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|
//
// Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#ifdef _WIN32
#include <RDGeneral/test.h>
#include <Windows.h>
#else
#include <unistd.h>
#include <fcntl.h>
#include <sys/time.h>
#include <sys/resource.h>
#endif
#include <stdio.h>
#include <string.h>
#include <time.h>
#include <string>
#include <iostream>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include "../RDKitBase.h"
#include "../FileParsers/FileParsers.h" //MOL single molecule !
#include "../FileParsers/MolSupplier.h" //SDF
#include "../SmilesParse/SmilesParse.h"
#include "../SmilesParse/SmilesWrite.h"
#include "../SmilesParse/SmartsWrite.h"
#include "FMCS.h"
#include "DebugTrace.h" //#ifdef VERBOSE_STATISTICS_ON
#include "../Substruct/SubstructMatch.h"
using namespace RDKit;
unsigned long long T0;
unsigned long long t0;
void printTime() {
unsigned long long t1 = nanoClock();
double sec = double(t1 - t0) / 1000000.;
printf("Time elapsed %.3lf seconds\n", sec);
t0 = nanoClock();
}
std::string getSmilesOnly(
const char* smiles,
std::string* id = nullptr) { // remove label, because RDKit parse FAILED
const char* sp = strchr(smiles, ' ');
unsigned n = (sp ? sp - smiles + 1 : strlen(smiles));
if (id) *id = std::string(smiles + n);
return std::string(smiles, n);
}
// UNIT Test Set:
//=========================================================================
void test1Basics() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "FMCS test1Basics()" << std::endl;
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"CC1CCC(N)CC1", "CC1CC(C)CC(C)C1", // OK test.sdf
};
for (auto& i : smi) {
std::string id;
mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i, &id))));
}
t0 = nanoClock();
MCSResult res = findMCS(mols);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 7 && res.NumBonds == 7);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test32() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS test32" << std::endl;
std::cout << "\n test32()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
//# Using CHEMBL1515359 CHEMBL1590658 CHEMBL1447567 CHEMBL1384017
// CHEMBL1456416 CHEMBL1308819 CHEMBL1703007 CHEMBL1707819 CHEMBL1500793
// CHEMBL1334715
// 32 . 1 31 33 0.82
// S(-N1-C-C-O-C-C-1)(-c1:c:c:c(-N(-C-C)-C-C):c(-N-C(-C=C-c2:c:c:c:c:c:2)=O):c:1)(=O)=O
"O=C(Nc1cc(S(N2CCOCC2)(=O)=O)ccc1N1CCOCC1)C=Cc1ccc(Cl)cc1 CHEMBL1515359",
"c1ccc(C=CC(Nc2cc(S(N3CCOCC3)(=O)=O)ccc2N2CCOCC2)=O)cc1 CHEMBL1590658",
"Cc1ccc(C=CC(=O)Nc2cc(S(N3CCOCC3)(=O)=O)ccc2N2CCOCC2)cc1 CHEMBL1447567",
"c1ccc(C=CC(Nc2cc(S(N3CCOCC3)(=O)=O)ccc2N2CCCC2)=O)cc1 CHEMBL1384017",
"O=C(C=Cc1ccc(F)cc1)Nc1cc(S(N2CCOCC2)(=O)=O)ccc1N1CCCC1 CHEMBL1456416",
"c1cc(F)cc(C=CC(=O)Nc2c(N3CCCC3)ccc(S(N3CCOCC3)(=O)=O)c2)c1 "
"CHEMBL1308819",
"CCN1CCN(c2ccc(S(N3CCOCC3)(=O)=O)cc2NC(=O)C=Cc2ccc(C)cc2)CC1 "
"CHEMBL1703007",
"c1cc(C=CC(=O)Nc2cc(S(N3CCOCC3)(=O)=O)ccc2N2CCOCC2)c([N+]([O-])=O)cc1 "
"CHEMBL1707819",
"N#CC(=Cc1ccccc1)C(=O)Nc1cc(S(N2CCOCC2)(=O)=O)ccc1N1CCCC1 CHEMBL1500793",
"C(=Cc1ccc2c(c1)OCO2)C(Nc1cc(S(=O)(=O)N2CCOCC2)ccc1N1CCOCC1)=O "
"CHEMBL1334715",
// 31 33 0.35 sec MCS: CCN(CC)c1ccc(cc1NC(=O)C=Cc1ccccc1)S(=O)(=O)N1CCOCC1
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
t0 = nanoClock();
MCSResult res = findMCS(mols);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 31 && res.NumBonds == 33);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test190() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS test190" << std::endl;
std::cout << "\n test190()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
// # 190
"COc1cc2nc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)ccc3)oc2cc1 CHEMBL1479679",
"COc1cc2nc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)c(C)cc3)oc2cc1 CHEMBL1333382",
"Cc1cc2oc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)ccc3)nc2cc1 CHEMBL1437584",
"COc1c(NC(=O)CSc2ccc(Cl)cc2)cc(-c2nc3ccccc3o2)cc1 CHEMBL1601350",
"Cc1cc2nc(-c3cccc(NC(=O)CSc4ccc(Cl)cc4)c3)oc2cc1C CHEMBL1398008",
"Cc1cc2oc(-c3cc(NC(=O)CSc4ccc(Cl)cc4)c(C)cc3)nc2cc1 CHEMBL1612903",
"COc1cc2nc(-c3cc(NC(=O)Cc4ccc(Cl)cc4)c(C)cc3)oc2cc1 CHEMBL1316483",
"Cc1c(NC(=O)CSc2ccc(Cl)cc2)cccc1-c1nc2cc(Cl)ccc2o1 CHEMBL1568754",
"COc1ccc2oc(-c3ccc(C)c(NC(=O)COc4cc(C)cc(C)c4)c3)nc2c1 CHEMBL1436972",
"Cc1ccc(SCC(=O)Nc2cc(-c3nc4cc(C)ccc4o3)c(O)cc2)cc1 CHEMBL1611932",
//# 19 21 1.37 sec MCS: CC(=O)Nc1cccc(c1)-c1nc2ccccc2o1
// 19 21 2.36 sec MCS: CC(=O)Nc1cccc(c1)-c1nc2ccccc2o1 19 atoms, 21 bonds
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
t0 = nanoClock();
MCSResult res = findMCS(mols);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 19 && res.NumBonds == 21);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test45() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS test45" << std::endl;
std::cout << "\n test45()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
// SLOW
// test 45 # Using CHEMBL551656 CHEMBL563796 CHEMBL561978 CHEMBL559467
// CHEMBL550503 CHEMBL562866 CHEMBL552190 CHEMBL181547 CHEMBL359567
// CHEMBL373316
// 45 . 1 30 32 27.01
// n12-C-c:c(-c:2:c:c2-C(-O)(-C-C)-C(-O-C-c:2:c:1=O)=O):n:c(:c:c:c-O):c(:c):c-C-C-C
"CCC1(O)c2cc3n(c(=O)c2COC1=O)Cc1c-3nc2ccc(OC)cc2c1C1CCCCC1 CHEMBL551656",
"CCC1(O)c2cc3n(c(=O)c2COC1=O)Cc1c-3nc2ccc(OC)cc2c1C1CCCC1 CHEMBL563796", // Q
"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(OC)cc1c2C1CCCCCC1 CHEMBL561978",
"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(OC)cc1c2C1CCC1 CHEMBL559467",
"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(O)cc1c2C1CCCC1 CHEMBL550503",
"CCC1(O)c2cc3n(c(=O)c2COC1=O)Cc1c-3nc2ccc(O)cc2c1C1CCCCCC1 CHEMBL562866",
"CCC1(O)C(=O)OCc2c1cc1n(c2=O)Cc2c-1nc1ccc(O)cc1c2C1CCCCC1 CHEMBL552190",
"CCC1(O)c2c(c(=O)n3c(c2)-c2nc4cc5c(cc4c(C4CCCC4)c2C3)OCO5)COC1=O "
"CHEMBL181547",
"CCC1(O)c2c(c(=O)n3c(c2)-c2nc4c(c(C5CCCCC5)c2C3)cc2c(c4)OCO2)COC1=O "
"CHEMBL359567",
"CCCc1c(OC)ccc2nc3c(c(CC)c21)Cn1c-3cc2c(c1=O)COC(=O)C2(O)CC CHEMBL373316",
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
t0 = nanoClock();
MCSResult res = findMCS(mols);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 31 && res.NumBonds == 33);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test3() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS test3" << std::endl;
std::cout << "\n test3()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
// TEST 3
"CN(C)c1ccc(CC(=O)NCCCCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL153934",
"CN(C)c1ccc(CC(=O)NCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL152361",
"CN(C)c1ccc(CC(=O)NCCCCCCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL157336",
"CN(C)c1ccc(CC(=O)NCCCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL157429",
"CN(C)c1ccc(CC(=O)NCCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL357551",
"CN(C)c1ccc(CC(=O)NCCCCCCCCCCCNC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL421974",
"CN(C)c1ccc(CC(NCCCCCC(NO)=O)=O)cc1 CHEMBL484488",
"CC(C)Cc1ccc(C(C)C(=O)NC23CC4CC(C2)CC(C3)C4)cc1 CHEMBL564780",
"c1cc([N+]([O-])=O)ccc1CC(=O)NC1CCCCCC1 CHEMBL1553142",
"CC1(C)NC(C)(C)CC(NC(=O)Cc2ccccc2)C1 CHEMBL1703640",
//# 3 . 1 14 14 0.08 sec MCS: CCCCNC(=O)Cc1ccccc1
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
t0 = nanoClock();
MCSResult res = findMCS(mols);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 14 && res.NumBonds == 14);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testRing1() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testRing1" << std::endl;
std::cout << "\ntestRing1()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"COCc1c(ncc2[nH]c3cccc(Oc4ccc(Cl)cc4)c3c12)C(=O)OC(C)C",
// "COCc1cnc(C(=O)OC(C)C)c2[nH]c3cc(Oc4ccc(Cl)cc4)ccc3c12", //
// original molecule
"COCc1cnc(C(=O)OC(C)C)c2[nH]ccc(Oc4ccc(Cl)cc4)cccc12", // ring 3 removed
};
for (auto& i : smi)
mols.push_back(
ROMOL_SPTR(SmilesToMol(getSmilesOnly(i)))); // with RING INFO
MCSParameters p;
p.BondCompareParameters.RingMatchesRingOnly = true;
p.BondCompareParameters.CompleteRingsOnly = true;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 12 && res.NumBonds == 12);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test504() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS test504" << std::endl;
std::cout << "\ntest504()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
// TEST 504
"C(CCNC(C1CC1[c:1]1[c:2]c(Cl)c(Cl)c[c:3]1)=O)CCN1CCC(NC(Nc2ccc(Cl)cc2)=O)"
"C1 CHEMBL545864", // - QUERY
"FC(F)(F)c1cc(NC(N2CCCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)ccc1Cl "
"CHEMBL528228",
"FC(F)(F)c1cc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)C2)=O)ccc1Cl "
"CHEMBL525875",
"Fc1ccc(NC(N2CCCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)cc1C(F)(F)F "
"CHEMBL527277",
"FC(F)(F)c1cc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)ccc1Cl "
"CHEMBL537333",
"Fc1ccc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)C2)=O)cc1C(F)(F)F "
"CHEMBL588077",
"FC(F)(F)c1ccc(NC(NC2CCN(CCCCCNC(C3CC3c3cc(Cl)c(Cl)cc3)=O)C2)=O)cc1 "
"CHEMBL525307",
"Fc1ccc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)cc1C(F)(F)F "
"CHEMBL581847",
"FC(F)(F)c1ccc(NC(NC2CCN(CCCCCNC(C3CC3c3cc(Cl)c(Cl)cc3)=O)CC2)=O)cc1 "
"CHEMBL579547",
"N#Cc1cccc(NC(NC2CCN(CCCCCNC(C3CC3c3ccc(Cl)c(Cl)c3)=O)CC2)=O)c1 "
"CHEMBL529994",
};
RWMol* qm = SmilesToMol(getSmilesOnly(smi[0]));
unsigned nq = qm->getNumAtoms();
for (size_t ai = 0; ai < nq; ai++) {
Atom* atom = qm->getAtomWithIdx(ai);
atom->setProp("molAtomMapNumber", (int)ai);
}
std::cout << "Query +MAP " << MolToSmiles(*qm) << "\n";
mols.push_back(ROMOL_SPTR(qm)); // with RING INFO
for (size_t i = 1; i < sizeof(smi) / sizeof(smi[0]); i++)
mols.push_back(
ROMOL_SPTR(SmilesToMol(getSmilesOnly(smi[i])))); // with RING INFO
t0 = nanoClock();
MCSResult res = findMCS(mols);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 34 && res.NumBonds == 36);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test18() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS test18" << std::endl;
std::cout << "\ntest18()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
// TEST 18
"Cc1nc(CN(C(C)c2ncccc2)CCCCN)ccc1 CHEMBL1682991", //-- QUERY
"Cc1ccc(CN(C(C)c2ccccn2)CCCCN)nc1 CHEMBL1682990",
"Cc1cccnc1CN(C(C)c1ccccn1)CCCCN CHEMBL1682998",
"CC(N(CCCCN)Cc1c(N)cccn1)c1ccccn1 CHEMBL1682987",
"Cc1cc(C)c(CN(C(C)c2ccccn2)CCCCN)nc1 CHEMBL1682992",
"Cc1cc(C(C)N(CCCCN)Cc2c(C)cccn2)ncc1 CHEMBL1682993",
"Cc1nc(C(C)N(CCCCN)Cc2nc3c([nH]2)cccc3)ccc1 CHEMBL1682878",
"CC(c1ncccc1)N(CCCCN)Cc1nc2c([nH]1)cccc2 CHEMBL1682867",
"CC(N(CCCCN)Cc1c(C(C)(C)C)cccn1)c1ccccn1 CHEMBL1682989",
"CC(N(CCCCN)Cc1c(C(F)(F)F)cccn1)c1ccccn1 CHEMBL1682988",
//# 18 . 20 20 0.04 sec. Python MCS: CC(c1ccccn1)N(CCCCN)Ccnccc
};
RWMol* qm = SmilesToMol(getSmilesOnly(smi[0]));
unsigned nq = qm->getNumAtoms();
for (size_t ai = 0; ai < nq; ai++) {
Atom* atom = qm->getAtomWithIdx(ai);
atom->setProp("molAtomMapNumber", (int)ai);
}
std::cout << "Query +MAP " << MolToSmiles(*qm) << "\n";
mols.push_back(ROMOL_SPTR(qm)); // with RING INFO
for (size_t i = 1; i < sizeof(smi) / sizeof(smi[0]); i++)
mols.push_back(
ROMOL_SPTR(SmilesToMol(getSmilesOnly(smi[i])))); // with RING INFO
t0 = nanoClock();
MCSResult res = findMCS(mols);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 21 && res.NumBonds == 21);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testThreshold() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testThreshold" << std::endl;
std::cout << "\ntestThreshold()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"CCC", "CCCO", "CCCN", "CC",
// "CCC", "CC", //th=0.5
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
findMCS(mols);
MCSParameters p;
p.Threshold = 0.7;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
p.Threshold = 1.0; // restore default value
TEST_ASSERT(res.NumAtoms == 3 && res.NumBonds == 2);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test330() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS test330" << std::endl;
std::cout << "\ntest330()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
// TEST 330 40 sec
"CCC(C)C(NC(=O)C(NC(C(CCC(O)=O)NC(=O)C(NC(=O)C(NC(C(CC(O)=O)NC(C(CC(C)C)"
"NC(C(Cc1ccccc1)NC(CN)=O)=O)=O)=O)C(C)CC)C(C)CC)=O)CCCCN)C(NC(C)C(NC("
"CCCCN)C(NC(CO)C(NC(Cc1c[nH]c2c1cccc2)C(O)=O)=O)=O)=O)=O CHEMBL1240742",
"CCC(C)C(NC(=O)C(NC(C(CCCCN)NC(=O)C(NC(=O)C(NC(C(CC(O)=O)NC(C(Cc1ccccc1)"
"NC(C(CC(C)C)NC(CN)=O)=O)=O)=O)C(C)CC)C(C)CC)=O)CCCCN)C(NC(C)C(NC(CCC(O)="
"O)C(NC(CO)C(NC(Cc1c[nH]c2c1cccc2)C(O)=O)=O)=O)=O)=O CHEMBL1240736",
"CCC(C)C(NC(CN)=O)C(NC(C(NC(CC(O)=O)C(NC(C(NC(C)C(NC(CCCCN)C(NC(C(NC(CC("
"C)C)C(NC(Cc1ccccc1)C(NC(CCC(O)=O)C(NC(CO)C(NC(Cc1c[nH]c2c1cccc2)C(O)=O)="
"O)=O)=O)=O)=O)CCCCN)=O)=O)=O)C(C)CC)=O)=O)C(C)CC)=O CHEMBL1240738",
"CCC(C)C(NC(CN)=O)C(NC(Cc1ccccc1)C(NC(CC(O)=O)C(NC(CCCCN)C(NC(CC(C)C)C("
"NC(C)C(NC(CCCCN)C(NC(CCC(O)=O)C(NC(C(NC(CO)C(NC(C(NC(Cc1c[nH]c2c1cccc2)"
"C(O)=O)=O)C(C)CC)=O)=O)C(C)CC)=O)=O)=O)=O)=O)=O)=O)=O CHEMBL1240740",
"CCC(C)C(NC(CN)=O)C(NC(Cc1c[nH]c2c1cccc2)C(NC(CO)C(NC(CC(O)=O)C(NC(CC(C)"
"C)C(NC(C)C(NC(CCC(O)=O)C(NC(C(NC(C(NC(CCCCN)C(NC(CCCCN)C(NC(Cc1ccccc1)C("
"O)=O)=O)=O)=O)C(C)CC)=O)C(C)CC)=O)=O)=O)=O)=O)=O)=O CHEMBL1240741",
"CCC(C)C(NC(=O)C(NC(=O)C(CCCCN)NC(C(CC(C)C)NC(C(Cc1c[nH]c2c1cccc2)NC(CN)="
"O)=O)=O)CCCCN)C(NC(CCC(O)=O)C(NC(CO)C(=O)NC(C(NC(C(NC(CC(O)=O)C(NC(C)C("
"NC(Cc1ccccc1)C(O)=O)=O)=O)=O)C(C)CC)=O)C(C)CC)=O)=O CHEMBL1240743",
"CCC(C)C(NC(C(CCC(O)=O)NC(C(CC(O)=O)NC(C(CC(C)C)NC(C(Cc1ccccc1)NC(C)=O)="
"O)=O)=O)=O)C(NC(Cc1c[nH]c2ccccc12)C(O)=O)=O CHEMBL431874",
"CCC(C)C(NC(C(CC(O)=O)NC(C(CC(C)C)NC(C(Cc1ccccc1)NC(C)=O)=O)=O)=O)C(NC("
"CCC(O)=O)C(NC(Cc1c[nH]c2ccccc12)C(O)=O)=O)=O CHEMBL262166",
"CCC(C)C(NC(C(CC(O)=O)NC(C(CC(C)C)NC(C(Cc1ccccc1)NC(C)=O)=O)=O)=O)C(NC("
"CCCCN)C(NC(Cc1c[nH]c2c1cccc2)C(O)=O)=O)=O CHEMBL313122",
"CCC(C)C(NC(C(CCCCN)NC(C(CC(O)=O)NC(C(CC(C)C)NC(C(Cc1ccccc1)NC(C)=O)=O)="
"O)=O)=O)C(NC(Cc1c[nH]c2c1cccc2)C(O)=O)=O CHEMBL314239",
//# 330 F 42 41 30.93 sec MCS:
//[#6]-[#6](-[#7]-[#6](-[#6](-[#6])-[#7]-[#6](-[#6](-[#6])-[#7]-[#6](-[#6](-[#6]-[#6]-[#6])-[#7]-[#6](-[#6](-[#6])-[#7]-[#6](-[#6])=[#8])=[#8])=[#8])=[#8])=[#8])-[#6](-[#7]-[#6](-[#6]-[#6](:[#6]):[#6]:[#6]:[#6]:[#6])-[#6](-[#8])=[#8])=[#8]
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
MCSParameters p;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 42 && res.NumBonds == 41);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testTarget_no_10188_30149() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testTarget_no_10188_30149" << std::endl;
std::cout << "\ntestTarget_no_10188_30149()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
// Target_no_10188_30149.txt // VERY SLOWER than Python
"CN(C)CCNC(=O)c1ccc(-c2n[nH]c3cc(Nc4ccccc4Cl)ccc32)cc1 CHEMBL399167",
"O=C(O)c1cccc(-c2[nH]nc3cc(Nc4ccccc4Cl)ccc32)c1 CHEMBL197613",
"c1ccc(Nc2ccc3c(c2)[nH]nc3-c2ccccc2)cc1 CHEMBL383177", /// == QUERY
"NC(=O)c1cccc(-c2[nH]nc3cc(Nc4ccccc4Cl)ccc32)c1 CHEMBL199136",
"Clc1ccccc1Nc1ccc2c(c1)n[nH]c2-c1ccccc1 CHEMBL440566",
"O=C(NCCCN1CCOCC1)c1cccc(-c2[nH]nc3cc(Nc4ccccc4Cl)ccc32)c1 CHEMBL198687",
"O=C(O)c1ccc(-c2[nH]nc3cc(Nc4ccccc4Cl)ccc32)cc1 CHEMBL197698",
"O=C(NC1CCNCC1)c1cccc(-c2n[nH]c3cc(Nc4ccccc4Cl)ccc32)c1 CHEMBL194806",
"COc1ccccc1Nc1ccc2c(c1)[nH]nc2-c1ccccc1 CHEMBL254443",
"CN(C)CCNC(=O)c1cccc(-c2[nH]nc3cc(Nc4ccccc4Cl)ccc32)c1 CHEMBL198821",
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
MCSParameters p;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 15 && res.NumBonds == 14);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testTarget_no_10188_49064() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testTarget_no_10188_49064" << std::endl;
std::cout << "\ntestTarget_no_10188_49064()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3cccc(O)c3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(F)cc3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(OC4OC(CO)C(O)C(O)C4O)cc3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(NC(=O)CCl)cc3)nc21",
"Cn1c2nc(Nc3ccc(NC(=O)CCN)cc3)ncc2cc(-c2c(Cl)cccc2Cl)c1=O",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3cccc(COCC(O)CO)c3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(O)cc3)nc21",
"CC(=O)Nc1ccc(Nc2ncc3cc(-c4c(Cl)cccc4Cl)c(=O)n(C)c3n2)cc1",
"Cn1c2nc(Nc3ccc(N)cc3)ncc2cc(-c2c(Cl)cccc2Cl)c1=O",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(NC(=O)CCNC(=O)OC(C)(C)C)cc3)"
"nc21",
"Cc1ccc(Nc2ncc3cc(-c4c(Cl)cccc4Cl)c(=O)n(C)c3n2)cc1",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3cccc(CO)c3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(NCC(O)CO)cc3)nc21",
"CCc1cccc(Nc2ncc3cc(-c4c(Cl)cccc4Cl)c(=O)n(C)c3n2)c1",
"Cn1c2nc(Nc3cccc(N)c3)ncc2cc(-c2c(Cl)cccc2Cl)c1=O",
"CC(=O)Nc1cccc(Nc2ncc3cc(-c4c(Cl)cccc4Cl)c(=O)n(C)c3n2)c1",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(CCO)cc3)nc21",
"Cn1c(=O)c(-c2c(Cl)cccc2Cl)cc2cnc(Nc3ccc(I)cc3)nc21",
"CN1CCN(C(=O)c2ccc(Nc3ncc4cc(-c5c(Cl)cccc5Cl)c(=O)n(C)c4n3)cc2)CC1",
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
MCSParameters p;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 15 && res.NumBonds == 14);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testSegFault() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testSegFault" << std::endl;
std::cout << "\ntestSegFault()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"CN(CCCN(C)CCc1ccccc1)CCOC(c1ccccc1)c1ccccc1",
"CN(CCCc1ccccc1)CCCN(C)CCOC(c1ccccc1)c1ccccc1",
"Fc1ccc(C(OCCNCCCNCCc2ccccc2)c2ccc(F)cc2)cc1",
"O=C(Cc1ccccc1)NCCCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1",
"O=C(Cc1ccccc1)NCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1",
"O=C(Cc1ccc(Br)cc1)NC=CNCCOC(c1ccc(F)cc1)c1ccc(F)cc1",
"O=C(Cc1ccc(F)cc1)NCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1",
"O=C(Cc1ccccc1)NCCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1",
"CN(CCOC(c1ccc(F)cc1)c1ccc(F)cc1)CCN(C)CCOC(c1ccc(F)cc1)c1ccc(F)cc1",
"COC(=O)C1C2CCC(CC1C(=O)Oc1ccccc1)N2C",
"O=C1CN(CCc2ccccc2)CCN1CCOC(c1ccc(F)cc1)c1ccc(F)cc1",
"CN(CCOC(c1ccccc1)c1ccccc1)CCN(C)CCc1ccc(F)cc1",
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
MCSParameters p;
p.BondCompareParameters.RingMatchesRingOnly = true;
p.BondCompareParameters.CompleteRingsOnly = true;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 6 && res.NumBonds == 6);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testAtomCompareIsotopes() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testAtomCompareIsotopes" << std::endl;
std::cout << "\ntestAtomCompareIsotopes()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"CC[13NH2]",
"CC[13CH3]",
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
MCSParameters p;
p.AtomTyper = MCSAtomCompareIsotopes;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 3 && res.NumBonds == 2);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testAtomCompareAnyAtom() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testAtomCompareAnyAtom" << std::endl;
std::cout << "\ntestAtomCompareAnyAtom()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"c1ccccc1C", "c1ccccc1O", "c1ccccc1Cl",
"c1ccccc1F", // opt
"c1ccccc1N", // opt
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
MCSParameters p;
p.AtomTyper = MCSAtomCompareAny;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 7 && res.NumBonds == 7);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testAtomCompareAnyAtomBond() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testAtomCompareAnyAtomBond"
<< std::endl;
std::cout << "\ntestAtomCompareAnyAtom()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"C1CCCCC1=C", "c1ccccc1O", "c1ccccc1Cl",
"c1ccccc1F", // opt
"c1ccccc1N", // opt
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
t0 = nanoClock();
MCSParameters p;
p.AtomTyper = MCSAtomCompareAny;
p.BondTyper = MCSBondCompareAny;
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 7 && res.NumBonds == 7);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testSimple() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testSimple" << std::endl;
std::cout << "\ntestSimple()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
// LONG TIME TEST for performance analisis (about 30 sec)
"CC(C)CC(NC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(C("
"CO)NC(C(NC(c1ccncc1)=O)NC(=O)C(Cc1ccc(Cl)cc1)NC=O)=O)=O)C(NC("
"CCCCNC(C)C)C(N1C(C(=O)NC(C)C(N)=O)CCC1)=O)=O CHEMBL439258 modified "
"QUERY", // CHEMBL439258
"CC(C)CC(NC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(=O)C(Cc1ccccc1)NC(C(CO)NC(C("
"NC(c1ccncc1)=O)NC(=O)C(Cc1ccc(Cl)cc1)NC(C(NC(C)=O)Cc1cc2ccccc2cc1)="
"O)=O)=O)C(NC(CCCCNC(C)C)C(N1C(C(=O)NC(C)C(N)=O)CCC1)=O)=O "
"CHEMBL439258", // CHEMBL439258
"CC(C)CC(NC(=O)CNC(=O)C(Cc1ccc(NC(C)=O)cc1)NC(C(CO)NC(C(NC(c1ccncc1)"
"=O)NC(=O)C(Cc1ccc(Cl)cc1)NC(C(NC(C)=O)Cc1cc2ccccc2cc1)=O)=O)=O)C("
"NC(CCCCNC(C)C)C(N1C(C(=O)NC(C)C(N)=O)CCC1)=O)=O CHEMBL439258 "
"modified", // CHEMBL439258
"CCCCC(NC(C(CCC(O)=O)NC(C(CC(C)C)NC(C(C(C)C)NC(=O)C(CCC(O)=O)NC(C("
"CCCN=C(N)N)NC(C(NC(=O)C(NC(C(NC(C1CCCNC(=O)CCC(N)C(=O)NC(CC(C)C)C(="
"O)NC(C(C)O)C(=O)N1)=O)Cc1c[nH]cn1)=O)CC(C)C)CC(C)C)=O)=O)=O)=O)=O)"
"C(NC(C)C(NC(CCCN=C(N)N)C(NC(C)C(NC(CCC(O)=O)C(NC(CCC(N)=O)C(NC(CC("
"C)C)C(NC(C)C(NC(CCC(N)=O)C(NC(CCC(N)=O)C(NC(C)C(NC(Cc1c[nH]cn1)C("
"NC(CO)C(NC(CC(N)=O)C(NC(CCCN=C(N)N)C(NC(CCCCN)C(NC(CC(C)C)C(NC("
"CCCC)C(NC(C(NC(C(C)CC)C(NC(C(N)=O)C(C)CC)=O)=O)CCC(O)=O)=O)=O)=O)="
"O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O CHEMBL438567",
"CCC(C)C(NC(CNC(=O)C(C)NC(=O)C(C)NC(C(Cc1nc[nH]c1)NC(C(CC(N)=O)NC("
"CNC(C(CO)NC(=O)C(C)NC(=O)C(CCC(N)=O)NC(C(NC(=O)C(NC(C(CCCN=C(N)N)"
"NC(C(CCC(N)=O)NC(C(NC(C(CCCN=C(N)N)NC(CNC(C(CCC(N)=O)NC(C(CC(C)C)"
"NC(C(C)N)=O)=O)=O)=O)=O)CC(C)C)=O)=O)=O)CC(C)C)CC(C)C)=O)=O)=O)=O)="
"O)=O)C(NC(CC(C)C)C(NC(C(O)C)C(NC(CCSC)C(O)=O)=O)=O)=O CHEMBL429374",
"CC(C)CC1NC(=O)C(CCCCN)NC(=O)C(Cc2ccc(O)cc2)NC(=O)CNC(=O)C2NC(=O)C("
"NC(C(C(C)C)NC(CNC(C3NC(=O)CC3)=O)=O)=O)CSSCC(C(O)=O)NC(=O)C3N("
"CCC3O)C(=O)C(Cc3ccccc3)NC(=O)C(CSSC2)NC1=O CHEMBL1076370",
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
MCSParameters p;
p.BondCompareParameters.RingMatchesRingOnly = true;
p.BondCompareParameters.CompleteRingsOnly = true;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 15 && res.NumBonds == 14);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testSimpleFast() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testSimpleFast" << std::endl;
std::cout << "\ntestSimpleFast()\n";
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
// SHORT TEST for 26 bonds.
// Python MCS = 26 bonds : COCc1cncc(c1):n:c1cccc(Oc2ccc(Cl)cc2)c1
// MCS 26: COCc1c-ncc(c1)nc1cccc(c1)Oc1ccc(Cl)cc1 24 atoms, 26 bonds
/// "COCC1=C(N=CC2=C1C1=C(OC3=CC=C(Cl)C=C3)C=CC=C1N2)C(=O)OC(C)C",
/// "COCC1=CN=C(C(=O)OC(C)C)C2=C1C1=CC=C(OC3=CC=C(Cl)C=C3)C=C1N2",
// The SAME, but pre AROMATIZATED (else PRECONDITION Exception with
// Implicit Hs / 16 bonds only)
"COCc1c(ncc2[nH]c3cccc(Oc4ccc(Cl)cc4)c3c12)C(=O)OC(C)C",
"COCc1cnc(C(=O)OC(C)C)c2[nH]c3cc(Oc4ccc(Cl)cc4)ccc3c12",
};
for (auto& i : smi) mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i))));
MCSParameters p;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 24 && res.NumBonds == 26);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void compareChirality(const char* target, const char* query,
bool useChirality) {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
std::cout << "test target = " << target << " query = " << query
<< " useChirality = " << useChirality << std::endl;
ROMOL_SPTR target_ptr(SmilesToMol(target));
ROMOL_SPTR query_ptr(SmartsToMol(query));
std::vector<std::pair<int, int>> vect;
bool sub_res = SubstructMatch(*target_ptr.get(), *query_ptr.get(), vect, true,
useChirality);
std::cout << "res sub = " << sub_res << " size=" << vect.size() << std::endl;
std::vector<ROMOL_SPTR> mols;
mols.push_back(target_ptr);
mols.push_back(query_ptr);
MCSParameters p;
p.AtomCompareParameters.MatchChiralTag = useChirality;
p.BondCompareParameters.MatchStereo = useChirality;
MCSResult mcs_res = findMCS(mols, &p);
std::cout << "MCS: " << mcs_res.SmartsString << " " << mcs_res.NumAtoms
<< " atoms, " << mcs_res.NumBonds << " bonds\n";
bool mcs_resb = query_ptr->getNumAtoms() == mcs_res.NumAtoms &&
query_ptr->getNumBonds() == mcs_res.NumBonds;
TEST_ASSERT(sub_res == mcs_resb);
if (sub_res != mcs_resb) { // || vect.size() != mcs_res.NumAtoms) {
BOOST_LOG(rdInfoLog) << "mcs_resb=" << mcs_resb
<< "\t*** TEST FAILED ***\n"; // exit(1);
}
}
void testSubMcsChirality(const char* target, const char* query) {
compareChirality(target, query, false);
compareChirality(target, query, true);
}
void testChirality() {
BOOST_LOG(rdInfoLog) << "\n-------------------------------------"
<< std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testChirality" << std::endl;
testSubMcsChirality("O[C@H](F)CCl", "C(F)C"); // MCS = CCF
testSubMcsChirality("CC[C@H](F)Cl", "CCC"); // MCS = CCC
testSubMcsChirality("CCC(F)Cl", "CC"); // MCS = CC
// GREG's tests:
testSubMcsChirality("C[C@H](F)CCl", "C[C@H](F)C");
testSubMcsChirality("C[C@H](F)CCl", "C[C@@H](F)C");
testSubMcsChirality(
"O[C@H](F)CCl",
"CC(F)C"); // DISMATCH. but actually it has non chiral MCS = CCF
testSubMcsChirality("O[C@H](F)CCl", "OC(F)C");
testSubMcsChirality("O[C@H](F)CCl", "O[C@H](F)C");
testSubMcsChirality("O[C@H](F)CCl", "O[C@@H](F)C");
testSubMcsChirality("OC(F)CCl", "OC(F)C");
testSubMcsChirality("OC(F)CCl", "O[C@H](F)C");
testSubMcsChirality("OC(F)CCl", "O[C@@H](F)C");
testSubMcsChirality(
"O[C@H](F)CCl",
"O[C@H]C"); // Is OCC = MCS ? Degree of [C@H] is different
testSubMcsChirality(
"O[C@H](F)CCl",
"O[C@@H]C"); // Is OCC = MCS ? Degree of [C@H] is different
// ADD-IN TESTS:
std::cout
<< "\n0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>>\n";
testSubMcsChirality(
"CC[C@H](F)Cl",
"CC[C@H]"); // actual MCS is CCC always. We lost last [C@H]
/* //TEMP (asymmetric implementation of match algorithm, that is incorrect for
FMCS task):
std::cout << "\nTEMP query/targ==MCS[asymmetric implementation of match
algorithm]\n";
std::cout << "1. <<<<<<<<< MCS: [#8]-[#6]-[#9] 3 atoms, 2 bonds >>>>>>>\n";
testSubMcsChirality ("O[C@H](F)", "OC(F)" ); // PASSED
/ / testSubMcsChirality ("OC(F)" , "O[C@H](F)"); // FAILED !!!
std::cout << "\n2.1<<<<<<<<< MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds
>>>>>>>\n";
testSubMcsChirality ("OC[C@H](F)C", "OC(F)C" ); // PASSED but incorrect
std::cout << "\n2.2<<<<<<<<< MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
>>>>>>>\n";
testSubMcsChirality ("OC(F)C" , "O[C@H](F)C"); // FAILED !!!
*/
std::cout << "\tdone" << std::endl;
}
void testJSONParameters() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing FMCS testJSONParameters" << std::endl;
MCSParameters pj;
parseMCSParametersJSON(nullptr, &pj);
parseMCSParametersJSON("{}", nullptr);
pj = MCSParameters(); // parsing of empty string keeps default values
parseMCSParametersJSON("", &pj);
TEST_ASSERT(pj.MaximizeBonds == true && pj.Threshold == 1.0 &&
pj.Timeout == (unsigned int)-1 &&
pj.AtomCompareParameters.MatchValences == false &&
pj.AtomCompareParameters.MatchChiralTag == false &&
pj.BondCompareParameters.MatchStereo == false &&
pj.BondCompareParameters.RingMatchesRingOnly == false &&
pj.BondCompareParameters.CompleteRingsOnly == false);
pj = MCSParameters();
const char json[] =
"{\"MaximizeBonds\": false, \"Threshold\": 0.7, \"Timeout\": 3"
", \"MatchValences\": true, \"MatchChiralTag\": true"
", \"MatchStereo\": true, \"RingMatchesRingOnly\": true, "
"\"CompleteRingsOnly\": true"
", \"InitialSeed\": \"CNC\""
"}";
parseMCSParametersJSON(json, &pj);
TEST_ASSERT(pj.MaximizeBonds == false && pj.Threshold == 0.7 &&
pj.Timeout == 3 &&
pj.AtomCompareParameters.MatchValences == true &&
pj.AtomCompareParameters.MatchChiralTag == true &&
pj.BondCompareParameters.MatchStereo == true &&
pj.BondCompareParameters.RingMatchesRingOnly == true &&
pj.BondCompareParameters.CompleteRingsOnly == true &&
0 == strcmp(pj.InitialSeed.c_str(), "CNC"));
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testGithubIssue481() {
BOOST_LOG(rdInfoLog) << "\n-------------------------------------"
<< std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing github #481 : order dependence in FMCS with chirality"
<< std::endl;
{
std::string s1 = "O[C@H](C)Cl";
std::string s2 = "O[C@@H](C)Cl";
ROMOL_SPTR ptr1(SmilesToMol(s1));
ROMOL_SPTR ptr2(SmilesToMol(s2));
std::vector<ROMOL_SPTR> mols;
mols.push_back(ptr1);
mols.push_back(ptr2);
BOOST_LOG(rdInfoLog) << "**** mols:" << s1 << " " << s2 << "\n";
//#688:
std::vector<std::pair<int, int>> vect;
ROMOL_SPTR mcs_mol(SmilesToMol("OCCl"));
bool sub_res = SubstructMatch(*ptr2, *mcs_mol, vect, true, false);
std::cout << "query=OCCl "
<< "SubstructMatch(useChirality=false) res =" << sub_res
<< " size=" << vect.size() << std::endl;
sub_res = SubstructMatch(*ptr2, *mcs_mol, vect, true, true);
std::cout << "query=OCCl "
<< "SubstructMatch(useChirality=true ) res =" << sub_res
<< " size=" << vect.size() << std::endl;
{
MCSParameters p;
p.AtomCompareParameters.MatchChiralTag = false;
p.BondCompareParameters.MatchStereo = false;
MCSResult mcs_res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << mcs_res.SmartsString << " "
<< mcs_res.NumAtoms << " atoms, " << mcs_res.NumBonds
<< " bonds\n";
TEST_ASSERT(mcs_res.NumAtoms == 4);
TEST_ASSERT(mcs_res.NumBonds == 3);
p.AtomCompareParameters.MatchChiralTag = true;
p.BondCompareParameters.MatchStereo = true;
mcs_res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << mcs_res.SmartsString << " "
<< mcs_res.NumAtoms << " atoms, " << mcs_res.NumBonds
<< " bonds\n";
TEST_ASSERT(mcs_res.NumAtoms == 3); //#688 was 2);
TEST_ASSERT(mcs_res.NumBonds == 2); //#688 was 1);
}
BOOST_LOG(rdInfoLog) << "------ REVERSE mols -------- \n";
mols.clear();
mols.push_back(ptr2);
mols.push_back(ptr1);
{
MCSParameters p;
p.AtomCompareParameters.MatchChiralTag = false;
p.BondCompareParameters.MatchStereo = false;
MCSResult mcs_res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << mcs_res.SmartsString << " "
<< mcs_res.NumAtoms << " atoms, " << mcs_res.NumBonds
<< " bonds\n";
TEST_ASSERT(mcs_res.NumAtoms == 4);
TEST_ASSERT(mcs_res.NumBonds == 3);
p.AtomCompareParameters.MatchChiralTag = true;
p.BondCompareParameters.MatchStereo = true;
mcs_res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << mcs_res.SmartsString << " "
<< mcs_res.NumAtoms << " atoms, " << mcs_res.NumBonds
<< " bonds\n";
TEST_ASSERT(mcs_res.NumAtoms == 3); //#688 was 2);
TEST_ASSERT(mcs_res.NumBonds == 2); //#688 was 1);
}
}
{
std::string s1 = "OC(C)Cl";
std::string s2 = "O[C@H](C)Cl";
ROMOL_SPTR ptr1(SmilesToMol(s1));
ROMOL_SPTR ptr2(SmilesToMol(s2));
std::vector<ROMOL_SPTR> mols;
mols.push_back(ptr1);
mols.push_back(ptr2);
BOOST_LOG(rdInfoLog) << "**** mols:" << s1 << " " << s2 << "\n";
{
MCSParameters p;
p.AtomCompareParameters.MatchChiralTag = false;
p.BondCompareParameters.MatchStereo = false;
MCSResult mcs_res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << mcs_res.SmartsString << " "
<< mcs_res.NumAtoms << " atoms, " << mcs_res.NumBonds
<< " bonds\n";
TEST_ASSERT(mcs_res.NumAtoms == 4);
TEST_ASSERT(mcs_res.NumBonds == 3);
p.AtomCompareParameters.MatchChiralTag = true;
p.BondCompareParameters.MatchStereo = true;
mcs_res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << mcs_res.SmartsString << " "
<< mcs_res.NumAtoms << " atoms, " << mcs_res.NumBonds
<< " bonds\n";
std::vector<std::pair<int, int>> vect;
bool sub_res =
SubstructMatch(*mols[1].get(), *mols[0].get(), vect, true, true);
if (sub_res == false) { // actualy == true & 4, 3 !!!
TEST_ASSERT(mcs_res.NumAtoms == 0);
TEST_ASSERT(mcs_res.NumBonds == 0);
}
}
BOOST_LOG(rdInfoLog) << "------ REVERSE mols -------- \n";
mols.clear();
mols.push_back(ptr2);
mols.push_back(ptr1);
{
MCSParameters p;
p.AtomCompareParameters.MatchChiralTag = false;
p.BondCompareParameters.MatchStereo = false;
MCSResult mcs_res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << mcs_res.SmartsString << " "
<< mcs_res.NumAtoms << " atoms, " << mcs_res.NumBonds
<< " bonds\n";
TEST_ASSERT(mcs_res.NumAtoms == 4);
TEST_ASSERT(mcs_res.NumBonds == 3);
p.AtomCompareParameters.MatchChiralTag = true;
p.BondCompareParameters.MatchStereo = true;
mcs_res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << mcs_res.SmartsString << " "
<< mcs_res.NumAtoms << " atoms, " << mcs_res.NumBonds
<< " bonds\n";
std::vector<std::pair<int, int>> vect;
bool sub_res =
SubstructMatch(*mols[1].get(), *mols[0].get(), vect, true, true);
if (sub_res == false) {
TEST_ASSERT(mcs_res.NumAtoms == 0);
TEST_ASSERT(mcs_res.NumBonds == 0);
}
}
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testInitialSeed() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "FMCS testInitialSeed()" << std::endl;
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"CC1CCC(N)CC1", "CC1CC(C)CC(C)C1", // OK test.sdf
};
for (auto& i : smi) {
std::string id;
mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i, &id))));
}
MCSParameters p;
p.InitialSeed = "CC";
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms == 7 && res.NumBonds == 7);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testInitialSeed2() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "FMCS testInitialSeed2()" << std::endl;
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
"Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1",
"COc1c(N2CCNC(C)C2)c(F)cc2c(=O)c(C(=O)O)cn(C3CC3)c12",
};
const char* initial_smarts = "CCNCCNcccccccnC1CC1";
BOOST_LOG(rdInfoLog) << "initial_smarts: " << initial_smarts << std::endl;
for (auto& i : smi) {
std::string id;
mols.push_back(ROMOL_SPTR(SmilesToMol(getSmilesOnly(i, &id))));
std::auto_ptr<ROMol> seed(SmartsToMol(initial_smarts));
MatchVectType match;
bool matched = SubstructMatch(*mols.back(), *seed, match);
BOOST_LOG(rdInfoLog) << (matched ? "RDKit MATCHED " : "RDKit DISmatched ")
<< i << std::endl;
}
MCSParameters p;
p.InitialSeed = initial_smarts;
t0 = nanoClock();
MCSResult res = findMCS(mols, &p);
std::cout << "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms != 0);
// Make Initial Seed from MCS
p.Verbose = true;
p.InitialSeed =
"[#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#"
"6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])"
"-[#6]"; // 25 atoms, 28 bonds
BOOST_LOG(rdInfoLog)
<< "\n\nFound MCS as the only initial seed (25 atoms, 28 bonds): \n"
<< p.InitialSeed << std::endl;
t0 = nanoClock();
res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << res.SmartsString << " " << res.NumAtoms
<< " atoms, " << res.NumBonds << " bonds\n";
printTime();
TEST_ASSERT(res.NumAtoms != 0);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testGithub631() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing github issue 631: FindMCS "
"matchChiralTag=True does not match self"
<< std::endl;
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {
// all examples derived from the bug report
"CN(C)[C@@H]1CCCNC1", // == MCS
"C1C=CCN1[C@@H]1CCCNC1",
"Cc1cc2c(cc1C)C(=O)N([C@@H]1CCC(=O)NC1=O)C2=O",
};
for (int pass = 0; pass < 2; ++pass, mols.clear())
for (auto& i : smi) {
RWMol* m = SmilesToMol(getSmilesOnly(i));
TEST_ASSERT(m);
if (0 == pass)
mols.clear(); // use a pair of the same molecules only. On the second
// pass use all.
mols.push_back(ROMOL_SPTR(m));
mols.push_back(ROMOL_SPTR(new ROMol(*m)));
{
MCSParameters p;
p.AtomCompareParameters.MatchChiralTag = false;
// p.Verbose = true;
MCSResult res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog)
<< "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n"
<< std::endl;
;
TEST_ASSERT(res.NumAtoms == mols[0]->getNumAtoms());
TEST_ASSERT(res.NumBonds == mols[0]->getNumBonds());
}
{
MCSParameters p;
p.AtomCompareParameters.MatchChiralTag = true;
// p.BondCompareParameters.MatchStereo = useChirality;
// p.Verbose = true;
MCSResult res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog)
<< "MCS: " << res.SmartsString << " " << res.NumAtoms << " atoms, "
<< res.NumBonds << " bonds\n"
<< std::endl;
;
TEST_ASSERT(res.NumAtoms == mols[0]->getNumAtoms());
TEST_ASSERT(res.NumBonds == mols[0]->getNumBonds());
}
BOOST_LOG(rdInfoLog) << "============================================"
<< std::endl;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testFormalChargeMatch() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing including formal charge in matches "
<< std::endl;
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {"CCNC", "CCN(C)C", "CC[N+](C)C"};
for (auto& i : smi) {
RWMol* m = SmilesToMol(getSmilesOnly(i));
TEST_ASSERT(m);
mols.push_back(ROMOL_SPTR(m));
}
{
// by default charge is not used.
MCSParameters p;
MCSResult res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << res.SmartsString << " " << res.NumAtoms
<< " atoms, " << res.NumBonds << " bonds\n"
<< std::endl;
;
TEST_ASSERT(res.NumAtoms == 4);
TEST_ASSERT(res.NumBonds == 3);
}
{
// check charge
MCSParameters p;
p.AtomCompareParameters.MatchFormalCharge = true;
MCSResult res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << res.SmartsString << " " << res.NumAtoms
<< " atoms, " << res.NumBonds << " bonds\n"
<< std::endl;
;
TEST_ASSERT(res.NumAtoms == 2);
TEST_ASSERT(res.NumBonds == 1);
}
BOOST_LOG(rdInfoLog) << "============================================"
<< std::endl;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testGithub2034() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github #2034: add test for ring--non-ring "
"matches at the atom level"
<< std::endl;
std::vector<ROMOL_SPTR> mols;
const char* smi[] = {"C1CC1N2CC2", "C1CC1N"};
for (auto& i : smi) {
auto m = SmilesToMol(getSmilesOnly(i));
TEST_ASSERT(m);
mols.push_back(ROMOL_SPTR(m));
}
{
// by default we're not doing ringMatchesRingOnly.
MCSResult res = findMCS(mols);
BOOST_LOG(rdInfoLog) << "MCS: " << res.SmartsString << " " << res.NumAtoms
<< " atoms, " << res.NumBonds << " bonds\n"
<< std::endl;
TEST_ASSERT(res.NumAtoms == 4);
TEST_ASSERT(res.NumBonds == 4);
}
{
MCSParameters p;
p.AtomCompareParameters.RingMatchesRingOnly = true;
// p.Verbose = true;
MCSResult res = findMCS(mols, &p);
BOOST_LOG(rdInfoLog) << "MCS: " << res.SmartsString << " " << res.NumAtoms
<< " atoms, " << res.NumBonds << " bonds\n"
<< std::endl;
TEST_ASSERT(res.NumAtoms == 3);
TEST_ASSERT(res.NumBonds == 3);
}
{
// set it:
bool maximizeBonds = true, verbose = false, matchValences = false,
ringMatchesRingOnly = true;
double threshold = 1.0;
unsigned timeout = 3000;
MCSResult res = findMCS(mols, maximizeBonds, threshold, timeout, verbose,
matchValences, ringMatchesRingOnly);
BOOST_LOG(rdInfoLog) << "MCS: " << res.SmartsString << " " << res.NumAtoms
<< " atoms, " << res.NumBonds << " bonds\n"
<< std::endl;
TEST_ASSERT(res.NumAtoms == 3);
TEST_ASSERT(res.NumBonds == 3);
}
BOOST_LOG(rdInfoLog) << "============================================"
<< std::endl;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
//====================================================================================================
//====================================================================================================
int main(int argc, const char* argv[]) {
(void)argc;
(void)argv;
// p.Verbose = true;
BOOST_LOG(rdInfoLog)
<< "*******************************************************\n";
BOOST_LOG(rdInfoLog) << "FMCS Unit Test \n";
// use maximum CPU resoures to increase time measuring accuracy and stability in
// multi process environment
#ifdef WIN32
// SetPriorityClass (GetCurrentProcess(), REALTIME_PRIORITY_CLASS );
SetThreadPriority(GetCurrentThread(), THREAD_PRIORITY_HIGHEST);
#else
setpriority(PRIO_PROCESS, getpid(), -20);
#endif
T0 = nanoClock();
t0 = nanoClock();
testJSONParameters();
test1Basics();
test32();
test190();
test3();
testSimpleFast();
testSimple();
testSegFault();
testThreshold();
testRing1();
testAtomCompareIsotopes();
testAtomCompareAnyAtom();
testAtomCompareAnyAtomBond();
test18();
test504();
// very SLOW optional tests:
// test330(); // SLOW test
// test45(); // SLOW test
testInitialSeed();
testInitialSeed2();
// chirality check:
testGithubIssue481();
testChirality();
testGithub631();
//---
testFormalChargeMatch();
testGithub2034();
unsigned long long t1 = nanoClock();
double sec = double(t1 - T0) / 1000000.;
printf("TOTAL Time elapsed %.2lf seconds\n", sec);
BOOST_LOG(rdInfoLog)
<< "*******************************************************\n";
return 0;
}
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