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Adds some features to the C# SWIG wrappers (#9274)

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This commit is contained in:
Gareth Jones
2026-05-14 01:07:56 -06:00
committed by GitHub
parent 24f0007757
commit 8e9adcd467
6 changed files with 257 additions and 1 deletions
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2
Code/GraphMol/MolStandardize/Tautomer.h
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@@ -449,6 +449,7 @@ class RDKIT_MOLSTANDARDIZE_EXPORT TautomerEnumerator {
/// When Iterable is TautomerEnumeratorResult we use the other non-templated
/// overload for efficiency (TautomerEnumeratorResult already has SMILES so no
/// need to recompute them)
/// caller owns the pointer
template <class Iterable,
typename std::enable_if<
!std::is_same<Iterable, TautomerEnumeratorResult>::value,
@@ -504,6 +505,7 @@ class RDKIT_MOLSTANDARDIZE_EXPORT TautomerEnumerator {
*/
/// When \p scoreFunc is empty (default), an optimized scorer is created
/// that pre-filters substructure patterns once for the input molecule.
/// caller owns the pointer
ROMol *canonicalize(
const ROMol &mol,
boost::function<int(const ROMol &mol)> scoreFunc = {}) const;

3
Code/JavaWrappers/ROMol.i
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@@ -77,6 +77,7 @@
%template(ROMol_Vect) std::vector< boost::shared_ptr<RDKit::ROMol> >;
%template(ROMol_Vect_Vect) std::vector< std::vector< boost::shared_ptr<RDKit::ROMol> > >;
%template(Atom_Vect) std::vector<RDKit::Atom*>;
%template(Const_Bond_Vect) std::vector<const RDKit::Bond*>;
%template(StereoGroup_Vect) std::vector<RDKit::StereoGroup>;
%template(UChar_Vect) std::vector<unsigned char>;
@@ -210,6 +211,8 @@
%newobject getBonds;
%newobject getAtomNeighbors;
%newobject getAtomBonds;
%newobject getDistanceMat;
%newobject getAdjacencyMatrix;
%{
#ifdef RDK_BUILD_COORDGEN_SUPPORT

18
Code/JavaWrappers/Tautomer.i Normal file
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@@ -0,0 +1,18 @@
%include "std_vector.i"
%{
#include <vector>
#include <GraphMol/MolStandardize/Tautomer.h>
%}
%shared_ptr(RDKit::ROMol)
%template(Sizet_Vect) std::vector<size_t>;
%ignore RDKit::MolStandardize::TautomerScoringFunctions::makeOptimizedScorer;
%shared_ptr(RDKit::MolStandardize::TautomerEnumerator)
%newobject RDKit::MolStandardize::tautomerEnumeratorFromParams;
%newobject RDKit::MolStandardize::getV1TautomerEnumerator;
%newobject RDKit::MolStandardize::TautomerEnumerator::pickCanonical;
%newobject RDKit::MolStandardize::TautomerEnumerator::canonicalize;
%include <GraphMol/MolStandardize/Tautomer.h>

3
Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i
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@@ -250,6 +250,7 @@ typedef unsigned long long int uintmax_t;
%include "../SubstructLibrary.i"
%include "../ScaffoldNetwork.i"
%include "../TautomerQuery.i"
%include "../Tautomer.i"
%include "../MolEnumerator.i"
%include "../SubstanceGroup.i"
%include "../MolHash.i"
@@ -288,6 +289,7 @@ typedef unsigned long long int uintmax_t;
%template(Double_Pair) std::pair<double,double>;
%template(UInt_Pair) std::pair<uint32_t, int >;
%template(Long_Pair) std::pair<boost::int64_t,int>;
%template(String_Pair) std::pair<std::string, std::string>;
/* map */
%template(String_String_Map) std::map<std::string,std::string>;
@@ -300,6 +302,7 @@ typedef unsigned long long int uintmax_t;
%template(UInt_Pair_Vect) std::vector<std::pair<uint32_t,int> >;
%template(Match_Vect) std::vector<std::pair<int32_t,int> >;
%template(Long_Pair_Vect) std::vector<std::pair<boost::int64_t,int> >;
%template(String_String_Pair_Vect) std::vector<std::pair<std::string,std::string> >;
/* vector vector */
%template(Int_Vect_Vect) std::vector<std::vector<int> >;

98
Code/JavaWrappers/csharp_wrapper/RdkitTests/TestMolStandardize.cs
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@@ -1,4 +1,5 @@
using GraphMolWrap;
using System.Collections.Generic;
using GraphMolWrap;
using Xunit;
@@ -43,5 +44,100 @@ namespace RdkitTests
RDKFuncs.canonicalTautomerInPlace(mol);
Assert.Equal("C[PH](C)=O", mol.MolToSmiles());
}
// Test that standardization rules for a guanidinium group work as expected when matching an Arginine query to a set of peptides
[Fact]
public void TestRMatchNormalize()
{
var cleanupParameters = new CleanupParameters();
cleanupParameters.doCanonical = true;
var replacements = cleanupParameters.normalizationData;
var replacement = new String_Pair("Standardize ARG",
"[#6:1][#6:2][#6:3][#7H1:4]-[#6X3:5](=[#7:6])-[#7:7]>>[#6:1][#6:2][#6:3][#7H0:4]=[#6X3:5](-[#7:6])-[#7:7]");
replacements.Add(replacement);
cleanupParameters.normalizationData = replacements;
// Record for R
var molFile = @"
ChemDraw06032117432D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 14 13 0 0 1
M V30 BEGIN ATOM
M V30 1 C 1.111765 -1.636387 0.000000 0
M V30 2 C 0.389632 -1.237272 0.000000 0
M V30 3 C 0.374442 -0.412275 0.000000 0
M V30 4 C -0.347639 -0.013245 0.000000 0
M V30 5 C -0.362863 0.811612 0.000000 0
M V30 6 N -0.273074 -1.636387 0.000000 0
M V30 7 O 1.111765 -2.461396 0.000000 0
M V30 8 N -1.084995 1.210729 0.000000 0
M V30 9 C -1.100270 2.035672 0.000000 0
M V30 10 N -0.393589 2.461396 0.000000 0
M V30 11 N -1.822349 2.434701 0.000000 0
M V30 12 R1 -0.995042 -1.237157 0.000000 0
M V30 13 R2 1.822349 -1.217228 0.000000 0
M V30 14 R3 0.320882 2.048896 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 6 12
M V30 2 1 1 13
M V30 3 2 7 1
M V30 4 1 1 2
M V30 5 1 2 6
M V30 6 1 2 3 CFG=1
M V30 7 1 3 4
M V30 8 1 4 5
M V30 9 1 5 8
M V30 10 2 8 9
M V30 11 1 9 11
M V30 12 1 9 10
M V30 13 1 10 14
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEABS ATOMS=(1 2)
M V30 END COLLECTION
M V30 END CTAB
M END
";
var q = RWMol.MolFromMolBlock(molFile);
q = RDKFuncs.normalize(q, cleanupParameters);
RDKFuncs.addHs(q);
foreach (var atom in q.getAtoms())
{
if (atom.getAtomicNum() != 0) continue;
atom.setAtomMapNum(0);
atom.setIsotope(0);
atom.clearProp("_MolFileRLabel");
}
var queryParameters = AdjustQueryParameters.noAdjustments();
queryParameters.makeDummiesQueries = true;
RDKFuncs.adjustQueryProperties(q, queryParameters);
var matchParameters = new SubstructMatchParameters
{
useChirality = true, specifiedStereoQueryMatchesUnspecified = true, useEnhancedStereo = true
};
List<string> smiles = new();
smiles.Add(
"O=C(N)CCC1NC(=O)C2N(C(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(NC1=O)CCCNC(=N)N)CO)C(O)C)CC(C)C)CCSC)CCC2");
smiles.Add(
"C[C@H](N[H])C(=O)N[C@H](C(=O)N[C@@H]1C(=O)N([C@@H](C)C(=O)N[C@H](C)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C=O)CC(O)=O)CSSC1)[C@@H](C)O)CCCCN[H])[C@@H](C)C(=O)O)CCCNC(N)=N");
smiles.Add(
"CSCC[C@@H]1NC(=O)[C@H](CC(C)C)NC(=O)[C@H]([C@@H](C)O)NC(=O)[C@H](CO)NC(=O)[C@H](CCCN=C(N)N)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@@H]2CCCN2C1=O");
smiles.Add(
"C[C@H](N)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N[C@H]1CSSC[C@@H](C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](C)C(=O)O)NC(=O)[C@H]([C@@H](C)O)NC(=O)[C@H](CCCCN)NC(=O)[C@H](C)NC(=O)[C@H](C)NC1=O");
foreach (var smi in smiles)
{
var mol = RWMol.MolFromSmiles(smi);
mol = RDKFuncs.normalize(mol, cleanupParameters);
RDKFuncs.addHs(mol);
var normalizedHits = mol.getSubstructMatches(q, matchParameters);
Assert.Equal(1, normalizedHits.Count);
}
}
}
}

134
Code/JavaWrappers/csharp_wrapper/RdkitTests/TestTautomer.cs Normal file
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@@ -0,0 +1,134 @@
using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Threading.Tasks;
using GraphMolWrap;
using Xunit;
namespace RdkitTests
{
public class TestTautomer
{
[Fact]
public void TestTautomerEnumeration()
{
var smiles1 = "CCCNC(=N)N";
var mol1 = RDKFuncs.SmilesToMol(smiles1);
var smiles2 = "CCCN=C(N)N";
var mol2 = RDKFuncs.SmilesToMol(smiles2);
Assert.Equal(0, mol1.getSubstructMatch(mol2).Count);
var enumerator = new TautomerEnumerator();
var tautomers1 = enumerator.enumerate(mol1);
var tautomers2 = enumerator.enumerate(mol2);
Assert.Equal(2, Convert.ToInt32(tautomers1.size()));
Assert.Equal(2, Convert.ToInt32(tautomers2.size()));
var mol1Matches = 0;
var mol2Matches = 0;
for (uint i = 0; i < 2; i++)
{
var mol1Tautomer = tautomers1.at(i);
if (mol2.getSubstructMatch(mol1Tautomer).Count > 0) mol2Matches++;
var mol2Tautomer = tautomers2.at(i);
if (mol1.getSubstructMatch(mol2Tautomer).Count > 0) mol1Matches++;
}
Assert.Equal(1, mol1Matches);
Assert.Equal(1, mol2Matches);
}
[Fact]
public void TestTautomerCanonicalization()
{
var smi =
"O=C(N)CCC1NC(=O)C2N(C(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(NC1=O)CCCNC(=N)N)CO)C(O)C)CC(C)C)CCSC)CCC2";
var mol = RWMol.MolFromSmiles(smi);
// Record for R
var molFile = @"
ChemDraw06032117432D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 14 13 0 0 1
M V30 BEGIN ATOM
M V30 1 C 1.111765 -1.636387 0.000000 0
M V30 2 C 0.389632 -1.237272 0.000000 0
M V30 3 C 0.374442 -0.412275 0.000000 0
M V30 4 C -0.347639 -0.013245 0.000000 0
M V30 5 C -0.362863 0.811612 0.000000 0
M V30 6 N -0.273074 -1.636387 0.000000 0
M V30 7 O 1.111765 -2.461396 0.000000 0
M V30 8 N -1.084995 1.210729 0.000000 0
M V30 9 C -1.100270 2.035672 0.000000 0
M V30 10 N -0.393589 2.461396 0.000000 0
M V30 11 N -1.822349 2.434701 0.000000 0
M V30 12 R1 -0.995042 -1.237157 0.000000 0
M V30 13 R2 1.822349 -1.217228 0.000000 0
M V30 14 R3 0.320882 2.048896 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 6 12
M V30 2 1 1 13
M V30 3 2 7 1
M V30 4 1 1 2
M V30 5 1 2 6
M V30 6 1 2 3 CFG=1
M V30 7 1 3 4
M V30 8 1 4 5
M V30 9 1 5 8
M V30 10 2 8 9
M V30 11 1 9 11
M V30 12 1 9 10
M V30 13 1 10 14
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEABS ATOMS=(1 2)
M V30 END COLLECTION
M V30 END CTAB
M END
";
var query = RWMol.MolFromMolBlock(molFile);
foreach (var atom in query.getAtoms())
{
if (atom.getAtomicNum() != 0)
{
continue;
}
atom.setIsotope(0U);
atom.setAtomMapNum(0);
}
var queryParameters = AdjustQueryParameters.noAdjustments();
queryParameters.makeDummiesQueries = true;
var matchParameters = new SubstructMatchParameters
{
useChirality = true, specifiedStereoQueryMatchesUnspecified = true, useEnhancedStereo = true
};
var cleanupParameters = new CleanupParameters();
cleanupParameters.tautomerRemoveBondStereo = false;
cleanupParameters.tautomerRemoveIsotopicHs = false;
cleanupParameters.tautomerReassignStereo = false;
cleanupParameters.tautomerRemoveSp3Stereo = false;
var canonMol = RDKFuncs.canonicalTautomer(mol, cleanupParameters);
RDKFuncs.addHs(canonMol);
var canonQuery = RDKFuncs.canonicalTautomer(query, cleanupParameters);
RDKFuncs.addHs(canonQuery);
RDKFuncs.adjustQueryProperties(canonQuery, queryParameters);
var canonMatches = canonMol.getSubstructMatches(canonQuery, matchParameters);
var numberCanonHits = canonMatches.Count;
Assert.Equal(1, numberCanonHits);
RDKFuncs.addHs(mol);
RDKFuncs.addHs(query);
RDKFuncs.adjustQueryProperties(query, queryParameters);
var matches = mol.getSubstructMatches(query, matchParameters);
var numberHits = matches.Count;
Assert.Equal(0, numberHits);
}
}
}