List of deadlink on MDAnalysis documentation

[mhmohona]

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]

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.