diff --git a/package/MDAnalysis/topology/CRDParser.py b/package/MDAnalysis/topology/CRDParser.py index 1867f0b6871..eb7b1c2418f 100644 --- 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 index 0ae6af833dd..4148a38c064 100644 --- 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 index a095bb2c4c6..f37a854c725 100644 --- 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 index df4beb4832b..6fa5bff616e 100644 --- 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 index 3cde90d27e4..8738d5e3ce9 100644 --- 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 index 541e6bb9c48..fbd7a6f602d 100644 --- 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 index f9d333db624..15ffeceb2f3 100644 --- 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 index e6e468f3b4c..9c9dd37976b 100644 --- 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 index 321a577343f..92e3709db1d 100644 --- 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 index 4cf652ab565..5a58f1b2454 100644 --- 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 index b13266279f7..7743ed04196 100644 --- 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 index 1579bebca6c..8349be9133b 100644 --- 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 index 14ddfefdec5..435ec5678c8 100644 --- 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 index 91773d6d21a..9ef6d3e6f95 100644 --- 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 index 6370b5e88e8..206f381e9e0 100644 --- 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 index b737d0019d3..5fe736fec6a 100644 --- 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 index 6cc4aa4f8d7..5b34609ea25 100644 --- 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.