├── .flake8 ├── .github ├── pull_request_template.md └── workflows │ └── pythonapp.yml ├── .gitignore ├── .readthedocs.yml ├── LICENSE ├── README.md ├── docs ├── Makefile ├── conf.py ├── index.rst ├── make.bat ├── modules.rst ├── olddocs │ ├── Makefile │ └── conf.py ├── polychrom.contactmaps.rst ├── polychrom.forcekits.rst ├── polychrom.forces.rst ├── polychrom.hdf5_format.rst ├── polychrom.legacy.contactmaps.rst ├── polychrom.legacy.forces.rst ├── polychrom.legacy.legacy_format.rst ├── polychrom.legacy.rst ├── polychrom.polymer_analyses.rst ├── polychrom.polymerutils.rst ├── polychrom.pymol_show.rst ├── polychrom.rst ├── polychrom.simulation.rst ├── polychrom.starting_conformations.rst ├── quickstart.rst └── requirements.txt ├── examples ├── customIntegrators │ ├── activeBD.py │ └── corr_noise.py ├── example │ └── example.py ├── loopExtrusion │ ├── LEF_Dynamics.pyx │ ├── README.md │ ├── directionalModel │ │ ├── flagshipNormLifetime.py │ │ └── showContactmap.py │ ├── extrusion_1D_newCode.ipynb │ ├── extrusion_1D_translocator.ipynb │ ├── extrusion_3D.ipynb │ ├── newSimulatorCode.py │ └── sample_contactmap.ipynb ├── storage_formats │ ├── hdf5_reporter.ipynb │ └── legacy_reporter.ipynb └── topological_simulation │ └── test_topological_simulation.ipynb ├── polychrom ├── __init__.py ├── __polymer_math.cpp ├── __polymer_math.h ├── _polymer_math.pyx ├── _polymer_math.so ├── cli │ ├── README.txt │ ├── dif │ ├── show │ ├── traj_convert.py │ └── xyz ├── contactmaps.py ├── contrib │ └── integrators.py ├── forcekits.py ├── forces.py ├── hdf5_format.py ├── installpymol.sh ├── legacy │ ├── __init__.py │ ├── contactmaps.py │ ├── forces.py │ ├── legacy_format.py │ └── polymerutils.py ├── lib │ ├── __init__.py │ └── extrusion.py ├── param_units.py ├── polymer_analyses.py ├── polymerutils.py ├── pymol_show.py ├── simulation.py └── starting_conformations.py ├── pyproject.toml ├── pytest.ini ├── requirements.txt ├── setup.py ├── tests ├── demo_test_bond_length.py ├── 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