Merge pull request #259 from lucas-diedrich/refactor_docs_II

[DOC] Refactor Docs II
MannLabs · Dec 11, 2024 · 1f08d58 · 1f08d58
2 parents 1a2e0e0 + 9288503
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diff --git a/docs/constants/atom.rst b/docs/constants/atom.rst
@@ -1,5 +1,5 @@
 alphabase.constants.atom
-===========================
+========================
 
 .. automodule:: alphabase.constants.atom
    :members:

diff --git a/docs/io/hdf.rst b/docs/io/hdf.rst
@@ -1,5 +1,5 @@
 alphabase.io.hdf
-===========================
+================
 
 .. automodule:: alphabase.io.hdf
    :members:

diff --git a/docs/io/tempmmap.rst b/docs/io/tempmmap.rst
@@ -1,5 +1,5 @@
 alphabase.io.tempmmap
-===========================
+=====================
 
 .. automodule:: alphabase.io.tempmmap
    :members:

diff --git a/docs/modules_io.rst b/docs/modules_io.rst
@@ -5,4 +5,4 @@ alphabase.io
    :maxdepth: 1
 
    io/hdf
-.. io/tempmmap
+   io/tempmmap
diff --git a/docs/nbs/peptide_smiles.ipynb b/docs/nbs/peptide_smiles.ipynb
@@ -353,7 +353,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Further usage:\n",
+    "## Further usage:\n",
     "\n",
     "### Molecular fingerprints\n",
     "\n",

diff --git a/docs/notebooks.rst b/docs/notebooks.rst
@@ -3,12 +3,41 @@ Tutorials and Notebooks
 
 Tutorials and notebooks about how to use AlphaBase.
 
+
+Basics
+------
+
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    tutorials/tutorial_basic_definitions
    tutorials/tutorial_dataframe_structures
+
+
+Spectral libraries
+------------------
+
+.. toctree::
+   :maxdepth: 1
+
    tutorials/tutorial_spectral_libraries
    nbs/library_from_fasta
+
+
+Reader
+------
+.. toctree::
+   :maxdepth: 1
+
    nbs/psm_readers
    nbs/library_reader
+
+
+Chemical structures
+-------------------
+.. toctree::
+   :maxdepth: 1
+
+   nbs/tutorial_smiles
+   nbs/peptide_smiles
+   nbs/adding_smiles
diff --git a/docs/protein/fasta.rst b/docs/protein/fasta.rst
@@ -1,5 +1,5 @@
 alphabase.protein.fasta
-===========================
+=======================
 
 The :obj:`SpecLibFasta <alphabase.protein.fasta.SpecLibFasta>`
 provides the highest level APIs based on all other

diff --git a/docs/protein/protein_level_decoy.rst b/docs/protein/protein_level_decoy.rst
@@ -1,5 +1,5 @@
 alphabase.protein.protein_level_decoy
-===========================
+=====================================
 
 Protein reverse decoy defined in
 :obj:`ProteinReverseDecoy <alphabase.protein.protein_level_decoy.ProteinReverseDecoy>`.

diff --git a/docs/psm_reader/maxquant_reader.rst b/docs/psm_reader/maxquant_reader.rst
@@ -1,5 +1,5 @@
 alphabase.psm_reader.maxquant_reader
-===========================================
+====================================
 
 .. automodule:: alphabase.psm_reader.maxquant_reader
    :members:

diff --git a/docs/psm_reader/msfragger_reader.rst b/docs/psm_reader/msfragger_reader.rst
@@ -1,5 +1,5 @@
 alphabase.psm_reader.msfragger_reader
-===========================================
+=====================================
 
 .. automodule:: alphabase.psm_reader.msfragger_reader
    :members:

diff --git a/docs/psm_reader/pfind_reader.rst b/docs/psm_reader/pfind_reader.rst
@@ -1,5 +1,5 @@
 alphabase.psm_reader.pfind_reader
-===================================
+=================================
 
 .. automodule:: alphabase.psm_reader.pfind_reader
    :members:

diff --git a/docs/psm_reader/psm_reader.rst b/docs/psm_reader/psm_reader.rst
@@ -1,5 +1,5 @@
 alphabase.psm_reader.psm_reader
-===================================
+===============================
 
 See examples in :doc:`psm_reader notebook <../nbs/psm_readers>`.
 

diff --git a/docs/spectral_library/base.rst b/docs/spectral_library/base.rst
@@ -1,5 +1,5 @@
 alphabase.spectral_library.base
-===================================
+===============================
 
 .. automodule:: alphabase.spectral_library.base
    :members:

diff --git a/docs/tutorials/tutorial_basic_definitions.ipynb b/docs/tutorials/tutorial_basic_definitions.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Tutorial: Basic Definations and Settings\n",
+    "# Tutorial: Basic Definitions and Settings\n",
     "\n",
     "Measuring m/z values is the elemental function of MS technologies, therefore the calculation of mass values for a peptide and its fragments becomes the most essential part in MS-based computational tools. AlphaBase calculates all mass values from atoms. And the masses of amino acids and modifications are calculated from their atom compositions, repectively. Eventually, the masses of peptides or precursors as well as their fragments can be calculated by the amino acid sequences with or without modifications (See figure below).\n",
     "\n",