Fix broken links in docs (#4941)

namiroues · IAlibay · web-flow · commit 8fb40ad226b3 · 2025-03-13T00:06:02.000Z
* Fixes #4940 * Fix broken links * docs: address review comments * use new genuine AMBER TRJ specs * link to GMX current docs --------- Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
diff --git a/package/MDAnalysis/coordinates/DLPoly.py b/package/MDAnalysis/coordinates/DLPoly.py
@@ -26,7 +26,7 @@
 
 Read DL Poly_ format coordinate files
 
-.. _Poly: http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/44516.aspx
+.. _Poly: https://www.sc.stfc.ac.uk/software/type/computational-materials-and-molecular-science/?searchquery=dl_poly
 """
 import numpy as np
 
diff --git a/package/MDAnalysis/coordinates/GRO.py b/package/MDAnalysis/coordinates/GRO.py
@@ -96,7 +96,7 @@
 
 
 .. _Gromacs: http://www.gromacs.org
-.. _GRO: http://manual.gromacs.org/current/online/gro.html
+.. _GRO: https://manual.gromacs.org/current/reference-manual/file-formats.html#gro
 .. _GRO format: http://chembytes.wikidot.com/g-grofile
 
 """
diff --git a/package/MDAnalysis/coordinates/GSD.py b/package/MDAnalysis/coordinates/GSD.py
@@ -36,7 +36,7 @@
 to be different to the one that was set at the first time step. No check on
 changes in particle identity or topology is currently implemented.
 
-.. _`HOOMD-blue`: http://codeblue.umich.edu/hoomd-blue/index.html
+.. _`HOOMD-blue`: https://glotzerlab.engin.umich.edu/hoomd-blue/
 
 Classes
 -------
diff --git a/package/MDAnalysis/coordinates/H5MD.py b/package/MDAnalysis/coordinates/H5MD.py
@@ -180,8 +180,8 @@
 .. _`H5PY`: http://docs.h5py.org/
 .. _`parallel h5py docs`: https://docs.h5py.org/en/stable/mpi.html
 .. _`mpi4py`: https://mpi4py.readthedocs.io/en/stable/index.html
-.. _`Build MPI from sources`: https://mpi4py.readthedocs.io/en/stable/appendix.html#building-mpi-from-sources
-.. _`Build HDF5 from sources`: https://support.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_parallel
+.. _`Build MPI from sources`: https://docs.open-mpi.org/en/v5.0.x/installing-open-mpi/downloading.html
+.. _`Build HDF5 from sources`: https://docs.h5py.org/en/latest/mpi.html
 .. _`Install mpi4py`: https://mpi4py.readthedocs.io/en/stable/install.html#requirements
 .. _`Build h5py from sources`: https://docs.h5py.org/en/stable/mpi.html#building-against-parallel-hdf5
 .. _`H5MD notation`: https://nongnu.org/h5md/modules/units.html
diff --git a/package/MDAnalysis/coordinates/INPCRD.py b/package/MDAnalysis/coordinates/INPCRD.py
@@ -27,7 +27,7 @@
 
 Read coordinates in Amber_ coordinate/restart file (suffix "inpcrd").
 
-.. _Amber: http://ambermd.org/formats.html#restart
+.. _Amber: https://ambermd.org/FileFormats.php
 
 
 Classes
diff --git a/package/MDAnalysis/coordinates/MMTF.py b/package/MDAnalysis/coordinates/MMTF.py
@@ -37,7 +37,7 @@
 .. autoclass:: MMTFReader
    :members:
 
-.. _MMTF: https://mmtf.rcsb.org/
+.. _MMTF: https://www.rcsb.org/news/feature/65a1af31c76ca3abcc925d0c
 
 """
 import warnings
diff --git a/package/MDAnalysis/coordinates/PDBQT.py b/package/MDAnalysis/coordinates/PDBQT.py
@@ -33,7 +33,7 @@
 available in this case).
 
 .. _PDBQT:
-   http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
+   https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf
 .. _AutoDock:
    http://autodock.scripps.edu/
 """
@@ -198,8 +198,7 @@ class PDBQTWriter(base.WriterBase):
     """PDBQT writer that implements a subset of the PDB_ 3.2 standard and the PDBQT_ spec.
 
     .. _PDB: http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
-    .. _PDBQT: http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
-
+    .. _PDBQT: https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf
 
     .. versionchanged:: 2.6.0
        Files are now written in `wt` mode, and keep extensions, allowing
diff --git a/package/MDAnalysis/coordinates/PQR.py b/package/MDAnalysis/coordinates/PQR.py
@@ -100,9 +100,9 @@
 In all cases the `dimensions` attribute will be set to `None`.
 
 
-.. _PQR:     https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html
-.. _APBS:    https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/index.html
-.. _PDB2PQR: https://apbs-pdb2pqr.readthedocs.io/en/latest/pdb2pqr/index.html
+.. _PQR:     https://apbs.readthedocs.io/en/latest/formats/pqr.html
+.. _APBS:    https://apbs.readthedocs.io/en/latest/
+.. _PDB2PQR: https://pdb2pqr.readthedocs.io/en/latest/
 .. _PDB:     http://www.wwpdb.org/documentation/file-format
 """
 import itertools
@@ -117,7 +117,7 @@ class PQRReader(base.SingleFrameReaderBase):
     """Read a PQR_ file into MDAnalysis.
 
     .. _PQR:
-        https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html
+        https://apbs.readthedocs.io/en/latest/formats/pqr.html
 
     .. versionchanged:: 0.11.0
        Frames now 0-based instead of 1-based
diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py
@@ -115,10 +115,10 @@
 .. Links
 
 .. _AMBER: http://ambermd.org
-.. _AMBER TRJ format: http://ambermd.org/formats.html#trajectory
+.. _AMBER TRJ format: https://ambermd.org/FileFormats.php#trajectory
 ..    The formats page was archived as
 ..    http://www.webcitation.org/query?url=http%3A%2F%2Fambermd.org%2Fformats.html&date=2018-02-11
-..    Use the archived version if the original disappears. [orbeckst]
+..    Use the archived version if the original (https://ambermd.org/FileFormats.php#trajectory) disappears. [orbeckst]
 .. _AMBER netcdf format: http://ambermd.org/netcdf/nctraj.xhtml
 ..    The formats page was archived as
 ..    http://www.webcitation.org/query?url=http%3A%2F%2Fambermd.org%2Fnetcdf%2Fnctraj.xhtml&date=2018-02-11
@@ -166,7 +166,7 @@ class TRJReader(base.ReaderBase):
     be set by passing the `dt` keyword argument to the constructor; it
     is assumed to be in ps. The default value is 1 ps.
 
-    .. _AMBER TRJ format: http://ambermd.org/formats.html#trajectory
+    .. _AMBER TRJ format: https://ambermd.org/FileFormats.php#trajectory
 
     .. versionchanged:: 0.11.0
        Frames now 0-based instead of 1-based.
diff --git a/package/MDAnalysis/coordinates/TRZ.py b/package/MDAnalysis/coordinates/TRZ.py
@@ -32,8 +32,8 @@
 the machine hardware architecture, MDAnalysis *always* reads and writes TRZ
 trajectories in *little-endian* byte order.
 
-.. _IBIsCO: http://www.theo.chemie.tu-darmstadt.de/ibisco/IBISCO.html
-.. _YASP: http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html
+.. _IBIsCO: https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21717
+.. _YASP: https://www.sciencedirect.com/science/article/abs/pii/0010465593901442
 
 Classes
 -------
diff --git a/package/MDAnalysis/coordinates/chemfiles.py b/package/MDAnalysis/coordinates/chemfiles.py
@@ -26,13 +26,10 @@
 MDAnalysis interoperates with the `chemfiles`_ library. The *chemfiles* C++ library
 supports an expanding set of file formats, some of which are not natively supported by
 MDAnalysis. Using the *CHEMFILES* reader you can use  `chemfiles`_ for the low-level
-file reading. Check the list of `chemfile-supported file formats <formats>`_.
+file reading. Check the list of `chemfile-supported file formats`_.
 
 .. _chemfiles: https://chemfiles.org
-.. _formats: https://chemfiles.org/chemfiles/0.10.0/formats.html#list-of-supported-formats
-.. NOTE: MDAnalysis currently restricts chemfiles to 0.10 <= version < 0.11. Update the link
-..       above to the latest documentation once this restriction is lifted.
-..       https://chemfiles.org/chemfiles/latest/formats.html#list-of-supported-formats
+.. _chemfile-supported file formats: https://chemfiles.org/chemfiles/latest/formats.html#list-of-supported-formats
 
 Using the CHEMFILES reader
 --------------------------
diff --git a/package/MDAnalysis/selections/gromacs.py b/package/MDAnalysis/selections/gromacs.py
@@ -34,7 +34,7 @@
 The index groups are named *mdanalysis001*, *mdanalysis002*, etc.
 
 .. _Gromacs: http://www.gromacs.org
-.. _ndx: http://www.gromacs.org/Documentation/File_Formats/Index_File
+.. _ndx: https://manual.gromacs.org/current/reference-manual/file-formats.html#ndx
 
 .. autoclass:: SelectionWriter
    :inherited-members:
diff --git a/package/MDAnalysis/topology/MMTFParser.py b/package/MDAnalysis/topology/MMTFParser.py
@@ -76,7 +76,7 @@
 .. autoclass:: MMTFParser
    :members:
 
-.. _Macromolecular Transmission Format (MMTF) format: https://mmtf.rcsb.org/
+.. _Macromolecular Transmission Format (MMTF) format: https://www.rcsb.org/news/feature/65a1af31c76ca3abcc925d0c
 """
 from collections import defaultdict
 import mmtf
diff --git a/package/MDAnalysis/topology/PDBQTParser.py b/package/MDAnalysis/topology/PDBQTParser.py
@@ -57,7 +57,7 @@
 
 
 .. _PDBQT:
-   http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
+   https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf 
 .. _AutoDock:
    http://autodock.scripps.edu/
 """
diff --git a/package/MDAnalysis/topology/PQRParser.py b/package/MDAnalysis/topology/PQRParser.py
@@ -42,7 +42,7 @@
 
 
 .. _PQR:     https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html
-.. _APBS:    https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/index.html
+.. _APBS:    https://apbs.readthedocs.io/en/latest/
 .. _PDB2PQR: https://apbs-pdb2pqr.readthedocs.io/en/latest/pdb2pqr/index.html
 .. _PDB:     http://www.wwpdb.org/documentation/file-format
 
diff --git a/package/MDAnalysis/topology/__init__.py b/package/MDAnalysis/topology/__init__.py
@@ -188,6 +188,13 @@
 
 .. _CHARMM: https://www.charmm.org/charmm/
 .. _HOOMD XML: http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html
+
+.. Note::
+
+   The HOOMD XML file format has been deprecated in favor of the GSD.
+   https://hoomd-blue.readthedocs.io/en/v2.9.3/module-deprecated-dump.html
+   Transitioning to the GSD file format is advisable for working with HOOMD-blue simulations.
+
 .. _HOOMD: http://glotzerlab.engin.umich.edu/hoomd-blue/
 .. _NAMD: http://www.ks.uiuc.edu/Research/namd/
 .. _LAMMPS: https://lammps.sandia.gov/
@@ -197,8 +204,8 @@
 .. _Tinker: https://dasher.wustl.edu/tinker/
 .. _DL_POLY: https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx
 .. _AutoDock: http://autodock.scripps.edu/
-.. _APBS: https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/
-.. _Macromolecular Transmission Format (MMTF): https://mmtf.rcsb.org/
+.. _APBS: https://apbs.readthedocs.io/en/latest/
+.. _Macromolecular Transmission Format (MMTF): https://www.rcsb.org/news/feature/65a1af31c76ca3abcc925d0c
 .. _FHI-AIMS: https://aimsclub.fhi-berlin.mpg.de/
 .. _GAMESS: https://www.msg.chem.iastate.edu/gamess/
 
diff --git a/package/MDAnalysis/units.py b/package/MDAnalysis/units.py
@@ -354,14 +354,14 @@ def __getitem__(self, key):
 #: *elementary_charge* in :data:`constants`.
 #: The `conversion factor to Amber charge units`_ is 18.2223.
 #:
-#: .. _`conversion factor to Amber charge units`: http://ambermd.org/formats.html#parm
+#: .. _`conversion factor to Amber charge units`: https://ambermd.org/FileFormats.php#parm.dat
 #:
 #: .. versionchanged:: 0.9.0
 #:    Use CODATA 2010 value for *elementary charge*, which differs from the previously used value
 #:    *e* =  1.602176487 x 10**(-19) C by 7.8000000e-27 C.
 chargeUnit_factor = {
     "e": 1.0,
-    "Amber": 18.2223,  # http://ambermd.org/formats.html#parm
+    "Amber": 18.2223,  # https://ambermd.org/FileFormats.php#parm.dat
     "C": constants["elementary_charge"],
     "As": constants["elementary_charge"],
 }
diff --git a/package/doc/sphinx/source/documentation_pages/overview.rst b/package/doc/sphinx/source/documentation_pages/overview.rst
@@ -38,7 +38,7 @@ of a protein and the radius of gyration of the backbone atoms are calculated::
         print(f"frame = {ts.frame}: d = {d} Angstroem, Rgyr = {rgyr} Angstroem")
 
 
-.. _NumPy:   http://numpy.scipy.org
+.. _NumPy:   https://numpy.org/
 .. _CHARMM:  http://www.charmm.org/
 .. _LAMMPS:  http://lammps.sandia.gov/
 .. _NAMD:    http://www.ks.uiuc.edu/Research/namd/
diff --git a/package/doc/sphinx/source/documentation_pages/selections_modules.rst b/package/doc/sphinx/source/documentation_pages/selections_modules.rst
@@ -122,4 +122,4 @@ Each module implements a :class:`SelectionWriter` for a specific format.
 .. _Gromacs: http://www.gromacs.org
 .. _VMD: http://www.ks.uiuc.edu/Research/vmd/
 .. _PyMOL: http://www.pymol.org
-.. _Jmol: http://wiki.jmol.org/
+.. _Jmol: https://jmol.sourceforge.net/
diff --git a/package/doc/sphinx/source/index.rst b/package/doc/sphinx/source/index.rst
@@ -35,11 +35,11 @@ written out in a range of formats.
 .. _LAMMPS:  http://lammps.sandia.gov/
 .. _NAMD:    http://www.ks.uiuc.edu/Research/namd/
 .. _Gromacs: http://www.gromacs.org/
-.. _`DL_POLY`: http://www.scd.stfc.ac.uk//44516.aspx
+.. _`DL_POLY`: https://www.sc.stfc.ac.uk/software/type/computational-materials-and-molecular-science/?searchquery=dl_poly
 .. _VMD: http://www.ks.uiuc.edu/Research/vmd/
 .. _PyMol: http://www.pymol.org/
-.. _PDB: http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html
-.. _XYZ format: http://openbabel.org/wiki/XYZ_%28format%29
+.. _PDB: https://www.wwpdb.org/documentation/file-formats-and-the-pdb
+.. _XYZ format: https://en.wikipedia.org/wiki/XYZ_file_format
 
 
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