From d392c755b74211280c398fc82a03fbeb5c6e248f Mon Sep 17 00:00:00 2001
From: badisa <badisa@users.noreply.github.com>
Date: Thu, 18 Sep 2025 08:41:16 -0600
Subject: [PATCH] Document Options in RGroupDcompose and other minor docs fixes
 (#8757)

* Adds missing options docstring

* Always be cleaning

* Fix typos in RGroupDecomposition module

* Update documentation on configuring doxygen

* Was a step that I couldn't find reference to besides in the Makefile

* Undo american spelling of labelling

* British spelling appears more consistent

* Fix style of RGroupDecompositionParameters parameter

* Also fixes a typo

* Remove unintentional use of docstring

* Was assigning documentation about the parameters to the
  RGroupDecomposition

* Remove empty string

* Apply suggestions from code review

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---
 .../RGroupDecomposition/Wrap/rdRGroupComposition.cpp  | 11 +++++++----
 Docs/Book/GettingStartedWithContributing.md           |  4 +++-
 Docs/Book/Makefile                                    |  2 +-
 Docs/Book_jp/Makefile                                 |  2 +-
 4 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp b/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp
index 60955e3dd..4b045056b 100644
--- a/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp
+++ b/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp
@@ -224,7 +224,7 @@ struct rgroupdecomp_wrapper {
         .export_values();
 
     python::enum_<RDKit::RGroupCoreAlignment>("RGroupCoreAlignment")
-        // DEPRECATED, remove the folowing line in release 2021.03
+        // DEPRECATED, remove the following line in release 2021.03
         .value("None", RDKit::NoAlignment)
         .value("NoAlignment", RDKit::NoAlignment)
         .value("MCS", RDKit::MCS)
@@ -287,7 +287,7 @@ struct rgroupdecomp_wrapper {
         "    - doTautomers: match all tautomers of a core against each "
         "input structure\n"
         "    - doEnumeration: expand input cores into enumerated mol bundles\n"
-        "    -allowMultipleRGroupsOnUnlabelled: permit more that one rgroup to "
+        "    - allowMultipleRGroupsOnUnlabelled: permit more than one rgroup to "
         "be attached to an unlabelled core atom";
     python::class_<RDKit::RGroupDecompositionParameters>(
         "RGroupDecompositionParameters", docString.c_str(),
@@ -350,7 +350,7 @@ struct rgroupdecomp_wrapper {
             &RDKit::RGroupDecompositionParameters::includeTargetMolInResults);
 
     python::class_<RDKit::RGroupDecompositionHelper, boost::noncopyable>(
-        "RGroupDecomposition", docString.c_str(),
+        "Class for doing RGroupDecomposition",
         python::init<python::object>(
             python::args("self", "cores"),
             "Construct from a molecule or sequence of molecules"))
@@ -398,7 +398,7 @@ struct rgroupdecomp_wrapper {
              "       columns[rgroup_label] = [ mols_or_smiles ]\n");
 
     docString =
-        "Decompose a collecion of molecules into their Rgroups\n"
+        "Decompose a collection of molecules into their Rgroups\n"
         "  ARGUMENTS:\n"
         "    - cores: a set of cores from most to least specific.\n"
         "             See RGroupDecompositionParameters for more details\n"
@@ -408,6 +408,9 @@ struct rgroupdecomp_wrapper {
         "molecules [default: False]\n"
         "    - asRows: return the results as rows (default) otherwise return "
         "columns\n"
+        "    - options: RGroupDecompositionParameters object that defines "
+        "the parameters for the decomposition.\n"
+        "             See RGroupDecompositionParameters for defaults\n"
         "\n"
         "  RETURNS: row_or_column_results, unmatched\n"
         "\n"
diff --git a/Docs/Book/GettingStartedWithContributing.md b/Docs/Book/GettingStartedWithContributing.md
index 901a72486..1b4a29a31 100644
--- a/Docs/Book/GettingStartedWithContributing.md
+++ b/Docs/Book/GettingStartedWithContributing.md
@@ -270,8 +270,10 @@ The RDKit docs support inclusion of Sphinx doctests to allow the result of a cod
 
 #### Build the Documentation
 
-To preview your changes to the RDKit documentation, build the docs locally. First set up your development environment by following the instructions in [Building RDKit for Development](#building-rdkit-for-development). Then change to the directory `Docs/Book`:
+To preview your changes to the RDKit documentation, build the docs locally. First set up your development environment by following the instructions in [Building RDKit for Development](#building-rdkit-for-development). Then run `doxygen` before changing to the directory `Docs/Book`:
   ```
+  # run doxygen
+  cd $RDBASE/Code/ && doxygen doxygen/doxygen.config
   cd $RDBASE/Docs/Book
   ```
 
diff --git a/Docs/Book/Makefile b/Docs/Book/Makefile
index edc4812f6..54835ad49 100644
--- a/Docs/Book/Makefile
+++ b/Docs/Book/Makefile
@@ -8,7 +8,7 @@ PAPER         =
 BUILDDIR      = _build
 
 # Created by running doxygen in the $RDBASE/Code directory as follows:
-#  doxygen doxygen.config
+#  doxygen doxygen/doxygen.config
 CPPAPIDOCSHOME   = $(RDBASE)/Code/docs
 
 # Internal variables.
diff --git a/Docs/Book_jp/Makefile b/Docs/Book_jp/Makefile
index d83708100..f7adc44b1 100644
--- a/Docs/Book_jp/Makefile
+++ b/Docs/Book_jp/Makefile
@@ -8,7 +8,7 @@ PAPER         =
 BUILDDIR      = _build
 
 # Created by running doxygen in the $RDBASE/Code directory as follows:
-#  doxygen doxygen.config
+#  doxygen doxygen/doxygen.config
 CPPAPIDOCSHOME   = $(RDBASE)/Code/docs
 
 # Internal variables.