LICENSE
MANIFEST.in
README.md
setup.py
pyRepliSage.egg-info/PKG-INFO
pyRepliSage.egg-info/SOURCES.txt
pyRepliSage.egg-info/dependency_links.txt
pyRepliSage.egg-info/entry_points.txt
pyRepliSage.egg-info/requires.txt
pyRepliSage.egg-info/top_level.txt
src/__init__.py
src/_version.py
src/banner.py
src/config.ini
src/logger.py
src/run.py
src/MC/__init__.py
src/MC/engine.py
src/MC/loops_energy.py
src/MC/moves.py
src/MC/normalization.py
src/MC/params.py
src/MC/potts_energy.py
src/MC/replication_energy.py
src/MC/replication_matrix.py
src/MC/results.py
src/MC/runner.py
src/MC/total_energy.py
src/MD/__init__.py
src/MD/dynamics.py
src/MD/forces.py
src/MD/md_plots.py
src/MD/model.py
src/MD/pipeline.py
src/MD/structures.py
src/MD/units.py
src/analysis/__init__.py
src/analysis/compartments.py
src/analysis/ensemble_metrics.py
src/analysis/folding_stats.py
src/analysis/heatmaps.py
src/analysis/lef_stats.py
src/analysis/mc_stats.py
src/analysis/potts_metrics.py
src/analysis/potts_order.py
src/analysis/rep_stats.py
src/analysis/structure_metrics.py
src/analysis/synchronization.py
src/analysis/tables.py
src/config/__init__.py
src/config/arg_defs.py
src/config/arg_types.py
src/config/loader.py
src/config/stress.py
src/config/writer.py
src/data/replication_timing_data.parquet
src/forcefields/classic_sm_ff.xml
src/io/__init__.py
src/io/structure_io.py
src/pipeline/__init__.py
src/pipeline/analysis_stage.py
src/pipeline/context.py
src/pipeline/figures_stage.py
src/pipeline/mc_stage.py
src/pipeline/md_stage.py
src/pipeline/orchestrator.py
src/pipeline/preproc_stage.py
src/pipeline/replication_stage.py
src/pipeline/viz3d_stage.py
src/plots/__init__.py
src/plots/diag_extra.py
src/plots/le_only.py
src/plots/loops.py
src/plots/mc_timeplots.py
src/plots/model_maps.py
src/plots/occupancy.py
src/plots/potts_order_fig.py
src/plots/rep_plots_pro.py
src/plots/rt_overview.py
src/plots/states.py
src/plots/story.py
src/plots/structure_figs.py
src/plots/style.py
src/plots/viz3d.py
src/preproc/__init__.py
src/preproc/bedpe.py
src/replication_simulation/__init__.py
src/replication_simulation/data_sources.py
src/replication_simulation/fork_propagation.py
src/replication_simulation/fork_simulator.py
src/replication_simulation/init_rate.py
src/replication_simulation/initiation.py
src/replication_simulation/input_checks.py
src/replication_simulation/rep_plots.py
src/replication_simulation/replikator.py
src/replication_simulation/simulator_class.py
src/replication_simulation/timing_io.py
src/replication_simulation/timing_stats.py
src/replication_simulation/validation.py
src/report/__init__.py
src/report/builder.py
src/report/findings.py
src/report/html_parts.py
src/report/mathml.py
src/report/text.py
src/report/theme.py
src/utils/__init__.py
src/utils/arrays.py
src/utils/constants.py
src/utils/files.py
src/utils/run_dirs.py
src/utils/sparse.py
src/viz3d/__init__.py
src/viz3d/data.py
src/viz3d/html_viewer.py
src/viz3d/palette.py
src/viz3d/video.py
src/viz3d/assets/viewer.css
src/viz3d/assets/viewer.html
src/viz3d/assets/viewer.js
src/viz3d/vendor/OrbitControls.js
src/viz3d/vendor/three.min.js
tests/test_config.py
tests/test_context_preproc.py
tests/test_io.py
tests/test_logger.py
tests/test_mc_energy_terms.py
tests/test_mc_equivalence.py
tests/test_mc_properties.py
tests/test_md.py
tests/test_pipeline_e2e.py
tests/test_pipeline_slow.py
tests/test_regression.py
tests/test_replication_utils.py
tests/test_replikator.py
tests/test_run_dirs.py
tests/test_stats_viz.py
tests/test_video_bar.py