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rdkit/Code/GraphMol/MolStandardize/testNormalize.cpp
Paolo Tosco 32dc126316 fixes #4281 (#4282) 
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
2021-07-09 15:33:02 +02:00

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//
// Copyright (C) 2018 Susan H. Leung
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h>
#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h>
#include "Normalize.h"
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/FileParseException.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/MolStandardize/MolStandardize.h>
#include <iostream>
#include <fstream>
using namespace RDKit;
using namespace MolStandardize;
void test1() {
BOOST_LOG(rdInfoLog) << "-----------------------\n test1" << std::endl;
std::string smi1, smi2, smi3, smi4, smi5, smi6, smi7;
Normalizer normalizer;
// Test sulfoxide normalization.
smi1 = "CS(C)=O";
std::shared_ptr<ROMol> m1(SmilesToMol(smi1));
ROMOL_SPTR normalized(normalizer.normalize(*m1));
TEST_ASSERT(MolToSmiles(*normalized) == "C[S+](C)[O-]");
// Test sulfone
smi2 = "C[S+2]([O-])([O-])O";
std::shared_ptr<ROMol> m2(SmilesToMol(smi2));
ROMOL_SPTR normalized2(normalizer.normalize(*m2));
TEST_ASSERT(MolToSmiles(*normalized2) == "CS(=O)(=O)O");
// Test 1,3-separated charges are recombined.
smi3 = "CC([O-])=[N+](C)C";
std::shared_ptr<ROMol> m3(SmilesToMol(smi3));
ROMOL_SPTR normalized3(normalizer.normalize(*m3));
TEST_ASSERT(MolToSmiles(*normalized3) == "CC(=O)N(C)C");
// Test 1,3-separated charges are recombined.
smi4 = "C[n+]1ccccc1[O-]";
std::shared_ptr<ROMol> m4(SmilesToMol(smi4));
ROMOL_SPTR normalized4(normalizer.normalize(*m4));
TEST_ASSERT(MolToSmiles(*normalized4) == "Cn1ccccc1=O");
// Test a case where 1,3-separated charges should not be recombined.
smi5 = "CC12CCCCC1(Cl)[N+]([O-])=[N+]2[O-]";
std::shared_ptr<ROMol> m5(SmilesToMol(smi5));
ROMOL_SPTR normalized5(normalizer.normalize(*m5));
TEST_ASSERT(MolToSmiles(*normalized5) ==
"CC12CCCCC1(Cl)[N+]([O-])=[N+]2[O-]");
// Test 1,5-separated charges are recombined.
smi6 = R"(C[N+](C)=C\C=C\[O-])";
std::shared_ptr<ROMol> m6(SmilesToMol(smi6));
ROMOL_SPTR normalized6(normalizer.normalize(*m6));
TEST_ASSERT(MolToSmiles(*normalized6) == "CN(C)C=CC=O");
// Test a case where 1,5-separated charges should not be recombined.
smi7 = "C[N+]1=C2C=[N+]([O-])C=CN2CCC1";
std::shared_ptr<ROMol> m7(SmilesToMol(smi7));
ROMOL_SPTR normalized7(normalizer.normalize(*m7));
TEST_ASSERT(MolToSmiles(*normalized7) == "C[N+]1=C2C=[N+]([O-])C=CN2CCC1");
// Failed on 1k normalize test sanitizeMol step
std::string smi8 = "O=c1cc([O-])[n+](C2OC(CO)C(O)C2O)c2sccn12";
std::shared_ptr<ROMol> m8(SmilesToMol(smi8));
ROMOL_SPTR normalized8(normalizer.normalize(*m8));
TEST_ASSERT(MolToSmiles(*normalized8) ==
"O=c1cc([O-])[n+](C2OC(CO)C(O)C2O)c2sccn12");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test2() {
BOOST_LOG(rdInfoLog) << "-----------------------\n test2" << std::endl;
std::string tfdata = R"DATA(// Name SMIRKS
Nitro to N+(O-)=O [N,P,As,Sb;X3:1](=[O,S,Se,Te:2])=[O,S,Se,Te:3]>>[*+1:1]([*-1:2])=[*:3]
Sulfone to S(=O)(=O) [S+2:1]([O-:2])([O-:3])>>[S+0:1](=[O-0:2])(=[O-0:3])
Pyridine oxide to n+O- [n:1]=[O:2]>>[n+:1][O-:2]
)DATA";
std::stringstream sstr(tfdata);
Normalizer nn(sstr, 10);
bool debugParse = false;
bool sanitize = false;
std::unique_ptr<ROMol> imol(
SmilesToMol("O=N(=O)CCN=N#N", debugParse, sanitize));
std::unique_ptr<ROMol> m2(nn.normalize(*imol));
TEST_ASSERT(MolToSmiles(*m2) == "N#N=NCC[N+](=O)[O-]");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testGithub2414() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing github #2414: "
"combinatorial explosion in Normalizer"
<< std::endl;
// pubchem sid 7638352
std::string molb = R"MOL(7638352
-OEChem-01301907472D
143151 0 0 0 0 0 0 0999 V2000
1.6643 -1.2092 0.0000 Rh 0 0 0 0 0 0 0 0 0 0 0 0
1.3553 -0.2582 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
2.4646 -6.2630 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
-1.7350 2.0001 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
-2.3172 0.8272 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
-3.9127 -3.0768 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.2298 -4.2734 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
6.5607 0.3263 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
3.1090 3.8378 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
3.3001 1.7525 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
6.7114 -2.6538 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.7500 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
2.6154 -0.9002 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
1.9734 -2.1603 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
2.8297 -7.9562 0.0000 Na 0 0 0 0 0 0 0 0 0 0 0 0
-2.6054 3.4976 0.0000 Na 0 0 0 0 0 0 0 0 0 0 0 0
-3.4723 2.1178 0.0000 Na 0 0 0 0 0 0 0 0 0 0 0 0
-5.3110 -2.0546 0.0000 Na 0 0 0 0 0 0 0 0 0 0 0 0
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8.2539 0.6914 0.0000 Na 0 0 0 0 0 0 0 0 0 0 0 0
3.2849 5.5609 0.0000 Na 0 0 0 0 0 0 0 0 0 0 0 0
3.9999 3.3368 0.0000 Na 0 0 0 0 0 0 0 0 0 0 0 0
8.4344 -2.8298 0.0000 Na 0 0 0 0 0 0 0 0 0 0 0 0
3.1359 -7.0042 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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3.1927 2.7467 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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2.3059 1.6450 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.1208 -3.5662 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.3019 -1.7415 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9511 -1.4410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5878 -2.5590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6154 -1.9002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5665 -1.2092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6440 0.5156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7824 -1.5725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3891 -3.1889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4326 -3.8246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.7479 -2.3977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.2346 1.4280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6750 -0.5782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3015 -2.7795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1039 -4.5658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8675 0.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6923 -2.1123 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1784 -3.4714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4829 -2.3977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7715 -2.1880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6383 0.4082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6948 -1.9819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2817 -4.1831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4538 -4.0297 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7933 -5.5219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8675 1.5027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1121 -0.1516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1729 -3.2648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7479 -3.4029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2637 -0.8485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8255 2.2412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4882 0.0126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1148 -3.3703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8675 1.5027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.4829 -3.4029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7275 -2.4986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2291 1.2214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5080 -1.3910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.1432 -4.9857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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4.8257 2.1420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4088 -0.3908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0156 -4.3706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4408 -2.3568 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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0.1461 0.7069 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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1.4940 1.6084 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0752 0.1312 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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2.4693 -3.3571 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.0437 -0.5060 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7979 -2.9766 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6820 -4.8926 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7153 -2.7275 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.3856 2.3732 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.3894 -2.4730 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0527 -5.8812 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.3504 -3.9003 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.9326 -3.4774 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.2233 1.1139 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.4203 -1.8005 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.9069 -6.5139 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5696 -5.3445 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2706 -7.4010 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0000 3.0104 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.8141 -0.5107 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.3573 -4.9945 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6154 -4.9106 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.4295 -2.1395 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.4135 2.9510 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.2178 0.1970 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.8246 -4.9584 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 12 1 0 0 0 0
1 13 1 0 0 0 0
1 14 1 0 0 0 0
3 24 1 0 0 0 0
3 33 2 0 0 0 0
3 34 2 0 0 0 0
3 78 1 0 0 0 0
4 25 1 0 0 0 0
4 35 2 0 0 0 0
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5 38 2 0 0 0 0
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6 27 1 0 0 0 0
6 39 2 0 0 0 0
6 40 2 0 0 0 0
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7 28 1 0 0 0 0
7 41 2 0 0 0 0
7 42 2 0 0 0 0
7 82 1 0 0 0 0
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8 43 2 0 0 0 0
8 44 2 0 0 0 0
8 83 1 0 0 0 0
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9 45 2 0 0 0 0
9 46 2 0 0 0 0
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10 31 1 0 0 0 0
10 47 2 0 0 0 0
10 48 2 0 0 0 0
10 85 1 0 0 0 0
11 32 1 0 0 0 0
11 49 2 0 0 0 0
11 50 2 0 0 0 0
11 86 1 0 0 0 0
12 51 1 0 0 0 0
12 52 1 0 0 0 0
12 53 1 0 0 0 0
12105 1 0 0 0 0
13 54 1 0 0 0 0
13 55 1 0 0 0 0
13 56 1 0 0 0 0
13106 1 0 0 0 0
14 57 1 0 0 0 0
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14107 1 0 0 0 0
15 24 1 0 0 0 0
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17 26 1 0 0 0 0
18 27 1 0 0 0 0
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20 29 1 0 0 0 0
21 30 1 0 0 0 0
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51 60 2 0 0 0 0
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M END)MOL";
std::string tfdata = R"DATA(// Name SMIRKS
Alkaline oxide to ions [Li,Na,K;+0:1]-[O+0:2]>>([*+1:1].[O-:2])
)DATA";
std::stringstream sstr(tfdata);
Normalizer nn(sstr, 10);
bool sanitize = false;
bool removeHs = false;
std::unique_ptr<ROMol> imol(MolBlockToMol(molb, sanitize, removeHs));
std::unique_ptr<ROMol> m2(nn.normalize(*imol));
TEST_ASSERT(m2);
auto p = "[Na]-O"_smarts;
TEST_ASSERT(p);
TEST_ASSERT(SubstructMatch(*imol, *p).size() == 9);
TEST_ASSERT(SubstructMatch(*m2, *p).size() == 0);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testNormalizeMultipleAltSmarts() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing that multiple SMARTS "
"matching the same group work"
<< std::endl;
std::string azideNormalizations = R"DATA(// Name SMARTS
Azide to N=N+=N- [N:2]=[N:3]#[N:4]>>[N:2]=[N+:3]=[N-:4]
Broken azide to N=N+=N- [N:2]=[N:3]=[N:4]>>[NH0:2]=[NH0+:3]=[NH0-:4])DATA";
std::stringstream azideNormalizationsStream(azideNormalizations);
std::stringstream captureLog;
rdInfoLog->SetTee(captureLog);
Normalizer nn(azideNormalizationsStream, 200);
const std::string brokenAzideSmi = "CN=[N+]=[NH-]";
const int debugParse = 0;
const bool sanitize = false;
ROMOL_SPTR brokenAzide(SmilesToMol(brokenAzideSmi, debugParse, sanitize));
ROMOL_SPTR normalizedAzide(nn.normalize(*brokenAzide));
rdInfoLog->ClearTee();
std::string line;
unsigned int count = 0;
while (std::getline(captureLog, line)) {
if (line.find("Rule applied: BrokenazidetoN=N+=N-") != std::string::npos) {
++count;
}
}
TEST_ASSERT(count == 1);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testGithub3460() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Github #3460: "
"Normalization rule incorrectly matches sulfones"
<< std::endl;
std::stringstream captureLog;
rdInfoLog->SetTee(captureLog);
Normalizer nn;
auto mol = "[O-][S+]1Nc2c(Cl)cc(Cl)c3c(Cl)cc(Cl)c(c23)N1"_smiles;
TEST_ASSERT(mol);
ROMOL_SPTR normalized(nn.normalize(*mol));
rdInfoLog->ClearTee();
auto logged = captureLog.str();
TEST_ASSERT(logged.find("Running Normalizer") != std::string::npos);
TEST_ASSERT(logged.find("Rule applied: C/S+NtoC/S=N+") == std::string::npos);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testEmptyMol() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Test that Normalizer "
"does not crash on an empty mol"
<< std::endl;
Normalizer nn;
std::unique_ptr<ROMol> emptyMol(new ROMol());
std::unique_ptr<ROMol> normalized(nn.normalize(*emptyMol));
TEST_ASSERT(!normalized->getNumAtoms());
}
void testGithub4281() {
BOOST_LOG(rdInfoLog)
<< "-----------------------\n Testing Github #3460: "
"Normalization rule incorrectly matches [N+]=O rather than n=O"
<< std::endl;
auto mol = "Cn1c(=O)c2nc[nH][n+](=O)c2n(C)c1=O"_smiles;
std::stringstream captureLog;
rdInfoLog->SetTee(captureLog);
Normalizer nn;
std::unique_ptr<ROMol> normalized(nn.normalize(*mol));
rdInfoLog->ClearTee();
auto logged = captureLog.str();
TEST_ASSERT(logged.find("FAILED sanitizeMol") == std::string::npos);
}
int main() {
RDLog::InitLogs();
#if 1
test1();
test2();
#endif
testGithub2414();
testNormalizeMultipleAltSmarts();
testGithub3460();
testEmptyMol();
testGithub4281();
return 0;
}
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