refactor

marrink-lab · Oct 9, 2024 · 9657bdf · 9657bdf
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Showing 9 changed files with 10 additions and 21 deletions.
diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -16,7 +16,6 @@ Welcome to VerMoUTH's documentation!
    file_formats
    tutorials/index
    api/modules
-   martinize2_tutorials/index
 
 
 Indices and tables

diff --git a/doc/source/martinize2_tutorials/index.rst b/doc/source/martinize2_tutorials/index.rst
diff --git a/...urce/martinize2_tutorials/basic_usage.rst → doc/source/tutorials/basic_usage.rst b/...urce/martinize2_tutorials/basic_usage.rst → doc/source/tutorials/basic_usage.rst
diff --git a/...martinize2_tutorials/elastic_examples.png → doc/source/tutorials/elastic_examples.png b/...martinize2_tutorials/elastic_examples.png → doc/source/tutorials/elastic_examples.png
diff --git a/...martinize2_tutorials/elastic_networks.rst → doc/source/tutorials/elastic_networks.rst b/...martinize2_tutorials/elastic_networks.rst → doc/source/tutorials/elastic_networks.rst
diff --git a/...source/martinize2_tutorials/go_models.rst → doc/source/tutorials/go_models.rst b/...source/martinize2_tutorials/go_models.rst → doc/source/tutorials/go_models.rst
diff --git a/doc/source/tutorials/index.rst b/doc/source/tutorials/index.rst
@@ -1,11 +1,18 @@
 Tutorials
 =========
-You can find some examples on how to use martinize 2 in the martinize-examples
+This page contains several examples of how martinize2 can be used to convert
+proteins from atomistic to a martini3 representation.
+
+You can find further examples on how to use martinize2 in the martinize-examples
 repository: https://github.com/marrink-lab/martinize-examples
 
 .. Organize the tutorials in directories, so it's easier to keep their files
     together
 
 .. toctree::
+    basic_usage
+    elastic_networks
+    go_models
+    mutations_and_modifications
     6_adding_residues_links/index
     7_adding_modifications/index
diff --git a/...tutorials/mutations_and_modifications.rst → ...tutorials/mutations_and_modifications.rst b/...tutorials/mutations_and_modifications.rst → ...tutorials/mutations_and_modifications.rst
diff --git a/...ce/martinize2_tutorials/water_biasing.rst → doc/source/tutorials/water_biasing.rst b/...ce/martinize2_tutorials/water_biasing.rst → doc/source/tutorials/water_biasing.rst
@@ -20,7 +20,7 @@ The documentation describes these features::
                           <start_resid_1>:<end_resid_1> <start_resid_2>:<end_resid_2>... (default: [])
     -idr-tune             Tune the idr regions with specific bonded potentials. (default: False)
 
-These flags can be specified in conjunction with the `Go model <go_models>`_.
+These flags can be specified in conjunction with the Go model.
 
 
 Water biasing for secondary structure
@@ -33,7 +33,7 @@ described above must be used.
 
 This will produce a coarse-grained model of your protein, with virtual sites along the backbone.
 The virtual sites will be defined in an external file, which should be included in your topology
-as per the `Go model <go_models>`_ instructions.
+as per the Go model instructions.
 
 There will also be a second file, defining the additional non-bonded interactions between
 water and the secondary structure elements defined in the command. In this case, any residue