CHANGELOG.md
LICENSE
MANIFEST.in
setup.cfg
setup.py
bioql/__init__.py
bioql/adme_predictor.py
bioql/advanced_qec.py
bioql/auditable_logs.py
bioql/batcher.py
bioql/billing_integration.py
bioql/bio_interpreter.py
bioql/bioisostere_db.py
bioql/cache.py
bioql/chemistry_qec.py
bioql/cli.py
bioql/cloud_auth.py
bioql/compiler.py
bioql/dashboard.py
bioql/drug_designer.py
bioql/drug_designer_v2.py
bioql/drug_discovery_templates.py
bioql/dynamic_bridge.py
bioql/enhanced_quantum.py
bioql/error_mitigation.py
bioql/logger.py
bioql/mapper.py
bioql/molecular_benchmarks.py
bioql/molecular_hamiltonian.py
bioql/molecular_utils.py
bioql/offtarget_panel.py
bioql/optimizer.py
bioql/pdb_generator.py
bioql/pipeline_orchestrator.py
bioql/profiler.py
bioql/provenance.py
bioql/qualtran_qec.py
bioql/quantum_chemistry.py
bioql/quantum_connector.py
bioql/quantum_fusion.py
bioql/remote_execution.py
bioql/resistance_profiler.py
bioql/similarity_search.py
bioql/simple_billing.py
bioql/tiered_billing.py
bioql.egg-info/PKG-INFO
bioql.egg-info/SOURCES.txt
bioql.egg-info/dependency_links.txt
bioql.egg-info/entry_points.txt
bioql.egg-info/not-zip-safe
bioql.egg-info/requires.txt
bioql.egg-info/top_level.txt
bioql/benchmarks/__init__.py
bioql/benchmarks/chemistry.py
bioql/benchmarks/quantum_advantage/__init__.py
bioql/benchmarks/quantum_advantage/accuracy_metrics.py
bioql/benchmarks/quantum_advantage/automated_runner.py
bioql/benchmarks/quantum_advantage/benchmark_suite.py
bioql/benchmarks/quantum_advantage/demo_benchmark.py
bioql/benchmarks/quantum_advantage/dft_comparison.py
bioql/benchmarks/quantum_advantage/performance_metrics.py
bioql/benchmarks/quantum_advantage/results_reporter.py
bioql/benchmarks/quantum_advantage/test_benchmarks.py
bioql/chem/__init__.py
bioql/chem/geometry 2.py
bioql/chem/geometry.py
bioql/chem/ligand_prep.py
bioql/chem/neutralize.py
bioql/chem/pharma_scores.py
bioql/chem/receptor_prep.py
bioql/circuits/__init__.py
bioql/circuits/base.py
bioql/circuits/catalog.py
bioql/circuits/algorithms/__init__.py
bioql/circuits/algorithms/grover.py
bioql/circuits/algorithms/vqe.py
bioql/circuits/composition/__init__.py
bioql/circuits/composition/composer.py
bioql/circuits/composition/modular.py
bioql/circuits/composition/stitching.py
bioql/circuits/drug_discovery/__init__.py
bioql/circuits/drug_discovery/adme_circuits.py
bioql/circuits/drug_discovery/binding_affinity.py
bioql/circuits/drug_discovery/docking_circuits.py
bioql/circuits/drug_discovery/pharmacophore.py
bioql/circuits/drug_discovery/toxicity_prediction.py
bioql/circuits/templates/__init__.py
bioql/circuits/templates/base.py
bioql/compilers/__init__.py
bioql/compilers/base.py
bioql/compilers/cirq_compiler.py
bioql/compilers/factory.py
bioql/compilers/qiskit_compiler.py
bioql/crispr_qai/__init__.py
bioql/crispr_qai/cli.py
bioql/crispr_qai/delivery_systems.py
bioql/crispr_qai/energies.py
bioql/crispr_qai/featurization.py
bioql/crispr_qai/guide_opt.py
bioql/crispr_qai/io.py
bioql/crispr_qai/ncbi_gene_fetcher.py
bioql/crispr_qai/offtarget_predictor.py
bioql/crispr_qai/phenotype.py
bioql/crispr_qai/regulatory_docs.py
bioql/crispr_qai/safety.py
bioql/crispr_qai/adapters/__init__.py
bioql/crispr_qai/adapters/base.py
bioql/crispr_qai/adapters/braket_adapter.py
bioql/crispr_qai/adapters/qiskit_adapter.py
bioql/crispr_qai/adapters/simulator.py
bioql/crispr_qai/examples/__init__.py
bioql/crispr_qai/examples/demo_advanced.py
bioql/crispr_qai/examples/demo_basic.py
bioql/docking/__init__.py
bioql/docking/pipeline 2.py
bioql/docking/pipeline.py
bioql/docking/quantum_runner.py
bioql/docking/real_vina.py
bioql/docking/vina_runner 2.py
bioql/docking/vina_runner.py
bioql/examples/aws_braket/AWS_BRAKET_SUCCESS.md
bioql/examples/aws_braket/QUICK_START.md
bioql/examples/aws_braket/README.md
bioql/examples/aws_braket/bell.qasm
bioql/examples/aws_braket/bioql_braket_integration.md
bioql/examples/aws_braket/braket_instructions.md
bioql/examples/aws_braket/setup_braket.sh
bioql/fmo_vqe/__init__.py
bioql/fmo_vqe/example_fmo_vqe.py
bioql/fmo_vqe/fragment_assembler.py
bioql/fmo_vqe/fragment_vqe.py
bioql/fmo_vqe/fragmentor.py
bioql/fmo_vqe/test_fmo_vqe.py
bioql/genomics/__init__.py
bioql/genomics/epigenetics.py
bioql/genomics/rna_seq.py
bioql/genomics/variant_calling.py
bioql/ir/__init__.py
bioql/ir/schema.py
bioql/ir/validators.py
bioql/llm/__init__.py
bioql/llm/agent_wrapper.py
bioql/llm/enhanced_agent.py
bioql/llm/vscode_assistant.py
bioql/llm/agents/__init__.py
bioql/llm/agents/code_generator.py
bioql/llm/agents/orchestrator.py
bioql/llm/models/__init__.py
bioql/llm/models/bioql_model.py
bioql/llm/models/evaluation.py
bioql/llm/models/inference.py
bioql/llm/models/serving.py
bioql/llm/models/training/__init__.py
bioql/llm/models/training/dataset.py
bioql/llm/models/training/trainer.py
bioql/llm/optimizers/__init__.py
bioql/llm/optimizers/hybrid_compiler.py
bioql/metabolomics/__init__.py
bioql/metabolomics/flux_analysis.py
bioql/metabolomics/metabolite_analysis.py
bioql/metabolomics/pathway_analysis.py
bioql/metabolomics/quantum_metabolomics.py
bioql/multiomics/__init__.py
bioql/multiomics/integration.py
bioql/multiomics/network_analysis.py
bioql/multiomics/quantum_integration.py
bioql/parser/__init__.py
bioql/parser/llm_parser.py
bioql/parser/mega_patterns.py
bioql/parser/nl_parser.py
bioql/parser/semantic_parser.py
bioql/parser/ultra_patterns.py
bioql/proteomics/__init__.py
bioql/proteomics/mass_spec.py
bioql/proteomics/protein_analysis.py
bioql/proteomics/protein_interaction.py
bioql/proteomics/ptm_prediction.py
bioql/proteomics/quantum_proteomics.py
bioql/proteomics/structure_prediction.py
bioql/qec/__init__.py
bioql/qec/error_mitigation.py
bioql/qec/metrics.py
bioql/qec/shor_code.py
bioql/qec/steane_code.py
bioql/qec/surface_code.py
bioql/transcorrelated_vqe/__init__.py
bioql/transcorrelated_vqe/tc_hamiltonian.py
bioql/transcorrelated_vqe/tc_vqe.py
bioql/transcorrelated_vqe/test_tc_vqe.py
bioql/transcorrelated_vqe/transcorrelation.py
bioql/visualization/__init__.py
bioql/visualization/qualtran_viz.py
bioql/visualization/resource_estimator.py
bioql/visualization/examples/__init__.py
bioql/visualization/examples/example_cost_analysis.py
bioql/visualization/examples/example_qec_comparison.py
bioql/visualization/examples/example_surface_code_viz.py
bioql/visualize/__init__ 2.py
bioql/visualize/__init__.py
bioql/visualize/py3dmol_viz 2.py
bioql/visualize/py3dmol_viz.py
bioql/visualize/pymol_viz.py
bioql/warm_start/__init__.py
bioql/warm_start/flow_vqe.py
bioql/warm_start/parameter_database.py
bioql/warm_start/similarity_matching.py
bioql/warm_start/test_warm_start.py
examples/advanced_features.py
examples/basic_usage.py
examples/billing_integration_examples.py
examples/cache_usage_example.py
examples/chemistry_benchmark_example.py
examples/complete_bioql_demo.py
examples/demo_bioql.py
examples/demo_unlimited_simulator.py
examples/dna_matching.py
examples/drug_discovery.py
examples/drug_discovery_circuits_example.py
examples/drug_discovery_example 2.py
examples/drug_discovery_example.py
examples/example_usage.py
examples/example_with_api_key.py
examples/h2_vqe_complete_example.py
examples/ibm_quantum_integration_example.py
examples/ionq_drug_discovery_demo.py
examples/ionq_simulators_test.py
examples/ionq_verified_demo.py
examples/profiler_example.py
examples/profiler_integration_demo.py
examples/protein_folding.py
examples/quick_test.py
examples/semantic_parser_demo.py
examples/test_docking_windows.py
examples/verified_working_demo.py
examples/glp1r_drug_discovery/scripts/compare_glp1_drugs.py
examples/glp1r_drug_discovery/scripts/generate_molecule_pdb.py
examples/glp1r_drug_discovery/scripts/glp1r_drug_design.py
examples/glp1r_drug_discovery/scripts/glp1r_simulator.py