.coverage
.pre-commit-config.yaml
AGENTS.md
CHANGELOG.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
USAGE.md
mypy.out
poetry.lock
pyproject.toml
requirements-dev.txt
requirements.txt
temperatures_suggested.json
tox.ini
typelog.txt
.github/workflows/ci.yml
.github/workflows/publish.yml
changelog.d/20250812_150601_61950289+kGorze_development.md
changelog.d/20250826_094526_solvation_option.md
example_programs/all_capabilities_demo.py
example_programs/find_conformations_with_msm.py
example_programs/free_energy_landscape.py
example_programs/reproducible_build.py
example_programs/run_shards_then_build.py
example_programs/verify_pmarlo.py
example_programs/programs_outputs/sharded_build/shards/shard_0002.json
src/pmarlo/__init__.py
src/pmarlo/_typing.py
src/pmarlo/_version.py
src/pmarlo/api.py
src/pmarlo/config.py
src/pmarlo/main.py
src/pmarlo/pipeline.py
src/pmarlo/progress.py
src/pmarlo/py.typed
src/pmarlo/results.py
src/pmarlo.egg-info/PKG-INFO
src/pmarlo.egg-info/SOURCES.txt
src/pmarlo.egg-info/dependency_links.txt
src/pmarlo.egg-info/entry_points.txt
src/pmarlo.egg-info/requires.txt
src/pmarlo.egg-info/top_level.txt
src/pmarlo/analysis/__init__.py
src/pmarlo/analysis/ck.py
src/pmarlo/cluster/__init__.py
src/pmarlo/cluster/micro.py
src/pmarlo/cv/base.py
src/pmarlo/cv/deeptica.py
src/pmarlo/cv/pairs.py
src/pmarlo/data/aggregate.py
src/pmarlo/data/emit.py
src/pmarlo/data/shard.py
src/pmarlo/engine/__init__.py
src/pmarlo/engine/build.py
src/pmarlo/experiments/__init__.py
src/pmarlo/experiments/benchmark_utils.py
src/pmarlo/experiments/cli.py
src/pmarlo/experiments/kpi.py
src/pmarlo/experiments/msm.py
src/pmarlo/experiments/replica_exchange.py
src/pmarlo/experiments/simulation.py
src/pmarlo/experiments/suite.py
src/pmarlo/experiments/utils.py
src/pmarlo/features/__init__.py
src/pmarlo/features/base.py
src/pmarlo/features/builtins.py
src/pmarlo/fes/__init__.py
src/pmarlo/fes/ramachandran.py
src/pmarlo/fes/surfaces.py
src/pmarlo/io/__init__.py
src/pmarlo/io/trajectory.py
src/pmarlo/manager/__init__.py
src/pmarlo/manager/checkpoint_manager.py
src/pmarlo/markov_state_model/__init__.py
src/pmarlo/markov_state_model/_base.py
src/pmarlo/markov_state_model/_ck.py
src/pmarlo/markov_state_model/_clustering.py
src/pmarlo/markov_state_model/_estimation.py
src/pmarlo/markov_state_model/_export.py
src/pmarlo/markov_state_model/_features.py
src/pmarlo/markov_state_model/_fes.py
src/pmarlo/markov_state_model/_its.py
src/pmarlo/markov_state_model/_loading.py
src/pmarlo/markov_state_model/_plots.py
src/pmarlo/markov_state_model/_states.py
src/pmarlo/markov_state_model/_tica.py
src/pmarlo/markov_state_model/_tram.py
src/pmarlo/markov_state_model/enhanced_msm.py
src/pmarlo/markov_state_model/pipeline.py
src/pmarlo/markov_state_model/utils.py
src/pmarlo/protein/__init__.py
src/pmarlo/protein/protein.py
src/pmarlo/reduce/__init__.py
src/pmarlo/reduce/reducers.py
src/pmarlo/replica_exchange/__init__.py
src/pmarlo/replica_exchange/config.py
src/pmarlo/replica_exchange/demux_metadata.py
src/pmarlo/replica_exchange/diagnostics.py
src/pmarlo/replica_exchange/exchange_engine.py
src/pmarlo/replica_exchange/platform_selector.py
src/pmarlo/replica_exchange/replica_exchange.py
src/pmarlo/replica_exchange/system_builder.py
src/pmarlo/replica_exchange/trajectory.py
src/pmarlo/reporting/__init__.py
src/pmarlo/reporting/export.py
src/pmarlo/reporting/plots.py
src/pmarlo/simulation/__init__.py
src/pmarlo/simulation/simulation.py
src/pmarlo/states/__init__.py
src/pmarlo/states/msm_bridge.py
src/pmarlo/states/picker.py
src/pmarlo/transform/__init__.py
src/pmarlo/transform/apply.py
src/pmarlo/transform/plan.py
src/pmarlo/transform/planner.py
src/pmarlo/transform/runner.py
src/pmarlo/utils/integrator.py
src/pmarlo/utils/msm_utils.py
src/pmarlo/utils/naming.py
src/pmarlo/utils/progress.py
src/pmarlo/utils/replica_utils.py
src/pmarlo/utils/seed.py
tests/__init__.py
tests/conftest.py
tests/temperatures_suggested.json
tests/test_aggregate_and_build.py
tests/test_bootstrap_counts.py
tests/test_build_api.py
tests/test_candidate_lag_ladder.py
tests/test_ck.py
tests/test_ck_fallback.py
tests/test_ck_tau_selection.py
tests/test_cluster_micro.py
tests/test_emit_shards.py
tests/test_experiments_kpi.py
tests/test_experiments_paths.py
tests/test_experiments_seed.py
tests/test_feature_extraction_seed.py
tests/test_features.py
tests/test_fes.py
tests/test_fes_pair_selection.py
tests/test_fes_periodic.py
tests/test_fes_result_api.py
tests/test_frame_accounting.py
tests/test_integration.py
tests/test_io_logging.py
tests/test_iterload_stream.py
tests/test_its_math.py
tests/test_ladder_retuning.py
tests/test_pipeline.py
tests/test_plan_serialization.py
tests/test_progress_reporting.py
tests/test_protein.py
tests/test_ramachandran.py
tests/test_ramachandran_wiring.py
tests/test_seed_reproducibility.py
tests/test_shard_io.py
tests/test_simulation.py
tests/test_temperature_ladder.py
tests/test_transform_reporter.py
tests/test_trig_expand_mapping.py
tests/data/3gd8-fixed.pdb
tests/data/3gd8.pdb
tests/data/traj.dcd
tests/integration/__init__.py
tests/integration/test_checkpoint_manager_retry.py
tests/integration/replica_exchange/__init__.py
tests/integration/replica_exchange/test_demux_metadata.py
tests/integration/replica_exchange/test_integration.py
tests/integration/replica_exchange/test_small_system.py
tests/reporting/test_export.py
tests/reporting/test_plots.py
tests/unit/__init__.py
tests/unit/test_results_serialization.py
tests/unit/test_states.py
tests/unit/cv/test_deeptica.py
tests/unit/cv/test_pairs.py
tests/unit/data/test_shard_bias.py
tests/unit/engine/test_learn_cv_integration.py
tests/unit/markov_state_model/__init__.py
tests/unit/markov_state_model/test_deeptime_backend.py
tests/unit/markov_state_model/test_its_plateau.py
tests/unit/markov_state_model/test_lag_window_formatter.py
tests/unit/markov_state_model/test_markov_state_model.py
tests/unit/markov_state_model/test_two_state_msm.py
tests/unit/reduce/test_reducers.py
tests/unit/replica_exchange/__init__.py
tests/unit/replica_exchange/test_checkpointing.py
tests/unit/replica_exchange/test_demux_integrity.py
tests/unit/replica_exchange/test_exchange_algorithm.py
tests/unit/replica_exchange/test_initialization.py
tests/unit/replica_exchange/test_runtime_budgeter.py
tests/unit/utils/test_msm_checks.py
tests/unit/utils/test_naming.py
utilities/lines.py