MasterMSM 2.0.1__tar.gz

mastermsm-2.0.1/CHANGELOG.md

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+# Changelog
+
+## [Unreleased]
+
+## [2.0.1] - 2026-11-15
+
+First release distributed on PyPI (`pip install MasterMSM`).
+
+### Packaging
+- `setup.py` replaced by `pyproject.toml`; the licence is stated as
+  GPL-2.0-or-later; extras `hdbscan` and `test`.
+- The test suite is installed with the package and runs with
+  `pytest --pyargs mastermsm`. Test trajectories are downloaded to
+  `$MASTERMSM_TEST_DATA`, the package folder or a per-user cache; tests
+  that need them are skipped if the download fails.
+- Releases are uploaded to PyPI from GitHub Actions.
+
+### Fixes
+- `test_interactive_stdin` no longer fails when IPython is not installed.
+
+### Fixes that change results
+- `FEWSM.map_trajectory`: frames in microstates outside the connected
+  set were silently dropped, joining the frames on either side. They are
+  now removed only at the start of a trajectory; elsewhere they inherit
+  the macrostate of the previous frame. A trajectory that never visits
+  the connected set is left out with a warning.
+
+## [2.0.0] - 2026-11-15
+
+Major release. The trajectory API has been redesigned and several fixes
+change numerical results, so analyses run with 1.x will not reproduce
+exactly. See "Breaking changes" and "Fixes that change results".
+
+### Breaking changes
+- `trajectory`: new feature -> dimensionality reduction -> discretization
+  workflow with the `Featurizer`, `DimRed` and `Discretizer` classes
+  (plus `Discretization`). `MultiTimeSeries` and its `joint_discretize*`
+  methods are removed; multiple trajectories are handled by the new classes.
+- `TimeSeries`: the discrete trajectory attribute is `distraj` (was
+  `dtraj`); `discretize` now takes `states`, `bounds` and `check`
+  (clustering moved to `Discretizer.kmeans` / `Discretizer.hdbscan`).
+- `MSM`: `do_count`/`calc_count_multi` replaced by `calc_count(nproc, sym)`;
+  `calc_eigsK`/`calc_eigsT` replaced by `calc_evals(neigs, evecs, errors)`;
+  `do_trans` computes eigenvectors by default; `do_rate` no longer takes
+  `evecs`; `boots(neigs, seed, nboots, block)` bootstraps trajectory blocks.
+- `SuperMSM`: `do_msm(lagts)` takes a list of lag times;
+  `convergence_test` and `ck_test` signatures changed; new `calc_evals`.
+- Python >= 3.10 required.
+
+### New features
+- `DimRed.doTICA`: time-lagged independent component analysis, alongside
+  `DimRed.doPCA` and `whiten`.
+- `Featurizer.add_torsions` (optional shift and sin/cos) and `add_contacts`.
+- `Discretizer.kmeans` and `Discretizer.hdbscan` (HDBSCAN is an optional
+  dependency, imported only when used; install with `pip install
+  ".[hdbscan]"`). It uses the standalone `hdbscan` package:
+  `sklearn.cluster.HDBSCAN` lacks `approximate_predict` and gives
+  different clusters for the same parameters.
+- Discretization protocols to compare discretizations of the same data.
+- Interactive check of Ramachandran state bounds for Buchete-Hummer
+  assignment (opt in with `check=True`).
+- `SuperMSM.ck_test` (Chapman-Kolmogorov test) implemented.
+- `examples/download_data.py` fetches model-potential data from OSF.
+- New example notebooks: TICA and discretization comparison for the
+  alanine pentapeptide; all example notebooks re-executed.
+
+### Fixes that change results
+- Relaxation times are computed from |lambda| of the transition matrix.
+- Leading unassigned frames in Buchete-Hummer assignment are dropped.
+- MLPB (`do_rate(method='MLPB')`): annealing schedule (no divide-by-zero),
+  Monte Carlo moves now reach all rates, rate step of 0.1 x mean positive
+  rate, counts restricted to the connected set.
+- Bootstrap: largest strongly connected component in each sample, seeding
+  per worker (reproducible errors with `seed`), fragment construction,
+  symmetrization and averaging of timescales across samples.
+- `FEWSM`: eigenvectors, trajectory mapping and metastability.
+- Complex eigenvalues/populations in `tauT`/`peqT`; `tauK`/`peqK` set after
+  `do_rate`; `acf_mode` zero-lag offset.
+- Singular C(0) is rejected in `DimRed.doTICA`.
+
+### Other fixes
+- MLPB likelihood uses `numpy.linalg.eigh` for the symmetrised rate matrix
+  (complex output from `eig` with NumPy >= 2.5).
+- NumPy 2 compatibility (`np.float`, `np.matrix` removed).
+
+### Removed
+- Example notebooks that no longer ran: `ala_dipeptide_discretize` and
+  `ala_pentapeptide_featurize` (unfinished drafts; their workflows are
+  covered by `ala_dipeptide`, `ala_pentapeptide_tica` and
+  `discretization_comparison`) and the Müller potential examples (their
+  data were not distributed).
+
+### Infrastructure
+- GitHub Actions CI on Linux and macOS, Python 3.10-3.12 (replaces Travis).
+- Test suite re-enabled and extended (MSM, MLPB, fewsm, TICA, protocols);
+  coverage reported to Codecov.
+- ReadTheDocs configuration; README, docs and contributors updated.
+
+### Note on version numbers
+Tag `v1.0.1` (June 2026) was created after `v1.2` (May 2022) and
+contains later code than `v1.2`. 2.0.0 supersedes both.
+
+## [1.2] - 2022-05-02
+## [1.1.1] - 2019-04-30
+## [1.1.0] - 2019-04-29
+## [1.0.0] - 2017-11-21
+First release.

mastermsm-2.0.1/LICENSE

@@ -0,0 +1,340 @@
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+

mastermsm-2.0.1/MANIFEST.in

@@ -0,0 +1,4 @@
+include CHANGELOG.md
+prune mastermsm/test/data
+global-exclude *.py[cod] __pycache__ .DS_Store .ipynb_checkpoints
+exclude mastermsm/test/index.html mastermsm/tester.ipynb

mastermsm-2.0.1/MasterMSM.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: MasterMSM
+Version: 2.0.1
+Summary: Algorithms to construct master equation / Markov state models
+Author-email: David De Sancho <daviddesancho@gmail.com>
+License-Expression: GPL-2.0-or-later
+Project-URL: Homepage, https://github.com/BioKT/MasterMSM
+Project-URL: Documentation, https://mastermsm.readthedocs.io
+Project-URL: Changelog, https://github.com/BioKT/MasterMSM/blob/master/CHANGELOG.md
+Keywords: markov state model,master equation,molecular dynamics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: networkx
+Requires-Dist: mdtraj
+Requires-Dist: scikit-learn
+Provides-Extra: hdbscan
+Requires-Dist: hdbscan; extra == "hdbscan"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: ipython; extra == "test"
+Dynamic: license-file
+
+[![CI](https://github.com/BioKT/MasterMSM/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/BioKT/MasterMSM/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/BioKT/MasterMSM/branch/master/graph/badge.svg)](https://codecov.io/gh/BioKT/MasterMSM)
+[![Documentation Status](https://readthedocs.org/projects/mastermsm/badge/?version=latest)](https://mastermsm.readthedocs.io/en/latest/?badge=latest)
+
+MasterMSM
+=========
+MasterMSM is a Python package for building Markov state models (MSMs)
+from molecular dynamics trajectories, using a formulation based on the
+chemical master equation. Besides the usual transition matrix, it
+estimates the rate matrix of the model, which gives direct access to
+rate coefficients, committors and reactive fluxes.
+
+Full documentation is at [mastermsm.readthedocs.io](https://mastermsm.readthedocs.io).
+
+Features
+--------
+*   **Trajectory handling**: read MD trajectories through
+    [MDTraj](https://mdtraj.org) or discrete state trajectories from
+    file.
+*   **Featurization and dimensionality reduction**: backbone torsions
+    and contacts; PCA and TICA.
+*   **Discretization**: assignment to Ramachandran basins with
+    transition-based assignment (suited to small peptides), k-means
+    and HDBSCAN clustering. Different protocols can be run on the same
+    data and compared.
+*   **Model estimation**: count and transition matrices at any lag
+    time; rate matrices from a Taylor expansion or from the maximum
+    likelihood propagator-based (MLPB) method; bootstrap errors for
+    relaxation times and equilibrium populations.
+*   **Validation**: convergence of relaxation times with lag time,
+    Chapman-Kolmogorov test, autocorrelation functions of the
+    eigenmodes.
+*   **Kinetics**: committors, reactive fluxes and rates between sets of
+    states; sensitivity analysis of the network.
+*   **Coarse-graining**: few-state models from the eigenvectors of the
+    MSM.
+
+Installation
+------------
+MasterMSM requires Python >= 3.10 and is installed from
+[PyPI](https://pypi.org/project/MasterMSM/) with `pip`:
+
+    pip install MasterMSM
+
+To work on the code, install it from source instead:
+
+    git clone https://github.com/BioKT/MasterMSM
+    cd MasterMSM
+    pip install -e .
+
+The dependencies are installed automatically by `pip`: numpy, scipy,
+matplotlib, networkx, [mdtraj](https://mdtraj.org) and scikit-learn.
+If you use conda, you may prefer to install them from conda-forge
+first:
+
+    conda install -c conda-forge numpy scipy matplotlib \
+        networkx mdtraj scikit-learn
+
+HDBSCAN clustering additionally needs the optional
+[hdbscan](https://github.com/scikit-learn-contrib/hdbscan) package
+(`pip install "MasterMSM[hdbscan]"`, or `pip install hdbscan`).
+
+Quick start
+-----------
+The script below builds an MSM for the alanine dipeptide from a short
+MD trajectory (downloaded from [OSF](https://osf.io/a2vc7) on first
+use).
+
+```python
+from mastermsm.trajectory import traj
+from mastermsm.msm import msm
+from mastermsm.fewsm import fewsm
+from mastermsm.test import download_data as dd
+
+if __name__ == "__main__":
+    # 1. Load the trajectory and assign frames to Ramachandran states
+    dd.download_osf_alaTB()
+    tr = traj.TimeSeries(top=dd._DATA_DIR + "/alaTB.gro",
+                         xtc=dd._DATA_DIR + "/alaTB.xtc")
+    tr.discretize(states=["A", "E", "L"])
+    tr.find_keys()
+
+    # 2. Build the MSM at a lag time of 10 ps (units of the trajectory)
+    smsm = msm.SuperMSM([tr])
+    lagt = 10
+    smsm.do_msm(lagt)
+    model = smsm.msms[lagt]
+    model.do_trans()          # transition matrix and its eigenvalues
+    model.boots()             # bootstrap errors
+    print(model.keep_keys)    # states in the model: ['A', 'E', 'L']
+    print(model.tauT)         # relaxation times, ~794 and ~55 ps
+    print(model.tau_std)
+    print(model.peqT)         # equilibrium populations
+
+    # 3. Rate matrix, committors and flux between E and A
+    model.do_rate()           # method='Taylor' (default) or 'MLPB'
+    print(model.rate)
+    model.do_pfold(FF=["A"], UU=["E"])
+    print(model.pfold, model.kf)
+
+    # 4. Coarse-grain into a two-state model
+    two_state = fewsm.FEWSM(parent=model, N=2)
+    print(two_state.macros)
+
+    # 5. Validate: relaxation times as a function of lag time
+    smsm.convergence_test(time=[5, 10, 20, 50, 100], error=True)
+    for lt in sorted(smsm.msms):
+        print(lt, smsm.msms[lt].tauT)
+```
+
+MasterMSM uses `multiprocessing`, so scripts need the
+`if __name__ == "__main__":` guard shown above. This is not required
+in a Jupyter notebook.
+
+Examples
+--------
+The [examples](examples) folder contains Jupyter notebooks:
+
+| Folder | Content |
+|--------|---------|
+| [alanine_dipeptide](examples/alanine_dipeptide) | Complete workflow on the simplest peptide model: discretization, MSM, validation, rate matrix (Taylor and MLPB) |
+| [alanine_pentapeptide](examples/alanine_pentapeptide) | Featurization, TICA and comparison of discretization protocols |
+| [bistable_potential](examples/bistable_potential) | Brownian dynamics on one and two dimensional two-state potentials |
+| [schutte_potential](examples/schutte_potential) | Brownian dynamics on the one dimensional Schütte potential |
+
+Most of the data are hosted at [OSF](https://osf.io/a2vc7); each
+notebook says where its data come from. The Brownian dynamics data
+for the bistable and Schütte potentials can be fetched with
+
+    python examples/download_data.py
+
+Testing
+-------
+The tests use `pytest` and download a small amount of MD data on the
+first run:
+
+    pip install pytest
+    pytest --pyargs mastermsm
+
+Contributing
+------------
+Development takes place on the `develop` branch; `master` holds the
+releases. Bug reports and pull requests (against `develop`) are welcome
+on [GitHub](https://github.com/BioKT/MasterMSM/issues).
+
+Citation
+--------
+If you use MasterMSM in your work, please cite:
+
+    @article{mastermsm,
+    author = "David De Sancho and Anne Aguirre",
+    title = "{MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics}",
+    year = "2019",
+    month = "6",
+    journal = "J. Chem. Inf. Model.",
+    url = "https://doi.org/10.1021/acs.jcim.9b00468",
+    doi = "10.1021/acs.jcim.9b00468"
+    }
+
+Contributors
+------------
+*   David De Sancho
+*   Anne Aguirre
+*   Ion Mitxelena
+
+License
+-------
+MasterMSM is distributed under the GNU General Public License,
+version 2. See [LICENSE](LICENSE).

mastermsm-2.0.1/MasterMSM.egg-info/SOURCES.txt

@@ -0,0 +1,25 @@
+CHANGELOG.md
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+MasterMSM.egg-info/PKG-INFO
+MasterMSM.egg-info/SOURCES.txt
+MasterMSM.egg-info/dependency_links.txt
+MasterMSM.egg-info/requires.txt
+MasterMSM.egg-info/top_level.txt
+mastermsm/__init__.py
+mastermsm/fewsm/__init__.py
+mastermsm/fewsm/fewsm.py
+mastermsm/fewsm/fewsm_lib.py
+mastermsm/msm/__init__.py
+mastermsm/msm/msm.py
+mastermsm/msm/msm_lib.py
+mastermsm/test/__init__.py
+mastermsm/test/download_data.py
+mastermsm/test/test_fewsm.py
+mastermsm/test/test_msm.py
+mastermsm/test/test_trajectory.py
+mastermsm/trajectory/__init__.py
+mastermsm/trajectory/traj.py
+mastermsm/trajectory/traj_lib.py