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Add safeSetattr to more params / options objects (#8842)

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* add safeSetattr to varios params objects

* added safeSetattr to further params / options
This commit is contained in:
Niels Maeder
2025-10-08 16:15:20 +02:00
committed by GitHub
parent b2fe43a9ad
commit db93262a3e
15 changed files with 49 additions and 22 deletions
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3
Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp
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@@ -563,7 +563,8 @@ BOOST_PYTHON_MODULE(rdChemReactions) {
.def_readwrite("agentWeight",
&RDKit::ReactionFingerprintParams::agentWeight)
.def_readwrite("includeAgents",
&RDKit::ReactionFingerprintParams::includeAgents);
&RDKit::ReactionFingerprintParams::includeAgents)
.def("__setattr__", &safeSetattr);
std::string docString =
R"DOC(A class for storing and applying chemical reactions.

3
Code/GraphMol/Depictor/Wrap/rdDepictor.cpp
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@@ -327,7 +327,8 @@ BOOST_PYTHON_MODULE(rdDepictor) {
"adjustMolBlockWedging is True")
.def_readwrite(
"useRingTemplates", &ConstrainedDepictionParams::useRingTemplates,
"use templates to generate coordinates of complex ring systems");
"use templates to generate coordinates of complex ring systems")
.def("__setattr__", &safeSetattr);
std::string docString;
docString =

3
Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp
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@@ -976,7 +976,8 @@ BOOST_PYTHON_MODULE(rdMolDescriptors) {
.setattr("atomTypes", atomPairTypes)
.setattr("numPathBits", RDKit::AtomPairs::numPathBits)
.setattr("numAtomPairFingerprintBits",
RDKit::AtomPairs::numAtomPairFingerprintBits);
RDKit::AtomPairs::numAtomPairFingerprintBits)
.def("__setattr__", &safeSetattr);
docString = "Returns the atom code (hash) for an atom";
python::def("GetAtomPairAtomCode", RDKit::AtomPairs::getAtomCode,
(python::arg("atom"), python::arg("branchSubtract") = 0,

10
Code/GraphMol/FMCS/Wrap/rdFMCS.cpp
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@@ -762,7 +762,9 @@ BOOST_PYTHON_MODULE(rdFMCS) {
"SMILES string to be used as the seed of the MCS")
.add_property("StoreAll", &RDKit::PyMCSParameters::getStoreAll,
&RDKit::PyMCSParameters::setStoreAll,
"toggles storage of degenerate MCSs");
"toggles storage of degenerate MCSs")
.def("__setattr__", &safeSetattr);
python::class_<RDKit::MCSAtomCompareParameters, boost::noncopyable>(
"MCSAtomCompareParameters",
@@ -787,7 +789,8 @@ BOOST_PYTHON_MODULE(rdFMCS) {
"results cannot include lone ring atoms")
.def_readwrite("MatchIsotope",
&RDKit::MCSAtomCompareParameters::MatchIsotope,
"use isotope atom queries in MCSResults");
"use isotope atom queries in MCSResults")
.def("__setattr__", &safeSetattr);
python::class_<RDKit::MCSBondCompareParameters, boost::noncopyable>(
"MCSBondCompareParameters",
@@ -811,7 +814,8 @@ BOOST_PYTHON_MODULE(rdFMCS) {
"won't match cyclodecane")
.def_readwrite("MatchStereo",
&RDKit::MCSBondCompareParameters::MatchStereo,
"include bond stereo in the comparison");
"include bond stereo in the comparison")
.def("__setattr__", &safeSetattr);
python::class_<RDKit::PyMCSProgress, boost::noncopyable>(
"MCSProgress",

4
Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp
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@@ -1384,7 +1384,9 @@ BOOST_PYTHON_MODULE(rdMolDraw2D) {
.def("setContourColour", &RDKit::setContourColour,
(python::arg("self"), python::arg("colour")))
.def("setColourMap", &RDKit::setColoursHelper,
(python::arg("self"), python::arg("colours")));
(python::arg("self"), python::arg("colours")))
.def("__setattr__", &safeSetattr);
docString = R"DOC(Generates and draws contours for a set of gaussians
- drawer: the MolDraw2D object to use

5
Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp
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@@ -11,6 +11,8 @@
#include <RDBoost/python.h>
#include <GraphMol/MolEnumerator/MolEnumerator.h>
#include <RDBoost/Wrap.h>
namespace python = boost::python;
using namespace RDKit;
namespace {
@@ -78,7 +80,8 @@ BOOST_PYTHON_MODULE(rdMolEnumerator) {
"seed for the random enumeration (not yet implemented")
.def("SetEnumerationOperator", &setEnumerationHelper,
python::args("self", "typ"),
"set the operator to be used for enumeration");
"set the operator to be used for enumeration")
.def("__setattr__", &safeSetattr);
python::def("Enumerate", &enumerateHelper1,
(python::arg("mol"), python::arg("maxPerOperation") = 0),
python::return_value_policy<python::manage_new_object>(),

6
Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp
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@@ -87,7 +87,8 @@ BOOST_PYTHON_MODULE(rdMolInterchange) {
.def_readwrite("useHCounts",
&RDKit::MolInterchange::JSONParseParameters::useHCounts,
"use atomic H counts from the JSON. You may want to set "
"this to False when parsing queries.");
"this to False when parsing queries.")
.def("__setattr__", &safeSetattr);
python::class_<RDKit::MolInterchange::JSONWriteParameters,
boost::noncopyable>("JSONWriteParameters",
@@ -95,7 +96,8 @@ BOOST_PYTHON_MODULE(rdMolInterchange) {
.def_readwrite(
"useRDKitExtensions",
&RDKit::MolInterchange::JSONWriteParameters::useRDKitExtensions,
"use RDKit extensions to the commonchem format");
"use RDKit extensions to the commonchem format")
.def("__setattr__", &safeSetattr);
std::string docString;
docString =

3
Code/GraphMol/MolProcessing/Wrap/rdMolProcessing.cpp
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@@ -76,7 +76,8 @@ BOOST_PYTHON_MODULE(rdMolProcessing) {
.def_readwrite("confId2D", &GeneralMolSupplier::SupplierOptions::confId2D,
"used for TDT files")
.def_readwrite("confId3D", &GeneralMolSupplier::SupplierOptions::confId3D,
"used for TDT files");
"used for TDT files")
.def("__setattr__", &safeSetattr);
python::def(
"GetFingerprintsForMolsInFile",

3
Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp
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@@ -460,7 +460,8 @@ BOOST_PYTHON_MODULE(rdMolStandardize) {
&RDKit::MolStandardize::CleanupParameters::
largestFragmentChooserCountHeavyAtomsOnly,
"whether LargestFragmentChooser should only count "
"heavy atoms (defaults to False)");
"heavy atoms (defaults to False)")
.def("__setattr__", &safeSetattr);
python::def("UpdateParamsFromJSON",
&RDKit::MolStandardize::updateCleanupParamsFromJSON,

3
Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp
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@@ -347,7 +347,8 @@ struct rgroupdecomp_wrapper {
&RDKit::RGroupDecompositionParameters::substructmatchParams)
.def_readwrite(
"includeTargetMolInResults",
&RDKit::RGroupDecompositionParameters::includeTargetMolInResults);
&RDKit::RGroupDecompositionParameters::includeTargetMolInResults)
.def("__setattr__", &safeSetattr);
python::class_<RDKit::RGroupDecompositionHelper, boost::noncopyable>(
"RGroupDecomposition",

6
Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp
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@@ -244,7 +244,8 @@ BOOST_PYTHON_MODULE(rdRascalMCES) {
" is > 0, it will over-ride the"
" similarityThreshold."
" Note that this refers to the"
" minimum number of BONDS in the MCES. Default=0.");
" minimum number of BONDS in the MCES. Default=0.")
.def("__setattr__", &safeSetattr);
docString =
"Find one or more MCESs between the 2 molecules given. Returns a list of "
@@ -290,7 +291,8 @@ BOOST_PYTHON_MODULE(rdRascalMCES) {
.def_readwrite(
"clusterMergeSim",
&RDKit::RascalMCES::RascalClusterOptions::clusterMergeSim,
"Two clusters are merged if the fraction of molecules they have in common is greater than this. Default=0.6.");
"Two clusters are merged if the fraction of molecules they have in common is greater than this. Default=0.6.")
.def("__setattr__", &safeSetattr);
docString =
"Use the RASCAL MCES similarity metric to do fuzzy clustering. Returns a list of lists "

3
Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp
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@@ -128,7 +128,8 @@ BOOST_PYTHON_MODULE(rdScaffoldNetwork) {
.def_readwrite("collectMolCounts",
&ScaffoldNetwork::ScaffoldNetworkParams::collectMolCounts,
"keep track of the number of molecules each scaffold was "
"found in");
"found in")
.def("__setattr__", &safeSetattr);
python::enum_<ScaffoldNetwork::EdgeType>("EdgeType")
.value("Fragment", ScaffoldNetwork::EdgeType::Fragment)

11
Code/GraphMol/Wrap/rdmolfiles.cpp
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@@ -1248,7 +1248,8 @@ BOOST_PYTHON_MODULE(rdmolfiles) {
.def_readwrite(
"scsrBaseHbondOptions",
&RDKit::v2::FileParsers::MolFromSCSRParams::scsrBaseHbondOptions,
"One of Ignore, UseSapAll(default) , UseSapOne, Auto");
"One of Ignore, UseSapAll(default) , UseSapOne, Auto")
.def("__setattr__", &safeSetattr);
docString =
"Construct a molecule from an SCSR Mol block.\n\n\
@@ -2581,8 +2582,9 @@ BOOST_PYTHON_MODULE(rdmolfiles) {
"choose CXSMILES fields to be included in the CXSMILES string (default=rdkit.Chem.rdmolfiles.CXSmilesFields.CX_ALL)")
.def_readwrite(
"restoreBondDirs", &RDKit::PNGMetadataParams::restoreBondDirs,
"choose what to do with bond dirs in the CXSMILES string (default=rdkit.Chem.rdmolfiles.RestoreBondDirOption.RestoreBondDirOptionClear)");
"choose what to do with bond dirs in the CXSMILES string (default=rdkit.Chem.rdmolfiles.RestoreBondDirOption.RestoreBondDirOptionClear)")
.def("__setattr__", &safeSetattr);
docString =
R"DOC(Construct a molecule from metadata in a PNG string.
@@ -2697,7 +2699,8 @@ BOOST_PYTHON_MODULE(rdmolfiles) {
"molecule is returned")
.def_readwrite(
"format", &RDKit::v2::CDXMLParser::CDXMLParserParams::format,
"ChemDraw format One of Auto, CDXML, CDX. For data streams, Auto defaults to CDXML");
"ChemDraw format One of Auto, CDXML, CDX. For data streams, Auto defaults to CDXML")
.def("__setattr__", &safeSetattr);
docString =
R"DOC(Construct a molecule from a cdxml file.

5
External/CoordGen/Wrap/rdCoordGen.cpp vendored
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@@ -16,6 +16,7 @@
#include <RDGeneral/Exceptions.h>
#include <GraphMol/RDKitBase.h>
#include <CoordGen/CoordGen.h>
#include <RDBoost/Wrap.h>
namespace python = boost::python;
@@ -90,7 +91,9 @@ struct coordgen_wrapper {
"controls sketcher precision")
.def_readwrite(
"treatNonterminalBondsToMetalAsZOBs",
&CoordGen::CoordGenParams::treatNonterminalBondsToMetalAsZeroOrder);
&CoordGen::CoordGenParams::treatNonterminalBondsToMetalAsZeroOrder)
.def("__setattr__", &safeSetattr);
python::def("SetDefaultTemplateFileDir", SetDefaultTemplateFileDir,
python::args("dir"));
docString =

3
External/FreeSASA/Wrap/rdFreeSASA.cpp vendored
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@@ -111,7 +111,8 @@ struct freesasa_wrapper {
python::args("self", "alg", "cls", "pr")))
.def_readwrite("algorithm", &FreeSASA::SASAOpts::algorithm)
.def_readwrite("classifier", &FreeSASA::SASAOpts::classifier)
.def_readwrite("probeRadius", &FreeSASA::SASAOpts::probeRadius);
.def_readwrite("probeRadius", &FreeSASA::SASAOpts::probeRadius)
.def("__setattr__", &safeSetattr);
docString =
"Classify the atoms in the molecule returning their radii if "