How obrien-lab-psu/ncledetector works
NCLEdetector is a Python toolkit for analyzing non-covalent lasso entanglements in protein structures and folding simulations, then comparing results with experiments and modeling populations. The principal workflow runs structure or trajectory analysis, derives entanglement and order-parameter features, and supports downstream clustering, MSM, and statistical analysis. The graph includes the documented resolution-conversion capability and the Jwalk components used for SASD calculations. Relationships are limited to README statements and SOURCE INDEX references; unsampled implementation details are not inferred.
Main entry points: order_params.py Order parameters · run_nativeNCLE.py Native NCLE · run_compare_sim2exp.py Sim-experiment workflow · _logging.py Logging helper
Components 19
Workflow entrypoints
- Native NCLE
scripts/run_nativeNCLE.py - Trajectory workflow
scripts/run_OP_on_simulation_traj.py - Sim-experiment workflow
scripts/run_compare_sim2exp.py - MSM workflow
scripts/run_MSM.py - Population workflow
scripts/run_population_modeling.py
Entanglement analysis
- Gaussian entanglement
NCLEdetector/gaussian_entanglement.py - Entanglement features
NCLEdetector/entanglement_features.py - Clustering and MSM
NCLEdetector/clustering.py - Experimental comparison
NCLEdetector/compare_sim2exp.py
Trajectory analysis
- Order parameters
NCLEdetector/order_params.py - Jwalk grid
NCLEdetector/Jwalk/GridTools.py - Jwalk structure tools
NCLEdetector/Jwalk/PDBTools.py - Jwalk surface tools
NCLEdetector/Jwalk/SurfaceTools.py - Jwalk SASD
NCLEdetector/Jwalk/SASDTools.py
Modeling and support
- Resolution conversion
NCLEdetector/change_resolution.py - Statistical modeling
NCLEdetector/statistics.py - Logging helper
NCLEdetector/_logging.py
Other components
- Researcher
- Analysis outputs
Connections 30
- Researcher → Native NCLE: runs
- Researcher → Trajectory workflow: runs
- Researcher → Sim-experiment workflow: runs
- Researcher → MSM workflow: runs
- Researcher → Population workflow: runs
- Native NCLE → Gaussian entanglement: calculates
scripts/run_nativeNCLE.py - Native NCLE → Clustering and MSM: uses
scripts/run_nativeNCLE.py - Native NCLE → Entanglement features: generates
scripts/run_nativeNCLE.py - Trajectory workflow → Order parameters: calculates
scripts/run_OP_on_simulation_traj.py - Order parameters → Jwalk grid: uses
NCLEdetector/order_params.py - Order parameters → Jwalk structure tools: uses
NCLEdetector/order_params.py - Order parameters → Jwalk surface tools: uses
NCLEdetector/order_params.py - Order parameters → Jwalk SASD: uses
NCLEdetector/order_params.py - Sim-experiment workflow → Experimental comparison: compares
scripts/run_compare_sim2exp.py - Sim-experiment workflow → Gaussian entanglement: uses
scripts/run_compare_sim2exp.py - Sim-experiment workflow → Clustering and MSM: uses
scripts/run_compare_sim2exp.py - MSM workflow → Clustering and MSM: builds
scripts/run_MSM.py - Population workflow → Statistical modeling: models
scripts/run_population_modeling.py - Population workflow → Analysis outputs: writes
- Native NCLE → Analysis outputs: writes
- Trajectory workflow → Analysis outputs: writes
- Sim-experiment workflow → Analysis outputs: writes
- MSM workflow → Analysis outputs: writes
- Resolution conversion → Analysis outputs: converts structures
- Statistical modeling → Analysis outputs: models
- Gaussian entanglement → Logging helper: configures
NCLEdetector/gaussian_entanglement.py - Clustering and MSM → Logging helper: configures
NCLEdetector/clustering.py - Experimental comparison → Logging helper: configures
NCLEdetector/compare_sim2exp.py - Order parameters → Logging helper: configures
NCLEdetector/order_params.py - Statistical modeling → Logging helper: configures
NCLEdetector/statistics.py