.. -*- coding: utf-8 -*- .. note: make sure that no lines accidentaly start with a single character .. followed by a period: reST interprets it as an enumerated list and .. messes up the formatting .. The references are accessible globally; you can cite these papers anywhere .. in the docs. .. _references: ************ References ************ MDAnalysis and the included algorithms are scientific software that are described in academic publications. **Please cite these papers when you use MDAnalysis in published work.** It is possible to :ref:`automatically generate a list of references ` for any program that uses MDAnalysis. This list (in common reference manager formats) contains the citations associated with the specific algorithms and libraries that were used in the program. Citations for the whole MDAnalysis library ========================================== When using MDAnalysis in published work, please cite :cite:p:`Michaud-Agrawal2011` and :cite:p:`Gowers2016`. (We are currently asking you to cite *both* papers if at all possible because the 2016 paper describes many updates to the original 2011 paper and neither paper on its own provides a comprehensive description of the library. We will publish a complete self-contained paper with the upcoming 1.0 release of MDAnalysis, which will then supersede these two citations.) .. bibliography:: :filter: False :style: MDA Michaud-Agrawal2011 Gowers2016 .. _references-components: Citations for included algorithms and modules ============================================= If you use the RMSD calculation (:mod:`MDAnalysis.analysis.rms`) or alignment code (:mod:`MDAnalysis.analysis.align`) that uses the :mod:`~MDAnalysis.lib.qcprot` module please also cite :cite:p:`a-Theobald2005` and :cite:p:`a-Liu2010`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Liu2010 Theobald2005 If you use the HELANAL_ algorithm in :mod:`MDAnalysis.analysis.helix_analysis` please cite :cite:p:`a-Bansal2000,a-Sugeta1967`. .. _HELANAL: https://web.archive.org/web/20100818185943/http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Bansal2000 Sugeta1967 If you use the GNM trajectory analysis code in :mod:`MDAnalysis.analysis.gnm` please cite :cite:p:`a-Hall2007`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Hall2007 If you use the water analysis code in :mod:`MDAnalysis.analysis.waterdynamics` please cite :cite:p:`a-ArayaSecchi2014`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ ArayaSecchi2014 If you use the Path Similarity Analysis (PSA) code in :mod:`MDAnalysis.analysis.psa` please :cite:p:`a-Seyler2015`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Seyler2015 If you use the implementation of the ENCORE ensemble analysis in :mod:`MDAnalysis.analysis.encore` please cite :cite:p:`a-Tiberti2015`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Tiberti2015 If you use the streamline visualization in :mod:`MDAnalysis.visualization.streamlines` and :mod:`MDAnalysis.visualization.streamlines_3D` please cite :cite:p:`a-Chavent2014`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Chavent2014 If you use the hydrogen bond analysis code in :mod:`MDAnalysis.analysis.hydrogenbonds.hbond_analysis` please cite :cite:p:`a-Smith2019`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Smith2019 If you use :meth:`~MDAnalysis.analysis.pca.PCA.rmsip` or :func:`~MDAnalysis.analysis.pca.rmsip` please cite :cite:p:`a-Amadei1999` and :cite:p:`a-Leo-Macias2005`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Amadei1999 Leo-Macias2005 If you use :meth:`~MDAnalysis.analysis.pca.PCA.cumulative_overlap` or :func:`~MDAnalysis.analysis.pca.cumulative_overlap` please cite :cite:p:`a-Yang2008`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Yang2008 If you use the Mean Squared Displacement analysis code in :mod:`MDAnalysis.analysis.msd` please cite :cite:p:`a-Calandrini2011` and :cite:p:`a-Buyl2018`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Calandrini2011 Buyl2018 If you calculate shape parameters using :meth:`~MDAnalysis.core.group.AtomGroup.shape_parameter`, :meth:`~MDAnalysis.core.group.ResidueGroup.shape_parameter`, :meth:`~MDAnalysis.core.group.SegmentGroup.shape_parameter`, or if you calculate asphericities using :meth:`~MDAnalysis.core.group.AtomGroup.asphericity`, :meth:`~MDAnalysis.core.group.ResidueGroup.asphericity`, :meth:`~MDAnalysis.core.group.SegmentGroup.asphericity`, please cite :cite:p:`a-Dima2004`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Dima2004 If you use use the dielectric analysis code in :class:`~MDAnalysis.analysis.dielectric.DielectricConstant` please cite :cite:p:`a-Neumann1983`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ Neumann1983 If you use H5MD files with :mod:`MDAnalysis.coordinates.H5MD`, please cite :cite:p:`a-deBuyl2014` and :cite:p:`a-Jakupovic2021`. .. bibliography:: :filter: False :style: MDA :keyprefix: a- :labelprefix: ᵃ deBuyl2014 Jakupovic2021 .. _citations-using-duecredit: Citations using Duecredit ========================= Citations can be automatically generated using duecredit_, depending on the packages used. Duecredit is easy to install via ``pip``. Simply type: .. code-block:: bash pip install duecredit duecredit_ will remain an optional dependency, i.e. any code using MDAnalysis will work correctly even without duecredit installed. A list of citations for ``yourscript.py`` can be obtained using simple commands. .. code-block:: bash cd /path/to/yourmodule python -m duecredit yourscript.py or set the environment variable :envvar:`DUECREDIT_ENABLE` .. code-block:: bash DUECREDIT-ENABLE=yes python yourscript.py Once the citations have been extracted (to a hidden file in the current directory), you can use the :program:`duecredit` program to export them to different formats. For example, one can display them in BibTeX format, using: .. code-block:: bash duecredit summary --format=bibtex **Please cite your use of MDAnalysis and the packages and algorithms that it uses. Thanks!** .. _duecredit: https://github.com/duecredit/duecredit