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MDAnalysis · Oct 19, 2024 · 948d75b · 948d75b
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diff --git a/package/MDAnalysis/topology/CRDParser.py b/package/MDAnalysis/topology/CRDParser.py
@@ -37,7 +37,7 @@
 
         By default, atomtypes and masses will be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
 .. _CRD: https://www.charmmtutorial.org/index.php/CHARMM:The_Basics
 
@@ -83,7 +83,7 @@ class CRDParser(TopologyReaderBase):
 
         By default, atomtypes and masses will be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
     .. versionchanged:: 2.8.0
        Type and mass are not longer guessed here. Until 3.0 these will still be

diff --git a/package/MDAnalysis/topology/DLPolyParser.py b/package/MDAnalysis/topology/DLPolyParser.py
@@ -34,7 +34,7 @@
 
         By default, atomtypes and masses will be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
 .. _Poly: http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/44516.aspx
 

diff --git a/package/MDAnalysis/topology/DMSParser.py b/package/MDAnalysis/topology/DMSParser.py
@@ -90,7 +90,7 @@ class DMSParser(TopologyReaderBase):
 
         By default, atomtypes will be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
     .. _DESRES: http://www.deshawresearch.com
     .. _Desmond: http://www.deshawresearch.com/resources_desmond.html

diff --git a/package/MDAnalysis/topology/ExtendedPDBParser.py b/package/MDAnalysis/topology/ExtendedPDBParser.py
@@ -82,7 +82,7 @@ class ExtendedPDBParser(PDBParser.PDBParser):
 
       By default, atomtypes and masses will be guessed on Universe creation.
       This may change in release 3.0.
-      See :ref:`Guessers`_ for more information.
+      See :ref:`Guessers` for more information.
 
 
     See Also

diff --git a/package/MDAnalysis/topology/FHIAIMSParser.py b/package/MDAnalysis/topology/FHIAIMSParser.py
@@ -71,7 +71,7 @@ class FHIAIMSParser(TopologyReaderBase):
 
         By default, atomtypes and masses will be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
     .. versionchanged:: 2.8.0
         Removed type and mass guessing (attributes guessing takes place now

diff --git a/package/MDAnalysis/topology/GMSParser.py b/package/MDAnalysis/topology/GMSParser.py
@@ -78,7 +78,7 @@ class GMSParser(TopologyReaderBase):
 
         By default, atomtypes and masses will be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
     .. versionadded:: 0.9.1
     .. versionchanged:: 2.8.0

diff --git a/package/MDAnalysis/topology/GROParser.py b/package/MDAnalysis/topology/GROParser.py
@@ -71,7 +71,7 @@ class GROParser(TopologyReaderBase):
 
         By default, atomtypes and masses will be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
     .. versionchanged:: 2.8.0
         Removed type and mass guessing (attributes guessing takes place now

diff --git a/package/MDAnalysis/topology/ITPParser.py b/package/MDAnalysis/topology/ITPParser.py
@@ -478,7 +478,7 @@ class ITPParser(TopologyReaderBase):
         By default, atomtypes and masses will be guessed on Universe creation
         if they are not read from the input file.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
     .. versionchanged:: 2.2.0
       no longer adds angles for water molecules with SETTLE constraint

diff --git a/package/MDAnalysis/topology/LAMMPSParser.py b/package/MDAnalysis/topology/LAMMPSParser.py
@@ -31,7 +31,7 @@
 
     By default, masses will be guessed on Universe creation if they are not read
     from the input file. This may change in release 3.0.
-    See :ref:`Guessers`_ for more information.
+    See :ref:`Guessers` for more information.
 
 .. _LAMMPS: http://lammps.sandia.gov/
 .. _data: DATA file format: :http://lammps.sandia.gov/doc/2001/data_format.html

diff --git a/package/MDAnalysis/topology/MMTFParser.py b/package/MDAnalysis/topology/MMTFParser.py
@@ -68,7 +68,7 @@
 
     By default, masses will be guessed on Universe creation.
     This may change in release 3.0.
-    See :ref:`Guessers`_ for more information.
+    See :ref:`Guessers` for more information.
 
 Classes
 -------

diff --git a/package/MDAnalysis/topology/MOL2Parser.py b/package/MDAnalysis/topology/MOL2Parser.py
@@ -82,7 +82,7 @@ class MOL2Parser(TopologyReaderBase):
 
         By default, masses will be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
 
     Notes

diff --git a/package/MDAnalysis/topology/PDBParser.py b/package/MDAnalysis/topology/PDBParser.py
@@ -41,7 +41,7 @@
     Otherwise, they will be guessed on Universe creation.
     By default, masses will also be guessed on Universe creation.
     This may change in release 3.0.
-    See :ref:`Guessers`_ for more information.
+    See :ref:`Guessers` for more information.
 
 
 .. Note::

diff --git a/package/MDAnalysis/topology/PDBQTParser.py b/package/MDAnalysis/topology/PDBQTParser.py
@@ -36,7 +36,7 @@
 
     By default, masses will be guessed on Universe creation.
     This may change in release 3.0.
-    See :ref:`Guessers`_ for more information.
+    See :ref:`Guessers` for more information.
 
 Notes
 -----

diff --git a/package/MDAnalysis/topology/PQRParser.py b/package/MDAnalysis/topology/PQRParser.py
@@ -86,7 +86,7 @@ class PQRParser(TopologyReaderBase):
         (e.g. GROMACS PQR files). Otherwise, they will be guessed on Universe
         creation. By default, masses will also be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
 
     .. versionchanged:: 0.9.0

diff --git a/package/MDAnalysis/topology/TXYZParser.py b/package/MDAnalysis/topology/TXYZParser.py
@@ -77,7 +77,7 @@ class TXYZParser(TopologyReaderBase):
 
         By default, masses will be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
     .. versionadded:: 0.17.0
     .. versionchanged:: 2.4.0

diff --git a/package/MDAnalysis/topology/XYZParser.py b/package/MDAnalysis/topology/XYZParser.py
@@ -63,7 +63,7 @@ class XYZParser(TopologyReaderBase):
 
         By default, atomtypes and masses will be guessed on Universe creation.
         This may change in release 3.0.
-        See :ref:`Guessers`_ for more information.
+        See :ref:`Guessers` for more information.
 
 
     .. versionadded:: 0.9.1

diff --git a/package/doc/sphinx/source/documentation_pages/guesser_modules.rst b/package/doc/sphinx/source/documentation_pages/guesser_modules.rst
@@ -18,7 +18,7 @@ Default behavior
 By default, MDAnalysis will guess the "mass" and "type" (atom type) attributes for all particles in the Universe
 using the :class:`~MDAnalysis.guesser.default_guesser.DefaultGuesser` at the time of Universe creation,
 if they are not read from the input file.
-Please see the :ref:`DefaultGuesser`_ for more information.
+Please see the :ref:`DefaultGuesser` for more information.