From 9a3aa466e43cc0cd359157cfb47bdae2484da55e Mon Sep 17 00:00:00 2001 From: github-actions Date: Sun, 14 Jul 2024 03:11:03 +0000 Subject: [PATCH] deploy: f3f13dcc5a31d6f618b91bd9dcd0df3bcf079e69 --- .doctrees/environment.pickle | Bin 3375516 -> 3375492 bytes .doctrees/mdakits.doctree | Bin 66313 -> 66301 bytes .doctrees/propkatraj.doctree | Bin 11576 -> 11564 bytes PathSimAnalysis.html | 28 ++-- ProLIF.html | 28 ++-- _sources/mdakits.rst.txt | 256 ++++++++++++++++---------------- _sources/propkatraj.rst.txt | 4 +- about.html | 4 +- lipyds.html | 28 ++-- maicos.html | 34 ++--- mda-tui.html | 32 ++-- mdachecker.html | 28 ++-- mdacli.html | 24 +-- mdaencore.html | 28 ++-- mdahole2.html | 28 ++-- mdakit-sasa.html | 28 ++-- mdakits.html | 120 +++++++-------- membrane-curvature.html | 34 ++--- openmm-mdanalysis-reporter.html | 34 ++--- propkatraj.html | 38 ++--- solvation-analysis.html | 32 ++-- spyrmsdkit.html | 28 ++-- transport-analysis.html | 34 ++--- waterdynamics.html | 24 +-- 24 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+181,8 @@

Installation instructions - - + +
diff --git a/ProLIF.html b/ProLIF.html index 9cb70850..1e2e0252 100644 --- a/ProLIF.html +++ b/ProLIF.html @@ -43,8 +43,8 @@ - - + + @@ -87,26 +87,26 @@

MDAKit Registry

@@ -182,8 +182,8 @@

Installation instructions - - + +
diff --git a/_sources/mdakits.rst.txt b/_sources/mdakits.rst.txt index 24789411..1d3a7949 100644 --- a/_sources/mdakits.rst.txt +++ b/_sources/mdakits.rst.txt @@ -17,46 +17,54 @@ Each of the MDAKits in the following table links to a page with more details abo - Keywords - Authors - CI badges - * - :ref:`membrane-curvature` - - membranes, curvature, molecular dynamics - - `membrane-curvature authors`_ - - |membrane-curvature_latest| |membrane-curvature_develop| * - :ref:`spyrmsdkit` - spyrmsd, RMSD, symmetry-corrected RMSD, drug discovery - `spyrmsdkit authors`_ - |spyrmsdkit_latest| |spyrmsdkit_develop| - * - :ref:`maicos` - - Molecular Dynamics, Confined Systems - - `maicos authors`_ - - |maicos_latest| |maicos_develop| - * - :ref:`mdaencore` - - ensemble, similarity, covariance, PCA - - `mdaencore authors`_ - - |mdaencore_latest| |mdaencore_develop| - * - :ref:`PathSimAnalysis` - - similarity, paths, metrics - - `PathSimAnalysis authors`_ - - |PathSimAnalysis_latest| |PathSimAnalysis_develop| + * - :ref:`transport-analysis` + - transport properties, molecular dynamics + - `transport-analysis authors`_ + - |transport-analysis_latest| |transport-analysis_develop| + * - :ref:`propkatraj` + - pKa, protein + - `propkatraj authors`_ + - |propkatraj_latest| |propkatraj_develop| + * - :ref:`openmm-mdanalysis-reporter` + - OpenMM, Reporters + - `openmm-mdanalysis-reporter authors`_ + - |openmm-mdanalysis-reporter_latest| |openmm-mdanalysis-reporter_develop| * - :ref:`mdakit-sasa` - SASA, FreeSASA, ShrakeRupley, LeeRichards - `mdakit-sasa authors`_ - |mdakit-sasa_latest| |mdakit-sasa_develop| - * - :ref:`mdachecker` - - structure analysis, conformation checks - - IAlibay - - |mdachecker_latest| |mdachecker_develop| - * - :ref:`solvation-analysis` - - chemistry, electrolytes, solvation structure - - orionarcher, hmacdope, laurlee, IAlibay - - |solvation-analysis_latest| |solvation-analysis_develop| * - :ref:`mdahole2` - pores, ion channels, transporters, HOLE - `mdahole2 authors`_ - |mdahole2_latest| |mdahole2_develop| + * - :ref:`mdaencore` + - ensemble, similarity, covariance, PCA + - `mdaencore authors`_ + - |mdaencore_latest| |mdaencore_develop| + * - :ref:`mda-tui` + - transformations, TUI + - `mda-tui authors`_ + - |mda-tui_latest| |mda-tui_develop| + * - :ref:`PathSimAnalysis` + - similarity, paths, metrics + - `PathSimAnalysis authors`_ + - |PathSimAnalysis_latest| |PathSimAnalysis_develop| * - :ref:`lipyds` - lipids, membranes - lilyminium - |lipyds_latest| |lipyds_develop| + * - :ref:`mdachecker` + - structure analysis, conformation checks + - IAlibay + - |mdachecker_latest| |mdachecker_develop| + * - :ref:`membrane-curvature` + - membranes, curvature, molecular dynamics + - `membrane-curvature authors`_ + - |membrane-curvature_latest| |membrane-curvature_develop| * - :ref:`waterdynamics` - water, hydrogenbonds, MSD - `waterdynamics authors`_ @@ -65,61 +73,42 @@ Each of the MDAKits in the following table links to a page with more details abo - command line interface, molecular-dynamics - `mdacli authors`_ - |mdacli_latest| |mdacli_develop| - * - :ref:`propkatraj` - - pKa, protein - - `propkatraj authors`_ - - |propkatraj_latest| |propkatraj_develop| - * - :ref:`mda-tui` - - transformations, TUI - - `mda-tui authors`_ - - |mda-tui_latest| |mda-tui_develop| + * - :ref:`maicos` + - Molecular Dynamics, Confined Systems + - `maicos authors`_ + - |maicos_latest| |maicos_develop| * - :ref:`ProLIF` - drug-design, cheminformatics, molecular-dynamics - Cédric Bouysset - |ProLIF_latest| |ProLIF_develop| - * - :ref:`transport-analysis` - - transport properties, molecular dynamics - - `transport-analysis authors`_ - - |transport-analysis_latest| |transport-analysis_develop| - * - :ref:`openmm-mdanalysis-reporter` - - OpenMM, Reporters - - `openmm-mdanalysis-reporter authors`_ - - |openmm-mdanalysis-reporter_latest| |openmm-mdanalysis-reporter_develop| + * - :ref:`solvation-analysis` + - chemistry, electrolytes, solvation structure + - orionarcher, hmacdope, laurlee, IAlibay + - |solvation-analysis_latest| |solvation-analysis_develop| .. toctree:: :maxdepth: 1 :hidden: - membrane-curvature spyrmsdkit - maicos - mdaencore - PathSimAnalysis + transport-analysis + propkatraj + openmm-mdanalysis-reporter mdakit-sasa - mdachecker - solvation-analysis mdahole2 + mdaencore + mda-tui + PathSimAnalysis lipyds + mdachecker + membrane-curvature waterdynamics mdacli - propkatraj - mda-tui + maicos ProLIF - transport-analysis - openmm-mdanalysis-reporter - - -.. _`membrane-curvature authors`: - https://github.com/MDAnalysis/membrane-curvature/blob/main/AUTHORS - -.. |membrane-curvature_latest| image:: https://img.shields.io/badge/latest-passed-green.svg - :alt: membrane-curvature develop CI status - :target: https://github.com/MDAnalysis/MDAKits/actions + solvation-analysis -.. |membrane-curvature_develop| image:: https://img.shields.io/badge/develop-passed-green.svg - :alt: membrane-curvature develop CI status - :target: https://github.com/MDAnalysis/MDAKits/actions .. _`spyrmsdkit authors`: https://github.com/RMeli/spyrmsdkit/blob/main/AUTHORS.md @@ -132,37 +121,37 @@ Each of the MDAKits in the following table links to a page with more details abo :alt: spyrmsdkit develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. _`maicos authors`: - https://gitlab.com/maicos-devel/maicos/-/blob/main/AUTHORS.rst +.. _`transport-analysis authors`: + https://github.com/MDAnalysis/transport-analysis/blob/main/AUTHORS.md -.. |maicos_latest| image:: https://img.shields.io/badge/latest-passed-green.svg - :alt: maicos develop CI status +.. |transport-analysis_latest| image:: https://img.shields.io/badge/latest-failed-red.svg + :alt: transport-analysis develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |maicos_develop| image:: https://img.shields.io/badge/develop-passed-green.svg - :alt: maicos develop CI status +.. |transport-analysis_develop| image:: https://img.shields.io/badge/develop-failed-red.svg + :alt: transport-analysis develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. _`mdaencore authors`: - https://github.com/MDAnalysis/mdaencore/blob/main/AUTHORS.md +.. _`propkatraj authors`: + https://github.com/Becksteinlab/propkatraj/blob/main/AUTHORS -.. |mdaencore_latest| image:: https://img.shields.io/badge/latest-passed-green.svg - :alt: mdaencore develop CI status +.. |propkatraj_latest| image:: https://img.shields.io/badge/latest-failed-red.svg + :alt: propkatraj develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |mdaencore_develop| image:: https://img.shields.io/badge/develop-passed-green.svg - :alt: mdaencore develop CI status +.. |propkatraj_develop| image:: https://img.shields.io/badge/develop-failed-red.svg + :alt: propkatraj develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. _`PathSimAnalysis authors`: - https://github.com/MDAnalysis/PathSimAnalysis/blob/main/AUTHORS.md +.. _`openmm-mdanalysis-reporter authors`: + https://github.com/sef43/openmm-mdanalysis-reporter/blob/main/AUTHORS.md -.. |PathSimAnalysis_latest| image:: https://img.shields.io/badge/latest-passed-green.svg - :alt: PathSimAnalysis develop CI status +.. |openmm-mdanalysis-reporter_latest| image:: https://img.shields.io/badge/latest-passed-green.svg + :alt: openmm-mdanalysis-reporter develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |PathSimAnalysis_develop| image:: https://img.shields.io/badge/develop-passed-green.svg - :alt: PathSimAnalysis develop CI status +.. |openmm-mdanalysis-reporter_develop| image:: https://img.shields.io/badge/develop-passed-green.svg + :alt: openmm-mdanalysis-reporter develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions .. _`mdakit-sasa authors`: @@ -176,31 +165,48 @@ Each of the MDAKits in the following table links to a page with more details abo :alt: mdakit-sasa develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |mdachecker_latest| image:: https://img.shields.io/badge/latest-passed-green.svg - :alt: mdachecker develop CI status +.. _`mdahole2 authors`: + https://github.com/MDAnalysis/mdahole2/blob/main/AUTHORS.md + +.. |mdahole2_latest| image:: https://img.shields.io/badge/latest-passed-green.svg + :alt: mdahole2 develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |mdachecker_develop| image:: https://img.shields.io/badge/develop-passed-green.svg - :alt: mdachecker develop CI status +.. |mdahole2_develop| image:: https://img.shields.io/badge/develop-passed-green.svg + :alt: mdahole2 develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |solvation-analysis_latest| image:: https://img.shields.io/badge/latest-passed-green.svg - :alt: solvation-analysis develop CI status +.. _`mdaencore authors`: + https://github.com/MDAnalysis/mdaencore/blob/main/AUTHORS.md + +.. |mdaencore_latest| image:: https://img.shields.io/badge/latest-passed-green.svg + :alt: mdaencore develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |solvation-analysis_develop| image:: https://img.shields.io/badge/develop-passed-green.svg - :alt: solvation-analysis develop CI status +.. |mdaencore_develop| image:: https://img.shields.io/badge/develop-passed-green.svg + :alt: mdaencore develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. _`mdahole2 authors`: - https://github.com/MDAnalysis/mdahole2/blob/main/AUTHORS.md +.. _`mda-tui authors`: + https://github.com/p-j-smith/mda-tui/blob/main/AUTHORS.md -.. |mdahole2_latest| image:: https://img.shields.io/badge/latest-passed-green.svg - :alt: mdahole2 develop CI status +.. |mda-tui_latest| image:: https://img.shields.io/badge/latest-passed-green.svg + :alt: mda-tui develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |mdahole2_develop| image:: https://img.shields.io/badge/develop-passed-green.svg - :alt: mdahole2 develop CI status +.. |mda-tui_develop| image:: https://img.shields.io/badge/develop-passed-green.svg + :alt: mda-tui develop CI status + :target: https://github.com/MDAnalysis/MDAKits/actions + +.. _`PathSimAnalysis authors`: + https://github.com/MDAnalysis/PathSimAnalysis/blob/main/AUTHORS.md + +.. |PathSimAnalysis_latest| image:: https://img.shields.io/badge/latest-passed-green.svg + :alt: PathSimAnalysis develop CI status + :target: https://github.com/MDAnalysis/MDAKits/actions + +.. |PathSimAnalysis_develop| image:: https://img.shields.io/badge/develop-passed-green.svg + :alt: PathSimAnalysis develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions .. |lipyds_latest| image:: https://img.shields.io/badge/latest-unavailable-inactive.svg @@ -211,6 +217,25 @@ Each of the MDAKits in the following table links to a page with more details abo :alt: lipyds develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions +.. |mdachecker_latest| image:: https://img.shields.io/badge/latest-passed-green.svg + :alt: mdachecker develop CI status + :target: https://github.com/MDAnalysis/MDAKits/actions + +.. |mdachecker_develop| image:: https://img.shields.io/badge/develop-passed-green.svg + :alt: mdachecker develop CI status + :target: https://github.com/MDAnalysis/MDAKits/actions + +.. _`membrane-curvature authors`: + https://github.com/MDAnalysis/membrane-curvature/blob/main/AUTHORS + +.. |membrane-curvature_latest| image:: https://img.shields.io/badge/latest-passed-green.svg + :alt: membrane-curvature develop CI status + :target: https://github.com/MDAnalysis/MDAKits/actions + +.. |membrane-curvature_develop| image:: https://img.shields.io/badge/develop-passed-green.svg + :alt: membrane-curvature develop CI status + :target: https://github.com/MDAnalysis/MDAKits/actions + .. _`waterdynamics authors`: https://github.com/MDAnalysis/waterdynamics/blob/main/AUTHORS.md @@ -233,26 +258,15 @@ Each of the MDAKits in the following table links to a page with more details abo :alt: mdacli develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. _`propkatraj authors`: - https://github.com/Becksteinlab/propkatraj/blob/main/AUTHORS - -.. |propkatraj_latest| image:: https://img.shields.io/badge/latest-passed-green.svg - :alt: propkatraj develop CI status - :target: https://github.com/MDAnalysis/MDAKits/actions - -.. |propkatraj_develop| image:: https://img.shields.io/badge/develop-passed-green.svg - :alt: propkatraj develop CI status - :target: https://github.com/MDAnalysis/MDAKits/actions - -.. _`mda-tui authors`: - https://github.com/p-j-smith/mda-tui/blob/main/AUTHORS.md +.. _`maicos authors`: + https://gitlab.com/maicos-devel/maicos/-/blob/main/AUTHORS.rst -.. |mda-tui_latest| image:: https://img.shields.io/badge/latest-passed-green.svg - :alt: mda-tui develop CI status +.. |maicos_latest| image:: https://img.shields.io/badge/latest-passed-green.svg + :alt: maicos develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |mda-tui_develop| image:: https://img.shields.io/badge/develop-passed-green.svg - :alt: mda-tui develop CI status +.. |maicos_develop| image:: https://img.shields.io/badge/develop-passed-green.svg + :alt: maicos develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions .. |ProLIF_latest| image:: https://img.shields.io/badge/latest-passed-green.svg @@ -263,25 +277,11 @@ Each of the MDAKits in the following table links to a page with more details abo :alt: ProLIF develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. _`transport-analysis authors`: - https://github.com/MDAnalysis/transport-analysis/blob/main/AUTHORS.md - -.. |transport-analysis_latest| image:: https://img.shields.io/badge/latest-failed-red.svg - :alt: transport-analysis develop CI status - :target: https://github.com/MDAnalysis/MDAKits/actions - -.. |transport-analysis_develop| image:: https://img.shields.io/badge/develop-failed-red.svg - :alt: transport-analysis develop CI status - :target: https://github.com/MDAnalysis/MDAKits/actions - -.. _`openmm-mdanalysis-reporter authors`: - https://github.com/sef43/openmm-mdanalysis-reporter/blob/main/AUTHORS.md - -.. |openmm-mdanalysis-reporter_latest| image:: https://img.shields.io/badge/latest-passed-green.svg - :alt: openmm-mdanalysis-reporter develop CI status +.. |solvation-analysis_latest| image:: https://img.shields.io/badge/latest-passed-green.svg + :alt: solvation-analysis develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |openmm-mdanalysis-reporter_develop| image:: https://img.shields.io/badge/develop-passed-green.svg - :alt: openmm-mdanalysis-reporter develop CI status +.. |solvation-analysis_develop| image:: https://img.shields.io/badge/develop-passed-green.svg + :alt: solvation-analysis develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions diff --git a/_sources/propkatraj.rst.txt b/_sources/propkatraj.rst.txt index d53d4211..ae959374 100644 --- a/_sources/propkatraj.rst.txt +++ b/_sources/propkatraj.rst.txt @@ -39,11 +39,11 @@ The source code of propkatraj can be installed using the following: .. _`propkatraj authors`: https://github.com/Becksteinlab/propkatraj/blob/main/AUTHORS -.. |propkatraj_latest| image:: https://img.shields.io/badge/latest-passed-green.svg +.. |propkatraj_latest| image:: https://img.shields.io/badge/latest-failed-red.svg :alt: propkatraj develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions -.. |propkatraj_develop| image:: https://img.shields.io/badge/develop-passed-green.svg +.. |propkatraj_develop| image:: https://img.shields.io/badge/develop-failed-red.svg :alt: propkatraj develop CI status :target: https://github.com/MDAnalysis/MDAKits/actions diff --git a/about.html b/about.html index 006ccd35..5e09d6f2 100644 --- a/about.html +++ b/about.html @@ -44,7 +44,7 @@ - + @@ -197,7 +197,7 @@

Why?