_graph.py
core/cyclization.py
core/data.py
core/derived_monomers.py
core/geometry_candidate.py
core/geometry_complex.py
core/geometry_inference.py
core/geometry_params.py
core/geometry_simple.py
core/identity_memo.py
core/local_monomer_inference.py
core/mmcif_chem_comp.py
core/mol2_compat.py
core/mol2_format.py
core/molecule.py
core/monomer_admin.py
core/monomer_resolution.py
core/native_mmcif_graph.py
core/overlay_collector.py
core/pdb_parser.py
core/pdb_utils.py
core/rigor.py
core/special_residues.py
core/structure_io.py
data/applicability_manifest.json
data/v5_evidence_dossier.json
data/templates/templates_index.json
data/templates/10_N-C/centroid_001.pdb
data/templates/10_N-C/centroid_002.pdb
data/templates/10_N-C/centroid_005.pdb
data/templates/10_N-C/centroid_006.pdb
data/templates/10_N-C/centroid_007.pdb
data/templates/10_N-C/centroid_008.pdb
data/templates/10_N-C/centroid_009.pdb
data/templates/10_N-C/centroid_010.pdb
data/templates/10_N-C/centroid_011.pdb
data/templates/10_N-C/centroid_015.pdb
data/templates/10_SC/centroid_001.pdb
data/templates/10_SC/centroid_002.pdb
data/templates/10_SC/centroid_003.pdb
data/templates/10_SC/centroid_004.pdb
data/templates/10_SC/centroid_005.pdb
data/templates/10_SC/centroid_006.pdb
data/templates/10_SC/centroid_007.pdb
data/templates/10_SC/centroid_008.pdb
data/templates/10_SC/centroid_009.pdb
data/templates/10_SC/centroid_011.pdb
data/templates/10_SC/centroid_012.pdb
data/templates/10_SC/centroid_013.pdb
data/templates/10_SC/centroid_014.pdb
data/templates/10_SC/centroid_015.pdb
data/templates/10_disulfide/centroid_001.pdb
data/templates/10_disulfide/centroid_002.pdb
data/templates/10_disulfide/centroid_003.pdb
data/templates/10_disulfide/centroid_004.pdb
data/templates/10_disulfide/centroid_005.pdb
data/templates/10_disulfide/centroid_006.pdb
data/templates/10_disulfide/centroid_007.pdb
data/templates/10_disulfide/centroid_008.pdb
data/templates/10_disulfide/centroid_009.pdb
data/templates/10_disulfide/centroid_010.pdb
data/templates/10_disulfide/centroid_011.pdb
data/templates/10_disulfide/centroid_012.pdb
data/templates/10_disulfide/centroid_013.pdb
data/templates/10_disulfide/centroid_014.pdb
data/templates/10_disulfide/centroid_015.pdb
data/templates/10_mixed/centroid_001.pdb
data/templates/10_none/centroid_001.pdb
data/templates/10_none/centroid_002.pdb
data/templates/10_none/centroid_003.pdb
data/templates/10_none/centroid_004.pdb
data/templates/10_none/centroid_005.pdb
data/templates/10_none/centroid_006.pdb
data/templates/10_none/centroid_007.pdb
data/templates/10_none/centroid_008.pdb
data/templates/10_none/centroid_009.pdb
data/templates/10_none/centroid_010.pdb
data/templates/10_none/centroid_011.pdb
data/templates/10_none/centroid_012.pdb
data/templates/10_none/centroid_013.pdb
data/templates/10_none/centroid_014.pdb
data/templates/10_none/centroid_015.pdb
data/templates/10_none/synthetic_001.pdb
data/templates/10_none/synthetic_002.pdb
data/templates/10_none/synthetic_003.pdb
data/templates/10_none/synthetic_004.pdb
data/templates/10_none/synthetic_005.pdb
data/templates/11_N-C/centroid_001.pdb
data/templates/11_N-C/centroid_004.pdb
data/templates/11_N-C/centroid_005.pdb
data/templates/11_N-C/centroid_006.pdb
data/templates/11_N-C/centroid_008.pdb
data/templates/11_N-C/centroid_009.pdb
data/templates/11_N-C/centroid_011.pdb
data/templates/11_SC/centroid_001.pdb
data/templates/11_SC/centroid_002.pdb
data/templates/11_SC/centroid_003.pdb
data/templates/11_SC/centroid_004.pdb
data/templates/11_SC/centroid_005.pdb
data/templates/11_SC/centroid_006.pdb
data/templates/11_SC/centroid_007.pdb
data/templates/11_SC/centroid_008.pdb
data/templates/11_SC/centroid_009.pdb
data/templates/11_SC/centroid_010.pdb
data/templates/11_SC/centroid_011.pdb
data/templates/11_SC/centroid_012.pdb
data/templates/11_SC/centroid_014.pdb
data/templates/11_SC/centroid_015.pdb
data/templates/11_disulfide/centroid_001.pdb
data/templates/11_disulfide/centroid_002.pdb
data/templates/11_disulfide/centroid_003.pdb
data/templates/11_disulfide/centroid_004.pdb
data/templates/11_disulfide/centroid_005.pdb
data/templates/11_disulfide/centroid_006.pdb
data/templates/11_disulfide/centroid_007.pdb
data/templates/11_disulfide/centroid_008.pdb
data/templates/11_disulfide/centroid_009.pdb
data/templates/11_disulfide/centroid_010.pdb
data/templates/11_disulfide/centroid_011.pdb
data/templates/11_disulfide/centroid_012.pdb
data/templates/11_disulfide/centroid_013.pdb
data/templates/11_disulfide/centroid_014.pdb
data/templates/11_disulfide/centroid_015.pdb
data/templates/11_none/centroid_001.pdb
data/templates/11_none/centroid_002.pdb
data/templates/11_none/centroid_003.pdb
data/templates/11_none/centroid_004.pdb
data/templates/11_none/centroid_005.pdb
data/templates/11_none/centroid_006.pdb
data/templates/11_none/centroid_007.pdb
data/templates/11_none/centroid_008.pdb
data/templates/11_none/centroid_009.pdb
data/templates/11_none/centroid_010.pdb
data/templates/11_none/centroid_011.pdb
data/templates/11_none/centroid_013.pdb
data/templates/11_none/centroid_015.pdb
data/templates/11_none/synthetic_001.pdb
data/templates/11_none/synthetic_002.pdb
data/templates/11_none/synthetic_003.pdb
data/templates/11_none/synthetic_004.pdb
data/templates/11_none/synthetic_005.pdb
data/templates/11_none/synthetic_006.pdb
data/templates/11_none/synthetic_007.pdb
data/templates/11_none/synthetic_008.pdb
data/templates/11_none/synthetic_009.pdb
data/templates/12_N-C/centroid_001.pdb
data/templates/12_N-C/centroid_002.pdb
data/templates/12_N-C/centroid_003.pdb
data/templates/12_N-C/centroid_004.pdb
data/templates/12_N-C/centroid_005.pdb
data/templates/12_N-C/centroid_006.pdb
data/templates/12_N-C/centroid_007.pdb
data/templates/12_N-C/centroid_009.pdb
data/templates/12_N-C/centroid_010.pdb
data/templates/12_N-C/centroid_012.pdb
data/templates/12_N-C/centroid_014.pdb
data/templates/12_SC/centroid_001.pdb
data/templates/12_SC/centroid_003.pdb
data/templates/12_SC/centroid_004.pdb
data/templates/12_SC/centroid_005.pdb
data/templates/12_SC/centroid_006.pdb
data/templates/12_SC/centroid_007.pdb
data/templates/12_SC/centroid_008.pdb
data/templates/12_SC/centroid_009.pdb
data/templates/12_SC/centroid_010.pdb
data/templates/12_SC/centroid_011.pdb
data/templates/12_SC/centroid_012.pdb
data/templates/12_SC/centroid_013.pdb
data/templates/12_SC/centroid_015.pdb
data/templates/12_disulfide/centroid_001.pdb
data/templates/12_disulfide/centroid_002.pdb
data/templates/12_disulfide/centroid_003.pdb
data/templates/12_disulfide/centroid_004.pdb
data/templates/12_disulfide/centroid_005.pdb
data/templates/12_disulfide/centroid_006.pdb
data/templates/12_disulfide/centroid_007.pdb
data/templates/12_disulfide/centroid_008.pdb
data/templates/12_disulfide/centroid_009.pdb
data/templates/12_disulfide/centroid_010.pdb
data/templates/12_disulfide/centroid_011.pdb
data/templates/12_disulfide/centroid_012.pdb
data/templates/12_disulfide/centroid_013.pdb
data/templates/12_disulfide/centroid_014.pdb
data/templates/12_disulfide/centroid_015.pdb
data/templates/12_mixed/centroid_001.pdb
data/templates/12_none/centroid_002.pdb
data/templates/12_none/centroid_003.pdb
data/templates/12_none/centroid_004.pdb
data/templates/12_none/centroid_005.pdb
data/templates/12_none/centroid_006.pdb
data/templates/12_none/centroid_007.pdb
data/templates/12_none/centroid_008.pdb
data/templates/12_none/centroid_009.pdb
data/templates/12_none/centroid_010.pdb
data/templates/12_none/centroid_011.pdb
data/templates/12_none/centroid_012.pdb
data/templates/12_none/centroid_014.pdb
data/templates/12_none/centroid_015.pdb
data/templates/12_none/synthetic_001.pdb
data/templates/12_none/synthetic_002.pdb
data/templates/13_N-C/centroid_003.pdb
data/templates/13_N-C/centroid_005.pdb
data/templates/13_N-C/centroid_007.pdb
data/templates/13_N-C/centroid_008.pdb
data/templates/13_N-C/centroid_010.pdb
data/templates/13_N-C/centroid_011.pdb
data/templates/13_N-C/centroid_012.pdb
data/templates/13_N-C/centroid_013.pdb
data/templates/13_N-C/centroid_014.pdb
data/templates/13_N-C/centroid_015.pdb
data/templates/13_SC/centroid_001.pdb
data/templates/13_SC/centroid_002.pdb
data/templates/13_SC/centroid_003.pdb
data/templates/13_SC/centroid_004.pdb
data/templates/13_SC/centroid_005.pdb
data/templates/13_SC/centroid_006.pdb
data/templates/13_SC/centroid_007.pdb
data/templates/13_SC/centroid_009.pdb
data/templates/13_SC/centroid_011.pdb
data/templates/13_SC/centroid_012.pdb
data/templates/13_SC/centroid_014.pdb
data/templates/13_SC/centroid_015.pdb
data/templates/13_disulfide/centroid_001.pdb
data/templates/13_disulfide/centroid_002.pdb
data/templates/13_disulfide/centroid_003.pdb
data/templates/13_disulfide/centroid_004.pdb
data/templates/13_disulfide/centroid_005.pdb
data/templates/13_disulfide/centroid_006.pdb
data/templates/13_disulfide/centroid_007.pdb
data/templates/13_disulfide/centroid_008.pdb
data/templates/13_disulfide/centroid_009.pdb
data/templates/13_disulfide/centroid_010.pdb
data/templates/13_disulfide/centroid_011.pdb
data/templates/13_disulfide/centroid_012.pdb
data/templates/13_disulfide/centroid_013.pdb
data/templates/13_disulfide/centroid_014.pdb
data/templates/13_disulfide/centroid_015.pdb
data/templates/13_mixed/centroid_001.pdb
data/templates/13_mixed/centroid_002.pdb
data/templates/13_mixed/centroid_003.pdb
data/templates/13_none/centroid_001.pdb
data/templates/13_none/centroid_002.pdb
data/templates/13_none/centroid_003.pdb
data/templates/13_none/centroid_004.pdb
data/templates/13_none/centroid_005.pdb
data/templates/13_none/centroid_006.pdb
data/templates/13_none/centroid_007.pdb
data/templates/13_none/centroid_008.pdb
data/templates/13_none/centroid_009.pdb
data/templates/13_none/centroid_010.pdb
data/templates/13_none/centroid_011.pdb
data/templates/13_none/centroid_012.pdb
data/templates/13_none/centroid_013.pdb
data/templates/13_none/centroid_014.pdb
data/templates/13_none/centroid_015.pdb
data/templates/13_none/synthetic_001.pdb
data/templates/13_none/synthetic_002.pdb
data/templates/13_none/synthetic_003.pdb
data/templates/13_none/synthetic_004.pdb
data/templates/14_N-C/centroid_001.pdb
data/templates/14_N-C/centroid_002.pdb
data/templates/14_N-C/centroid_003.pdb
data/templates/14_N-C/centroid_004.pdb
data/templates/14_N-C/centroid_005.pdb
data/templates/14_N-C/centroid_006.pdb
data/templates/14_N-C/centroid_007.pdb
data/templates/14_N-C/centroid_008.pdb
data/templates/14_N-C/centroid_010.pdb
data/templates/14_N-C/centroid_011.pdb
data/templates/14_N-C/centroid_012.pdb
data/templates/14_N-C/centroid_014.pdb
data/templates/14_N-C/centroid_015.pdb
data/templates/14_N-C/synthetic_001.pdb
data/templates/14_N-C/synthetic_002.pdb
data/templates/14_N-C/synthetic_003.pdb
data/templates/14_N-C/synthetic_004.pdb
data/templates/14_SC/centroid_001.pdb
data/templates/14_SC/centroid_002.pdb
data/templates/14_SC/centroid_003.pdb
data/templates/14_SC/centroid_004.pdb
data/templates/14_SC/centroid_005.pdb
data/templates/14_SC/centroid_006.pdb
data/templates/14_SC/centroid_007.pdb
data/templates/14_SC/centroid_010.pdb
data/templates/14_SC/centroid_011.pdb
data/templates/14_SC/centroid_012.pdb
data/templates/14_SC/centroid_013.pdb
data/templates/14_SC/centroid_014.pdb
data/templates/14_SC/centroid_015.pdb
data/templates/14_disulfide/centroid_001.pdb
data/templates/14_disulfide/centroid_002.pdb
data/templates/14_disulfide/centroid_003.pdb
data/templates/14_disulfide/centroid_004.pdb
data/templates/14_disulfide/centroid_005.pdb
data/templates/14_disulfide/centroid_006.pdb
data/templates/14_disulfide/centroid_007.pdb
data/templates/14_disulfide/centroid_008.pdb
data/templates/14_disulfide/centroid_009.pdb
data/templates/14_disulfide/centroid_010.pdb
data/templates/14_disulfide/centroid_011.pdb
data/templates/14_disulfide/centroid_012.pdb
data/templates/14_disulfide/centroid_013.pdb
data/templates/14_disulfide/centroid_014.pdb
data/templates/14_disulfide/centroid_015.pdb
data/templates/14_mixed/centroid_001.pdb
data/templates/14_mixed/centroid_002.pdb
data/templates/14_mixed/centroid_003.pdb
data/templates/14_none/centroid_001.pdb
data/templates/14_none/centroid_002.pdb
data/templates/14_none/centroid_003.pdb
data/templates/14_none/centroid_004.pdb
data/templates/14_none/centroid_005.pdb
data/templates/14_none/centroid_006.pdb
data/templates/14_none/centroid_007.pdb
data/templates/14_none/centroid_008.pdb
data/templates/14_none/centroid_009.pdb
data/templates/14_none/centroid_010.pdb
data/templates/14_none/centroid_011.pdb
data/templates/14_none/centroid_012.pdb
data/templates/14_none/centroid_013.pdb
data/templates/14_none/centroid_014.pdb
data/templates/14_none/centroid_015.pdb
data/templates/14_none/synthetic_001.pdb
data/templates/14_none/synthetic_002.pdb
data/templates/14_none/synthetic_003.pdb
data/templates/15_N-C/centroid_002.pdb
data/templates/15_N-C/centroid_003.pdb
data/templates/15_N-C/centroid_004.pdb
data/templates/15_N-C/centroid_005.pdb
data/templates/15_N-C/centroid_006.pdb
data/templates/15_N-C/centroid_008.pdb
data/templates/15_N-C/centroid_015.pdb
data/templates/15_N-C/synthetic_001.pdb
data/templates/15_N-C/synthetic_002.pdb
data/templates/15_N-C/synthetic_003.pdb
data/templates/15_N-C/synthetic_004.pdb
data/templates/15_N-C/synthetic_005.pdb
data/templates/15_N-C/synthetic_006.pdb
data/templates/15_N-C/synthetic_007.pdb
data/templates/15_N-C/synthetic_008.pdb
data/templates/15_N-C/synthetic_009.pdb
data/templates/15_N-C/synthetic_010.pdb
data/templates/15_N-C/synthetic_011.pdb
data/templates/15_N-C/synthetic_012.pdb
data/templates/15_N-C/synthetic_013.pdb
data/templates/15_N-C/synthetic_014.pdb
data/templates/15_N-C/synthetic_015.pdb
data/templates/15_N-C/synthetic_016.pdb
data/templates/15_N-C/synthetic_017.pdb
data/templates/15_N-C/synthetic_018.pdb
data/templates/15_N-C/synthetic_019.pdb
data/templates/15_N-C/synthetic_020.pdb
data/templates/15_N-C/synthetic_021.pdb
data/templates/15_N-C/synthetic_022.pdb
data/templates/15_N-C/synthetic_023.pdb
data/templates/15_N-C/synthetic_024.pdb
data/templates/15_N-C/synthetic_025.pdb
data/templates/15_N-C/synthetic_026.pdb
data/templates/15_N-C/synthetic_027.pdb
data/templates/15_N-C/synthetic_028.pdb
data/templates/15_N-C/synthetic_029.pdb
data/templates/15_N-C/synthetic_030.pdb
data/templates/15_N-C/synthetic_031.pdb
data/templates/15_N-C/synthetic_032.pdb
data/templates/15_N-C/synthetic_033.pdb
data/templates/15_N-C/synthetic_034.pdb
data/templates/15_N-C/synthetic_035.pdb
data/templates/15_N-C/synthetic_036.pdb
data/templates/15_N-C/synthetic_037.pdb
data/templates/15_N-C/synthetic_038.pdb
data/templates/15_N-C/synthetic_039.pdb
data/templates/15_N-C/synthetic_040.pdb
data/templates/15_N-C/synthetic_041.pdb
data/templates/15_N-C/synthetic_042.pdb
data/templates/15_N-C/synthetic_043.pdb
data/templates/15_N-C/synthetic_044.pdb
data/templates/15_N-C/synthetic_045.pdb
data/templates/15_N-C/synthetic_046.pdb
data/templates/15_N-C/synthetic_047.pdb
data/templates/15_N-C/synthetic_048.pdb
data/templates/15_N-C/synthetic_049.pdb
data/templates/15_N-C/synthetic_050.pdb
data/templates/15_N-C/synthetic_051.pdb
data/templates/15_N-C/synthetic_052.pdb
data/templates/15_N-C/synthetic_053.pdb
data/templates/15_N-C/synthetic_054.pdb
data/templates/15_N-C/synthetic_055.pdb
data/templates/15_N-C/synthetic_056.pdb
data/templates/15_N-C/synthetic_057.pdb
data/templates/15_N-C/synthetic_058.pdb
data/templates/15_SC/centroid_001.pdb
data/templates/15_SC/centroid_002.pdb
data/templates/15_SC/centroid_003.pdb
data/templates/15_SC/centroid_004.pdb
data/templates/15_SC/centroid_005.pdb
data/templates/15_SC/centroid_007.pdb
data/templates/15_SC/centroid_008.pdb
data/templates/15_SC/centroid_010.pdb
data/templates/15_SC/centroid_011.pdb
data/templates/15_SC/centroid_012.pdb
data/templates/15_SC/centroid_013.pdb
data/templates/15_SC/centroid_014.pdb
data/templates/15_disulfide/centroid_001.pdb
data/templates/15_disulfide/centroid_002.pdb
data/templates/15_disulfide/centroid_003.pdb
data/templates/15_disulfide/centroid_004.pdb
data/templates/15_disulfide/centroid_005.pdb
data/templates/15_disulfide/centroid_006.pdb
data/templates/15_disulfide/centroid_007.pdb
data/templates/15_disulfide/centroid_008.pdb
data/templates/15_disulfide/centroid_009.pdb
data/templates/15_disulfide/centroid_010.pdb
data/templates/15_disulfide/centroid_011.pdb
data/templates/15_disulfide/centroid_012.pdb
data/templates/15_disulfide/centroid_015.pdb
data/templates/15_mixed/centroid_012.pdb
data/templates/15_mixed/centroid_013.pdb
data/templates/15_none/centroid_001.pdb
data/templates/15_none/centroid_002.pdb
data/templates/15_none/centroid_003.pdb
data/templates/15_none/centroid_004.pdb
data/templates/15_none/centroid_005.pdb
data/templates/15_none/centroid_006.pdb
data/templates/15_none/centroid_007.pdb
data/templates/15_none/centroid_008.pdb
data/templates/15_none/centroid_009.pdb
data/templates/15_none/centroid_010.pdb
data/templates/15_none/centroid_011.pdb
data/templates/15_none/centroid_012.pdb
data/templates/15_none/centroid_013.pdb
data/templates/15_none/centroid_014.pdb
data/templates/15_none/centroid_015.pdb
data/templates/15_none/synthetic_001.pdb
data/templates/15_none/synthetic_002.pdb
data/templates/15_none/synthetic_003.pdb
data/templates/15_none/synthetic_004.pdb
data/templates/15_none/synthetic_005.pdb
data/templates/15_none/synthetic_006.pdb
data/templates/15_none/synthetic_007.pdb
data/templates/15_none/synthetic_008.pdb
data/templates/15_none/synthetic_009.pdb
data/templates/15_none/synthetic_010.pdb
data/templates/15_none/synthetic_011.pdb
data/templates/15_none/synthetic_012.pdb
data/templates/15_none/synthetic_013.pdb
data/templates/15_none/synthetic_014.pdb
data/templates/15_none/synthetic_015.pdb
data/templates/15_none/synthetic_016.pdb
data/templates/15_none/synthetic_017.pdb
data/templates/15_none/synthetic_018.pdb
data/templates/15_none/synthetic_019.pdb
data/templates/15_none/synthetic_020.pdb
data/templates/15_none/synthetic_021.pdb
data/templates/15_none/synthetic_022.pdb
data/templates/15_none/synthetic_023.pdb
data/templates/15_none/synthetic_024.pdb
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data/torsion_priors/torsion_definitions.json
data/torsion_priors/torsion_prior_manifest_runtime.json
data/torsion_priors/torsion_priors_runtime.json
docking/__init__.py
docking/box.py
docking/build_template_library.py
docking/build_torsion_priors.py
docking/compress_template_library.py
docking/flexibility.py
docking/ligand_pdbqt.py
docking/mol2_input.py
docking/mol2_pdbqt.py
docking/pdbqt_validation.py
docking/protonation.py
docking/receptor_pdbqt.py
docking/template_library.py
docking/template_view.py
docking/torsion_budget.py
docking/torsion_observations.py
docking/torsion_prior.py
docking/vina.py
docking/vina_wrapper.py
docking/workflow.py
export/__init__.py
export/conformer.py
export/conformer_ensemble.py
gui/__init__.py
gui/__main__.py
gui/main_window.py
gui/params_panel.py
gui/render.py
gui/workers.py
libraries/caps.csv
libraries/core.csv
libraries/curated_cycpep.csv
libraries/helm_gpt.csv
libraries/manifest.json
libraries/nnaa_diverse.csv
libraries/special.csv
paths/__init__.py
paths/_map_utils.py
paths/path_a.py
paths/path_b.py
paths/path_c.py
paths/path_f.py
paths/path_g.py
paths/path_h.py
paths/residue_template_factory.py
rdpepper/__init__.py
rdpepper/__main__.py
rdpepper/application.py
rdpepper/cli.py
rdpepper/gui.py
rdpepper.egg-info/PKG-INFO
rdpepper.egg-info/SOURCES.txt
rdpepper.egg-info/dependency_links.txt
rdpepper.egg-info/entry_points.txt
rdpepper.egg-info/requires.txt
rdpepper.egg-info/top_level.txt
schemas/candidate_assessment.schema.json
schemas/exact_v1.schema.json
schemas/v5_artifact.schema.json