CHANGELOG.md
LICENSE
MANIFEST.in
RAPID_IMPLEMENTATION_COMPLETE.md
README.md
pyproject.toml
setup.cfg
setup.py
bioql/__init__.py
bioql/advanced_qec.py
bioql/batcher.py
bioql/billing_integration.py
bioql/bio_interpreter.py
bioql/cache.py
bioql/chemistry_qec.py
bioql/cli.py
bioql/cloud_auth.py
bioql/compiler.py
bioql/dashboard.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/optimizer.py
bioql/profiler.py
bioql/provenance.py
bioql/qualtran_qec.py
bioql/quantum_chemistry.py
bioql/quantum_connector.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/chem/__init__.py
bioql/chem/geometry 2.py
bioql/chem/geometry.py
bioql/chem/ligand_prep.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/docking/__init__.py
bioql/docking/pipeline 2.py
bioql/docking/pipeline.py
bioql/docking/quantum_runner.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/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/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/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/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
docs/ADMIN_SETUP.md
docs/AGENT_FILE_REVIEW_FIX.md
docs/AGENT_FINAL_STATUS.md
docs/AGENT_INTEGRATION.md
docs/ARCHITECTURE_DIAGRAM.md
docs/AUTONOMOUS_AGENT.md
docs/AZURE_QUANTUM_CLI_SETUP.md
docs/AZURE_QUANTUM_NEXT_STEPS.md
docs/AZURE_QUANTUM_STATUS.md
docs/AZURE_SUBSCRIPTION_ISSUE_SOLVED.md
docs/BILLING_INTEGRATION_COMPLETE.md
docs/BILLING_SETUP_STATUS.md
docs/BIOQL_MODEL_TRAINING_SUMMARY.md
docs/BIOQL_PRICING.md
docs/BIOQL_REAL_FEATURES.md
docs/BIOQL_SUMMARY.md
docs/BIOQL_V3.1.0_COMPLETE_API.md
docs/BIOQL_V3_README.md
docs/BIOQL_VSCODE_INTEGRATION_READY.md
docs/BIOQL_VSCODE_V2_CHAT.md
docs/CACHE_IMPLEMENTATION_SUMMARY.md
docs/CACHE_QUICK_REFERENCE.md
docs/CHANGELOG 2.md
docs/CHANGELOG.md
docs/CODE_REVIEW_REPORT.md
docs/COMPREHENSIVE_STATUS.md
docs/CONNECT_MODAL_TO_BILLING.md
docs/COST_TRACKING_IMPLEMENTATION.md
docs/CRITICAL_FIX_APPLIED.md
docs/DEEPSEEK_FINETUNED_MODEL.md
docs/DEEPSEEK_PRODUCTION_READY.md
docs/DEPLOYMENT_SUCCESS.md
docs/DRUG_DISCOVERY_CIRCUITS.md
docs/DRUG_DISCOVERY_QUICKSTART.md
docs/ESTADO_FINAL_MODELO.md
docs/FILE_PATH_REVIEW_FIXED.md
docs/FINAL_FIX.md
docs/FINAL_SUCCESS_REPORT.md
docs/FIXES_APPLIED.md
docs/FOUNDATIONAL_MODEL.md
docs/IBM_QUANTUM_INTEGRATION_SUMMARY.md
docs/IDE_EXTENSIONS_GUIDE.md
docs/IMPLEMENTATION_SUMMARY.md
docs/INDEX.md
docs/INSTALLATION.md
docs/INSTALL_AND_TEST.md
docs/INSTALL_VSCODE_AGENT.md
docs/INSTALL_VSCODE_EXTENSION.md
docs/INTEGRATION_SUMMARY.md
docs/INTEGRATION_TESTING_INDEX.md
docs/INTEGRATION_TEST_REPORT.md
docs/INTERACTIVE_CLI_GUIDE.md
docs/IONQ_ACCESS_REQUEST.md
docs/MODAL_ISSUE.md
docs/MODAL_SETUP.md
docs/MODAL_TRAINING_GUIDE.md
docs/MODELO_MEJORADO_PLAN.md
docs/MODELO_V2_ESTADO_FINAL.md
docs/MODEL_FIX_SOLUTION.md
docs/PRICING.md
docs/PRICING_MODEL.md
docs/PRICING_SYSTEM_V2_SUMMARY.md
docs/PRODUCTION_READY_SUMMARY.md
docs/PROFILER_MODULE.md
docs/PROJECT_COMPLETION_SUMMARY 2.md
docs/PROJECT_COMPLETION_SUMMARY.md
docs/PROJECT_STRUCTURE.md
docs/README 2.md
docs/README.md
docs/README_API_KEY_MODEL.md
docs/RESUMEN_FINAL_ESTADO.md
docs/RETRAINING_V2.md
docs/SEMANTIC_PARSER_GUIDE.md
docs/TECHNICAL_REFERENCE 2.md
docs/TEST_SUITE_SUMMARY.md
docs/VALIDATION_REPORT.md
docs/VERIFICATION_REPORT.md
docs/VSCODE_ASSISTANT_GUIDE.md
docs/VSCODE_EXTENSION_FINAL.md
docs/VSCODE_READY_TO_USE.md
docs/monetization_plan.md
docs/📚_INDEX_COMPLETO.md
docs/admin/ADMIN_MANUAL.md
docs/admin/BILLING_STATUS.md
docs/demo/API_KEY_ONLY.txt
docs/demo/DEMO_CREDENTIALS.md
docs/demo/DEMO_EXECUTIVE_SUMMARY.md
docs/demo/DEMO_INDEX.txt
docs/demo/DEMO_PACKAGE_COMPLETE.md
docs/demo/DEMO_README.txt
docs/demo/FINAL_WORKING_DEMO.md
docs/demo/START_HERE.md
docs/ionq/IONQ_QUICK_START.txt
docs/ionq/IONQ_SIMULATORS_GUIDE.md
docs/ionq/IONQ_WORKING_GUIDE.md
docs/monitor/INICIAR_MONITOR.txt
docs/monitor/MONITOR_SYSTEM_SUMMARY.md
docs/monitor/QUICK_START_MONITOR.md
docs/monitor/SERVICE_MONITOR_GUIDE.md
docs/technical/TECHNICAL_REFERENCE.md
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