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List of deadlink on MDAnalysis documentation #4735

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mhmohona opened this issue Oct 17, 2024 · 1 comment
Open

List of deadlink on MDAnalysis documentation #4735

mhmohona opened this issue Oct 17, 2024 · 1 comment

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@mhmohona
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I checked MDAnalysis Documentation and found several links that are either broken, lead to 404 errors, or are inaccessible -

# Error Anchor Text Linked From Broken Link
1 404 Not Found XYZ format Stable Index http://openbabel.org/wiki/XYZ_(format)
2 -1 Timeout NumPy Stable Index http://numpy.scipy.org/
3 -1 Timeout IPython Overview http://ipython.scipy.org/
4 404 Not Found examples Overview https://github.com/MDAnalysis/MDAnalysisCookbook/tree/master/examples/
5 404 Not Found rmsfit_qcp.py Overview https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/rmsfit_qcp.py
6 404 Not Found blocks.py Overview https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/blocks.py
7 404 Not Found potential_profile.py Overview https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/potential_profile.py
8 404 Not Found nativecontacts.py Overview https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/nativecontacts.py
9 404 Not Found membrane-leaflets.py Overview https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/membrane-leaflets.py
10 404 Not Found multimers-analysis.py Overview https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/multimers-analysis.py
11 404 Not Found dcd2xtc.py Overview https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/dcd2xtc.py
12 404 Not Found amber2dcd.py Overview https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/amber2dcd.py
13 404 Not Found make_MthK_tetramer.py Overview https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/make_MthK_tetramer.py
14 404 Not Found PDB Stable Index https://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html
15 -1 Not Found HELANAL References http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.html
16 404 Not Found scipy Visualization Modules https://scipy.org/scipylib/index.html
17 -1 Not Found Jmol Selections Modules https://wiki.jmol.org/index.php/Main_Page
18 404 Not Found APBS Topology Init https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/
19 -1 Not Found HOOMD XML Topology Init http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html
20 -1 Not Found Macromolecular Transmission Format (MMTF) Topology Init https://mmtf.rcsb.org/
21 -1 Not Found FHI-AIMS Topology Init https://aimsclub.fhi-berlin.mpg.de/
22 404 Not Found conversion factor to Amber charge units Units https://ambermd.org/formats.html
23 -1 Timeout MinActionPath result for AdK Contacts http://lorentz.dynstr.pasteur.fr/joel/adenylate.php
24 -1 Not Found CRD CRD Parser https://www.charmmtutorial.org/index.php/CHARMM:The_Basics
25 -1 Not Found GAMESS-UK GMS Parser http://www.cfs.dl.ac.uk/
26 -1 Not Found HOOMD HoomdXML Parser http://codeblue.umich.edu/hoomd-blue/index.html
27 404 Not Found PQR PQR Parser https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html
28 404 Not Found PDB2PQR PQR Parser https://apbs-pdb2pqr.readthedocs.io/en/latest/pdb2pqr/index.html
29 404 Not Found APBS PQR https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/index.html
30 -1 Not Found IBIsCO TRZ http://www.theo.chemie.tu-darmstadt.de/ibisco/IBISCO.html
31 -1 Not Found YASP TRZ http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html
32 404 Not Found chemfile-supported file formats Chemfiles https://docs.mdanalysis.org/stable/documentation_pages/coordinates/formats
33 404 Not Found ndx Gromacs https://www.gromacs.org/Documentation/File_Formats/Index_File
34 403 Forbidden Video (4:55 to 8:05) RDKit https://www.youtube.com/watch?v=5b5wYmK4URU&feature=youtu.be
35 410 Gone Christoph Gohlke Transformations https://www.lfd.uci.edu/~gohlke/
36 -1 Not Found qcp QCProt https://theobald.brandeis.edu/qcp/
37 404 Not Found MDAnalysisCookbook Leaflet Analysis https://github.com/MDAnalysis/MDAnalysisCookbook/tree/master/examples
38 -1 Timeout Chimera Density Analysis https://www.cgl.ucsf.edu/chimera/
39 404 Not Found Carbohydrate Naming Convention in Glycam WBridge Analysis https://glycam.ccrc.uga.edu/documents/FutureNomenclature.htm
40 404 Not Found MDAnalysis.analysis.encore.clustering.affinityprop Modules Index https://docs.mdanalysis.org/stable/_modules/MDAnalysis/analysis/encore/clustering/affinityprop.html
41 404 Not Found MDAnalysis.analysis.encore.cutils Modules Index https://docs.mdanalysis.org/stable/_modules/MDAnalysis/analysis/encore/cutils.html
42 404 Not Found MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed Modules Index https://docs.mdanalysis.org/stable/_modules/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.html
43 404 Not Found MDAnalysis.coordinates.timestep Modules Index https://docs.mdanalysis.org/stable/_modules/MDAnalysis/coordinates/timestep.html
44 404 Not Found MDAnalysis.lib._augment Modules Index https://docs.mdanalysis.org/stable/_modules/MDAnalysis/lib/_augment.html
45 404 Not Found MDAnalysis.lib._cutil Modules Index https://docs.mdanalysis.org/stable/_modules/MDAnalysis/lib/_cutil.html
46 404 Not Found MDAnalysis.lib.formats.libdcd Modules Index https://docs.mdanalysis.org/stable/_modules/MDAnalysis/lib/formats/libdcd.html
47 404 Not Found MDAnalysis.lib.formats.libmdaxdr Modules Index https://docs.mdanalysis.org/stable/_modules/MDAnalysis/lib/formats/libmdaxdr.html
48 404 Not Found MDAnalysis.lib.nsgrid Modules Index https://docs.mdanalysis.org/stable/_modules/MDAnalysis/lib/nsgrid.html
49 404 Not Found MDAnalysis.lib.qcprot Modules Index https://docs.mdanalysis.org/stable/_modules/MDAnalysis/lib/qcprot.html
50 404 Not Found builtins Modules Index https://docs.mdanalysis.org/stable/_modules/builtins.html
51 404 Not Found PATH HOLE2 https://matplotlib.org/stable/users/faq/environment_variables_faq.html
52 404 Not Found chemfile-supported file formats Chemfiles https://docs.mdanalysis.org/2.3.0/documentation_pages/coordinates/formats
53 404 Not Found MDAnalysis.analysis.encore.clustering.affinityprop Modules Index https://docs.mdanalysis.org/2.3.0/_modules/MDAnalysis/analysis/encore/clustering/affinityprop.html
54 404 Not Found MDAnalysis.analysis.encore.cutils Modules Index https://docs.mdanalysis.org/2.3.0/_modules/MDAnalysis/analysis/encore/cutils.html
55 404 Not Found MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed Modules Index https://docs.mdanalysis.org/2.3.0/_modules/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.html
56 404 Not Found MDAnalysis.coordinates.timestep Modules Index https://docs.mdanalysis.org/2.3.0/_modules/MDAnalysis/coordinates/timestep.html
57 404 Not Found MDAnalysis.lib._augment Modules Index https://docs.mdanalysis.org/2.3.0/_modules/MDAnalysis/lib/_augment.html
58 404 Not Found MDAnalysis.lib._cutil Modules Index https://docs.mdanalysis.org/2.3.0/_modules/MDAnalysis/lib/_cutil.html
59 404 Not Found MDAnalysis.lib.formats.libdcd Modules Index https://docs.mdanalysis.org/2.3.0/_modules/MDAnalysis/lib/formats/libdcd.html
60 404 Not Found MDAnalysis.lib.formats.libmdaxdr Modules Index https://docs.mdanalysis.org/2.3.0/_modules/MDAnalysis/lib/formats/libmdaxdr.html
61 404 Not Found MDAnalysis.lib.nsgrid Modules Index https://docs.mdanalysis.org/2.3.0/_modules/MDAnalysis/lib/nsgrid.html
62 404 Not Found MDAnalysis.lib.qcprot Modules Index https://docs.mdanalysis.org/2.3.0/_modules/MDAnalysis/lib/qcprot.html
63 404 Not Found builtins Modules Index https://docs.mdanalysis.org/2.3.0/_modules/builtins.html
64 -1 Timeout Shoemake K., Quaternions Transformations https://www.ljll.math.upmc.fr/~frey/papers/scientific visualisation/Shoemake K., Quaternions.pdf
65 404 Not Found Intel Developer's Manual Transformations https://www.intel.com/content/www/us/en/404.html?ref=https://www.intel.com/cd/ids/developer/asmo-na/eng/293748.html

I am ready to start working on fixing these issues, but I would appreciate some feedback or suggestions before proceeding. Also, if there are preferred sources to replace outdated links, please provide them.

@orbeckst
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We'd very much appreciated help fixing links!

Perhaps start with a PR for one part of the library, e.g. "fix dead links in MDAnalysis.coordinates". Use your best guess for a replacement and then we can discuss alternatives when reviewing.

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