EntDetect 1.2.0__tar.gz → 1.2.1__tar.gz

entdetect-1.2.1/EntDetect.egg-info/PKG-INFO

@@ -0,0 +1,188 @@
+Metadata-Version: 2.4
+Name: EntDetect
+Version: 1.2.1
+Summary: Entanglement Detection in Protein Structures
+Home-page: https://github.com/obrien-lab-psu/EntDetect
+Project-URL: Source, https://github.com/obrien-lab-psu/EntDetect
+Project-URL: Bug Tracker, https://github.com/obrien-lab-psu/EntDetect/issues
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: biopython
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: MDAnalysis
+Requires-Dist: mdtraj
+Requires-Dist: parmed
+Requires-Dist: numba
+Requires-Dist: topoly
+Requires-Dist: geom_median
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: scikit-learn
+Requires-Dist: networkx
+Requires-Dist: pyyaml
+Requires-Dist: tqdm
+Requires-Dist: requests
+Requires-Dist: statsmodels
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: summary
+
+# EntDetect
+
+A comprehensive Python package for studying non-covalent lasso entanglements in protein folding through molecular dynamics simulations and experimental data analysis.
+
+## Overview
+
+EntDetect provides a complete toolkit for analyzing protein entanglements across multiple scales - from individual structures to large-scale proteomic datasets. The package enables researchers to:
+
+- **Identify and characterize** native entanglements in protein structures
+- **Calculate order parameters** for simulation trajectories (Q, G, K, SASA, Jwalk, XP)
+- **Build Markov State Models** from coarse-grained simulation ensembles
+- **Compare simulations to experiments** using LiP-MS and XL-MS data
+- **Perform population-level analysis** across heterogeneous protein datasets
+- **Coarse-grain and back-map** between atomic resolutions
+
+## Key Features
+
+- **Multi-scale Analysis**: From single proteins to proteome-wide studies
+- **Experimental Integration**: Direct comparison with mass spectrometry data
+- **Advanced Clustering**: Non-native entanglement clustering and MSM construction
+- **Statistical Methods**: Monte Carlo simulations and logistic regression modeling
+- **Flexible Resolution**: Seamless conversion between all-atom and coarse-grained representations
+
+## Installation
+
+Create a new conda environment and install EntDetect (from this repo checkout):
+
+```bash
+conda env create -f environment.yml
+conda activate entdetect
+```
+
+Notes:
+- The provided conda environment targets Python 3.11 for best compatibility with the scientific stack.
+- Run `conda env create` from the EntDetect repo root (the environment file uses `pip -e .`).
+- If you prefer installing into an existing env, use `pip install -e .` from the repo root.
+
+macOS (Miniconda) notes:
+- The default `environment.yml` is intended to work on both Linux and macOS via conda-forge.
+- If you hit solver/build issues on macOS, try:
+
+```bash
+conda env create -f environment-mac.yml
+conda activate entdetect
+```
+
+- On Apple Silicon, if a dependency is missing for `osx-arm64`, a common workaround is:
+
+```bash
+CONDA_SUBDIR=osx-64 conda env create -f environment-mac.yml
+conda activate entdetect
+```
+
+## Tutorials
+
+Step-by-step, runnable tutorials covering all four analysis workflows are in `Documentation/`. Start here:
+
+- [Documentation/index.md](Documentation/index.md) — master index with environment setup, path variables, and links to all workflows
+
+For quick CLI reference, every script supports `--help`:
+
+```bash
+python scripts/run_nativeNCLE.py --help
+python scripts/run_OP_on_simulation_traj.py --help
+```
+
+## Package Structure
+
+```
+EntDetect/
+├── EntDetect/                    # Main package
+│   ├── __init__.py
+│   ├── gaussian_entanglement.py  # Core entanglement calculations
+│   ├── clustering.py             # Entanglement clustering methods
+│   ├── order_params.py          # Order parameter calculations
+│   ├── compare_sim2exp.py       # Simulation-experiment comparison
+│   ├── statistics.py            # Statistical analysis methods
+│   ├── entanglement_features.py # Feature generation
+│   ├── change_resolution.py     # Resolution conversion
+│   └── utilities.py             # Helper functions
+├── scripts/                     # Example workflow scripts
+├── Documentation/               # Detailed module documentation
+└── TestingGrounds/             # Test data and examples
+```
+
+## Core Modules
+
+- **`gaussian_entanglement`**: Calculate Gaussian linking numbers and identify entanglements
+- **`clustering`**: Cluster native and non-native entanglements, build MSMs
+- **`order_params`**: Compute Q, G, K, SASA, Jwalk, and cross-linking propensity
+- **`compare_sim2exp`**: Integrate LiP-MS and XL-MS experimental data
+- **`statistics`**: Population modeling and Monte Carlo analysis
+- **`entanglement_features`**: Generate structural features for entanglements
+- **`change_resolution`**: Convert between all-atom and coarse-grained representations
+
+## Documentation
+
+Detailed documentation for each module:
+
+- [Tutorial index](Documentation/index.md)
+- [Workflow 1: Native NCLE detection](Documentation/workflow1_native_ncle.md)
+- [Workflow 2: Trajectory analysis](Documentation/workflow2_trajectory_analysis.md)
+- [Workflow 3: Sim-to-experiment comparison](Documentation/workflow3_sim2exp.md)
+- [Workflow 4: Population-level analysis](Documentation/workflow4_population.md)
+- [Gaussian Entanglement](Documentation/gaussian_entanglement.md)
+- [Clustering](Documentation/clustering.md)
+- [Order Parameters](Documentation/order_params.md)
+- [Simulation-Experiment Comparison](Documentation/compare_sim2exp.md)
+- [Statistical Analysis](Documentation/statistics.md)
+- [Entanglement Features](Documentation/entanglement_features.md)
+- [Resolution Conversion](Documentation/change_resolution.md)
+- [Utilities](Documentation/utilities.md)
+
+## Requirements
+
+- Python 3.8+
+- NumPy
+- Pandas
+- SciPy
+- MDAnalysis
+- OpenMM (for force field operations)
+- Matplotlib (for visualization)
+- See `environment.yml` for complete dependencies
+
+## Citation
+
+If you use EntDetect in your research, please cite:
+
+```bibtex
+@software{entdetect2024,
+  title={EntDetect: A Python Package for Protein Entanglement Analysis},
+  author={Ian Sitarik},
+  author={Yang Jiang},
+  author={Hyebin Song},
+  author={Edward O'Brien},
+  year={2026},
+  url={https://github.com/obrien-lab-psu/EntDetect}
+}
+```
+
+## Contributing
+
+Contributions are welcome! Please see our contributing guidelines and submit pull requests for any improvements.
+
+## License
+
+This project is licensed under the MIT License - see the LICENSE file for details.
+
+## Support
+
+For questions and support, please open an issue on GitHub or contact the developers. 
+  
+

entdetect-1.2.1/PKG-INFO

@@ -0,0 +1,188 @@
+Metadata-Version: 2.4
+Name: EntDetect
+Version: 1.2.1
+Summary: Entanglement Detection in Protein Structures
+Home-page: https://github.com/obrien-lab-psu/EntDetect
+Project-URL: Source, https://github.com/obrien-lab-psu/EntDetect
+Project-URL: Bug Tracker, https://github.com/obrien-lab-psu/EntDetect/issues
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: biopython
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: MDAnalysis
+Requires-Dist: mdtraj
+Requires-Dist: parmed
+Requires-Dist: numba
+Requires-Dist: topoly
+Requires-Dist: geom_median
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: scikit-learn
+Requires-Dist: networkx
+Requires-Dist: pyyaml
+Requires-Dist: tqdm
+Requires-Dist: requests
+Requires-Dist: statsmodels
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: summary
+
+# EntDetect
+
+A comprehensive Python package for studying non-covalent lasso entanglements in protein folding through molecular dynamics simulations and experimental data analysis.
+
+## Overview
+
+EntDetect provides a complete toolkit for analyzing protein entanglements across multiple scales - from individual structures to large-scale proteomic datasets. The package enables researchers to:
+
+- **Identify and characterize** native entanglements in protein structures
+- **Calculate order parameters** for simulation trajectories (Q, G, K, SASA, Jwalk, XP)
+- **Build Markov State Models** from coarse-grained simulation ensembles
+- **Compare simulations to experiments** using LiP-MS and XL-MS data
+- **Perform population-level analysis** across heterogeneous protein datasets
+- **Coarse-grain and back-map** between atomic resolutions
+
+## Key Features
+
+- **Multi-scale Analysis**: From single proteins to proteome-wide studies
+- **Experimental Integration**: Direct comparison with mass spectrometry data
+- **Advanced Clustering**: Non-native entanglement clustering and MSM construction
+- **Statistical Methods**: Monte Carlo simulations and logistic regression modeling
+- **Flexible Resolution**: Seamless conversion between all-atom and coarse-grained representations
+
+## Installation
+
+Create a new conda environment and install EntDetect (from this repo checkout):
+
+```bash
+conda env create -f environment.yml
+conda activate entdetect
+```
+
+Notes:
+- The provided conda environment targets Python 3.11 for best compatibility with the scientific stack.
+- Run `conda env create` from the EntDetect repo root (the environment file uses `pip -e .`).
+- If you prefer installing into an existing env, use `pip install -e .` from the repo root.
+
+macOS (Miniconda) notes:
+- The default `environment.yml` is intended to work on both Linux and macOS via conda-forge.
+- If you hit solver/build issues on macOS, try:
+
+```bash
+conda env create -f environment-mac.yml
+conda activate entdetect
+```
+
+- On Apple Silicon, if a dependency is missing for `osx-arm64`, a common workaround is:
+
+```bash
+CONDA_SUBDIR=osx-64 conda env create -f environment-mac.yml
+conda activate entdetect
+```
+
+## Tutorials
+
+Step-by-step, runnable tutorials covering all four analysis workflows are in `Documentation/`. Start here:
+
+- [Documentation/index.md](Documentation/index.md) — master index with environment setup, path variables, and links to all workflows
+
+For quick CLI reference, every script supports `--help`:
+
+```bash
+python scripts/run_nativeNCLE.py --help
+python scripts/run_OP_on_simulation_traj.py --help
+```
+
+## Package Structure
+
+```
+EntDetect/
+├── EntDetect/                    # Main package
+│   ├── __init__.py
+│   ├── gaussian_entanglement.py  # Core entanglement calculations
+│   ├── clustering.py             # Entanglement clustering methods
+│   ├── order_params.py          # Order parameter calculations
+│   ├── compare_sim2exp.py       # Simulation-experiment comparison
+│   ├── statistics.py            # Statistical analysis methods
+│   ├── entanglement_features.py # Feature generation
+│   ├── change_resolution.py     # Resolution conversion
+│   └── utilities.py             # Helper functions
+├── scripts/                     # Example workflow scripts
+├── Documentation/               # Detailed module documentation
+└── TestingGrounds/             # Test data and examples
+```
+
+## Core Modules
+
+- **`gaussian_entanglement`**: Calculate Gaussian linking numbers and identify entanglements
+- **`clustering`**: Cluster native and non-native entanglements, build MSMs
+- **`order_params`**: Compute Q, G, K, SASA, Jwalk, and cross-linking propensity
+- **`compare_sim2exp`**: Integrate LiP-MS and XL-MS experimental data
+- **`statistics`**: Population modeling and Monte Carlo analysis
+- **`entanglement_features`**: Generate structural features for entanglements
+- **`change_resolution`**: Convert between all-atom and coarse-grained representations
+
+## Documentation
+
+Detailed documentation for each module:
+
+- [Tutorial index](Documentation/index.md)
+- [Workflow 1: Native NCLE detection](Documentation/workflow1_native_ncle.md)
+- [Workflow 2: Trajectory analysis](Documentation/workflow2_trajectory_analysis.md)
+- [Workflow 3: Sim-to-experiment comparison](Documentation/workflow3_sim2exp.md)
+- [Workflow 4: Population-level analysis](Documentation/workflow4_population.md)
+- [Gaussian Entanglement](Documentation/gaussian_entanglement.md)
+- [Clustering](Documentation/clustering.md)
+- [Order Parameters](Documentation/order_params.md)
+- [Simulation-Experiment Comparison](Documentation/compare_sim2exp.md)
+- [Statistical Analysis](Documentation/statistics.md)
+- [Entanglement Features](Documentation/entanglement_features.md)
+- [Resolution Conversion](Documentation/change_resolution.md)
+- [Utilities](Documentation/utilities.md)
+
+## Requirements
+
+- Python 3.8+
+- NumPy
+- Pandas
+- SciPy
+- MDAnalysis
+- OpenMM (for force field operations)
+- Matplotlib (for visualization)
+- See `environment.yml` for complete dependencies
+
+## Citation
+
+If you use EntDetect in your research, please cite:
+
+```bibtex
+@software{entdetect2024,
+  title={EntDetect: A Python Package for Protein Entanglement Analysis},
+  author={Ian Sitarik},
+  author={Yang Jiang},
+  author={Hyebin Song},
+  author={Edward O'Brien},
+  year={2026},
+  url={https://github.com/obrien-lab-psu/EntDetect}
+}
+```
+
+## Contributing
+
+Contributions are welcome! Please see our contributing guidelines and submit pull requests for any improvements.
+
+## License
+
+This project is licensed under the MIT License - see the LICENSE file for details.
+
+## Support
+
+For questions and support, please open an issue on GitHub or contact the developers. 
+  
+

{entdetect-1.2.0 → entdetect-1.2.1}/setup.py

@@ -1,9 +1,19 @@
 from setuptools import setup, find_packages
 
+with open('README.md', 'r', encoding='utf-8') as f:
+    long_description = f.read()
+
 setup(
     name='EntDetect',
-    version='1.2.0',
+    version='1.2.1',
     description='Entanglement Detection in Protein Structures',
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    url='https://github.com/obrien-lab-psu/EntDetect',
+    project_urls={
+        'Source': 'https://github.com/obrien-lab-psu/EntDetect',
+        'Bug Tracker': 'https://github.com/obrien-lab-psu/EntDetect/issues',
+    },
     packages=find_packages(),
     include_package_data=True,
     package_data={

entdetect-1.2.0/EntDetect.egg-info/PKG-INFO

@@ -1,26 +0,0 @@
-Metadata-Version: 2.4
-Name: EntDetect
-Version: 1.2.0
-Summary: Entanglement Detection in Protein Structures
-License-File: LICENSE
-Requires-Dist: biopython
-Requires-Dist: numpy
-Requires-Dist: scipy
-Requires-Dist: pandas
-Requires-Dist: MDAnalysis
-Requires-Dist: mdtraj
-Requires-Dist: parmed
-Requires-Dist: numba
-Requires-Dist: topoly
-Requires-Dist: geom_median
-Requires-Dist: matplotlib
-Requires-Dist: seaborn
-Requires-Dist: scikit-learn
-Requires-Dist: networkx
-Requires-Dist: pyyaml
-Requires-Dist: tqdm
-Requires-Dist: requests
-Requires-Dist: statsmodels
-Dynamic: license-file
-Dynamic: requires-dist
-Dynamic: summary

entdetect-1.2.0/PKG-INFO

@@ -1,26 +0,0 @@
-Metadata-Version: 2.4
-Name: EntDetect
-Version: 1.2.0
-Summary: Entanglement Detection in Protein Structures
-License-File: LICENSE
-Requires-Dist: biopython
-Requires-Dist: numpy
-Requires-Dist: scipy
-Requires-Dist: pandas
-Requires-Dist: MDAnalysis
-Requires-Dist: mdtraj
-Requires-Dist: parmed
-Requires-Dist: numba
-Requires-Dist: topoly
-Requires-Dist: geom_median
-Requires-Dist: matplotlib
-Requires-Dist: seaborn
-Requires-Dist: scikit-learn
-Requires-Dist: networkx
-Requires-Dist: pyyaml
-Requires-Dist: tqdm
-Requires-Dist: requests
-Requires-Dist: statsmodels
-Dynamic: license-file
-Dynamic: requires-dist
-Dynamic: summary