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_("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_( "RGroupDecompositionParameters", docString.c_str(), @@ -350,7 +350,7 @@ struct rgroupdecomp_wrapper { &RDKit::RGroupDecompositionParameters::includeTargetMolInResults); python::class_( - "RGroupDecomposition", docString.c_str(), + "Class for doing RGroupDecomposition", python::init( 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.