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jones-garethjones-gareth
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Adds some features to the C# SWIG wrappers (rdkit#9274)
1 parent 24f0007 commit 8e9adcd

6 files changed

Lines changed: 257 additions & 1 deletion

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‎Code/GraphMol/MolStandardize/Tautomer.h‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -449,6 +449,7 @@ class RDKIT_MOLSTANDARDIZE_EXPORT TautomerEnumerator {
449449
/// When Iterable is TautomerEnumeratorResult we use the other non-templated
450450
/// overload for efficiency (TautomerEnumeratorResult already has SMILES so no
451451
/// need to recompute them)
452+
/// caller owns the pointer
452453
template <class Iterable,
453454
typename std::enable_if<
454455
!std::is_same<Iterable, TautomerEnumeratorResult>::value,
@@ -504,6 +505,7 @@ class RDKIT_MOLSTANDARDIZE_EXPORT TautomerEnumerator {
504505
*/
505506
/// When \p scoreFunc is empty (default), an optimized scorer is created
506507
/// that pre-filters substructure patterns once for the input molecule.
508+
/// caller owns the pointer
507509
ROMol *canonicalize(
508510
const ROMol &mol,
509511
boost::function<int(const ROMol &mol)> scoreFunc = {}) const;

‎Code/JavaWrappers/ROMol.i‎

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@@ -77,6 +77,7 @@
7777
%template(ROMol_Vect) std::vector< boost::shared_ptr<RDKit::ROMol> >;
7878
%template(ROMol_Vect_Vect) std::vector< std::vector< boost::shared_ptr<RDKit::ROMol> > >;
7979
%template(Atom_Vect) std::vector<RDKit::Atom*>;
80+
%template(Const_Bond_Vect) std::vector<const RDKit::Bond*>;
8081
%template(StereoGroup_Vect) std::vector<RDKit::StereoGroup>;
8182
%template(UChar_Vect) std::vector<unsigned char>;
8283

@@ -210,6 +211,8 @@
210211
%newobject getBonds;
211212
%newobject getAtomNeighbors;
212213
%newobject getAtomBonds;
214+
%newobject getDistanceMat;
215+
%newobject getAdjacencyMatrix;
213216

214217
%{
215218
#ifdef RDK_BUILD_COORDGEN_SUPPORT

‎Code/JavaWrappers/Tautomer.i‎

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@@ -0,0 +1,18 @@
1+
%include "std_vector.i"
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3+
%{
4+
#include <vector>
5+
#include <GraphMol/MolStandardize/Tautomer.h>
6+
%}
7+
8+
%shared_ptr(RDKit::ROMol)
9+
%template(Sizet_Vect) std::vector<size_t>;
10+
%ignore RDKit::MolStandardize::TautomerScoringFunctions::makeOptimizedScorer;
11+
%shared_ptr(RDKit::MolStandardize::TautomerEnumerator)
12+
%newobject RDKit::MolStandardize::tautomerEnumeratorFromParams;
13+
%newobject RDKit::MolStandardize::getV1TautomerEnumerator;
14+
%newobject RDKit::MolStandardize::TautomerEnumerator::pickCanonical;
15+
%newobject RDKit::MolStandardize::TautomerEnumerator::canonicalize;
16+
17+
%include <GraphMol/MolStandardize/Tautomer.h>
18+

‎Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -250,6 +250,7 @@ typedef unsigned long long int uintmax_t;
250250
%include "../SubstructLibrary.i"
251251
%include "../ScaffoldNetwork.i"
252252
%include "../TautomerQuery.i"
253+
%include "../Tautomer.i"
253254
%include "../MolEnumerator.i"
254255
%include "../SubstanceGroup.i"
255256
%include "../MolHash.i"
@@ -288,6 +289,7 @@ typedef unsigned long long int uintmax_t;
288289
%template(Double_Pair) std::pair<double,double>;
289290
%template(UInt_Pair) std::pair<uint32_t, int >;
290291
%template(Long_Pair) std::pair<boost::int64_t,int>;
292+
%template(String_Pair) std::pair<std::string, std::string>;
291293

292294
/* map */
293295
%template(String_String_Map) std::map<std::string,std::string>;
@@ -300,6 +302,7 @@ typedef unsigned long long int uintmax_t;
300302
%template(UInt_Pair_Vect) std::vector<std::pair<uint32_t,int> >;
301303
%template(Match_Vect) std::vector<std::pair<int32_t,int> >;
302304
%template(Long_Pair_Vect) std::vector<std::pair<boost::int64_t,int> >;
305+
%template(String_String_Pair_Vect) std::vector<std::pair<std::string,std::string> >;
303306

304307
/* vector vector */
305308
%template(Int_Vect_Vect) std::vector<std::vector<int> >;

‎Code/JavaWrappers/csharp_wrapper/RdkitTests/TestMolStandardize.cs‎

Lines changed: 97 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,5 @@
1-
using GraphMolWrap;
1+
using System.Collections.Generic;
2+
using GraphMolWrap;
23
using Xunit;
34

45

@@ -43,5 +44,100 @@ public void TestCanonicalTautomer()
4344
RDKFuncs.canonicalTautomerInPlace(mol);
4445
Assert.Equal("C[PH](C)=O", mol.MolToSmiles());
4546
}
47+
48+
// Test that standardization rules for a guanidinium group work as expected when matching an Arginine query to a set of peptides
49+
[Fact]
50+
public void TestRMatchNormalize()
51+
{
52+
var cleanupParameters = new CleanupParameters();
53+
cleanupParameters.doCanonical = true;
54+
var replacements = cleanupParameters.normalizationData;
55+
var replacement = new String_Pair("Standardize ARG",
56+
"[#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]");
57+
replacements.Add(replacement);
58+
cleanupParameters.normalizationData = replacements;
59+
// Record for R
60+
var molFile = @"
61+
ChemDraw06032117432D
62+
63+
0 0 0 0 0 0 V3000
64+
M V30 BEGIN CTAB
65+
M V30 COUNTS 14 13 0 0 1
66+
M V30 BEGIN ATOM
67+
M V30 1 C 1.111765 -1.636387 0.000000 0
68+
M V30 2 C 0.389632 -1.237272 0.000000 0
69+
M V30 3 C 0.374442 -0.412275 0.000000 0
70+
M V30 4 C -0.347639 -0.013245 0.000000 0
71+
M V30 5 C -0.362863 0.811612 0.000000 0
72+
M V30 6 N -0.273074 -1.636387 0.000000 0
73+
M V30 7 O 1.111765 -2.461396 0.000000 0
74+
M V30 8 N -1.084995 1.210729 0.000000 0
75+
M V30 9 C -1.100270 2.035672 0.000000 0
76+
M V30 10 N -0.393589 2.461396 0.000000 0
77+
M V30 11 N -1.822349 2.434701 0.000000 0
78+
M V30 12 R1 -0.995042 -1.237157 0.000000 0
79+
M V30 13 R2 1.822349 -1.217228 0.000000 0
80+
M V30 14 R3 0.320882 2.048896 0.000000 0
81+
M V30 END ATOM
82+
M V30 BEGIN BOND
83+
M V30 1 1 6 12
84+
M V30 2 1 1 13
85+
M V30 3 2 7 1
86+
M V30 4 1 1 2
87+
M V30 5 1 2 6
88+
M V30 6 1 2 3 CFG=1
89+
M V30 7 1 3 4
90+
M V30 8 1 4 5
91+
M V30 9 1 5 8
92+
M V30 10 2 8 9
93+
M V30 11 1 9 11
94+
M V30 12 1 9 10
95+
M V30 13 1 10 14
96+
M V30 END BOND
97+
M V30 BEGIN COLLECTION
98+
M V30 MDLV30/STEABS ATOMS=(1 2)
99+
M V30 END COLLECTION
100+
M V30 END CTAB
101+
M END
102+
";
103+
var q = RWMol.MolFromMolBlock(molFile);
104+
q = RDKFuncs.normalize(q, cleanupParameters);
105+
RDKFuncs.addHs(q);
106+
foreach (var atom in q.getAtoms())
107+
{
108+
if (atom.getAtomicNum() != 0) continue;
109+
atom.setAtomMapNum(0);
110+
atom.setIsotope(0);
111+
atom.clearProp("_MolFileRLabel");
112+
}
113+
114+
var queryParameters = AdjustQueryParameters.noAdjustments();
115+
queryParameters.makeDummiesQueries = true;
116+
RDKFuncs.adjustQueryProperties(q, queryParameters);
117+
var matchParameters = new SubstructMatchParameters
118+
{
119+
useChirality = true, specifiedStereoQueryMatchesUnspecified = true, useEnhancedStereo = true
120+
};
121+
List<string> smiles = new();
122+
smiles.Add(
123+
"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");
124+
smiles.Add(
125+
"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");
126+
smiles.Add(
127+
"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");
128+
smiles.Add(
129+
"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");
130+
foreach (var smi in smiles)
131+
{
132+
var mol = RWMol.MolFromSmiles(smi);
133+
134+
mol = RDKFuncs.normalize(mol, cleanupParameters);
135+
RDKFuncs.addHs(mol);
136+
137+
var normalizedHits = mol.getSubstructMatches(q, matchParameters);
138+
Assert.Equal(1, normalizedHits.Count);
139+
}
140+
}
46141
}
142+
47143
}

‎Code/JavaWrappers/csharp_wrapper/RdkitTests/TestTautomer.cs‎

Lines changed: 134 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,134 @@
1+
using System;
2+
using System.Collections.Generic;
3+
using System.Linq;
4+
using System.Text;
5+
using System.Threading.Tasks;
6+
using GraphMolWrap;
7+
using Xunit;
8+
9+
namespace RdkitTests
10+
{
11+
public class TestTautomer
12+
{
13+
[Fact]
14+
public void TestTautomerEnumeration()
15+
{
16+
var smiles1 = "CCCNC(=N)N";
17+
var mol1 = RDKFuncs.SmilesToMol(smiles1);
18+
var smiles2 = "CCCN=C(N)N";
19+
var mol2 = RDKFuncs.SmilesToMol(smiles2);
20+
Assert.Equal(0, mol1.getSubstructMatch(mol2).Count);
21+
22+
var enumerator = new TautomerEnumerator();
23+
var tautomers1 = enumerator.enumerate(mol1);
24+
var tautomers2 = enumerator.enumerate(mol2);
25+
Assert.Equal(2, Convert.ToInt32(tautomers1.size()));
26+
Assert.Equal(2, Convert.ToInt32(tautomers2.size()));
27+
28+
var mol1Matches = 0;
29+
var mol2Matches = 0;
30+
for (uint i = 0; i < 2; i++)
31+
{
32+
var mol1Tautomer = tautomers1.at(i);
33+
if (mol2.getSubstructMatch(mol1Tautomer).Count > 0) mol2Matches++;
34+
var mol2Tautomer = tautomers2.at(i);
35+
if (mol1.getSubstructMatch(mol2Tautomer).Count > 0) mol1Matches++;
36+
}
37+
38+
Assert.Equal(1, mol1Matches);
39+
Assert.Equal(1, mol2Matches);
40+
}
41+
42+
[Fact]
43+
public void TestTautomerCanonicalization()
44+
{
45+
var smi =
46+
"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";
47+
var mol = RWMol.MolFromSmiles(smi);
48+
// Record for R
49+
var molFile = @"
50+
ChemDraw06032117432D
51+
52+
0 0 0 0 0 0 V3000
53+
M V30 BEGIN CTAB
54+
M V30 COUNTS 14 13 0 0 1
55+
M V30 BEGIN ATOM
56+
M V30 1 C 1.111765 -1.636387 0.000000 0
57+
M V30 2 C 0.389632 -1.237272 0.000000 0
58+
M V30 3 C 0.374442 -0.412275 0.000000 0
59+
M V30 4 C -0.347639 -0.013245 0.000000 0
60+
M V30 5 C -0.362863 0.811612 0.000000 0
61+
M V30 6 N -0.273074 -1.636387 0.000000 0
62+
M V30 7 O 1.111765 -2.461396 0.000000 0
63+
M V30 8 N -1.084995 1.210729 0.000000 0
64+
M V30 9 C -1.100270 2.035672 0.000000 0
65+
M V30 10 N -0.393589 2.461396 0.000000 0
66+
M V30 11 N -1.822349 2.434701 0.000000 0
67+
M V30 12 R1 -0.995042 -1.237157 0.000000 0
68+
M V30 13 R2 1.822349 -1.217228 0.000000 0
69+
M V30 14 R3 0.320882 2.048896 0.000000 0
70+
M V30 END ATOM
71+
M V30 BEGIN BOND
72+
M V30 1 1 6 12
73+
M V30 2 1 1 13
74+
M V30 3 2 7 1
75+
M V30 4 1 1 2
76+
M V30 5 1 2 6
77+
M V30 6 1 2 3 CFG=1
78+
M V30 7 1 3 4
79+
M V30 8 1 4 5
80+
M V30 9 1 5 8
81+
M V30 10 2 8 9
82+
M V30 11 1 9 11
83+
M V30 12 1 9 10
84+
M V30 13 1 10 14
85+
M V30 END BOND
86+
M V30 BEGIN COLLECTION
87+
M V30 MDLV30/STEABS ATOMS=(1 2)
88+
M V30 END COLLECTION
89+
M V30 END CTAB
90+
M END
91+
";
92+
93+
var query = RWMol.MolFromMolBlock(molFile);
94+
foreach (var atom in query.getAtoms())
95+
{
96+
if (atom.getAtomicNum() != 0)
97+
{
98+
continue;
99+
}
100+
101+
atom.setIsotope(0U);
102+
atom.setAtomMapNum(0);
103+
}
104+
105+
var queryParameters = AdjustQueryParameters.noAdjustments();
106+
queryParameters.makeDummiesQueries = true;
107+
var matchParameters = new SubstructMatchParameters
108+
{
109+
useChirality = true, specifiedStereoQueryMatchesUnspecified = true, useEnhancedStereo = true
110+
};
111+
112+
var cleanupParameters = new CleanupParameters();
113+
cleanupParameters.tautomerRemoveBondStereo = false;
114+
cleanupParameters.tautomerRemoveIsotopicHs = false;
115+
cleanupParameters.tautomerReassignStereo = false;
116+
cleanupParameters.tautomerRemoveSp3Stereo = false;
117+
var canonMol = RDKFuncs.canonicalTautomer(mol, cleanupParameters);
118+
RDKFuncs.addHs(canonMol);
119+
var canonQuery = RDKFuncs.canonicalTautomer(query, cleanupParameters);
120+
RDKFuncs.addHs(canonQuery);
121+
RDKFuncs.adjustQueryProperties(canonQuery, queryParameters);
122+
var canonMatches = canonMol.getSubstructMatches(canonQuery, matchParameters);
123+
var numberCanonHits = canonMatches.Count;
124+
Assert.Equal(1, numberCanonHits);
125+
126+
RDKFuncs.addHs(mol);
127+
RDKFuncs.addHs(query);
128+
RDKFuncs.adjustQueryProperties(query, queryParameters);
129+
var matches = mol.getSubstructMatches(query, matchParameters);
130+
var numberHits = matches.Count;
131+
Assert.Equal(0, numberHits);
132+
}
133+
}
134+
}

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