LICENSE
MANIFEST.in
README.md
neurocgmd.py
pyproject.toml
ai_control/__init__.py
ai_control/chemistry_governor.py
ai_control/controller.py
ai_control/policies.py
ai_control/resource_allocator.py
ai_control/stability_monitor.py
benchmarks/reference_cases/data/1BRS.pdb
benchmarks/reference_cases/data/6M0J.pdb
chemistry/__init__.py
chemistry/interface_logic.py
chemistry/residue_semantics.py
compartments/__init__.py
compartments/domain_models.py
compartments/registry.py
compartments/routing.py
config/__init__.py
config/protein_mapping.py
config/run_manifest.py
config/runtime.py
core/__init__.py
core/constants.py
core/exceptions.py
core/interfaces.py
core/project_manifest.py
core/state.py
core/state_registry.py
core/types.py
core/units.py
examples/barnase_20ns.toml
examples/barnase_barstar.toml
examples/quick_test.toml
examples/spike_ace2.toml
forcefields/__init__.py
forcefields/base_forcefield.py
forcefields/bonded_potentials.py
forcefields/hybrid_engine.py
forcefields/material_templates.py
forcefields/nonbonded_potentials.py
forcefields/protein_import_forcefield.py
forcefields/protein_shadow_profiles.py
forcefields/spatial_semantic_profiles.py
forcefields/trusted_sources.py
forcefields/universal_forcefield.py
forcefields/universal_types.py
graph/__init__.py
graph/adjacency_utils.py
graph/connectivity_rules.py
graph/edge_models.py
graph/graph_manager.py
graph/message_passing.py
integrators/__init__.py
integrators/baoab.py
integrators/base.py
integrators/langevin.py
io/__init__.py
io/checkpoint_writer.py
io/export_registry.py
io/pdb_loader.py
io/trajectory_writer.py
memory/__init__.py
memory/episode_registry.py
memory/replay_buffer.py
memory/trace_store.py
ml/__init__.py
ml/differentiable_hooks.py
ml/ensemble_uncertainty.py
ml/live_features.py
ml/neural_residual_model.py
ml/online_trainer.py
ml/residual_model.py
ml/scalable_residual.py
ml/uncertainty_model.py
neurocgmd.egg-info/PKG-INFO
neurocgmd.egg-info/SOURCES.txt
neurocgmd.egg-info/dependency_links.txt
neurocgmd.egg-info/entry_points.txt
neurocgmd.egg-info/requires.txt
neurocgmd.egg-info/top_level.txt
optimization/__init__.py
optimization/backend_execution.py
optimization/backend_registry.py
optimization/compute_backend.py
optimization/profiling.py
optimization/scaling_hooks.py
physics/__init__.py
physics/constraints.py
physics/electrostatics.py
physics/neighbor_list.py
physics/periodic_boundary.py
physics/production_evaluator.py
physics/backends/__init__.py
physics/backends/contracts.py
physics/backends/dispatch.py
physics/backends/reference_backend.py
physics/energies/__init__.py
physics/energies/bonded.py
physics/energies/nonbonded.py
physics/forces/__init__.py
physics/forces/bonded_forces.py
physics/forces/composite.py
physics/forces/nonbonded_forces.py
physics/kernels/__init__.py
physics/kernels/bonded.py
physics/kernels/constraints.py
physics/kernels/electrostatics.py
physics/kernels/integration.py
physics/kernels/nonbonded.py
plasticity/__init__.py
plasticity/engine.py
plasticity/hebbian.py
plasticity/pruning.py
plasticity/reinforcement.py
plasticity/stdp.py
plasticity/traces.py
prepare/__init__.py
prepare/ions.py
prepare/models.py
prepare/pipeline.py
prepare/protonation.py
prepare/solvation.py
qcloud/__init__.py
qcloud/adaptive_refinement.py
qcloud/cloud_state.py
qcloud/event_analyzer.py
qcloud/protein_shadow_tuning.py
qcloud/qcloud_coupling.py
qcloud/region_selector.py
qcloud/shadow_cloud.py
qcloud/shadow_correction.py
qcloud/shadow_mapping.py
qcloud/spatial_semantic_field.py
sampling/__init__.py
sampling/enhanced_sampling.py
sampling/production_engine.py
sampling/production_loop.py
sampling/simulation_loop.py
sampling/stage_runner.py
sampling/scenarios/__init__.py
sampling/scenarios/barnase_barstar.py
sampling/scenarios/complex_assembly.py
sampling/scenarios/contracts.py
sampling/scenarios/imported_protein.py
sampling/scenarios/spike_ace2.py
scripts/__init__.py
scripts/build_docs.py
scripts/full_pipeline_demo.py
scripts/import_protein_system.py
scripts/live_dashboard.py
scripts/neurocgmd.py
scripts/plot_analysis_png.py
scripts/plot_architecture.py
scripts/plot_binding.py
scripts/plot_scientific_validation.py
scripts/plot_small_protein_benchmark.py
scripts/plot_style.py
scripts/run_small_protein_benchmark.py
scripts/tune_spatial_transfer.py
scripts/validate_scaffold.py
spring/__init__.py
spring/engine.py
spring/main.py
spring/visualize.py
spring/bridges/__init__.py
spring/bridges/neurocgmd_bridge.py
spring/demos/__init__.py
spring/demos/chain_fold.py
spring/demos/graph_color.py
spring/demos/tile_puzzle.py
spring/demos/tsp.py
tests/test_ai_control.py
tests/test_arbitrary_protein_pipeline.py
tests/test_backend_compute_spine.py
tests/test_backend_parity.py
tests/test_baoab_integrator.py
tests/test_barnase_barstar_scenario.py
tests/test_chemistry_layer.py
tests/test_compartments.py
tests/test_complex_assembly_scenario.py
tests/test_core_state.py
tests/test_core_types.py
tests/test_differentiable_hooks.py
tests/test_enhanced_features.py
tests/test_forcefield_foundation.py
tests/test_graph_layer.py
tests/test_memory_layer.py
tests/test_ml_layer.py
tests/test_molecular_observables.py
tests/test_neighbor_list.py
tests/test_neural_ml.py
tests/test_neurocgmd_cli.py
tests/test_optimization_layer.py
tests/test_plasticity_layer.py
tests/test_preparation_pipeline.py
tests/test_production_engine.py
tests/test_production_loop_and_analysis.py
tests/test_production_md.py
tests/test_project_manifest.py
tests/test_protein_shadow_tuning.py
tests/test_protein_transfer_tuning.py
tests/test_qcloud_framework.py
tests/test_reference_cases.py
tests/test_run_manifest.py
tests/test_scaffold.py
tests/test_scalable_ml_residual.py
tests/test_scientific_validation.py
tests/test_shadow_fidelity_layer.py
tests/test_simulation_loop.py
tests/test_small_protein_benchmark.py
tests/test_spatial_semantic_forcefield.py
tests/test_spike_ace2_scenario.py
tests/test_spring_bridge.py
tests/test_stdp_and_gnn.py
tests/test_structure_metrics.py
tests/test_topology.py
tests/test_transition_analysis.py
tests/test_universal_forcefield.py
tests/test_validation_benchmarks.py
tests/test_visualization.py
topology/__init__.py
topology/beads.py
topology/bonds.py
topology/protein_coarse_mapping.py
topology/protein_import_models.py
topology/system_topology.py
validation/__init__.py
validation/adaptive_analysis.py
validation/backend_parity.py
validation/drift_checks.py
validation/fidelity_checks.py
validation/molecular_observables.py
validation/protein_transfer_tuning.py
validation/sanity_checks.py
validation/scientific_validation.py
validation/statistical_mechanics.py
validation/structure_metrics.py
validation/transition_analysis.py
visualization/__init__.py
visualization/benchmark_report_views.py
visualization/graph_views.py
visualization/problem_views.py
visualization/trajectory_views.py
visualization/validation_report_views.py