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Replace links with refs #406

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7e9b1ad
replace links with refs
lilyminium Mar 1, 2025
0044448
found more links
lilyminium Mar 1, 2025
d7cea50
make linter happy
lilyminium Mar 1, 2025
30f40b8
Update script to strip numpy typing and re-execute notebooks (#408)
lilyminium Mar 5, 2025
41e52af
add additional dependencies (#410)
lilyminium Mar 10, 2025
388606e
Add some preliminary guesser docs (#409)
lilyminium Mar 10, 2025
6834ed6
Update preparing_releases_and_hotfixes.rst (#413)
IAlibay Mar 12, 2025
5d74304
Add 2.9 release notes (#414)
IAlibay Mar 24, 2025
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17 changes: 7 additions & 10 deletions doc/source/examples/analysis/alignment_and_rms/README.rst
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Expand Up @@ -10,10 +10,13 @@ The :mod:`MDAnalysis.analysis.align` and :mod:`MDAnalysis.analysis.rms`
modules contain the functions used for aligning structures,
aligning trajectories, and calculating root mean squared quantities.

Demonstrations of alignment are in `align_structure <aligning_structure_to_another.ipynb>`__,
`align_trajectory_first <aligning_trajectory_to_frame.ipynb>`__, and `align_trajectory <aligning_trajectory.ipynb>`__. Another example of
generating an average structure from an alignment is demonstrated in
`rmsf <rmsf.ipynb>`__. Typically, trajectories need to be aligned for RMSD and
Demonstrations of alignment are in
:ref:`/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb`,
:ref:`/examples/analysis/alignment_and_rms/aligning_trajectory_to_frame.ipynb`,
and :ref:`/examples/analysis/alignment_and_rms/aligning_trajectory.ipynb`.
Another example of generating an average structure from an alignment is demonstrated in
:ref:`/examples/analysis/alignment_and_rms/rmsf.ipynb`.
Typically, trajectories need to be aligned for RMSD and
RMSF values to make sense.

.. note::
Expand All @@ -32,9 +35,3 @@ RMSF values to make sense.
/examples/analysis/alignment_and_rms/rmsd
/examples/analysis/alignment_and_rms/pairwise_rmsd
/examples/analysis/alignment_and_rms/rmsf

.. _rmsd: /examples/analysis/alignment_and_rms/rmsd.ipynb
.. _pairwise: /examples/analysis/alignment_and_rms/pairwise_rmsd.ipynb
.. _align_structure: aligning_structure_to_another.ipynb
.. _align_trajectory: aligning_trajectory.ipynb
.. _align_trajectory_frame: aligning_trajectory_to_frame.ipynb
8 changes: 4 additions & 4 deletions doc/source/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb
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"name": "stdout",
"output_type": "stream",
"text": [
"(21.712154435976014, 6.817293751703919)\n"
"(np.float64(21.712154435976014), 6.817293751703919)\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"(18.991465038265208, 16.603704620787127)\n"
"(np.float64(18.991465038265208), 16.603704620787127)\n"
]
}
],
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"metadata": {
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"display_name": "Python 3.9.15 ('mda-user-guide')",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -502,7 +502,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.15"
"version": "3.10.16"
},
"toc": {
"base_numbering": 1,
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6 changes: 5 additions & 1 deletion doc/source/examples/analysis/trajectory_similarity/README.rst
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Expand Up @@ -5,7 +5,11 @@
Trajectory similarity
======================

A molecular dynamics trajectory with :math:`N` atoms can be considered through a path through :math:`3N`-dimensional molecular configuration space. MDAnalysis contains a number of algorithms to compare the conformational ensembles of different trajectories. Most of these are in the :mod:`MDAnalysis.analysis.encore` module (:cite:`tiberti_encore_2015`) and compare estimated probability distributions to measure similarity. The `path similarity analysis </examples/analysis/trajectory_similarity/psa.html>`_ compares the RMSD between pairs of structures in conformation transition paths. :mod:`MDAnalysis.analysis.encore` also contains functions for evaluating the conformational convergence of a trajectory using the `similarity over conformation clusters </examples/analysis/trajectory_similarity/clustering_ensemble_similarity.html>`_ or `similarity in a reduced dimensional space </examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity.html>`_.
A molecular dynamics trajectory with :math:`N` atoms can be considered through a path through :math:`3N`-dimensional molecular configuration space. MDAnalysis contains a number of algorithms to compare the conformational ensembles of different trajectories. Most of these are in the :mod:`MDAnalysis.analysis.encore` module (:cite:`tiberti_encore_2015`) and compare estimated probability distributions to measure similarity.
The :ref:`/examples/analysis/trajectory_similarity/psa.ipynb` tutorial compares the RMSD between pairs of structures in conformation transition paths.
:mod:`MDAnalysis.analysis.encore` also contains functions for evaluating the conformational convergence of a trajectory using the
:ref:`similarity over conformation clusters </examples/analysis/trajectory_similarity/clustering_ensemble_similarity.ipynb>`
or :ref:`similarity in a reduced dimensional space </examples/analysis/trajectory_similarity/dimension_reduction_ensemble_similarity.ipynb>`.


.. toctree::
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66 changes: 27 additions & 39 deletions doc/source/examples/analysis/trajectory_similarity/harmonic_ensemble_similarity.ipynb
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Expand Up @@ -49,7 +49,17 @@
"shell.execute_reply": "2021-05-19T06:01:12.662787Z"
}
},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/lily/micromamba/envs/mda-user-guide-dev/lib/python3.10/site-packages/MDAnalysis/analysis/encore/__init__.py:45: DeprecationWarning: Deprecation in version 2.8.0\n",
"MDAnalysis.analysis.encore is deprecated in favour of the MDAKit mdaencore (https://www.mdanalysis.org/mdaencore/) and will be removed in MDAnalysis version 3.0.0.\n",
" warnings.warn(wmsg, category=DeprecationWarning)\n"
]
}
],
"source": [
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
Expand Down Expand Up @@ -96,7 +106,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/home/pbarletta/mambaforge/envs/mda-user-guide/lib/python3.9/site-packages/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behaviour will be changed in 3.0 to be the same as other readers\n",
"/Users/lily/micromamba/envs/mda-user-guide-dev/lib/python3.10/site-packages/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.\n",
" warnings.warn(\"DCDReader currently makes independent timesteps\"\n"
]
}
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"shell.execute_reply": "2021-05-19T06:03:04.424122Z"
}
},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/lily/micromamba/envs/mda-user-guide-dev/lib/python3.10/site-packages/MDAnalysis/coordinates/memory.py:535: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911\n",
" warnings.warn(\n"
]
}
],
"source": [
"hes, details = encore.hes([u1, u2, u3, u4],\n",
" select='backbone',\n",
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"name": "stdout",
"output_type": "stream",
"text": [
" 0.0 24955.7 1879874.5 145622.3 \n",
" 0.0 24955.7 1879874.9 145622.3 \n",
" 24955.7 0.0 1659867.5 161102.3 \n",
" 1879874.5 1659867.5 0.0 9900092.7 \n",
" 145622.3 161102.3 9900092.7 0.0 \n"
" 1879874.9 1659867.5 0.0 9900093.4 \n",
" 145622.3 161102.3 9900093.4 0.0 \n"
]
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],
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"\n",
"[4] Beckstein O, Denning EJ, Perilla JR, Woolf TB. Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions. *J Mol Biol*. 2009;394(1):160–176. [doi:10.1016/j.jmb.2009.09.009](https://dx.doi.org/10.1016%2Fj.jmb.2009.09.009)\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## References\n",
"\n",
"[1] Oliver Beckstein, Elizabeth&nbsp;J. Denning, Juan&nbsp;R. Perilla, and Thomas&nbsp;B. Woolf.\n",
"Zipping and <span class=\"bibtex-protected\">Unzipping</span> of <span class=\"bibtex-protected\">Adenylate</span> <span class=\"bibtex-protected\">Kinase</span>: <span class=\"bibtex-protected\">Atomistic</span> <span class=\"bibtex-protected\">Insights</span> into the <span class=\"bibtex-protected\">Ensemble</span> of <span class=\"bibtex-protected\">Open</span>↔<span class=\"bibtex-protected\">Closed</span> <span class=\"bibtex-protected\">Transitions</span>.\n",
"<em>Journal of Molecular Biology</em>, 394(1):160–176, November 2009.\n",
"00107.\n",
"URL: <a href=\"https://linkinghub.elsevier.com/retrieve/pii/S0022283609011164\">https://linkinghub.elsevier.com/retrieve/pii/S0022283609011164</a>, <a href=\"https://doi.org/10.1016/j.jmb.2009.09.009\">doi:10.1016/j.jmb.2009.09.009</a>.\n",
"\n",
"[2] Richard&nbsp;J. Gowers, Max Linke, Jonathan Barnoud, Tyler J.&nbsp;E. Reddy, Manuel&nbsp;N. Melo, Sean&nbsp;L. Seyler, Jan Domański, David&nbsp;L. Dotson, Sébastien Buchoux, Ian&nbsp;M. Kenney, and Oliver Beckstein.\n",
"<span class=\"bibtex-protected\">MDAnalysis</span>: <span class=\"bibtex-protected\">A</span> <span class=\"bibtex-protected\">Python</span> <span class=\"bibtex-protected\">Package</span> for the <span class=\"bibtex-protected\">Rapid</span> <span class=\"bibtex-protected\">Analysis</span> of <span class=\"bibtex-protected\">Molecular</span> <span class=\"bibtex-protected\">Dynamics</span> <span class=\"bibtex-protected\">Simulations</span>.\n",
"<em>Proceedings of the 15th Python in Science Conference</em>, pages 98–105, 2016.\n",
"00152.\n",
"URL: <a href=\"https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html\">https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html</a>, <a href=\"https://doi.org/10.25080/Majora-629e541a-00e\">doi:10.25080/Majora-629e541a-00e</a>.\n",
"\n",
"[3] Naveen Michaud-Agrawal, Elizabeth&nbsp;J. Denning, Thomas&nbsp;B. Woolf, and Oliver Beckstein.\n",
"<span class=\"bibtex-protected\">MDAnalysis</span>: <span class=\"bibtex-protected\">A</span> toolkit for the analysis of molecular dynamics simulations.\n",
"<em>Journal of Computational Chemistry</em>, 32(10):2319–2327, July 2011.\n",
"00778.\n",
"URL: <a href=\"http://doi.wiley.com/10.1002/jcc.21787\">http://doi.wiley.com/10.1002/jcc.21787</a>, <a href=\"https://doi.org/10.1002/jcc.21787\">doi:10.1002/jcc.21787</a>.\n",
"\n",
"[4] Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, and Kresten Lindorff-Larsen.\n",
"<span class=\"bibtex-protected\">ENCORE</span>: <span class=\"bibtex-protected\">Software</span> for <span class=\"bibtex-protected\">Quantitative</span> <span class=\"bibtex-protected\">Ensemble</span> <span class=\"bibtex-protected\">Comparison</span>.\n",
"<em>PLOS Computational Biology</em>, 11(10):e1004415, October 2015.\n",
"00031.\n",
"URL: <a href=\"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004415\">https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004415</a>, <a href=\"https://doi.org/10.1371/journal.pcbi.1004415\">doi:10.1371/journal.pcbi.1004415</a>."
]
}
],
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"display_name": "Python 3.9.15 ('mda-user-guide')",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -371,7 +359,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.15"
"version": "3.10.16"
},
"toc": {
"base_numbering": 1,
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