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rdkit/Code/GraphMol/ChemReactions/testReaction.cpp
Ricardo Rodriguez 7b7a8a4e17 Refactor iostreams includes (#8846) 
* refactor iostreams includes

* restore ostream to MonomerInfo.cpp
2025-10-08 16:08:01 +02:00

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//
// Copyright (c) 2007-2025, Novartis Institutes for BioMedical Research Inc.
// and other RDKit contributors
// 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.
//
#include <RDGeneral/test.h>
#include <GraphMol/test_fixtures.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <string>
#include <Geometry/point.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/ChemReactions/ReactionPickler.h>
#include <GraphMol/ChemReactions/ReactionRunner.h>
#include <GraphMol/ChemReactions/ReactionUtils.h>
#include <GraphMol/ChemReactions/SanitizeRxn.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/Atom.h>
#include <fstream>
using namespace RDKit;
void test1Basics() {
ROMol *mol = nullptr;
ChemicalReaction rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing ChemicalReaction infrastructure"
<< std::endl;
smi = "[C:1](=[O:2])O";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 1);
smi = "[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 2);
smi = "[C:1](=[O:2])[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addProductTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumProductTemplates() == 1);
smi = "C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn.initReactantMatchers();
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
reacts.clear();
smi = "CC(C(=O)O)C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
reacts.clear();
smi = "CC(C(=O)O)C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "NCN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test2SimpleReactions() {
ROMol *mol = nullptr;
ChemicalReaction rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing simple reactions" << std::endl;
smi = "[C:1](=[O:2])O";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 1);
smi = "[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 2);
smi = "[C:1](=[O:2])[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addProductTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumProductTemplates() == 1);
smi = "C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn.initReactantMatchers();
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
reacts.clear();
smi = "CC(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
reacts.clear();
smi = "CC(C(=O)O)C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[1].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 9);
TEST_ASSERT(prods[1][0]->getNumAtoms() == 9);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[1][0]));
reacts.clear();
smi = "CC(C(=O)O)C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "NCN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[1].size() == 1);
TEST_ASSERT(prods[2].size() == 1);
TEST_ASSERT(prods[3].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 10);
TEST_ASSERT(prods[1][0]->getNumAtoms() == 10);
TEST_ASSERT(prods[2][0]->getNumAtoms() == 10);
TEST_ASSERT(prods[3][0]->getNumAtoms() == 10);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[1][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[2][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[3][0]));
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test3RingFormation() {
ROMol *mol = nullptr;
ChemicalReaction rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing ring formation reactions" << std::endl;
smi = "[C:1]=[C:2]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 1);
smi = "[C:3]=[C:4][C:5]=[C:6]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 2);
smi = "[C:1]1[C:2][C:3][C:4]=[C:5][C:6]1";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addProductTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumProductTemplates() == 1);
smi = "C=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "C=CC=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn.initReactantMatchers();
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 6);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[1][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[2][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[3][0]));
reacts.clear();
smi = "CC=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "C=CC=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 7);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[1][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[2][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[3][0]));
reacts.clear();
smi = "CC=C[Cl]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "[F]C=CC=C[Br]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 10);
for (unsigned int i = 0; i < prods.size(); i++) {
unsigned int nDifferent = 0;
for (unsigned int j = 0; j < prods.size(); j++) {
if (MolToSmiles(*prods[i][0]) != MolToSmiles(*prods[j][0])) {
nDifferent += 1;
}
}
TEST_ASSERT(nDifferent == 2);
}
reacts.clear();
smi = "C1C=CCCC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "C=CC=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 10);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[1][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[2][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[3][0]));
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test4MultipleProducts() {
ROMol *mol = nullptr;
ChemicalReaction rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing reactions forming multiple products"
<< std::endl;
// yes, I know this is bogus... it's a test!
smi = "[N:1][C:2][C:3](=[O:4])[O:5]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 1);
smi = "[N:6][C:7][C:8](=[O:9])[O:10]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 2);
smi = "[N:1]1[C:2][C:3](=[O:4])[N:6][C:7][C:8]1=[O:9]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addProductTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumProductTemplates() == 1);
smi = "[O:5][O:10]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addProductTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumProductTemplates() == 2);
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn.initReactantMatchers();
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 8);
TEST_ASSERT(prods[0][1]->getNumAtoms() == 2);
smi = MolToSmiles(*prods[0][0]);
std::cerr << "smi: " << smi << std::endl;
TEST_ASSERT(smi == "O=C1CNC(=O)CN1");
TEST_ASSERT(MolToSmiles(*prods[0][1]) == "OO");
reacts.clear();
smi = "COC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "COC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
MolOps::sanitizeMol(*(static_cast<RWMol *>(prods[0][0].get())));
MolOps::sanitizeMol(*(static_cast<RWMol *>(prods[0][1].get())));
std::cerr << "1: " << MolToSmiles(*prods[0][0]) << std::endl;
std::cerr << "2: " << MolToSmiles(*prods[0][1]) << std::endl;
TEST_ASSERT(prods[0][0]->getNumAtoms() == 8);
TEST_ASSERT(prods[0][1]->getNumAtoms() == 4);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "O=C1CNC(=O)CN1");
TEST_ASSERT(MolToSmiles(*prods[0][1]) == "COOC");
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test5Salts() {
ROMol *mol = nullptr;
ChemicalReaction rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing salt handling" << std::endl;
smi = "[C:1](=[O:2])O";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 1);
smi = "[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 2);
smi = "[C:1](=[O:2])[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addProductTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumProductTemplates() == 1);
smi = "C(=O)O.[ClH]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN.C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn.initReactantMatchers();
prods = rxn.runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test6DaylightParser() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Daylight parser" << std::endl;
smi = "[C:1](=[O:2])O.[N:3][C:4]>>[C:1](=[O:2])[N:3][C:4]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
smi = "C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
delete rxn;
reacts.clear();
smi =
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>>[N:1]1[C:2]["
"C:3](=[O:4])[N:6][C:7][C:8]1=[O:9].[O:5][O:10]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 8);
TEST_ASSERT(prods[0][1]->getNumAtoms() == 2);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "O=C1CNC(=O)CN1");
TEST_ASSERT(MolToSmiles(*prods[0][1]) == "OO");
delete rxn;
reacts.clear();
smi =
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10].[N:1]1[C:2]["
"C:3](=[O:4])[N:6][C:7][C:8]1=[O:9].[O:5][O:10]";
try {
rxn = RxnSmartsToChemicalReaction(smi);
} catch (ChemicalReactionParserException &) {
}
smi =
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>>[N:1]1[C:2]["
"C:3](=[O:4])[N:6][C:7][C:8]1=[O:9]>>[O:5][O:10]";
try {
rxn = RxnSmartsToChemicalReaction(smi);
} catch (ChemicalReactionParserException &) {
}
smi =
"[Q:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>>[N:1]1[C:2]["
"C:3](=[O:4])[N:6][C:7][C:8]1=[O:9].[O:5][O:10]";
try {
rxn = RxnSmartsToChemicalReaction(smi);
} catch (ChemicalReactionParserException &) {
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test7MDLParser() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing MDL parser" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/AmideBond.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
smi = "C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
delete rxn;
reacts.clear();
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/cyclization1.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 8);
std::cerr << MolToSmiles(*prods[0][0]) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "O=C1CNC(=O)CN1");
delete rxn;
reacts.clear();
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/cyclization1.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 8);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "O=C1CNC(=O)CN1");
delete rxn;
reacts.clear();
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/cyclization2.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
smi = "CC=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "C=CC=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 7);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[1][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[2][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[3][0]));
reacts.clear();
smi = "CC=C[Cl]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "[F]C=CC=C[Br]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 10);
for (unsigned int i = 0; i < prods.size(); i++) {
unsigned int nDifferent = 0;
for (unsigned int j = 0; j < prods.size(); j++) {
if (MolToSmiles(*prods[i][0]) != MolToSmiles(*prods[j][0])) {
nDifferent += 1;
}
}
TEST_ASSERT(nDifferent == 2);
}
reacts.clear();
smi = "C1C=CCCC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "C=CC=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 10);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[1][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[2][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[3][0]));
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test8Validation() {
ChemicalReaction *rxn;
unsigned int nWarn, nError;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Reaction Validation." << std::endl;
smi = "[C:1](=[O:2])O.[N:3][C:4]>>[C:1](=[O:2])[N:3][C:4]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, true));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
delete rxn;
smi = "[C:1](=[O:2])[O:5].[N:3][C:4]>>[C:1](=[O:2])[N:3][C:4]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, true));
TEST_ASSERT(nWarn == 1);
TEST_ASSERT(nError == 0);
delete rxn;
smi = "[C:1](=[O:2])O.[N:1][C:4]>>[C:1](=[O:2])[N:3][C:4]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(!rxn->validate(nWarn, nError, true));
TEST_ASSERT(nWarn == 1);
TEST_ASSERT(nError == 1);
delete rxn;
smi = "[C:1](=[O:2])O.[N:3][C:4]>>[C:1](=[O:2])[N:3][C:5]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, true));
TEST_ASSERT(nWarn == 2);
TEST_ASSERT(nError == 0);
delete rxn;
smi = "[C:1](=[O:2])O.[N:3][C:4]>>[C:1](=[O:2])[N:3][C:1]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 2);
TEST_ASSERT(nError == 0);
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test9ProductQueries() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing handling of query atoms in the products"
<< std::endl;
smi = "[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[*:3]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
smi = "C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(2)->getAtomicNum() == 7);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "CNC=O");
delete rxn;
smi = "[C:1](=[O:2])O.[N:3]>>[C:1](=[*:2])[*:3]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(2)->getAtomicNum() == 7);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "CNC=O");
delete rxn;
smi = "[C:1](=[O:2])O.[N:3]>>[*:1](=[*:2])[*:3]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(2)->getAtomicNum() == 7);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "CNC=O");
delete rxn;
smi =
"[*:1]1:[*:2]:[*:3]:[*:4]:[*:5]:[*:6]:1>>[*:1]1:[*:2]:[*:3]:[*:4]:[*:5]:["
"*:6]:1C";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
reacts.clear();
smi = "c1ccccc1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 12);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 7);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(prods[0][0]->getAtomWithIdx(1)->getIsAromatic());
TEST_ASSERT(prods[0][0]->getBondBetweenAtoms(0, 1)->getIsAromatic());
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test10ChiralityDaylight() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Chirality handling" << std::endl;
{ // default behavior, make no changes w.r.t. stereochem
std::string smi =
"[F:1][C:2]([Cl:3])([Br:4])[I:5]>>[*:1][C:2]([*:3])([*:4])[*:5]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "F[C@](Cl)(Br)I";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@](Cl)(Br)I");
reacts.clear();
smi = "F[C@@](Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@@](Cl)(Br)I");
reacts.clear();
smi = "FC(Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "FC(Cl)(Br)I");
delete rxn;
}
{ // a reaction that retains stereochem
std::string smi =
"[F:1][C@:2]([Cl:3])([Br:4])[I:5]>>[*:1][C@:2]([*:3])([*:4])[*:5]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "F[C@](Cl)(Br)I";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@](Cl)(Br)I");
reacts.clear();
smi = "F[C@@](Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@@](Cl)(Br)I");
reacts.clear();
smi = "FC(Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "FC(Cl)(Br)I");
delete rxn;
}
{ // a reaction that inverts stereochem
std::string smi =
"[F:1][C@:2]([Cl:3])([Br:4])[I:5]>>[*:1][C@@:2]([*:3])([*:4])[*:5]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "F[C@](Cl)(Br)I";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@@](Cl)(Br)I");
reacts.clear();
smi = "F[C@@](Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@](Cl)(Br)I");
reacts.clear();
smi = "FC(Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "FC(Cl)(Br)I");
delete rxn;
}
{ // a reaction that induces/sets stereochem
std::string smi =
"[F:1][C:2]([Cl:3])([Br:4])[I:5]>>[*:1][C@@:2]([*:3])([*:4])[*:5]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "F[C@](Cl)(Br)I";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@@](Cl)(Br)I");
reacts.clear();
smi = "F[C@@](Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@@](Cl)(Br)I");
reacts.clear();
smi = "FC(Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@@](Cl)(Br)I");
delete rxn;
}
{ // a reaction that induces/sets stereochem
std::string smi =
"[F:1][C:2]([Cl:3])([Br:4])[I:5]>>[*:1][C@:2]([*:3])([*:4])[*:5]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "F[C@](Cl)(Br)I";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@](Cl)(Br)I");
reacts.clear();
smi = "F[C@@](Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@](Cl)(Br)I");
reacts.clear();
smi = "FC(Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@](Cl)(Br)I");
delete rxn;
}
{ // a reaction that removes stereochem
std::string smi =
"[F:1][C@:2]([Cl:3])([Br:4])[I:5]>>[*:1][C:2]([*:3])([*:4])[*:5]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "F[C@](Cl)(Br)I";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "FC(Cl)(Br)I");
reacts.clear();
smi = "F[C@@](Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "FC(Cl)(Br)I");
reacts.clear();
smi = "FC(Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "FC(Cl)(Br)I");
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test11ChiralityRxn() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Chirality handling (rxn)" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/SN2_FlagProd.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
reacts.clear();
smi = "F[C@@](Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "[OH-]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
TEST_ASSERT(prods[0][1]->getNumAtoms() == 1);
TEST_ASSERT(prods[0][1]->getNumBonds() == 0);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "O[C@](F)(Cl)I");
TEST_ASSERT(MolToSmiles(*prods[0][1], true) == "[Br-]");
fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/SN2_FlagProd.retain.rxn";
delete rxn;
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
TEST_ASSERT(prods[0][1]->getNumAtoms() == 1);
TEST_ASSERT(prods[0][1]->getNumBonds() == 0);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "O[C@@](F)(Cl)I");
TEST_ASSERT(MolToSmiles(*prods[0][1], true) == "[Br-]");
// this has the chirality flag in the reactants, which is ignored, so the
// chirality is preserved:
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/SN2_FlagReact.rxn";
delete rxn;
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumBonds() == 4);
TEST_ASSERT(prods[0][1]->getNumAtoms() == 1);
TEST_ASSERT(prods[0][1]->getNumBonds() == 0);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "O[C@@](F)(Cl)I");
TEST_ASSERT(MolToSmiles(*prods[0][1], true) == "[Br-]");
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test12DoubleBondStereochem() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi, stereo;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing handling of double bond stereochemistry"
<< std::endl;
for (const bool useLegacy : {true, false}) {
smi = "[C:1](=[O:2])-[O;H0]>>[C:1](=[O:2])[X]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
UseLegacyStereoPerceptionFixture fx(useLegacy);
reacts.clear();
smi = "COC(=O)/C=C/Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
MolOps::assignStereochemistry(*mol);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 6);
TEST_ASSERT(prods[0][0]->getNumBonds() == 5);
prods[0][0]->updatePropertyCache();
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
if (useLegacy) {
TEST_ASSERT(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOE);
} else {
TEST_ASSERT(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOTRANS);
}
Bond *stereoBond = prods[0][0]->getBondWithIdx(3);
INT_VECT stereoAtomsRef{{0, 5}};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
reacts.clear();
// FIX: note that the handling of this situation, where we match double
// bonds that have stereochem indicated, is currently not completely correct
// since the stereochem querying stuff doesn't match C/C=C\Cl when C\C=C/Cl
// is provided as a query.
delete rxn;
smi = "[Cl:3]\\[C:1]=[C:2]/[C:4]>>[Cl:3]\\[C:1]=[C:2]\\[C:4]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
reacts.clear();
smi = "Cl\\C=C/C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
MolOps::assignStereochemistry(*mol);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
prods[0][0]->updatePropertyCache();
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
if (useLegacy) {
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOZ);
} else {
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOCIS);
}
stereoBond = prods[0][0]->getBondWithIdx(1);
stereoAtomsRef = {0, 3};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
reacts.clear();
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test13Issue1748846() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi, stereo;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing sf.net Issue 1748846: bad bond orders in reaction products"
<< std::endl;
smi = "c1ccccc1[C:1].[*:2][At]>>c1ccccc1[C:1][*:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
reacts.clear();
smi = "c1ccccc1C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "[At]OC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() > 0);
BOOST_LOG(rdInfoLog) << prods[0].size() << std::endl;
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 9);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(prods[0][0]->getBondBetweenAtoms(0, 1)->getBondType() ==
Bond::AROMATIC);
TEST_ASSERT(prods[0][0]->getBondBetweenAtoms(1, 2)->getBondType() ==
Bond::AROMATIC);
smi = MolToSmiles(*prods[0][0], true);
TEST_ASSERT(smi == "COCc1ccccc1");
delete rxn;
smi = "[c:3][C:1].[*:2][At]>>[c:3][C:1][*:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
reacts.clear();
smi = "c1ccccc1C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "[At]OC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() > 0);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 9);
smi = MolToSmiles(*prods[0][0], true);
TEST_ASSERT(smi == "COCc1ccccc1");
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test14Issue1804420() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi, stereo;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing sf.net Issue 1804420: bad handling of query "
"atoms in products."
<< std::endl;
// NOTE that this bug was actually in the smarts parser, so this is really
// just another reaction test... still, more tests are better
smi = "[N;D3;R:1]-!@[*:2]>>[At][N:1].[*:2][At]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
TEST_ASSERT((*rxn->beginReactantTemplates())
->getAtomWithIdx(0)
->hasProp(common_properties::molAtomMapNumber));
reacts.clear();
smi = "C1CCN1CCC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
smi = MolToSmiles(*prods[0][0], true);
TEST_ASSERT(smi == "[At]N1CCC1");
TEST_ASSERT(prods[0][1]->getNumAtoms() == 4);
smi = MolToSmiles(*prods[0][1], true);
TEST_ASSERT(smi == "CCC[At]");
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test15Issue1882749() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
unsigned int nWarn, nError;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing sf.net Issue 1882749: property handling in products."
<< std::endl;
smi = "[N:1]-!@*>>[N;+1,+0:1][#0]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 1);
TEST_ASSERT(nError == 0);
delete rxn;
smi = "[N:1]-!@*>>[N;-1:1]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
reacts.clear();
smi = "C1CCN1CCC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getFormalCharge() == -1);
delete rxn;
smi = "[N;D3:1]-!@*>>[N;H1:1]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getNumExplicitHs() == 1);
delete rxn;
smi = "[N;D3:1]-!@*>>[15N:1]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getAtomicNum() == 7);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getIsotope() == 15);
std::cerr << " mass: " << prods[0][0]->getAtomWithIdx(0)->getMass()
<< std::endl;
TEST_ASSERT(feq(prods[0][0]->getAtomWithIdx(0)->getMass(), 15.0001));
delete rxn;
smi = "[N;D3:1]-!@*>>[15N;-1:1]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getFormalCharge() == -1);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getIsotope() == 15);
TEST_ASSERT(feq(prods[0][0]->getAtomWithIdx(0)->getMass(), 15.0001));
reacts.clear();
smi = "CS(=O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
delete rxn;
smi = "[S:1]=[O:2]>>[S;+2:1]-[O;-:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getFormalCharge() == +2);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(1)->getFormalCharge() == -1);
reacts.clear();
smi = "CO";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
delete rxn;
smi = "[O:1]>>[O:1][13C]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 3);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(1)->getIsotope() == 13);
TEST_ASSERT(feq(prods[0][0]->getAtomWithIdx(1)->getMass(), 13.00335));
reacts.clear();
smi = "CO";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
delete rxn;
smi = "[O:1]>>[O:1][3#0]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 3);
MolOps::sanitizeMol(*(static_cast<RWMol *>(prods[0][0].get())));
TEST_ASSERT(prods[0][0]->getAtomWithIdx(1)->getIsotope() == 3);
TEST_ASSERT(feq(prods[0][0]->getAtomWithIdx(1)->getMass(), 0.000));
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "[3*]OC");
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test16Exceptions() {
ChemicalReaction *rxn;
std::string rxnB;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing parser exception handling" << std::endl;
rxnB =
"$RXN\n"
"\n"
" ISIS 082120061354\n"
"\n"
" 2 1\n"
"$MOL\n"
"\n"
" -ISIS- 08210613542D\n"
"\n"
" 4 2 0 0 0 0 0 0 0 0999 V2000\n"
" -1.4340 -0.6042 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" -0.8639 -0.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.4340 0.0542 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0\n"
" 1 2 1 0 0 0 0\n"
" 1 3 2 0 0 0 0\n"
"M END\n"
"$MOL\n"
"\n"
" -ISIS- 08210613542D\n"
"\n"
" 1 0 0 0 0 0 0 0 0 0999 V2000\n"
" 2.2125 -0.7833 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0\n"
"M END\n"
"$MOL\n"
"\n"
" -ISIS- 08210613542D\n"
"\n"
" 3 2 0 0 0 0 0 0 0 0999 V2000\n"
" 9.5282 -0.8083 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0\n"
" 8.9579 -0.4792 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" 8.9579 0.1792 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0\n"
" 1 2 1 0 0 0 0\n"
" 2 3 2 0 0 0 0\n"
"M END\n";
rxn = (ChemicalReaction *)0x1;
try {
rxn = RxnBlockToChemicalReaction(rxnB);
} catch (ChemicalReactionParserException &) {
rxn = (ChemicalReaction *)nullptr;
}
TEST_ASSERT(!rxn);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test17Issue1920627() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
ROMOL_SPTR prod;
std::string smi, cip;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing sf.net Issue 1920627: chirality flip in reactions."
<< std::endl;
smi = "[C:1](=[O:2])>>[C:1](=[S:2])";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
reacts.clear();
smi = "C[C@](Cl)(CO)CC(=O)NC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getNumAtoms() == 10);
TEST_ASSERT(prod->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
reacts.clear();
smi = "C[C@H](CO)CC(=O)NC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getNumAtoms() == 9);
TEST_ASSERT(prod->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
// make sure the above two tests work "backwards":
reacts.clear();
smi = "C[C@@](Cl)(CO)CC(=O)NC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getNumAtoms() == 10);
TEST_ASSERT(prod->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
reacts.clear();
smi = "C[C@@H](CO)CC(=O)NC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getNumAtoms() == 9);
TEST_ASSERT(prod->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
// do some "restructuring" and make sure things still work:
reacts.clear();
smi = "[C@@](C)(Cl)(CO)CC(=O)NC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getNumAtoms() == 10);
TEST_ASSERT(prod->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
reacts.clear();
smi = "[C@H](C)(CO)CC(=O)NC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getNumAtoms() == 9);
TEST_ASSERT(prod->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
reacts.clear();
smi = "C(=O)N[C@@H](CC)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(3)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getNumAtoms() == 7);
TEST_ASSERT(prod->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(3)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
reacts.clear();
smi = "C(=O)N[C@@H](CC)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(3)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getNumAtoms() == 7);
TEST_ASSERT(prod->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(3)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test18PropertyTransfer() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
ROMOL_SPTR prod;
std::string smi, cip;
unsigned int nWarn, nError;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing property transfer in reactions."
<< std::endl;
// ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ -----
// start with sf.net Issue 1934052: propagation of isotope information
smi = "[C:1]>>[C:1]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
reacts.clear();
smi = "C";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 1);
TEST_ASSERT(feq(prod->getAtomWithIdx(0)->getMass(), 12, .1));
reacts.clear();
smi = "[13CH4]";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 1);
TEST_ASSERT(feq(prod->getAtomWithIdx(0)->getMass(), 13, .1));
delete rxn;
smi = "[12C:1]>>[13C:1]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
reacts.clear();
smi = "[12CH4]";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 1);
TEST_ASSERT(prod->getAtomWithIdx(0)->getIsotope() == 13);
TEST_ASSERT(feq(prod->getAtomWithIdx(0)->getMass(), 13.003, .001));
reacts.clear();
smi = "[13CH4]";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 0);
delete rxn;
smi = "[13C:1]>>[12C:1]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
reacts.clear();
smi = "[13CH4]";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 1);
TEST_ASSERT(prod->getAtomWithIdx(0)->getIsotope() == 12);
TEST_ASSERT(feq(prod->getAtomWithIdx(0)->getMass(), 12, .001));
reacts.clear();
smi = "C";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 0);
delete rxn;
smi = "[C:1]>>[12C:1]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
reacts.clear();
smi = "C";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 1);
TEST_ASSERT(prod->getAtomWithIdx(0)->getIsotope() == 12);
TEST_ASSERT(feq(prod->getAtomWithIdx(0)->getMass(), 12, .001));
reacts.clear();
smi = "[13CH4]";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 1);
TEST_ASSERT(prod->getAtomWithIdx(0)->getIsotope() == 12);
TEST_ASSERT(feq(prod->getAtomWithIdx(0)->getMass(), 12, .001));
delete rxn;
smi = "[C:1](=[O:2])>>[C:1](=[S:2])";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
reacts.clear();
smi = "C=O";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 2);
TEST_ASSERT(feq(prod->getAtomWithIdx(0)->getMass(), 12, .1));
TEST_ASSERT(feq(prod->getAtomWithIdx(1)->getMass(), 32, .1));
// ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ -----
// now look at some other properties
delete rxn;
smi = "[c;H1:1][n:2]>>[c:1](O)[n:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
reacts.clear();
smi = "c1ccccn1";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 7);
smi = MolToSmiles(*prod);
std::cerr << smi << std::endl;
TEST_ASSERT(smi == "Oc1ccccn1");
reacts.clear();
smi = "c1ccc[nH]1";
mol = SmilesToMol(smi);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 6);
smi = MolToSmiles(*prod);
std::cerr << smi << std::endl;
TEST_ASSERT(smi == "Oc1ccc[nH]1");
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test19Issue2050085() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
ROMOL_SPTR prod;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing sf.net Issue 2050085: recap failing on chiral molecules."
<< std::endl;
smi = "[N;!D1;+0](-!@[*:1])-!@[*:2]>>*[*:1].[*:2]*";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
reacts.clear();
smi = "C1CC1N[C@H](C)F";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 2);
MolOps::sanitizeMol(*(static_cast<RWMol *>(prods[0][0].get())));
MolOps::sanitizeMol(*(static_cast<RWMol *>(prods[0][1].get())));
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 4);
prod = prods[0][1];
TEST_ASSERT(prod->getNumAtoms() == 4);
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test20BondQueriesInProduct() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
ROMOL_SPTR prod;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing bond queries in the product." << std::endl;
smi = "[O:1]~[C:2]>>[O:1]~[C:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
reacts.clear();
smi = "OCC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(static_cast<RWMol *>(prods[0][0].get())));
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 3);
TEST_ASSERT(prod->getBondBetweenAtoms(0, 1)->getBondType() == Bond::SINGLE);
reacts.clear();
smi = "O=CC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(static_cast<RWMol *>(prods[0][0].get())));
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 3);
TEST_ASSERT(prod->getBondBetweenAtoms(0, 1)->getBondType() == Bond::DOUBLE);
delete rxn;
smi = "[O:1]~[C:2]>>[O:1][C:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
reacts.clear();
smi = "OCC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(static_cast<RWMol *>(prods[0][0].get())));
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 3);
TEST_ASSERT(prod->getBondBetweenAtoms(0, 1)->getBondType() == Bond::SINGLE);
reacts.clear();
smi = "O=CC";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(static_cast<RWMol *>(prods[0][0].get())));
prod = prods[0][0];
TEST_ASSERT(prod->getNumAtoms() == 3);
TEST_ASSERT(prod->getBondBetweenAtoms(0, 1)->getBondType() == Bond::SINGLE);
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test21Issue2540021() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing sf.net Issue 2540021: bad handling of atoms with explicit Hs."
<< std::endl;
{
std::string smi = "[#7;!H0:1]>>[#7:1]C";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "C1=CNC=C1";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
TEST_ASSERT(prod->getNumAtoms() == 6);
TEST_ASSERT(prod->getAtomWithIdx(0)->getAtomicNum() == 7);
TEST_ASSERT(
prod->getAtomWithIdx(0)->getValence(Atom::ValenceType::IMPLICIT) == 0);
TEST_ASSERT(
prod->getAtomWithIdx(0)->getValence(Atom::ValenceType::EXPLICIT) == 3);
TEST_ASSERT(prod->getAtomWithIdx(0)->getNoImplicit() == false);
delete rxn;
}
{
std::string smi =
"[c:1]1[c:2][n;H1:3][c:4][n:5]1>>[c:1]1[c:2][n:3][c:4](C)[n:5]1";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "C1=CNC=N1";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
TEST_ASSERT(prod->getNumAtoms() == 6);
TEST_ASSERT(prod->getAtomWithIdx(2)->getAtomicNum() == 7);
TEST_ASSERT(prod->getAtomWithIdx(2)->getNumExplicitHs() == 1);
TEST_ASSERT(prod->getAtomWithIdx(5)->getAtomicNum() == 7);
TEST_ASSERT(prod->getAtomWithIdx(5)->getNumExplicitHs() == 0);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test22DotsToRemoveBonds() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing using dots in the products to remove bonds."
<< std::endl;
{
/* 08/05/14
* This test is changed due to a new behavior of the smarts reaction parser
* which now
* allows using parenthesis in products as well
* original smiles:
* std::string smi = "[C:1]1[O:2][N:3]1>>[C:1]1[O:2].[N:3]1"; */
std::string smi = "[C:1]1[O:2][N:3]1>>([C:1]1[O:2].[N:3]1)";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "C1ON1";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
TEST_ASSERT(prod->getNumAtoms() == 3);
TEST_ASSERT(prod->getAtomWithIdx(0)->getAtomicNum() == 6);
TEST_ASSERT(prod->getAtomWithIdx(1)->getAtomicNum() == 8);
TEST_ASSERT(prod->getAtomWithIdx(2)->getAtomicNum() == 7);
TEST_ASSERT(prod->getBondBetweenAtoms(0, 1));
TEST_ASSERT(prod->getBondBetweenAtoms(0, 2));
TEST_ASSERT(!prod->getBondBetweenAtoms(1, 2));
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test23Pickling() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing pickling and depickling reactions."
<< std::endl;
{
std::string smi;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
/* 08/05/14
* This test is changed due to a new behavior of the smarts reaction parser
* which now allows using parenthesis in products as well original smiles:
* std::string smi = "[C:1]1[O:2][N:3]1>>[C:1]1[O:2].[N:3]1"; */
smi = "[C:1]1[O:2][N:3]1>>([C:1]1[O:2].[N:3]1)";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
std::string pkl;
ReactionPickler::pickleReaction(rxn, pkl);
delete rxn;
rxn = new ChemicalReaction();
ReactionPickler::reactionFromPickle(pkl, rxn);
rxn->initReactantMatchers();
reacts.clear();
smi = "C1ON1";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
TEST_ASSERT(prod->getNumAtoms() == 3);
TEST_ASSERT(prod->getAtomWithIdx(0)->getAtomicNum() == 6);
TEST_ASSERT(prod->getAtomWithIdx(1)->getAtomicNum() == 8);
TEST_ASSERT(prod->getAtomWithIdx(2)->getAtomicNum() == 7);
TEST_ASSERT(prod->getBondBetweenAtoms(0, 1));
TEST_ASSERT(prod->getBondBetweenAtoms(0, 2));
TEST_ASSERT(!prod->getBondBetweenAtoms(1, 2));
// test construction from a pickle:
delete rxn;
rxn = new ChemicalReaction(pkl);
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
TEST_ASSERT(prod->getNumAtoms() == 3);
TEST_ASSERT(prod->getAtomWithIdx(0)->getAtomicNum() == 6);
TEST_ASSERT(prod->getAtomWithIdx(1)->getAtomicNum() == 8);
TEST_ASSERT(prod->getAtomWithIdx(2)->getAtomicNum() == 7);
TEST_ASSERT(prod->getBondBetweenAtoms(0, 1));
TEST_ASSERT(prod->getBondBetweenAtoms(0, 2));
TEST_ASSERT(!prod->getBondBetweenAtoms(1, 2));
delete rxn;
}
{
std::string rdbase = getenv("RDBASE");
std::string fName;
std::string smi;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/cyclization1.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
std::string pkl;
ReactionPickler::pickleReaction(rxn, pkl);
delete rxn;
rxn = new ChemicalReaction();
ReactionPickler::reactionFromPickle(pkl, rxn);
TEST_ASSERT(!rxn->isInitialized());
rxn->initReactantMatchers();
TEST_ASSERT(rxn->isInitialized());
// quick test of github issue #249
ReactionPickler::pickleReaction(rxn, pkl);
delete rxn;
rxn = new ChemicalReaction();
ReactionPickler::reactionFromPickle(pkl, rxn);
TEST_ASSERT(rxn->isInitialized());
smi = "OC(=O)CN";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 8);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "O=C1CNC(=O)CN1");
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test24AtomFlags() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing preservation of atom flags from rxn files."
<< std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
unsigned int nWarn, nError;
{
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/atomflags.rxn";
ChemicalReaction *rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
TEST_ASSERT(
rxn->beginReactantTemplates()->get()->getAtomWithIdx(0)->hasProp(
common_properties::molAtomMapNumber));
TEST_ASSERT((++(rxn->beginReactantTemplates()))
->get()
->getAtomWithIdx(0)
->hasProp(common_properties::molAtomMapNumber));
TEST_ASSERT((++(rxn->beginReactantTemplates()))
->get()
->getAtomWithIdx(1)
->hasProp(common_properties::molAtomMapNumber));
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test25Conformers() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing transfer of conformer data from reactants->products."
<< std::endl;
unsigned int nWarn, nError;
{
std::string smi;
smi = "[C:1]=[O:2].[N:3]>>[O:2]=[C:1][N:3]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
ROMol *mol;
Conformer *conf;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
reacts.clear();
smi = "C(=O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
conf = new Conformer(3);
conf->setAtomPos(0, RDGeom::Point3D(1, 0, 0));
conf->setAtomPos(1, RDGeom::Point3D(1, 1, 0));
conf->setAtomPos(2, RDGeom::Point3D(1, 0, 1));
mol->addConformer(conf, true);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
conf = new Conformer(2);
conf->setAtomPos(0, RDGeom::Point3D(-1, 0, 0));
conf->setAtomPos(1, RDGeom::Point3D(-1, 1, 0));
mol->addConformer(conf, true);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumConformers() == 1);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(0).x == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(0).y == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(0).z == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(1).x == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(1).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(1).z == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(2).x == -1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(2).y == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(2).z == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(3).x == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(3).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(3).z == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(4).x == -1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(4).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(4).z == 0.0);
// test when only the first reactant has a conf:
reacts.clear();
smi = "C(=O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
conf = new Conformer(3);
conf->setAtomPos(0, RDGeom::Point3D(1, 0, 0));
conf->setAtomPos(1, RDGeom::Point3D(1, 1, 0));
conf->setAtomPos(2, RDGeom::Point3D(1, 0, 1));
mol->addConformer(conf, true);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumConformers() == 1);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(0).x == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(0).y == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(0).z == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(1).x == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(1).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(1).z == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(2).x == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(2).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(2).z == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(3).x == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(3).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(3).z == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(4).x == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(4).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(4).z == 0.0);
// test when only the second reactant has a conf:
reacts.clear();
smi = "C(=O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
conf = new Conformer(2);
conf->setAtomPos(0, RDGeom::Point3D(-1, 0, 0));
conf->setAtomPos(1, RDGeom::Point3D(-1, 1, 0));
mol->addConformer(conf, true);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumConformers() == 1);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(0).x == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(0).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(0).z == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(1).x == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(1).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(1).z == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(2).x == -1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(2).y == 1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(2).z == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(3).x == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(3).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(3).z == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(4).x == -1.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(4).y == 0.0);
TEST_ASSERT(prods[0][0]->getConformer().getAtomPos(4).z == 0.0);
// and, of course, when neither has a conformer:
reacts.clear();
smi = "C(=O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 5);
TEST_ASSERT(prods[0][0]->getNumConformers() == 0);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test26V3000MDLParser() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing v3000 MDL parser" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/v3k.AmideBond.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
smi = "C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
delete rxn;
reacts.clear();
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/v3k.cyclization1.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 8);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "O=C1CNC(=O)CN1");
delete rxn;
reacts.clear();
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/v3k.cyclization1.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 8);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "O=C1CNC(=O)CN1");
delete rxn;
reacts.clear();
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/v3k.cyclization2.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
smi = "CC=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "C=CC=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 7);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[1][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[2][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[3][0]));
reacts.clear();
smi = "CC=C[Cl]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "[F]C=CC=C[Br]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 10);
for (unsigned int i = 0; i < prods.size(); i++) {
unsigned int nDifferent = 0;
for (unsigned int j = 0; j < prods.size(); j++) {
if (MolToSmiles(*prods[i][0]) != MolToSmiles(*prods[j][0])) {
nDifferent += 1;
}
}
TEST_ASSERT(nDifferent == 2);
}
reacts.clear();
smi = "C1C=CCCC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "C=CC=C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 4);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 10);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[1][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[2][0]));
TEST_ASSERT(MolToSmiles(*prods[0][0]) == MolToSmiles(*prods[3][0]));
delete rxn;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test27SmartsWriter() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing reaction SMARTS writer." << std::endl;
unsigned int nWarn, nError;
{
std::string smi;
smi = "[C:1]=[O:2].[N:3]>>[O:2]=[C:1]~[N:3]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi = ChemicalReactionToRxnSmarts(*rxn);
TEST_ASSERT(smi == "[C:1]=[O:2].[N:3]>>[O:2]=[C:1]~[N:3]");
delete rxn;
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test28RxnDepictor() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing reaction depictor." << std::endl;
unsigned int nWarn, nError;
{
std::string smi;
smi =
"[C:10]1[C:11][C:12]1[C:1]=[O:2].[N:3][C:20]([C:21])[C:22]>>[O:2]=[C:1]"
"([C:10]1[C:11][C:12]1)[N:3][C:20]([C:21])[C:22]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
for (RDKit::MOL_SPTR_VECT::const_iterator templIt =
rxn->beginReactantTemplates();
templIt != rxn->endReactantTemplates(); ++templIt) {
TEST_ASSERT((*templIt)->getNumConformers() == 0);
}
for (RDKit::MOL_SPTR_VECT::const_iterator templIt =
rxn->beginProductTemplates();
templIt != rxn->endProductTemplates(); ++templIt) {
TEST_ASSERT((*templIt)->getNumConformers() == 0);
}
RDDepict::compute2DCoordsForReaction(*rxn);
for (RDKit::MOL_SPTR_VECT::const_iterator templIt =
rxn->beginReactantTemplates();
templIt != rxn->endReactantTemplates(); ++templIt) {
TEST_ASSERT((*templIt)->getNumConformers() == 1);
TEST_ASSERT(!(*templIt)->getConformer().is3D());
}
for (RDKit::MOL_SPTR_VECT::const_iterator templIt =
rxn->beginProductTemplates();
templIt != rxn->endProductTemplates(); ++templIt) {
TEST_ASSERT((*templIt)->getNumConformers() == 1);
TEST_ASSERT(!(*templIt)->getConformer().is3D());
}
delete rxn;
}
{ // make sure the depiction doesn't screw up the reaction itself
std::string rdbase = getenv("RDBASE");
std::string fName;
std::string smi;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/cyclization1.rxn";
rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
RDDepict::compute2DCoordsForReaction(*rxn);
smi = "OC(=O)CN";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 8);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "O=C1CNC(=O)CN1");
delete rxn;
}
{
std::string smi = "[#7;!H0:1]>>[#7:1]C";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "C1=CNC=C1";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
RDDepict::compute2DCoordsForReaction(*rxn);
rxn->initReactantMatchers();
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
TEST_ASSERT(prod->getNumAtoms() == 6);
TEST_ASSERT(prod->getAtomWithIdx(0)->getAtomicNum() == 7);
TEST_ASSERT(
prod->getAtomWithIdx(0)->getValence(Atom::ValenceType::IMPLICIT) == 0);
TEST_ASSERT(
prod->getAtomWithIdx(0)->getValence(Atom::ValenceType::EXPLICIT) == 3);
TEST_ASSERT(prod->getAtomWithIdx(0)->getNoImplicit() == false);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test29RxnWriter() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing RXN file writer." << std::endl;
unsigned int nWarn, nError;
{
std::string rdbase = getenv("RDBASE");
std::string fName;
std::string smi;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/AmideBond.rxn";
ChemicalReaction *rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi = ChemicalReactionToRxnSmarts(*rxn);
TEST_ASSERT(smi == "[#6:2](-[#8])=[#8:1].[#7:3]>>[#7:3]-[#6:2]=[#8:1]")
std::string mb;
mb = ChemicalReactionToRxnBlock(*rxn);
delete rxn;
rxn = RxnBlockToChemicalReaction(mb);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test30ReactProdQueries() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing reactant and product queries." << std::endl;
{
ROMol *mol;
unsigned int nWarn, nError, which;
std::string smi;
smi =
"[c;H:1]:[c:2](:[c;H:3])Br.[C:4](=[O:5])Cl>>[c:1]:[c:2]([c:3])-[C:4]=["
"O:5]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi = "c1ccccc1Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(isMoleculeReactantOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == 0);
TEST_ASSERT(isMoleculeReactantOfReaction(*rxn, *mol));
delete (mol);
smi = "c1ccccc1Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!isMoleculeReactantOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == rxn->getNumReactantTemplates());
TEST_ASSERT(!isMoleculeReactantOfReaction(*rxn, *mol));
delete (mol);
smi = "c1ccncc1Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(isMoleculeReactantOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == 0);
delete (mol);
smi = "c1cccnc1Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!isMoleculeReactantOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == rxn->getNumReactantTemplates());
delete (mol);
smi = "c1cccc(C)c1Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!isMoleculeReactantOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == rxn->getNumReactantTemplates());
delete (mol);
smi = "ClC(=O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(isMoleculeReactantOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == 1);
delete (mol);
smi = "C(=O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!isMoleculeReactantOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == rxn->getNumReactantTemplates());
delete (mol);
smi = "c1ccccc1C(=O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(isMoleculeProductOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == 0);
TEST_ASSERT(isMoleculeProductOfReaction(*rxn, *mol));
delete (mol);
smi = "c1cccnc1C(=O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!isMoleculeProductOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == rxn->getNumProductTemplates());
TEST_ASSERT(!isMoleculeProductOfReaction(*rxn, *mol));
delete (mol);
delete (rxn);
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test31Issue3140490() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 3140490." << std::endl;
{
unsigned int nWarn, nError;
std::string smi;
smi = "[O:1]>>[N:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "OC";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(!prods[0][0]->getAtomWithIdx(0)->hasProp(
common_properties::molAtomMapNumber));
TEST_ASSERT(!prods[0][0]->getAtomWithIdx(1)->hasProp(
common_properties::molAtomMapNumber));
delete (rxn);
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test32Replacements() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing string replacement in parsing." << std::endl;
{
std::map<std::string, std::string> repls;
repls["{amine}"] = "$([N;!H0;$(N-[#6]);!$(N-[!#6;!#1]);!$(N-C=[O,N,S])])";
unsigned int nWarn, nError;
std::string smi;
smi = "[{amine}:1]>>[*:1]-C";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, &repls);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "CCN";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
delete (rxn);
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test33ReactingAtoms1() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing getReactingAtoms() 1." << std::endl;
{ // basics
std::string smi;
smi = "[O:1][C:2]>>[N:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 1);
delete rxn;
}
{ // no changes
std::string smi;
smi = "[O:1][C:2]>>[O:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 0);
delete rxn;
}
{ // make sure atomic number queries work:
std::string smi;
smi = "[#8:1][C:2]>>[O:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 0);
delete rxn;
}
{ // query in the reactants, dummy in product
std::string smi;
smi = "[O,N:1][C:2]>>[*:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 0);
delete rxn;
}
{ // recursive query in the reactants without an atomic number query
std::string smi;
smi = "[$(O):1][C:2]>>[O:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 1);
delete rxn;
}
{ // recursive query with atomic number query
std::string smi;
smi = "[O;$(O):1][C:2]>>[O:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 0);
delete rxn;
}
{ // recursive query with atomic number query, alternate ordering
// FIX: this returns a changed atom (since we don't know the atomic
// number of the atom) but probably shouldn't
std::string smi;
smi = "[$(O);O:1][C:2]>>[O:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 1);
delete rxn;
}
{ // recursive query in the reactants, dummy in products
std::string smi;
smi = "[$(O):1][C:2]>>[*:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 0);
delete rxn;
}
{ // query with degree/H info in the reactants:
std::string smi;
smi = "[O;H1:1][C:2]>>[O:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 0);
delete rxn;
}
{ // dummy in the reactants, dummy in products
std::string smi;
smi = "[*:1][C:2]>>[*:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 0);
delete rxn;
}
{ // two reactants, one changes
std::string smi;
smi = "[O:1][C:2].[N:3]>>[N:1][C:2].[N:3]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 2);
TEST_ASSERT(ratoms[0].size() == 1);
TEST_ASSERT(ratoms[1].size() == 0);
delete rxn;
}
{ // two reactants, one changes, reordered
std::string smi;
smi = "[O:1][C:2].[N:3]>>[N:3].[N:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 2);
TEST_ASSERT(ratoms[0].size() == 1);
TEST_ASSERT(ratoms[1].size() == 0);
delete rxn;
}
{ // dummies for duplicating atom properties
std::string smi;
smi = "[O:1][C:2].[N:3]>>[N:1][C:2].[*:3]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 2);
TEST_ASSERT(ratoms[0].size() == 1);
TEST_ASSERT(ratoms[1].size() == 0);
delete rxn;
}
{ // query in the reactants, dummy in products
std::string smi;
smi = "[O,N:1][C:2]>>[*:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 0);
delete rxn;
}
{ // changed degree
std::string smi;
smi = "[O:1][C:2].[N:3]>>[N:1][C:2].[*:3]C";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 2);
TEST_ASSERT(ratoms[0].size() == 1);
TEST_ASSERT(ratoms[1].size() == 1);
delete rxn;
}
{ // unmapped atoms in reactants:
std::string smi;
smi = "[O:1]C>>[O:1]C";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 2);
delete rxn;
}
{ // don't return info about unmapped atoms:
std::string smi;
smi = "[O:1]C>>[O:1]C";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn, true);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 1);
delete rxn;
}
{ // changing atom order
std::string smi;
smi = "[C:1]-[C:2]>>[C:2]-[C:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 0);
delete rxn;
}
{ // changing bond order
std::string smi;
smi = "[C:1]-[C:2]>>[C:1]=[C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 2);
delete rxn;
}
{ // changing bond orders
std::string smi;
smi = "[C:1]-[C:2]=[C:3]>>[C:1]=[C:2]-[C:3]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 3);
delete rxn;
}
{ // query bond order
std::string smi;
smi = "[C:1]-[C:2]>>[C:1]~[C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 0);
delete rxn;
}
{ // changing connectivity
std::string smi;
smi = "[C:1]-[C:2]-[C:3]>>[C:1]~[C:3]~[C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 3);
delete rxn;
}
{ // changing connectivity 2
std::string smi;
smi = "[C:1]1[C:2][C:3]1>>[C:1][C:2][C:3]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 1);
TEST_ASSERT(ratoms[0].size() == 2);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test34ReactingAtoms2() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing getReactingAtoms() 2" << std::endl;
{
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/AmideBond.rxn";
ChemicalReaction *rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 2);
TEST_ASSERT(ratoms[0].size() == 2);
TEST_ASSERT(ratoms[1].size() == 1);
delete rxn;
}
{
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/cyclization1.rxn";
ChemicalReaction *rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
VECT_INT_VECT ratoms = getReactingAtoms(*rxn);
TEST_ASSERT(ratoms.size() == 2);
TEST_ASSERT(ratoms[0].size() == 3);
TEST_ASSERT(ratoms[1].size() == 3);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test35ParensInReactants1() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing grouping parens in reactants1" << std::endl;
{
std::string smi = "[C:1].[C:2]>>[C:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
{
std::string smi = "([C:1].[C:2])>>[C:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
{
std::string smi = "([C:1].C(=O)O).[C:2]>>[C:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
{
std::string smi = "[C:1](=O)O.[C:2]>>[C:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
{
std::string smi = "[C:1](=O)O.([C:2])>>[C:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
{
std::string smi = "[C:1](=O)O.([C:2].N)>>[C:1][C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
{
std::string smi = "([C:1](=O)O.[C:2]>>[C:1][C:2]";
ChemicalReaction *rxn = nullptr;
try {
rxn = RxnSmartsToChemicalReaction(smi);
} catch (const ChemicalReactionParserException &) {
rxn = nullptr;
}
TEST_ASSERT(!rxn);
delete rxn;
}
{
std::string smi = "[C:1](=O)O.([C:2]>>[C:1][C:2]";
ChemicalReaction *rxn = nullptr;
try {
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(!rxn);
} catch (const ChemicalReactionParserException &) {
;
}
delete rxn;
}
{
std::string smi = "[C:1](=O)O).[C:2]>>[C:1][C:2]";
ChemicalReaction *rxn = nullptr;
try {
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(!rxn);
} catch (const ChemicalReactionParserException &) {
;
}
delete rxn;
}
{
std::string smi = "[C:1](=O)O.[C:2])>>[C:1][C:2]";
ChemicalReaction *rxn = nullptr;
try {
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(!rxn);
} catch (const ChemicalReactionParserException &) {
;
}
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test36ParensInReactants2() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing grouping parens in reactants2" << std::endl;
{
std::string smi = "([C:1].[O:2])>>[C:1][O:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "CNO";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 3);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test37ProtectOption() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing use of _protected property on atoms."
<< std::endl;
{
unsigned int nWarn, nError;
std::string smi = "[O:1]>>[N:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "OCO";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[1].size() == 1);
reacts[0]->getAtomWithIdx(0)->setProp(common_properties::_protected, 1);
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
delete (rxn);
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test38AddRecursiveQueriesToReaction() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing use of adding recursive queries to a reaction." << std::endl;
{
ROMol *mol = nullptr;
ChemicalReaction rxn;
MOL_SPTR_VECT reacts;
std::string smi;
smi = "[C:1](=[O:2])";
mol = SmartsToMol(smi);
mol->getAtomWithIdx(0)->setProp("replaceme", "foo");
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 1);
smi = "[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 2);
smi = "[C:1](=[O:2])[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addProductTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumProductTemplates() == 1);
std::string smi2 = "CCl";
ROMOL_SPTR q1(SmilesToMol(smi2));
std::map<std::string, ROMOL_SPTR> mp;
mp["foo"] = q1;
bool ok = false;
try {
addRecursiveQueriesToReaction(rxn, mp, "replaceme");
} catch (ChemicalReactionException &) {
ok = true;
}
TEST_ASSERT(ok);
rxn.initReactantMatchers();
addRecursiveQueriesToReaction(rxn, mp, "replaceme");
MatchVectType mv;
std::string msmi = "C(=O)Cl";
ROMol *mmol = SmilesToMol(msmi);
TEST_ASSERT(SubstructMatch(*mmol, *(*(rxn.beginReactantTemplates())), mv));
delete mmol;
msmi = "C(=O)O";
mmol = SmilesToMol(msmi);
TEST_ASSERT(!SubstructMatch(*mmol, *(*(rxn.beginReactantTemplates())), mv));
delete mmol;
}
{
ROMol *mol = nullptr;
ChemicalReaction rxn;
MOL_SPTR_VECT reacts;
std::string smi;
smi = "[C:1](=[O:2])";
mol = SmartsToMol(smi);
mol->getAtomWithIdx(0)->setProp("replaceme", "foo");
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 1);
smi = "[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 2);
smi = "[C:1](=[O:2])[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addProductTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumProductTemplates() == 1);
std::string smi2 = "CO";
ROMOL_SPTR q1(SmilesToMol(smi2));
std::map<std::string, ROMOL_SPTR> mp;
mp["foo"] = q1;
rxn.initReactantMatchers();
std::vector<std::vector<std::pair<unsigned int, std::string>>> labels;
addRecursiveQueriesToReaction(rxn, mp, "replaceme", &labels);
TEST_ASSERT(labels.size() == 2);
TEST_ASSERT(labels[0][0].second == "foo");
}
{
ROMol *mol = nullptr;
ChemicalReaction rxn;
MOL_SPTR_VECT reacts;
std::string smi;
smi = "[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 1);
smi = "[C:1](=[O:2])";
mol = SmartsToMol(smi);
mol->getAtomWithIdx(0)->setProp("replaceme", "foo");
TEST_ASSERT(mol);
rxn.addReactantTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumReactantTemplates() == 2);
smi = "[C:1](=[O:2])[N:3][C:4]";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn.addProductTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn.getNumProductTemplates() == 1);
std::string smi2 = "CO";
ROMOL_SPTR q1(SmilesToMol(smi2));
std::map<std::string, ROMOL_SPTR> mp;
mp["foo"] = q1;
rxn.initReactantMatchers();
std::vector<std::vector<std::pair<unsigned int, std::string>>> labels;
addRecursiveQueriesToReaction(rxn, mp, "replaceme", &labels);
TEST_ASSERT(labels.size() == 2);
TEST_ASSERT(labels[1][0].second == "foo");
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test39InnocentChiralityLoss() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing loss of chirality on innocent atoms."
<< std::endl;
{
ChemicalReaction *rxn =
RxnSmartsToChemicalReaction("[C:2][C:1]=O>>[C:2][C:1]=S");
unsigned int nWarn, nError;
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
{
std::string smi = "Cl[C@H](F)C=O";
ROMol *mol = SmilesToMol(smi);
MOL_SPTR_VECT reacts;
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
smi = MolToSmiles(*prods[0][0], false);
TEST_ASSERT(smi == "FC(Cl)C=S");
smi = MolToSmiles(*prods[0][0], true);
TEST_ASSERT(smi == "F[C@@H](Cl)C=S");
}
{
std::string smi = "O=C[C@@H](F)Cl";
ROMol *mol = SmilesToMol(smi);
MOL_SPTR_VECT reacts;
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
smi = MolToSmiles(*prods[0][0], false);
TEST_ASSERT(smi == "FC(Cl)C=S");
smi = MolToSmiles(*prods[0][0], true);
TEST_ASSERT(smi == "F[C@@H](Cl)C=S");
}
{
std::string smi = "F[C@H](C=O)Cl";
ROMol *mol = SmilesToMol(smi);
MOL_SPTR_VECT reacts;
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
smi = MolToSmiles(*prods[0][0], false);
TEST_ASSERT(smi == "FC(Cl)C=S");
smi = MolToSmiles(*prods[0][0], true);
TEST_ASSERT(smi == "F[C@@H](Cl)C=S");
}
delete rxn;
}
{
// in this case the atom isn't actually innocent, but we can handle it
// anyway because
// only one bond changes
ChemicalReaction *rxn = RxnSmartsToChemicalReaction("[C:1]-O>>[C:1]-S");
unsigned int nWarn, nError;
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
{
std::string smi = "Cl[C@H](F)O";
ROMol *mol = SmilesToMol(smi);
MOL_SPTR_VECT reacts;
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
smi = MolToSmiles(*prods[0][0], false);
TEST_ASSERT(smi == "FC(S)Cl");
smi = MolToSmiles(*prods[0][0], true);
TEST_ASSERT(smi == "F[C@H](S)Cl");
}
delete rxn;
}
{
// another non-innocent atom
ChemicalReaction *rxn = RxnSmartsToChemicalReaction("[C:1]-O>>[C:1]");
unsigned int nWarn, nError;
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
{
std::string smi = "Cl[C@H](F)O";
ROMol *mol = SmilesToMol(smi);
MOL_SPTR_VECT reacts;
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
smi = MolToSmiles(*prods[0][0], false);
TEST_ASSERT(smi == "FCCl");
smi = MolToSmiles(*prods[0][0], true);
TEST_ASSERT(smi == "FCCl");
}
delete rxn;
}
{
// one of the original bug report cases:
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(
"[C:1](=[O:2])[C:3][C:4]([OH:5])[#6:6]>>[C:1](=[O:2])[C:3][H].[C:4](=["
"O:5])[#6:6]");
unsigned int nWarn, nError;
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
{
std::string smi = "CC(O)[C@](N)(F)C(C)=O";
ROMol *mol = SmilesToMol(smi);
MOL_SPTR_VECT reacts;
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
smi = MolToSmiles(*prods[0][0], false);
TEST_ASSERT(smi == "[H]C(N)(F)C(C)=O");
smi = MolToSmiles(*prods[0][0], true);
TEST_ASSERT(smi == "[H][C@](N)(F)C(C)=O");
}
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test40AgentsInSmarts() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing handling of agents in reaction smarts"
<< std::endl;
// This was github #222
{
ChemicalReaction *rxn;
std::string smi;
smi = "[C:1](=[O:2])O.[N:3][C:4]>[Pd]>[C:1](=[O:2])[N:3][C:4]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test41Github233() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing github 233: chirality not preserved in nonmapped atoms"
<< std::endl;
{
ChemicalReaction *rxn;
std::string smi;
smi = "[F:1][C:2]([C:3])[I:4]>>[F:1][C:2]([C:3][C@H]([OH])Br)[Cl:4]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
unsigned int nWarn, nError;
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi = "FC(C)I";
ROMol *mol = SmilesToMol(smi);
MOL_SPTR_VECT reacts;
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(static_cast<RWMol *>(prods[0][0].get())));
smi = MolToSmiles(*prods[0][0], true);
TEST_ASSERT(smi == "O[C@H](Br)CC(F)Cl");
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test42ReactionSmiles() {
ROMol *mol = nullptr;
ChemicalReaction *rxn;
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Daylight parser" << std::endl;
smi = "[C:1](=[O:2])O.[N:3][C:4]>>[C:1](=[O:2])[N:3][C:4]";
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
smi = "C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 4);
TEST_ASSERT(prods[0][0]->getNumBonds() == 3);
delete rxn;
reacts.clear();
smi =
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>>[N:1]1[C:2]["
"C:3](=[O:4])[N:6][C:7][C:8]1=[O:9].[O:5][O:10]";
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "OC(=O)CN";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 8);
TEST_ASSERT(prods[0][1]->getNumAtoms() == 2);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "O=C1CNC(=O)CN1");
TEST_ASSERT(MolToSmiles(*prods[0][1]) == "OO");
delete rxn;
reacts.clear();
smi =
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10].[N:1]1[C:2]["
"C:3](=[O:4])[N:6][C:7][C:8]1=[O:9].[O:5][O:10]";
try {
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
} catch (ChemicalReactionParserException &) {
}
smi =
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>>[N:1]1[C:2]["
"C:3](=[O:4])[N:6][C:7][C:8]1=[O:9]>>[O:5][O:10]";
try {
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
} catch (ChemicalReactionParserException &) {
}
smi =
"[Q:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>>[N:1]1[C:2]["
"C:3](=[O:4])[N:6][C:7][C:8]1=[O:9].[O:5][O:10]";
try {
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
} catch (ChemicalReactionParserException &) {
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test43Github243() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing github 243: dummy labels copied into products" << std::endl;
{
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/github243.rxn";
ChemicalReaction *rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
std::string smi = "CCCN";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(9)->getAtomicNum() == 6);
TEST_ASSERT(!prods[0][0]->getAtomWithIdx(9)->hasProp(
common_properties::dummyLabel));
TEST_ASSERT(!prods[0][0]->getAtomWithIdx(9)->hasProp(
common_properties::_MolFileRLabel));
TEST_ASSERT(prods[0][0]->getAtomWithIdx(9)->getIsotope() == 0);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(10)->getAtomicNum() == 0);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(10)->hasProp(
common_properties::dummyLabel));
TEST_ASSERT(prods[0][0]->getAtomWithIdx(10)->hasProp(
common_properties::_MolFileRLabel));
delete (rxn);
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test44Github290() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing github 290: seg fault while parsing rxn"
<< std::endl;
{
auto *rxn = new ChemicalReaction();
delete rxn;
}
{
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/bogus_github290.rxn";
bool failed = false;
try {
RxnFileToChemicalReaction(fName);
} catch (ChemicalReactionParserException &) {
failed = true;
}
TEST_ASSERT(failed);
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test45SmilesWriter() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing reaction SMILES writer." << std::endl;
unsigned int nWarn, nError;
{
std::string smi;
smi = "[C:1]=[O:2].[N:3]>>[N:3]~[C:1]=[O:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
std::string res = "";
for (MOL_SPTR_VECT::const_iterator iter = rxn->beginReactantTemplates();
iter != rxn->endReactantTemplates(); ++iter) {
if (iter != rxn->beginReactantTemplates()) {
res += ".";
}
res += MolToSmiles(**iter, true);
}
res += ">>";
for (MOL_SPTR_VECT::const_iterator iter = rxn->beginProductTemplates();
iter != rxn->endProductTemplates(); ++iter) {
if (iter != rxn->beginProductTemplates()) {
res += ".";
}
res += MolToSmiles(**iter, true);
}
smi = ChemicalReactionToRxnSmiles(*rxn);
TEST_ASSERT(smi == res)
TEST_ASSERT(smi == "[C:1]=[O:2].[N:3]>>[C:1](=[O:2])~[N:3]");
delete rxn;
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
delete rxn;
}
{
std::string smi;
smi = "C=O.N>>N~C=O";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
std::string res = "";
for (MOL_SPTR_VECT::const_iterator iter = rxn->beginReactantTemplates();
iter != rxn->endReactantTemplates(); ++iter) {
if (iter != rxn->beginReactantTemplates()) {
res += ".";
}
res += MolToSmiles(**iter, true);
}
res += ">>";
for (MOL_SPTR_VECT::const_iterator iter = rxn->beginProductTemplates();
iter != rxn->endProductTemplates(); ++iter) {
if (iter != rxn->beginProductTemplates()) {
res += ".";
}
res += MolToSmiles(**iter, true);
}
smi = ChemicalReactionToRxnSmiles(*rxn);
TEST_ASSERT(smi == res)
TEST_ASSERT(smi == "C=O.N>>N~C=O");
delete rxn;
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
{
std::string smi;
smi = "[S,C]=O.N>>N~[S,C]=O";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, false);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
std::string res = "";
for (MOL_SPTR_VECT::const_iterator iter = rxn->beginReactantTemplates();
iter != rxn->endReactantTemplates(); ++iter) {
if (iter != rxn->beginReactantTemplates()) {
res += ".";
}
res += MolToSmiles(**iter, true);
}
res += ">>";
for (MOL_SPTR_VECT::const_iterator iter = rxn->beginProductTemplates();
iter != rxn->endProductTemplates(); ++iter) {
if (iter != rxn->beginProductTemplates()) {
res += ".";
}
res += MolToSmiles(**iter, true);
}
smi = ChemicalReactionToRxnSmiles(*rxn, false);
TEST_ASSERT(smi == res)
TEST_ASSERT(smi != "C=O.N>>N~C=O");
TEST_ASSERT(smi == "*=O.N>>N~*=O");
delete rxn;
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test46Agents() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing handling of reaction agents." << std::endl;
unsigned int nWarn, nError;
{
std::string smi;
ROMol *mol = nullptr;
smi = "[C:1]=[O:2].[N:3]>[OH2].[Na].[Cl]>[N:3]~[C:1]=[O:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 3);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi = "C(=O)O";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn->addAgentTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn->getNumAgentTemplates() == 4);
delete rxn;
}
{
std::string smi;
smi = ">[OH2].[Na].[Cl]>";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 0);
TEST_ASSERT(rxn->getNumProductTemplates() == 0);
TEST_ASSERT(rxn->getNumAgentTemplates() == 3);
delete rxn;
}
{
std::string smi;
ROMol *mol = nullptr;
MOL_SPTR_VECT agents;
smi = "[C:1]=[O:2].[N:3]>>[N:3]~[C:1]=[O:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi = "C(=O)O";
mol = SmartsToMol(smi);
TEST_ASSERT(mol);
rxn->addAgentTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn->getNumAgentTemplates() == 1);
delete rxn;
}
{
std::string smi;
ROMol *mol = nullptr;
unsigned int nWarn, nError, which;
MOL_SPTR_VECT agents;
smi = "[C:1]=[O:2].[N:3]>[OH2].[Na].[Cl]>[N:3]~[C:1]=[O:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 3);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi = "O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(isMoleculeAgentOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == 0);
TEST_ASSERT(isMoleculeAgentOfReaction(*rxn, *mol));
delete (mol);
smi = "C(=O)N";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!isMoleculeAgentOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == rxn->getNumAgentTemplates());
TEST_ASSERT(!isMoleculeAgentOfReaction(*rxn, *mol));
delete (mol);
smi = "C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!isMoleculeAgentOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == rxn->getNumAgentTemplates());
TEST_ASSERT(!isMoleculeAgentOfReaction(*rxn, *mol));
delete (mol);
smi = "C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
rxn->addAgentTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn->getNumAgentTemplates() == 4);
smi = "C(=O)O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(isMoleculeAgentOfReaction(*rxn, *mol, which));
TEST_ASSERT(which == 3);
delete (mol);
delete rxn;
}
{
std::string smi1, smi2;
smi1 = "[C:1]=[O:2].[N:3]>[OH2].[Na].[Cl]>[N:3]~[C:1]=[O:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi1, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 3);
rxn->initReactantMatchers();
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi2 = "[C:1]=[O:2].[N:3]>>[N:3]~[C:1]=[O:2]";
ChemicalReaction *rxnq = RxnSmartsToChemicalReaction(smi2, nullptr, true);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq->getNumReactantTemplates() == 2);
TEST_ASSERT(rxnq->getNumProductTemplates() == 1);
TEST_ASSERT(rxnq->getNumAgentTemplates() == 0);
rxnq->initReactantMatchers();
TEST_ASSERT(rxnq->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *rxnq, true));
delete rxn;
delete rxnq;
}
{
std::string smi1;
smi1 = "[C:1]=[O:2].[N:3].C(=O)O>[OH2].[Na].[Cl]>[N:3]~[C:1]=[O:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi1, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 3);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 3);
rxn->initReactantMatchers();
rxn->removeUnmappedReactantTemplates();
rxn->removeUnmappedProductTemplates();
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 4);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test47TestReactionMoleculeConversion() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing the conversion of a molecule with Rxn role "
"to a reaction and vice versa."
<< std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/ChemReactions/testData/";
{
std::string fName;
fName = rdbase + "rxn1.mol";
ROMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 18);
TEST_ASSERT(m->getNumBonds() == 16);
ChemicalReaction *rxn = RxnMolToChemicalReaction(*m);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
ROMol *mol = ChemicalReactionToRxnMol(*rxn);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(0)->getProp<int>(
common_properties::molRxnRole) == 1);
TEST_ASSERT(
mol->getAtomWithIdx(10)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(10)->getProp<int>(
common_properties::molRxnRole) == 2);
std::string smi1 = MolToSmiles(*m);
std::string smi2 = MolToSmiles(*mol);
TEST_ASSERT(smi1 == smi2)
std::string smi3 = ChemicalReactionToRxnSmiles(*rxn);
ChemicalReaction *rxn2 = RxnMolToChemicalReaction(*mol);
std::string smi4 = ChemicalReactionToRxnSmiles(*rxn2);
TEST_ASSERT(smi3 == smi4)
delete rxn;
delete rxn2;
delete m;
delete mol;
}
{
// test molecule with bond between reactant and product, same test as having
// different rxn roles in one fragment
std::string fName;
fName = rdbase + "rxn1_1.mol";
ROMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 18);
TEST_ASSERT(m->getNumBonds() == 17);
ChemicalReaction *rxn = RxnMolToChemicalReaction(*m);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 0);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
delete rxn;
delete m;
}
{
// test for molecule with correct rxn role for only one reactant
std::string fName;
fName = rdbase + "rxn1_2.mol";
ROMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms() == 18);
TEST_ASSERT(m->getNumBonds() == 16);
ChemicalReaction *rxn = RxnMolToChemicalReaction(*m);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
delete rxn;
delete m;
;
}
{
// test for molecule with correct rxn role for only one reactant
std::string smi = "[C:1][C:2]>>[C:1].[C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
ROMol *mol = ChemicalReactionToRxnMol(*rxn);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(0)->getProp<int>(
common_properties::molRxnRole) == 1);
TEST_ASSERT(mol->getAtomWithIdx(2)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(2)->getProp<int>(
common_properties::molRxnRole) == 2);
TEST_ASSERT(mol->getAtomWithIdx(3)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(3)->getProp<int>(
common_properties::molRxnRole) == 2);
delete rxn;
delete mol;
smi = "[C:1][C:2]>[Na]>[C:1].[C:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
TEST_ASSERT(rxn->getNumAgentTemplates() == 1);
mol = ChemicalReactionToRxnMol(*rxn);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(0)->getProp<int>(
common_properties::molRxnRole) == 1);
TEST_ASSERT(mol->getAtomWithIdx(2)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(2)->getProp<int>(
common_properties::molRxnRole) == 2);
TEST_ASSERT(mol->getAtomWithIdx(4)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(4)->getProp<int>(
common_properties::molRxnRole) == 3);
delete rxn;
delete mol;
smi = "[C:1][C:2]>>";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 0);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
mol = ChemicalReactionToRxnMol(*rxn);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(0)->getProp<int>(
common_properties::molRxnRole) == 1);
delete rxn;
delete mol;
smi = ">>[C:1].[C:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn->getNumReactantTemplates() == 0);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
mol = ChemicalReactionToRxnMol(*rxn);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(0)->getProp<int>(
common_properties::molRxnRole) == 2);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::molRxnRole));
TEST_ASSERT(mol->getAtomWithIdx(1)->getProp<int>(
common_properties::molRxnRole) == 2);
delete rxn;
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test48ParensInProducts1() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing grouping parens in products1" << std::endl;
{
std::string smi = "[C:1][C:2]>>[C:1].[C:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
delete rxn;
}
{
std::string smi = "[C:1][C:2]>>([C:1].[C:2])";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
{
std::string smi = "([C:1].C(=O)O).[C:2]>>([C:1].[C:2]).C(=O)O";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
delete rxn;
}
{
std::string smi = "[C:1](=O)O.[C:2]>>[C:1][C:2].C(=O)O";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
delete rxn;
}
{
std::string smi = "[C:1](=O)O.([C:2])>>[C:1][C:2].(C(=O)O)";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
delete rxn;
}
{
std::string smi = "[C:1](=O)O.([C:2].N)>>[C:1][C:2].(C(=O)O.N)";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
delete rxn;
}
{
std::string smi = "[C:1](=O)O.[C:2]>>([C:1][C:2]";
ChemicalReaction *rxn = nullptr;
try {
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(!rxn);
} catch (const ChemicalReactionParserException &) {
;
}
delete rxn;
}
{
std::string smi = "[C:1](=O)O.[C:2]>>[C:1].([C:2]";
ChemicalReaction *rxn = nullptr;
try {
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(!rxn);
} catch (const ChemicalReactionParserException &) {
;
}
delete rxn;
}
{
std::string smi = "[C:1](=O)O.[C:2]>>[C:1][C:2])";
ChemicalReaction *rxn = nullptr;
try {
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(!rxn);
} catch (const ChemicalReactionParserException &) {
;
}
delete rxn;
}
{
std::string smi = "[C:1](=O)O.[C:2]>>[C:1]).[C:2]";
ChemicalReaction *rxn = nullptr;
try {
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(!rxn);
} catch (const ChemicalReactionParserException &) {
;
}
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test49ParensInProducts2() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing grouping parens in products2" << std::endl;
{
std::string smi = "[C:1][O:2]>>([C:1].[O:2])";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "C1NO1";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 3);
TEST_ASSERT(prods[0][0]->getNumBonds() == 2);
delete rxn;
}
{
std::string smi = "([N:1].[O:2])>>([N:1]C.[O:2]CCC)";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "Nn1ccc(O)c1";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
TEST_ASSERT(reacts[0]->getNumAtoms() == 7);
TEST_ASSERT(reacts[0]->getNumBonds() == 7);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 11);
TEST_ASSERT(prods[0][0]->getNumBonds() == 11);
smi = "CCCOc1ccn(NC)c1";
auto *p00 = static_cast<RWMol *>(prods[0][0].get());
MolOps::sanitizeMol(*p00);
TEST_ASSERT(MolToSmiles(*p00) == smi);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test50RNXFileParserWithEmptyAgentColumn() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing RNX file parser with empty agent column"
<< std::endl;
{
std::string rdbase = getenv("RDBASE");
std::string fName;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/rxn2.mol";
ChemicalReaction *rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test51RNXSmilesFromPatentData() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing RNX from patent data" << std::endl;
unsigned int nWarn, nError;
{
// product atom-mapping numbers found multiple times, validation should fail
std::string smi =
"[Na+].[Na+].[NH2:23][CH2:22][CH2:21][CH2:20][CH2:19][CH2:18][CH2:17]["
"CH2:16][CH2:15][CH2:14][NH2:13].O=C([O-])[O-].[Cl:12][c:8]1[cH:9][cH:"
"10][c:11]2[c:2](Cl)[n:3][cH:4][n:5][c:6]2[cH:7]1>CC(C)O>[Cl:12][c:8]1["
"cH:9][cH:10][c:11]2[c:6]([cH:7]1)[n:5][cH:4][n:3][c:2]2[NH:23][CH2:22]"
"[CH2:21][CH2:20][CH2:19][CH2:18][CH2:17][CH2:16][CH2:15][CH2:14][NH:"
"13][c:2]1[n:3][cH:4][n:5][c:6]2[cH:7][c:8]([Cl:12])[cH:9][cH:10][c:11]"
"21";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
delete rxn;
}
{
// test removing reactant without heavyatoms to agents
std::string smi =
"[S].[H][H].[CH3:2][CH2:1][O:3][C:4](=[O:20])[c:5]1[c:6]([O:17][CH2:18]"
"[CH3:19])[cH:7][c:8]([C:14](=[O:15])Cl)[cH:9][c:10]1[O:11][CH2:12]["
"CH3:13].c1ccc2ncccc2c1>[Pd+2].[Ba+2].O=S(=O)([O-])[O-].O=S(=O)([O-])["
"O-]>[CH3:2][CH2:1][O:3][C:4](=[O:20])[c:5]1[c:6]([O:17][CH2:18][CH3:"
"19])[cH:7][c:8]([CH:14]=[O:15])[cH:9][c:10]1[O:11][CH2:12][CH3:13]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
rxn->initReactantMatchers();
rxn->removeUnmappedReactantTemplates();
rxn->removeUnmappedProductTemplates();
delete rxn;
}
{
// reactant atom-mapping numbers found multiple times, validation should
// fail
std::string smi =
"[BrH:1].[CH3:24][CH2:23][CH2:22][CH2:21][CH2:20][C:19](=[O:25])O[C:19]"
"(=[O:25])[CH2:20][CH2:21][CH2:22][CH2:23][CH3:24].[CH3:16][CH:15]1[N:"
"14]([CH3:17])[CH:13]2[CH2:18][C:9]1([c:5]1[cH:6][cH:7][cH:8][c:3]([OH:"
"2])[cH:4]1)[CH2:10][CH2:11][CH2:12]2>c1ccncc1>[BrH:1].[CH3:24][CH2:23]"
"[CH2:22][CH2:21][CH2:20][C:19](=[O:25])[O:2][c:3]1[cH:8][cH:7][cH:6]["
"c:5]([C:9]23[CH2:18][CH:13]([CH2:12][CH2:11][CH2:10]2)[N:14]([CH3:17])"
"[CH:15]3[CH3:16])[cH:4]1";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(!rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError != 0);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test52RedundantProductMappingNumbersAndRunReactants() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing products redundant atom mapping numbers in run_reactants"
<< std::endl;
unsigned int nWarn, nError;
{
std::string smi = "[C:1]-[OH:2]>>[C:1]-[O:2]-[C:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "N[13CH2]O";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
smi = "N[13CH2]O[13CH2]N";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
delete rxn;
}
{
std::string smi = "[C:1]-[OH:2]>>[C:1]-[O:2]-[C:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "[13CH3]O";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getNumAtoms() == 3);
TEST_ASSERT(prods[0][0]->getNumBonds() == 2);
smi = "[13CH3]O[13CH3]";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
delete rxn;
}
{
std::string smi = "[O:1]-[C:2]>>[O:1]-[C:2]-C-[C:2]-[O:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "[13C]1OCN1";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[1].size() == 1);
smi = "C1N[13C](C[13C]2NCO2)O1";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
smi = "C(C1N[13C]O1)C1N[13C]O1";
TEST_ASSERT(MolToSmiles(*prods[1][0], true) == smi);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test53ReactionSubstructureMatching() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing reaction substructure matching w/o agents"
<< std::endl;
{
std::string smi = "c1ccccc1>>c1ccncc1";
ChemicalReaction *query_rxn =
RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(query_rxn);
TEST_ASSERT(query_rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(query_rxn->getNumProductTemplates() == 1);
TEST_ASSERT(query_rxn->getNumAgentTemplates() == 0);
smi = "CCC.c1ccccc1>>CCC.c1ccncc1";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, false));
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, true));
delete rxn;
smi = "c1ccccc1.CCC>>CCC.c1ccncc1";
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, false));
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, true));
delete rxn;
smi = "c1ccccc1.CCC>>c1ccncc1.CCC";
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, false));
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, true));
delete rxn;
smi = "CCC.c1ccccc1.C(=O)O>>CCC.c1ccncc1.C(=O)O";
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 3);
TEST_ASSERT(rxn->getNumProductTemplates() == 3);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, false));
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, true));
delete rxn;
smi = "CCC.C(=O)O.c1ccccc1>>CCC.c1ccncc1.C(=O)O";
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, false));
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, true));
delete rxn;
smi = "CCC.C(=O)O.c1ccccc1>>CCC.C(=O)O.c1ccncc1";
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, false));
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, true));
delete rxn;
smi = "CCC.c1ccccc1.C(=O)O>NC=O>CCC.c1ccncc1.C(=O)O";
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 3);
TEST_ASSERT(rxn->getNumProductTemplates() == 3);
TEST_ASSERT(rxn->getNumAgentTemplates() == 1);
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, false));
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, true));
delete query_rxn;
smi = "c1ccccc1>NC=O>c1ccncc1";
query_rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(query_rxn);
TEST_ASSERT(query_rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(query_rxn->getNumProductTemplates() == 1);
TEST_ASSERT(query_rxn->getNumAgentTemplates() == 1);
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, false));
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, true));
delete rxn;
smi = "CCC.c1ccccc1.C(=O)O>>CCC.c1ccncc1.C(=O)O";
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 3);
TEST_ASSERT(rxn->getNumProductTemplates() == 3);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *query_rxn, false));
TEST_ASSERT(!hasReactionSubstructMatch(*rxn, *query_rxn, true));
delete rxn;
smi = "CCC.c1ccccc1.C(=O)O>>CCC.c1ncncc1.C(=O)O";
rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 3);
TEST_ASSERT(rxn->getNumProductTemplates() == 3);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
TEST_ASSERT(!hasReactionSubstructMatch(*rxn, *query_rxn, false));
TEST_ASSERT(!hasReactionSubstructMatch(*rxn, *query_rxn, true));
delete rxn;
delete query_rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test54RedundantProductMappingNumbersAndRSChirality() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing products with redundant atom mapping numbers and chirality"
<< std::endl;
unsigned int nWarn, nError;
std::string smi, cip;
{
// perserve the stereo chemistry of the reactant in the product
smi = "[C:1][O:2]>>[C:1][O:2]N[O:2][C:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "[OH][C@](F)(Cl)Br";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
std::cout << MolToSmiles(*prods[0][0], true) << std::endl;
smi = "F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getAtomWithIdx(0)->getAtomicNum() == 6);
TEST_ASSERT(prod->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(0)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
TEST_ASSERT(prod->getAtomWithIdx(4)->getAtomicNum() == 6);
TEST_ASSERT(prod->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
delete rxn;
}
{
// invert the stereo chemistry of one carbon of the reactant in the product
smi = "[C@:1][O:2]>>[C@:1][O:2]N[O:2][C@@:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "[OH][C@](F)(Cl)Br";
ROMol *mol = SmilesToMol(smi);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
std::cout << MolToSmiles(*prods[0][0], true) << std::endl;
smi = "F[C@](Cl)(Br)ONO[C@](F)(Cl)Br";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getAtomWithIdx(0)->getAtomicNum() == 6);
TEST_ASSERT(prod->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(0)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
TEST_ASSERT(prod->getAtomWithIdx(4)->getAtomicNum() == 6);
TEST_ASSERT(prod->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(4)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
delete rxn;
}
{
// Both carbons in the product (mapped with #2), should be (S)
smi =
"[OH:5][C@:2]([F:3])([Cl:1])[Br:4]>>[F:3][C@@:2]([Cl:1])([Br:4])[O:5]N["
"O:5][C@:2]([F:3])([Cl:1])[Br:4]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
MOL_SPTR_VECT reacts;
rxn->initReactantMatchers();
reacts.clear();
smi = "[OH][C@](F)(Cl)Br";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
std::cout << MolToSmiles(*prods[0][0], true) << std::endl;
smi = "F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
TEST_ASSERT(prod->getAtomWithIdx(7)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(7)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
delete rxn;
}
{
// One carbon in the product (mapped with #2) should be (S), the other (R)
smi =
"[OH:5][C@:2]([F:3])([Cl:1])[Br:4]>>[F:3][C@@:2]([Cl:1])([Br:4])[O:5]N["
"O:5][C@@:2]([F:3])([Cl:1])[Br:4]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
MOL_SPTR_VECT reacts;
rxn->initReactantMatchers();
reacts.clear();
smi = "[OH][C@](F)(Cl)Br";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
std::cout << MolToSmiles(*prods[0][0], true) << std::endl;
smi = "F[C@](Cl)(Br)ONO[C@](F)(Cl)Br";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
TEST_ASSERT(prod->getAtomWithIdx(7)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(7)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
delete rxn;
}
{
// Both carbons in the product (mapped with #2), should be (S)
smi =
"[OH:5][C@:2]([F:3])([Cl:1])[Br:4]>>[F:3][C@@:2]([Cl:1])([Br:4])[O:5]["
"C@:2]([F:3])([Cl:1])[Br:4]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
MOL_SPTR_VECT reacts;
rxn->initReactantMatchers();
reacts.clear();
smi = "[OH][C@](F)(Cl)Br";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
std::cout << MolToSmiles(*prods[0][0], true) << std::endl;
smi = "F[C@@](Cl)(Br)O[C@](F)(Cl)Br";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
TEST_ASSERT(prod->getAtomWithIdx(5)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(5)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
delete rxn;
}
{
// One carbon in the product (mapped with #2) should be (S), the other (R)
smi =
"[OH:5][C@:2]([F:3])([Cl:1])[Br:4]>>[F:3][C@@:2]([Cl:1])([Br:4])[O:5]["
"C@@:2]([F:3])([Cl:1])[Br:4]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
MOL_SPTR_VECT reacts;
rxn->initReactantMatchers();
reacts.clear();
smi = "[OH][C@](F)(Cl)Br";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
std::cout << MolToSmiles(*prods[0][0], true) << std::endl;
smi = "F[C@](Cl)(Br)O[C@](F)(Cl)Br";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
MolOps::assignStereochemistry(*prod);
TEST_ASSERT(prod->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(1)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "S");
TEST_ASSERT(prod->getAtomWithIdx(5)->hasProp(common_properties::_CIPCode));
prod->getAtomWithIdx(5)->getProp(common_properties::_CIPCode, cip);
TEST_ASSERT(cip == "R");
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test55RedundantProductMappingNumbersAndEZStereochemistry() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing products with redundant atom mapping numbers and chirality"
<< std::endl;
unsigned int nWarn, nError;
std::string smi;
{
// both double bonds in the product are (E)
smi =
"[CH3:1]\\[CH:2]=[CH:3]\\[CH3:4]>>[CH3:1]\\[CH:2]=[CH:3]\\[CH2:4][CH2:"
"4]\\[CH:3]=[CH:2]\\[CH3:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
MOL_SPTR_VECT reacts;
rxn->initReactantMatchers();
reacts.clear();
smi = "[CH3]\\[CH]=[CH]\\[CH3]";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[1].size() == 1);
smi = "C/C=C/CC/C=C/C";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
TEST_ASSERT(MolToSmiles(*prods[1][0], true) == smi);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
Bond *stereoBond = prod->getBondWithIdx(1);
INT_VECT stereoAtomsRef{{0, 3}};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
stereoBond = prod->getBondWithIdx(5);
stereoAtomsRef = {4, 7};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
prod = prods[1][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
stereoBond = prod->getBondWithIdx(1);
stereoAtomsRef = {0, 3};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
stereoBond = prod->getBondWithIdx(5);
stereoAtomsRef = {4, 7};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
delete rxn;
}
{
// both double bonds in the product are (E)
smi =
"[CH3:1]\\[CH:2]=[CH:3]\\[CH3:4]>>[CH3:1]\\[CH:2]=[CH:3]\\[CH2:4][CH2:"
"4]\\[CH:3]=[CH:2]/[CH3:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
MOL_SPTR_VECT reacts;
rxn->initReactantMatchers();
reacts.clear();
smi = "[CH3]\\[CH]=[CH]\\[CH3]";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[1].size() == 1);
smi = "C/C=C\\CC/C=C/C";
// std::cerr<<MolToSmiles(*prods[0][0],true)<<std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
TEST_ASSERT(MolToSmiles(*prods[1][0], true) == smi);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
Bond *stereoBond = prod->getBondWithIdx(1);
INT_VECT stereoAtomsRef{{0, 3}};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
stereoBond = prod->getBondWithIdx(5);
stereoAtomsRef = {4, 7};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOCIS);
prod = prods[1][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
stereoBond = prod->getBondWithIdx(1);
stereoAtomsRef = {0, 3};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
stereoBond = prod->getBondWithIdx(5);
stereoAtomsRef = {4, 7};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOCIS);
delete rxn;
}
{
// both double bonds in the product are (E)
smi =
"[CH3:1]\\[CH:2]=[CH:3]\\[CH3:4]>>[CH3:1]\\[CH:2]=[CH:3]\\[CH:3]=[CH:2]"
"\\[CH3:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi, nullptr, true);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn != 0);
TEST_ASSERT(nError == 0);
MOL_SPTR_VECT reacts;
rxn->initReactantMatchers();
reacts.clear();
smi = "[CH3]\\[CH]=[CH]\\[CH3]";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
reacts.push_back(ROMOL_SPTR(mol));
TEST_ASSERT(reacts.size() == 1);
std::vector<MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[1].size() == 1);
smi = "C/C=C/C=C/C";
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == smi);
TEST_ASSERT(MolToSmiles(*prods[1][0], true) == smi);
ROMOL_SPTR prod = prods[0][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
Bond *stereoBond = prod->getBondWithIdx(1);
INT_VECT stereoAtomsRef{{0, 3}};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
stereoBond = prod->getBondWithIdx(3);
stereoAtomsRef = {2, 5};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
prod = prods[1][0];
MolOps::sanitizeMol(*(static_cast<RWMol *>(prod.get())));
stereoBond = prod->getBondWithIdx(1);
stereoAtomsRef = {0, 3};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
stereoBond = prod->getBondWithIdx(3);
stereoAtomsRef = {2, 5};
TEST_ASSERT(stereoBond->getStereoAtoms() == stereoAtomsRef);
TEST_ASSERT(stereoBond->getStereo() == Bond::STEREOTRANS);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test56TestOldPickleVersion() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing old pickle file with new agent version"
<< std::endl;
unsigned int nWarn, nError;
{
std::string pklName = getenv("RDBASE");
pklName += "/Code/GraphMol/ChemReactions/testData/testpickle.bin";
std::ifstream inStream(pklName.c_str(), std::ios_base::binary);
auto *rxn = new ChemicalReaction();
ReactionPickler::reactionFromPickle(inStream, rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
rxn->initReactantMatchers();
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test57IntroductionOfNewChiralCenters() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing introduction of new atoms with chirality"
<< std::endl;
{ // a reaction that induces new atoms with stereochem
std::string smi =
"[F:1][C:2]([Cl:3])([Br:4])[I:5]>>[F:1][C@@:2]([Cl:3])([N:4][C@:6]([Cl:"
"7])[Br:8])[I:5]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "FC(Cl)(Br)I";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "F[C@](Cl)(I)N[C@H](Cl)Br");
delete rxn;
}
{ // a reaction that induces new atoms with stereochem
std::string rdbase = getenv("RDBASE");
std::string fName;
fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/testRXNChirality.rxn";
ChemicalReaction *rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
BOOST_LOG(rdInfoLog) << ChemicalReactionToRxnSmiles(*rxn) << std::endl;
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.clear();
fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/testRXNChirality1.sdf";
ROMol *mol = MolFileToMol(fName);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "C[C@H](F)CCC[C@@H](C)Cl");
delete rxn;
}
{ // a reaction that induces new atoms with stereochem
std::string rdbase = getenv("RDBASE");
std::string fName;
fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/testRXNChirality2.sdf";
ROMol *mol = MolFileToMol(fName);
auto *rxn = new ChemicalReaction();
rxn->addReactantTemplate(ROMOL_SPTR(mol));
fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/testRXNChirality3.sdf";
mol = MolFileToMol(fName);
rxn->addProductTemplate(ROMOL_SPTR(mol));
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
BOOST_LOG(rdInfoLog) << ChemicalReactionToRxnSmiles(*rxn) << std::endl;
rxn->initReactantMatchers();
updateProductsStereochem(rxn);
MOL_SPTR_VECT reacts;
reacts.clear();
fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/testRXNChirality1.sdf";
mol = MolFileToMol(fName);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
BOOST_LOG(rdInfoLog) << MolToSmiles(*prods[0][0], true) << std::endl;
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "C[C@H](F)CCC[C@@H](C)Cl");
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test58MolFileValueRoundTrip() {
ChemicalReaction *rxn;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing round trip molFileValue" << std::endl;
const char *rxnB =
"$RXN\n"
"\n"
" ISIS 090220091541\n"
"\n"
" 2 1\n"
"$MOL\n"
"\n"
" -ISIS- 09020915412D\n"
"\n"
" 3 2 0 0 0 0 0 0 0 0999 V2000\n"
" -2.9083 -0.4708 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0\n"
" -2.3995 -0.1771 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" -2.4042 0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 2 3 2 0 0 0 0\n"
"V 2 aldehyde\n"
"M RGP 1 1 1\n"
"M END\n"
"$MOL\n"
"\n"
" -ISIS- 09020915412D\n"
"\n"
" 2 1 0 0 0 0 0 0 0 0999 V2000\n"
" 2.8375 -0.2500 0.0000 R# 0 0 0 0 0 0 0 0 0 3 0 0\n"
" 3.3463 0.0438 0.0000 N 0 0 0 0 0 0 0 0 0 4 0 0\n"
" 1 2 1 0 0 0 0\n"
"V 2 aldehyde\n"
"M RGP 1 1 2\n"
"M END\n"
"$MOL\n"
"\n"
" -ISIS- 09020915412D\n"
"\n"
" 4 3 0 0 0 0 0 0 0 0999 V2000\n"
" 13.3088 0.9436 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" 13.8206 1.2321 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0\n"
" 13.3028 0.3561 0.0000 N 0 0 0 0 0 0 0 0 0 4 0 0\n"
" 12.7911 0.0676 0.0000 R# 0 0 0 0 0 0 0 0 0 3 0 0\n"
" 1 3 1 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 3 4 1 0 0 0 0\n"
"M RGP 2 2 1 4 2\n"
"M END";
rxn = RxnBlockToChemicalReaction(rxnB);
// check the mol file values
for (MOL_SPTR_VECT::const_iterator template_mol =
rxn->beginReactantTemplates();
template_mol != rxn->endReactantTemplates(); ++template_mol) {
const Atom *at = (*template_mol)->getAtomWithIdx(1);
TEST_ASSERT(at->hasProp(common_properties::molFileValue));
TEST_ASSERT(at->getProp<std::string>(common_properties::molFileValue) ==
"aldehyde");
}
ChemicalReaction *rxn2 =
RxnBlockToChemicalReaction(ChemicalReactionToRxnBlock(*rxn));
for (MOL_SPTR_VECT::const_iterator template_mol =
rxn2->beginReactantTemplates();
template_mol != rxn2->endReactantTemplates(); ++template_mol) {
const Atom *at = (*template_mol)->getAtomWithIdx(1);
TEST_ASSERT(at->hasProp(common_properties::molFileValue));
TEST_ASSERT(at->getProp<std::string>(common_properties::molFileValue) ==
"aldehyde");
}
delete rxn;
delete rxn2;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test59ReactionCanonicalization() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing canonicatization of reactions" << std::endl;
{ // with mapping numbers
std::string smi =
"[K+].[NH4+].[C:2]([CH:4]([CH2:9][CH3:10])[CH2:5][C:6]([OH:8])=[O:7])#["
"N:3]>Cl.[OH-]>[CH2:2]([CH:4]([CH2:9][CH3:10])[CH2:5][C:6]([OH:8])=[O:"
"7])[NH2:3].[K+].[NH4+]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 3);
TEST_ASSERT(rxn->getNumProductTemplates() == 3);
TEST_ASSERT(rxn->getNumAgentTemplates() == 2);
std::string rxnsmi = ChemicalReactionToRxnSmiles(*rxn);
delete rxn;
rxn = RxnSmartsToChemicalReaction(rxnsmi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 3);
TEST_ASSERT(rxn->getNumProductTemplates() == 3);
TEST_ASSERT(rxn->getNumAgentTemplates() == 2);
std::string rxnsmi2 = ChemicalReactionToRxnSmiles(*rxn);
TEST_ASSERT(rxnsmi == rxnsmi2);
delete rxn;
}
{ // without mapping numbers
std::string smi =
"[K+].[NH4+].CCC(CC(O)=O)C#N>Cl.[OH-]>CCC(CC(O)=O)CN.[K+].[NH4+]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 3);
TEST_ASSERT(rxn->getNumProductTemplates() == 3);
TEST_ASSERT(rxn->getNumAgentTemplates() == 2);
std::string rxnsmi = ChemicalReactionToRxnSmiles(*rxn);
delete rxn;
rxn = RxnSmartsToChemicalReaction(rxnsmi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 3);
TEST_ASSERT(rxn->getNumProductTemplates() == 3);
TEST_ASSERT(rxn->getNumAgentTemplates() == 2);
std::string rxnsmi2 = ChemicalReactionToRxnSmiles(*rxn);
TEST_ASSERT(rxnsmi == rxnsmi2);
delete rxn;
}
}
void test60RunSingleReactant() {
const std::string smirks_thiourea =
"[N;$(N-[#6]):3]=[C;$(C=S):1].[N;$(N[#6]);!$(N=*);!$([N-]);!$(N#*);!$(["
"ND3]);!$([ND4]);!$(N[O,N]);!$(N[C,S]=[S,O,N]):2]>>[N:3]-[C:1]-[N+0:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smirks_thiourea);
rxn->initReactantMatchers();
const std::string smi1 = "C=CCN=C=S";
const std::string smi2 = "NCc1ncc(Cl)cc1Br";
ROMOL_SPTR reag1(SmilesToMol(smi1));
ROMOL_SPTR reag2(SmilesToMol(smi2));
std::vector<MOL_SPTR_VECT> prods;
{
ROMOL_SPTR expected_result(SmilesToMol("C=CCNC(N)=S"));
ROMOL_SPTR expected_sidechain_result(SmilesToMol("[*:1]=S.[*:3]CC=C"));
const bool isomericSmiles = true;
std::string expected = MolToSmiles(*expected_result, isomericSmiles);
std::string expected_sidechain =
MolToSmiles(*expected_sidechain_result, isomericSmiles);
prods = rxn->runReactant(reag1, 0);
TEST_ASSERT(prods.size() > 0);
for (auto &prod : prods) {
for (size_t prodidx = 0; prodidx < prod.size(); prodidx++) {
TEST_ASSERT(prodidx < 1);
TEST_ASSERT(MolToSmiles(*prod[prodidx]) == expected);
ROMol *sidechain = reduceProductToSideChains(prod[prodidx]);
std::string smi = MolToSmiles(*sidechain, isomericSmiles);
TEST_ASSERT(smi == expected_sidechain);
delete sidechain;
}
}
prods = rxn->runReactant(reag2, 0);
TEST_ASSERT(prods.size() == 0)
}
{
ROMOL_SPTR expected_result(SmilesToMol("NCNCc1ncc(Cl)cc1Br"));
ROMOL_SPTR expected_sidechain_result(SmilesToMol("[*:2]Cc1ncc(Cl)cc1Br"));
const bool isomericSmiles = true;
std::string expected = MolToSmiles(*expected_result, isomericSmiles);
std::string expected_sidechain =
MolToSmiles(*expected_sidechain_result, isomericSmiles);
prods = rxn->runReactant(reag2, 1);
TEST_ASSERT(prods.size() > 0);
for (auto &prod : prods) {
for (size_t prodidx = 0; prodidx < prod.size(); prodidx++) {
TEST_ASSERT(prodidx < 1);
TEST_ASSERT(MolToSmiles(*prod[prodidx]) == expected);
ROMol *sidechain = reduceProductToSideChains(prod[prodidx]);
std::string smi = MolToSmiles(*sidechain, isomericSmiles);
TEST_ASSERT(smi == expected_sidechain);
delete sidechain;
}
}
prods = rxn->runReactant(reag1, 1);
TEST_ASSERT(prods.size() == 0)
}
delete rxn;
}
void test61Github685() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing github685: SMARTS reaction triggers "
"invariant violation on chiral compounds"
<< std::endl;
{
std::string smi =
"[C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[Cl:6].[C:2][C:3]([O:4])([N:5])["
"C:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
rxn->initReactantMatchers();
{
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "CCC(O)(N)Cl";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "Cl");
TEST_ASSERT(MolToSmiles(*prods[0][1], true) == "CC(C)(N)O");
}
{
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "CC[C@](O)(N)Cl";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "Cl");
TEST_ASSERT(MolToSmiles(*prods[0][1], true) ==
"CC(C)(N)O"); // we lose the chirality because there's an
// unspecified bond in the products
}
delete rxn;
}
{ // the original example
std::string smi =
"[#1;D1R0:4][#8;H1D2R0:3][#6;H0D3R0:2](=[#8;H0D1R0:5])[#6;D4;H1,H0,H2:"
"1]([#6:7])[#6,#1D1AR0,ClH0D1AR0,FH0D1AR0,BrH0D1AR0:6]>>[*:3]=[*:2]=[*:"
"5].[*:4]-[*:1](-[*:6])-[*:7]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
TEST_ASSERT(rxn->getNumAgentTemplates() == 0);
rxn->initReactantMatchers();
{
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "CC(N)C(=O)O";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::addHs(*mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "O=C=O");
TEST_ASSERT(MolToSmiles(*prods[0][1], true) ==
"[H]N([H])C([H])([H])C([H])([H])[H]");
}
{
MOL_SPTR_VECT reacts;
reacts.clear();
smi = "C[C@@H](N)C(=O)O";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::addHs(*mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(MolToSmiles(*prods[0][0], true) == "O=C=O");
TEST_ASSERT(MolToSmiles(*prods[0][1], true) ==
"[H]N([H])C([H])([H])C([H])([H])[H]");
}
delete rxn;
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void test62Github975() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing github975: Unnecessary warnings in rxn.validate()"
<< std::endl;
{
unsigned int nWarn, nError;
std::string smi = "[N,O:1]>>[N+0,O+0:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, true));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
delete rxn;
smi = "[N,O:1][C,N:2]>>[N+0,O+0:1][C+0,N+1:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, true));
TEST_ASSERT(nWarn == 1);
TEST_ASSERT(nError == 0);
delete rxn;
}
{
unsigned int nWarn, nError;
std::string smi = "[N,O:1]>>[NH,OH:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, true));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
delete rxn;
smi = "[N,O:1][C,N:2]>>[NH,OH:1][CH2,NH:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, true));
TEST_ASSERT(nWarn == 1);
TEST_ASSERT(nError == 0);
delete rxn;
}
{
unsigned int nWarn, nError;
std::string smi = "[N,O:1]>>[14N,14O:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, true));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
delete rxn;
smi = "[N,O:1][C,N:2]>>[14N,14O:1][12C,14N:2]";
rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->validate(nWarn, nError, true));
TEST_ASSERT(nWarn == 1);
TEST_ASSERT(nError == 0);
delete rxn;
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void test63CopyConstructor() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing copy constructor" << std::endl;
{
std::string smi =
"[C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[Cl:6].[C:2][C:3]([O:4])([N:5])["
"C:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
std::string smi1 = ChemicalReactionToRxnSmiles(*rxn);
TEST_ASSERT(rxn);
auto *rxn_new = new ChemicalReaction(*rxn);
removeMappingNumbersFromReactions(*rxn_new);
std::string smi2 = ChemicalReactionToRxnSmiles(*rxn);
std::string new_smi = ChemicalReactionToRxnSmiles(*rxn_new);
std::cerr << "smi1 " << smi1 << std::endl;
std::cerr << "smi2 " << smi2 << std::endl;
TEST_ASSERT(smi1 == smi2);
TEST_ASSERT(smi2 != new_smi);
TEST_ASSERT(new_smi == "CCC(N)(O)Cl>>CC(C)(N)O.Cl");
delete rxn;
delete rxn_new;
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void test64Github1266() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing github 1266: Reactions don't modify isotope "
"unless chemical element is specified for the product"
<< std::endl;
{
std::string smi = "[13:1]>>[14:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
{
MOL_SPTR_VECT reacts;
smi = "C[13CH3]";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
std::vector<MOL_SPTR_VECT> prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getIsotope() == 14);
}
delete rxn;
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void test65SanitizeUnmappedHs() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Tests sanitize reaction (unmapped Hs) " << std::endl;
const std::string unmappedHs =
"$RXN\n"
"\n"
" Marvin 031701170941\n"
"\n"
" 1 1\n"
"$MOL\n"
"\n"
" Mrv1583 03171709412D \n"
"\n"
" 16 16 0 0 0 0 999 V2000\n"
" -2.5620 0.5265 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n"
" -2.4235 -0.2868 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" -3.0587 -0.8133 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0\n"
" -3.8322 -0.5265 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0\n"
" -3.3355 0.8133 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0\n"
" -1.7581 0.7120 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -3.0942 1.6022 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.5124 0.9090 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.3663 -1.1553 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -3.3000 -1.6022 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -3.8242 1.4780 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -2.2307 1.2821 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -3.9706 0.2868 0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0\n"
" -2.5700 -1.4780 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -1.6500 -0.5736 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -4.6278 -0.3082 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 5 1 1 0 0 0 0\n"
" 1 6 1 0 0 0 0\n"
" 1 12 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 15 1 0 0 0 0\n"
" 3 4 1 0 0 0 0\n"
" 3 10 1 0 0 0 0\n"
" 3 14 1 0 0 0 0\n"
" 4 9 1 0 0 0 0\n"
" 4 13 1 0 0 0 0\n"
" 4 16 1 0 0 0 0\n"
" 5 7 1 0 0 0 0\n"
" 5 11 1 0 0 0 0\n"
" 13 5 1 0 0 0 0\n"
" 13 8 1 0 0 0 0\n"
"M END\n"
"$MOL\n"
"\n"
" Mrv1583 03171709412D \n"
"\n"
" 6 6 0 0 0 0 999 V2000\n"
" 3.8966 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n"
" 4.6111 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" 4.6111 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0\n"
" 3.8966 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0\n"
" 3.1821 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0\n"
" 3.1821 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0\n"
" 1 2 1 0 0 0 0\n"
" 6 1 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 3 4 1 0 0 0 0\n"
" 4 5 1 0 0 0 0\n"
" 5 6 1 0 0 0 0\n"
"M END";
ChemicalReaction *rxn = RxnBlockToChemicalReaction(unmappedHs);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts1, hreacts1, reacts2, hreacts2;
std::vector<MOL_SPTR_VECT> prods;
reacts1.push_back(ROMOL_SPTR(SmilesToMol("C1CCCCC1")));
hreacts1.push_back(ROMOL_SPTR(MolOps::addHs(*reacts1[0].get())));
reacts2.push_back(ROMOL_SPTR(SmilesToMol("C1CCCCC1Cl")));
hreacts2.push_back(ROMOL_SPTR(MolOps::addHs(*reacts2[0].get())));
// test with and without AddHs
prods = rxn->runReactants(reacts1);
TEST_ASSERT(prods.size() == 0);
prods = rxn->runReactants(hreacts1);
TEST_ASSERT(prods.size() == 768);
prods = rxn->runReactants(reacts2);
TEST_ASSERT(prods.size() == 0);
prods = rxn->runReactants(hreacts2);
TEST_ASSERT(prods.size() == 128);
// Test after sanitization (way fewer matches than with AddHs..)
RxnOps::sanitizeRxn(*rxn);
prods = rxn->runReactants(reacts1);
TEST_ASSERT(prods.size() == 12);
prods = rxn->runReactants(reacts2);
TEST_ASSERT(prods.size() == 4);
delete rxn;
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void test66SanitizeMappedHs() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Tests sanitize reaction (mapped hs in react but not prod) "
<< std::endl;
// H's are mapped in reactant but do not exist in product,
// they can be merged
const std::string unmappedHs =
"$RXN\n"
"\n"
" Marvin 031701170941\n"
"\n"
" 1 1\n"
"$MOL\n"
"\n"
" Mrv1583 03171709412D \n"
"\n"
" 16 16 0 0 0 0 999 V2000\n"
" -2.5620 0.5265 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n"
" -2.4235 -0.2868 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" -3.0587 -0.8133 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0\n"
" -3.8322 -0.5265 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0\n"
" -3.3355 0.8133 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0\n"
" -1.7581 0.7120 0.0000 H 0 0 0 0 0 0 0 0 0 7 0 0\n"
" -3.0942 1.6022 0.0000 H 0 0 0 0 0 0 0 0 0 8 0 0\n"
" -4.5124 0.9090 0.0000 H 0 0 0 0 0 0 0 0 0 9 0 0\n"
" -4.3663 -1.1553 0.0000 H 0 0 0 0 0 0 0 0 0 10 0 0\n"
" -3.3000 -1.6022 0.0000 H 0 0 0 0 0 0 0 0 0 11 0 0\n"
" -3.8242 1.4780 0.0000 H 0 0 0 0 0 0 0 0 0 12 0 0\n"
" -2.2307 1.2821 0.0000 H 0 0 0 0 0 0 0 0 0 13 0 0\n"
" -3.9706 0.2868 0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0\n"
" -2.5700 -1.4780 0.0000 H 0 0 0 0 0 0 0 0 0 14 0 0\n"
" -1.6500 -0.5736 0.0000 H 0 0 0 0 0 0 0 0 0 15 0 0\n"
" -4.6278 -0.3082 0.0000 H 0 0 0 0 0 0 0 0 0 16 0 0\n"
" 1 2 1 0 0 0 0\n"
" 5 1 1 0 0 0 0\n"
" 1 6 1 0 0 0 0\n"
" 1 12 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 15 1 0 0 0 0\n"
" 3 4 1 0 0 0 0\n"
" 3 10 1 0 0 0 0\n"
" 3 14 1 0 0 0 0\n"
" 4 9 1 0 0 0 0\n"
" 4 13 1 0 0 0 0\n"
" 4 16 1 0 0 0 0\n"
" 5 7 1 0 0 0 0\n"
" 5 11 1 0 0 0 0\n"
" 13 5 1 0 0 0 0\n"
" 13 8 1 0 0 0 0\n"
"M END\n"
"$MOL\n"
"\n"
" Mrv1583 03171709412D \n"
"\n"
" 6 6 0 0 0 0 999 V2000\n"
" 3.8966 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n"
" 4.6111 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" 4.6111 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0\n"
" 3.8966 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0\n"
" 3.1821 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0\n"
" 3.1821 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0\n"
" 1 2 1 0 0 0 0\n"
" 6 1 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 3 4 1 0 0 0 0\n"
" 4 5 1 0 0 0 0\n"
" 5 6 1 0 0 0 0\n"
"M END";
ChemicalReaction *rxn = RxnBlockToChemicalReaction(unmappedHs);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts1, hreacts1, reacts2, hreacts2;
std::vector<MOL_SPTR_VECT> prods;
reacts1.push_back(ROMOL_SPTR(SmilesToMol("C1CCCCC1")));
hreacts1.push_back(ROMOL_SPTR(MolOps::addHs(*reacts1[0].get())));
reacts2.push_back(ROMOL_SPTR(SmilesToMol("C1CCCCC1Cl")));
hreacts2.push_back(ROMOL_SPTR(MolOps::addHs(*reacts2[0].get())));
// test with and without AddHs
prods = rxn->runReactants(reacts1);
TEST_ASSERT(prods.size() == 0);
prods = rxn->runReactants(hreacts1);
TEST_ASSERT(prods.size() == 768);
prods = rxn->runReactants(reacts2);
TEST_ASSERT(prods.size() == 0);
prods = rxn->runReactants(hreacts2);
TEST_ASSERT(prods.size() == 128);
// Test after sanitization (way fewer matches than with AddHs..)
RxnOps::sanitizeRxn(*rxn);
prods = rxn->runReactants(reacts1);
TEST_ASSERT(prods.size() == 12);
prods = rxn->runReactants(reacts2);
TEST_ASSERT(prods.size() == 4);
delete rxn;
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void test67SanitizeMappedHsInReactantAndProd() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Tests sanitize reaction (mapped hs in react and prod) " << std::endl;
// H's are mapped in reactant and in prod
// they can be merged
const std::string unmappedHs =
"$RXN\n"
"\n"
" Marvin 031701171002\n"
"\n"
" 1 1\n"
"$MOL\n"
"\n"
" Mrv1583 03171710022D \n"
"\n"
" 16 16 0 0 0 0 999 V2000\n"
" -3.1881 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n"
" -2.4736 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" -2.4736 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0\n"
" -3.1881 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0\n"
" -3.9025 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0\n"
" -2.8178 1.5622 0.0000 H 0 0 0 0 0 0 0 0 0 7 0 0\n"
" -4.3559 1.1018 0.0000 H 0 0 0 0 0 0 0 0 0 8 0 0\n"
" -4.6170 -0.8250 0.0000 H 0 0 0 0 0 0 0 0 0 9 0 0\n"
" -3.5583 -1.5622 0.0000 H 0 0 0 0 0 0 0 0 0 10 0 0\n"
" -2.0203 -1.1018 0.0000 H 0 0 0 0 0 0 0 0 0 11 0 0\n"
" -4.7262 0.4605 0.0000 H 0 0 0 0 0 0 0 0 0 12 0 0\n"
" -3.5583 1.5622 0.0000 H 0 0 0 0 0 0 0 0 0 13 0 0\n"
" -3.9025 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0\n"
" -1.6500 -0.4605 0.0000 H 0 0 0 0 0 0 0 0 0 14 0 0\n"
" -1.7591 0.8250 0.0000 H 0 0 0 0 0 0 0 0 0 15 0 0\n"
" -2.8178 -1.5622 0.0000 H 0 0 0 0 0 0 0 0 0 16 0 0\n"
" 1 2 1 0 0 0 0\n"
" 5 1 1 0 0 0 0\n"
" 1 6 1 0 0 0 0\n"
" 1 12 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 15 1 0 0 0 0\n"
" 3 4 1 0 0 0 0\n"
" 3 10 1 0 0 0 0\n"
" 3 14 1 0 0 0 0\n"
" 4 9 1 0 0 0 0\n"
" 4 13 1 0 0 0 0\n"
" 4 16 1 0 0 0 0\n"
" 5 7 1 0 0 0 0\n"
" 5 11 1 0 0 0 0\n"
" 13 5 1 0 0 0 0\n"
" 13 8 1 0 0 0 0\n"
"M END\n"
"$MOL\n"
"\n"
" Mrv1583 03171710022D \n"
"\n"
" 17 17 0 0 0 0 999 V2000\n"
" 4.1309 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n"
" 4.8454 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" 4.8454 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0\n"
" 4.1309 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0\n"
" 3.4165 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0\n"
" 3.4165 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0\n"
" 4.5012 1.5622 0.0000 H 0 0 0 0 0 0 0 0 0 13 0 0\n"
" 3.7607 1.5622 0.0000 H 0 0 0 0 0 0 0 0 0 7 0 0\n"
" 5.6690 0.4605 0.0000 H 0 0 0 0 0 0 0 0 0 15 0 0\n"
" 5.2987 1.1018 0.0000 H 0 0 0 0 0 0 0 0 0 17 0 0\n"
" 5.2987 -1.1018 0.0000 H 0 0 0 0 0 0 0 0 0 14 0 0\n"
" 3.7607 -1.5622 0.0000 H 0 0 0 0 0 0 0 0 0 16 0 0\n"
" 2.9631 -1.1018 0.0000 H 0 0 0 0 0 0 0 0 0 9 0 0\n"
" 2.5929 -0.4605 0.0000 H 0 0 0 0 0 0 0 0 0 18 0 0\n"
" 2.7020 0.8250 0.0000 H 0 0 0 0 0 0 0 0 0 8 0 0\n"
" 4.5012 -1.5622 0.0000 H 0 0 0 0 0 0 0 0 0 10 0 0\n"
" 5.6690 -0.4605 0.0000 H 0 0 0 0 0 0 0 0 0 11 0 0\n"
" 1 2 1 0 0 0 0\n"
" 6 1 1 0 0 0 0\n"
" 1 7 1 0 0 0 0\n"
" 1 8 1 0 0 0 0\n"
" 2 9 1 0 0 0 0\n"
" 2 10 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 3 4 1 0 0 0 0\n"
" 3 11 1 0 0 0 0\n"
" 3 17 1 0 0 0 0\n"
" 4 5 1 0 0 0 0\n"
" 4 12 1 0 0 0 0\n"
" 4 16 1 0 0 0 0\n"
" 5 6 1 0 0 0 0\n"
" 5 14 1 0 0 0 0\n"
" 5 13 1 0 0 0 0\n"
" 6 15 1 0 0 0 0\n"
"M END\n";
ChemicalReaction *rxn = RxnBlockToChemicalReaction(unmappedHs);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts1, hreacts1, reacts2, hreacts2;
std::vector<MOL_SPTR_VECT> prods;
reacts1.push_back(ROMOL_SPTR(SmilesToMol("C1CCCCC1")));
hreacts1.push_back(ROMOL_SPTR(MolOps::addHs(*reacts1[0].get())));
reacts2.push_back(ROMOL_SPTR(SmilesToMol("C1CCCCC1Cl")));
hreacts2.push_back(ROMOL_SPTR(MolOps::addHs(*reacts2[0].get())));
// test with and without AddHs
prods = rxn->runReactants(reacts1);
TEST_ASSERT(prods.size() == 0);
prods = rxn->runReactants(hreacts1);
TEST_ASSERT(prods.size() == 768);
prods = rxn->runReactants(reacts2);
TEST_ASSERT(prods.size() == 0);
prods = rxn->runReactants(hreacts2);
TEST_ASSERT(prods.size() == 128);
// Test after sanitization (way fewer matches than with AddHs..)
RxnOps::sanitizeRxn(*rxn);
prods = rxn->runReactants(reacts1);
TEST_ASSERT(prods.size() == 12);
prods = rxn->runReactants(reacts2);
TEST_ASSERT(prods.size() == 4);
delete rxn;
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void test68MappedHToHeavy() {
const std::string rxnblock =
"$RXN\n"
"\n"
" Marvin 031701171005\n"
"\n"
" 1 1\n"
"$MOL\n"
"\n"
" Mrv1583 03171710052D \n"
"\n"
" 3 2 0 0 0 0 999 V2000\n"
" -1.2721 -0.0116 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n"
" -1.9866 -0.4241 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" -1.2721 0.8134 0.0000 H 0 0 0 0 0 0 0 0 0 3 0 0\n"
" 2 1 1 0 0 0 0\n"
" 1 3 1 0 0 0 0\n"
"M END\n"
"$MOL\n"
"\n"
" Mrv1583 03171710052D \n"
"\n"
" 3 2 0 0 0 0 999 V2000\n"
" 2.3886 -0.0563 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n"
" 1.6741 -0.4688 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n"
" 2.3886 0.7688 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0\n"
" 2 1 1 0 0 0 0\n"
" 1 3 1 0 0 0 0\n"
"M END\n";
ChemicalReaction *rxn = RxnBlockToChemicalReaction(rxnblock);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts1, hreacts1, reacts2, hreacts2;
std::vector<MOL_SPTR_VECT> prods;
reacts1.push_back(ROMOL_SPTR(SmilesToMol("CC")));
hreacts1.push_back(ROMOL_SPTR(MolOps::addHs(*reacts1[0].get())));
// test with and without AddHs
prods = rxn->runReactants(reacts1);
TEST_ASSERT(prods.size() == 0);
prods = rxn->runReactants(hreacts1);
TEST_ASSERT(prods.size() == 6);
std::stringstream sstrm;
rdWarningLog->SetTee(sstrm);
RxnOps::sanitizeRxn(*rxn);
std::string s = sstrm.str();
std::cerr << s << std::endl;
TEST_ASSERT(s.find("Reaction has explicit hydrogens, reactants will need "
"explicit hydrogens (addHs)") != std::string::npos);
rdWarningLog->ClearTee();
delete rxn;
}
void test69Github1387() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Tests github1387: Bond from reactant not added to product"
<< std::endl;
{
const std::string smarts =
"([*:1]-[O:2][CH3:3].[*:4]-[O:5][CH3:6])>>([*:1]-[O:2][C:3]C.[*:4]-[O:"
"5][C:6]C)";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smarts);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
{ // this always worked
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
reacts.push_back(ROMOL_SPTR(SmilesToMol("COCCCOC")));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
std::vector<int> mapping;
unsigned int nPieces = MolOps::getMolFrags(*prods[0][0], mapping);
TEST_ASSERT(nPieces = 2);
TEST_ASSERT(prods[0][0]->getBondBetweenAtoms(0, 4) == nullptr);
}
{ // the bug:
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
reacts.push_back(ROMOL_SPTR(SmilesToMol("COCCOC")));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
std::vector<int> mapping;
unsigned int nPieces = MolOps::getMolFrags(*prods[0][0], mapping);
TEST_ASSERT(nPieces = 2);
TEST_ASSERT(prods[0][0]->getBondBetweenAtoms(0, 4) != nullptr);
}
{ // the bug, plus a ring closure:
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
reacts.push_back(ROMOL_SPTR(SmilesToMol("COC1CCC1OC")));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
std::vector<int> mapping;
unsigned int nPieces = MolOps::getMolFrags(*prods[0][0], mapping);
TEST_ASSERT(nPieces = 2);
TEST_ASSERT(prods[0][0]->getBondBetweenAtoms(0, 4) != nullptr);
}
delete rxn;
}
{ // reorder the same reaction
const std::string smarts =
"([O:2](-[*:1])[CH3:3].[CH3:6][O:5]-[*:4])>>(C[C:3][O:2]-[*:1].[*:4]"
"-[O:5][C:6]C)";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smarts);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
{ // this always worked
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
reacts.push_back(ROMOL_SPTR(SmilesToMol("COCCCOC")));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
std::vector<int> mapping;
unsigned int nPieces = MolOps::getMolFrags(*prods[0][0], mapping);
TEST_ASSERT(nPieces = 2);
TEST_ASSERT(prods[0][0]->getBondBetweenAtoms(3, 4) == nullptr);
}
{ // the bug:
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
reacts.push_back(ROMOL_SPTR(SmilesToMol("COCCOC")));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
std::vector<int> mapping;
unsigned int nPieces = MolOps::getMolFrags(*prods[0][0], mapping);
TEST_ASSERT(nPieces = 2);
TEST_ASSERT(prods[0][0]->getBondBetweenAtoms(3, 4) != nullptr);
}
{ // the bug, plus a ring closure:
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
reacts.push_back(ROMOL_SPTR(SmilesToMol("COC1CCC1OC")));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2);
TEST_ASSERT(prods[0].size() == 1);
std::vector<int> mapping;
unsigned int nPieces = MolOps::getMolFrags(*prods[0][0], mapping);
TEST_ASSERT(nPieces = 2);
TEST_ASSERT(prods[0][0]->getBondBetweenAtoms(3, 4) != nullptr);
}
delete rxn;
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void test70Github1544() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Tests github1544: ChemicalReaction code not calling "
"setNoImplicit() when H counts are set"
<< std::endl;
{
const std::string smarts = "[CH3:1]>>[CH2:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smarts);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
{
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
reacts.push_back(ROMOL_SPTR(SmilesToMol("Cc1ccccc1")));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getNoImplicit());
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "[CH2]c1ccccc1");
}
delete rxn;
}
{ // test that the change also works when the degree on the atom changes
const std::string smarts = "[CH3:1][*:2]>>[CH2:1].[*:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smarts);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
{
MOL_SPTR_VECT reacts;
std::vector<MOL_SPTR_VECT> prods;
reacts.push_back(ROMOL_SPTR(SmilesToMol("Cc1ccccc1")));
prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 2);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getNoImplicit());
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "[CH2]");
TEST_ASSERT(MolToSmiles(*prods[0][1]) == "c1ccccc1");
}
delete rxn;
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void testSanitizeException() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing sanitizerxn exception" << std::endl;
// This is a marvinjs conversion of the following smirks:
// {indole}\t[*;Br,I;$(*c1ccccc1)]-[c:1]:[c:2]-[NH2:3].[CH1:5]#[C;$(C-[#6]):4]>>[c:1]1:[c:2]-[N:3]-[C:4]=[C:5]-1\tc1cc(I)c(N)cc1\tCC#C
// From Hartenfeller et. al., J. Chem. Inf. Model., 2012, 52 (5), p 1167-1178
std::string rxnB =
"$RXN\n\n Marvin 102501170854\n\n 2 1\n$MOL\n\n Mrv1583 "
"10251708542D \n\n 4 3 0 0 0 0 999 V2000\n "
"-4.2429 -0.3572 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n "
"-5.0679 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n "
"-5.4804 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n "
"-6.3054 0.3572 0.0000 N 0 0 0 3 0 0 0 0 0 3 0 0\n 1 "
" 2 1 0 0 0 0\n 2 3 4 0 0 0 0\n 3 4 1 0 0 0 0\nM MRV "
"SMA 1 [*;A]\nM MRV SMA 4 [#7H2;A:3]\nM END\n$MOL\n\n Mrv1583 "
"10251708542D \n\n 2 1 0 0 0 0 999 V2000\n "
"-1.6500 0.0000 0.0000 C 0 0 0 2 0 0 0 0 0 5 0 0\n "
"-2.4750 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0\n 1 "
" 2 3 0 0 0 0\nM MRV SMA 1 [#6H1:5]\nM END\n$MOL\n\n Mrv1583 "
"10251708542D \n\n 5 5 0 0 0 0 999 V2000\n "
"3.3782 0.6348 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0\n "
"4.0456 0.1498 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0\n "
"3.7907 -0.6348 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0\n "
"2.9657 -0.6348 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0\n "
"2.7107 0.1498 0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0\n 1 "
"2 4 0 0 0 0\n 1 5 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 "
"1 0 0 0 0\n 4 5 2 0 0 0 0\nM END\n";
ChemicalReaction *rxn = RxnBlockToChemicalReaction(rxnB);
RxnOps::sanitizeRxn(*rxn);
delete rxn;
}
void testReactionProperties() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Tests reaction properties" << std::endl;
{
const std::string smarts = "[CH3:1]>>[CH2:1]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smarts);
TEST_ASSERT(rxn);
TEST_ASSERT(!rxn->hasProp("fooprop"));
rxn->setProp("fooprop", 3);
TEST_ASSERT(rxn->hasProp("fooprop"));
TEST_ASSERT(rxn->getProp<int>("fooprop") == 3);
{
std::string pkl;
ReactionPickler::pickleReaction(rxn, pkl);
auto *lrxn = new ChemicalReaction();
ReactionPickler::reactionFromPickle(pkl, lrxn);
TEST_ASSERT(!lrxn->hasProp("fooprop"));
delete lrxn;
}
{
std::string pkl;
ReactionPickler::pickleReaction(rxn, pkl, PicklerOps::AllProps);
auto *lrxn = new ChemicalReaction();
ReactionPickler::reactionFromPickle(pkl, lrxn);
TEST_ASSERT(lrxn->hasProp("fooprop"));
TEST_ASSERT(lrxn->getProp<int>("fooprop") == 3);
delete lrxn;
}
delete rxn;
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void testGithub1950() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github #1950: Query features in products of "
"rxn files not properly handled"
<< std::endl;
std::string rdbase = getenv("RDBASE");
{ // the original report
auto fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/github1950_1.rxn";
auto rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
MOL_SPTR_VECT reacts;
std::string smi = "c1ccccc1Cl";
auto mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CCO";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
auto prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2); // symmetric, so two products
TEST_ASSERT(prods[0].size() == 1);
smi = MolToSmiles(*prods[0][0]);
TEST_ASSERT(smi == "CCOc1ccccc1");
delete rxn;
}
{ // a modification using MRV SMA
auto fName =
rdbase + "/Code/GraphMol/ChemReactions/testData/github1950_2.rxn";
std::cerr << "-------------" << std::endl;
auto rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
MOL_SPTR_VECT reacts;
std::string smi = "c1ccccc1Cl";
auto mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CCO";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
auto prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2); // symmetric, so two products
TEST_ASSERT(prods[0].size() == 1);
smi = MolToSmiles(*prods[0][0]);
std::cerr << smi << std::endl;
TEST_ASSERT(smi == "CCOc1ccccc1");
delete rxn;
}
{ // make sure we didn't break anything,
// this is roughly the same reaction as SMARTS
std::string smarts =
"Cl[#6:2]=,:[#6,#7:3].[#8:5]-[#6:4]>>[#6:4]-[#8:5]-[#6:2]~[*:3]";
auto rxn = RxnSmartsToChemicalReaction(smarts);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
MOL_SPTR_VECT reacts;
std::string smi = "c1ccccc1Cl";
auto mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
smi = "CCO";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
rxn->initReactantMatchers();
auto prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 2); // symmetric, so two products
TEST_ASSERT(prods[0].size() == 1);
smi = MolToSmiles(*prods[0][0]);
TEST_ASSERT(smi == "CCOc1ccccc1");
delete rxn;
}
BOOST_LOG(rdInfoLog) << "Done" << std::endl;
}
void testGithub1869() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing github #1869 and #1955: parens around "
"reactant/product fragments."
<< std::endl;
{
std::string smi;
// nonsense test case
smi = "([C:1].[Cl:2]).[N:3]-[C:4]>>[Cl:2]-[C:1].([N:3].[C:4])";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
rxn->initReactantMatchers();
unsigned int nWarn, nError;
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi = ChemicalReactionToRxnSmarts(*rxn);
TEST_ASSERT(smi ==
"([C:1].[Cl:2]).[N:3]-[C:4]>>[Cl:2]-[C:1].([N:3].[C:4])");
delete rxn;
}
{ // #1869 example
std::string smi;
smi = "[R:1]~;!@[*:2]>>([*:1].[*:2])";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
unsigned int nWarn, nError;
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi = ChemicalReactionToRxnSmarts(*rxn);
TEST_ASSERT(smi == "[R:1]!@[*:2]>>([*:1].[*:2])");
delete rxn;
}
{ // #1955 example
std::string smi;
smi = "([C:1].[C:2]).([C:3][C:4])>>[#6:1]-[#6:2]-[#6:3]-[#6:4]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
unsigned int nWarn, nError;
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0);
TEST_ASSERT(nError == 0);
smi = ChemicalReactionToRxnSmarts(*rxn);
TEST_ASSERT(smi == "([C:1].[C:2]).[C:3][C:4]>>[#6:1]-[#6:2]-[#6:3]-[#6:4]");
delete rxn;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testGithub1269() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing github #1269: preserve reactant atom idx in products"
<< std::endl;
{
// nonsense test case
std::string sma = "[C:1]>>[O:1]Cl";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(sma);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
std::string smi = "NC";
auto mol = SmilesToMol(smi);
TEST_ASSERT(mol);
reacts.push_back(ROMOL_SPTR(mol));
auto prods = rxn->runReactants(reacts);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getAtomicNum() == 8);
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->hasProp(
common_properties::reactantAtomIdx));
TEST_ASSERT(prods[0][0]->getAtomWithIdx(0)->getProp<unsigned int>(
"react_atom_idx") == 1);
TEST_ASSERT(!prods[0][0]->getAtomWithIdx(1)->hasProp(
common_properties::reactantAtomIdx));
TEST_ASSERT(prods[0][0]->getAtomWithIdx(2)->hasProp(
common_properties::reactantAtomIdx));
TEST_ASSERT(prods[0][0]->getAtomWithIdx(2)->getProp<unsigned int>(
"react_atom_idx") == 0);
delete rxn;
}
}
void testGithub1868() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github #1868: Atom index out of range error"
<< std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/v3k.AmideBond.rxn";
for (int i = 0; i < 1000; ++i) {
std::unique_ptr<ChemicalReaction> rxn(RxnFileToChemicalReaction(fName));
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
for (auto v : rxn->getReactants()) {
MolToSmiles(*v.get());
}
for (auto v : rxn->getProducts()) {
MolToSmiles(*v.get());
}
}
}
bool check_bond_stereo(const ROMOL_SPTR &mol, unsigned bond_idx,
int start_anchor_idx, int end_anchor_idx,
Bond::BondStereo stereo) {
auto *bond = mol->getBondWithIdx(bond_idx);
std::vector<int> stereo_atoms_ref{{start_anchor_idx, end_anchor_idx}};
return Bond::BondType::DOUBLE == bond->getBondType() &&
stereo == bond->getStereo() &&
stereo_atoms_ref == bond->getStereoAtoms();
}
ROMOL_SPTR run_simple_reaction(const std::string &reaction,
const ROMOL_SPTR &reactant) {
std::unique_ptr<ChemicalReaction> rxn{RxnSmartsToChemicalReaction(reaction)};
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
const auto prods = rxn->runReactant(reactant, 0);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
return prods[0][0];
};
void run_gist_reaction_tests(const std::vector<RWMOL_SPTR> &mols) {
TEST_ASSERT(check_bond_stereo(mols[0], 1, 0, 3, Bond::BondStereo::STEREOE));
TEST_ASSERT(check_bond_stereo(mols[1], 1, 0, 3, Bond::BondStereo::STEREOE));
TEST_ASSERT(check_bond_stereo(mols[2], 2, 2, 4, Bond::BondStereo::STEREOZ));
TEST_ASSERT(check_bond_stereo(mols[3], 1, 0, 3, Bond::BondStereo::STEREOE));
// StereoAtoms atoms get set such that TRANS == E and CIS == Z
{ // Example 1: reaction that does not affect double bond or neighboring
// single bonds
const std::string reaction(R"([Br:1]>>[F:1])");
{
// 1a
const auto product = run_simple_reaction(reaction, mols[0]);
TEST_ASSERT(
check_bond_stereo(product, 2, 4, 1, Bond::BondStereo::STEREOTRANS));
}
{
// 1b
const auto product = run_simple_reaction(reaction, mols[1]);
TEST_ASSERT(
check_bond_stereo(product, 1, 3, 0, Bond::BondStereo::STEREOTRANS));
}
}
{ // Example 2: reaction that does affect neighboring single bonds
const std::string reaction(R"([C:2][Br:1]>>[C:2][F:1])");
{
// 2a
const auto product = run_simple_reaction(reaction, mols[1]);
TEST_ASSERT(
check_bond_stereo(product, 1, 3, 1, Bond::BondStereo::STEREOTRANS));
}
{
// 2b
const auto product = run_simple_reaction(reaction, mols[2]);
TEST_ASSERT(
check_bond_stereo(product, 2, 1, 4, Bond::BondStereo::STEREOCIS));
}
}
{ // Example 3: reaction that affects the double bond itself
const std::string reaction(R"([C:1]=[N:2]>>[C:1]=[C:2])");
auto product = run_simple_reaction(reaction, mols[3]);
TEST_ASSERT(
check_bond_stereo(product, 0, 2, 3, Bond::BondStereo::STEREOTRANS));
}
}
void strip_bond_directions(RWMOL_SPTR &mol) {
for (auto &bond : mol->bonds()) {
if (bond->getBondDir() == Bond::BondDir::ENDDOWNRIGHT ||
bond->getBondDir() == Bond::BondDir::ENDUPRIGHT) {
bond->setBondDir(Bond::BondDir::NONE);
}
}
}
void testBondStereoGistExamples() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing Bond Stereo propagation across reactions in gist examples"
<< std::endl;
// Examples from
// https://gist.github.com/greglandrum/1c7d933537fd97f14a5c1ec3419f8d7a
// All these mols have Z stereo, except mol3, which is Z
auto mol1 = RWMOL_SPTR(SmilesToMol(R"(C/C=C/C[Br])"));
auto mol2 = RWMOL_SPTR(SmilesToMol(R"(C/C=C/[Br])"));
auto mol3 = RWMOL_SPTR(SmilesToMol(R"(C/C(Br)=C/C)"));
auto mol4 = RWMOL_SPTR(SmilesToMol(R"(C/C=N/F)"));
std::vector<RWMOL_SPTR> mols{mol1, mol2, mol3, mol4};
run_gist_reaction_tests(mols);
// Now, strip bond directions and rerun the same tests to make sure tests
// yield the same results without bond directions in the reactants
for (auto &mol : mols) {
strip_bond_directions(mol);
}
run_gist_reaction_tests(mols);
}
void testStereoBondIsomerization() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Stereo Bond isomerization" << std::endl;
auto mol = RWMOL_SPTR(SmilesToMol(R"(C/C(Br)=C(Cl)/F)"));
strip_bond_directions(mol);
TEST_ASSERT(check_bond_stereo(mol, 2, 2, 4, Bond::BondStereo::STEREOE));
// StereoAtoms will get set to the end of the directed bonds in the products
{ // Try a null reaction
const std::string reaction(
R"([C:1]/[C:2](-[Br:3])=[C:4](\[Cl:5])-[F:6]>>[C:1]/[C:2](-[Br:3])=[C:4](\[Cl:5])-[F:6])");
const auto product = run_simple_reaction(reaction, mol);
TEST_ASSERT(
check_bond_stereo(product, 2, 0, 4, Bond::BondStereo::STEREOCIS));
}
{ // Flip the bond stereo (second bond direction is flipped in the product)
const std::string reaction(
R"([C:1]/[C:2](-[Br:3])=[C:4](\[Cl:5])-[F:6]>>[C:1]/[C:2](-[Br:3])=[C:4](/[Cl:5])-[F:6])");
const auto product = run_simple_reaction(reaction, mol);
TEST_ASSERT(
check_bond_stereo(product, 2, 0, 4, Bond::BondStereo::STEREOTRANS));
}
{ // This should fail, but doesn't:
// we attempt a null reaction on the opposite isomer of the reactant (second
// bond direction is flipped), but it sill works because RDKit cannot match
// SMARTS bond directions in the reactant, but still can force them onto the
// products of the reaction.
const std::string reaction(
R"([C:1]/[C:2](-[Br:3])=[C:4](/[Cl:5])-[F:6]>>[C:1]/[C:2](-[Br:3])=[C:4](/[Cl:5])-[F:6])");
const auto product = run_simple_reaction(reaction, mol);
TEST_ASSERT(
check_bond_stereo(product, 2, 0, 4, Bond::BondStereo::STEREOTRANS));
}
{ // Isomerize swapping the directed bond to the other atom
// Note that the stereo is the same, but we changed the stereoatom it is
// referred to!
const std::string reaction(
R"([C:1]/[C:2](-[Br:3])=[C:4](\[Cl:5])-[F:6]>>[C:1]/[C:2](-[Br:3])=[C:4](-[Cl:5])\[F:6])");
const auto product = run_simple_reaction(reaction, mol);
TEST_ASSERT(
check_bond_stereo(product, 2, 0, 5, Bond::BondStereo::STEREOCIS));
}
// From here on, StereoAtoms set to reactant's StereoAtoms (= highest CIPs)
{ // One-side reaction isomerization (no double bond in reaction)
const std::string reaction(R"([C:1](\[Cl:2])-[F:3]>>[C:1](/[Cl:2])-[F:3])");
const auto product = run_simple_reaction(reaction, mol);
TEST_ASSERT(
check_bond_stereo(product, 2, 5, 1, Bond::BondStereo::STEREOTRANS));
}
{ // One-side reaction isomerization II (double bond in the reaction)
const std::string reaction(
R"([C:1]=[C:2](\[Cl:3])-[F:4]>>[C:1]=[C:2](/[Cl:3])-[F:4])");
const auto product = run_simple_reaction(reaction, mol);
TEST_ASSERT(
check_bond_stereo(product, 0, 5, 2, Bond::BondStereo::STEREOTRANS));
}
}
void testOtherBondStereo() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Other Bond Stereo reaction cases"
<< std::endl;
auto mol = RWMOL_SPTR(SmilesToMol(R"(C/C=C/[Br])"));
strip_bond_directions(mol);
TEST_ASSERT(check_bond_stereo(mol, 1, 0, 3, Bond::BondStereo::STEREOE));
{ // Reaction changes order of the stereo bond
const std::string reaction(R"([C:1]=[C:2]>>[C:1]-[C:2])");
std::unique_ptr<ChemicalReaction> rxn{
RxnSmartsToChemicalReaction(reaction)};
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
const auto product_sets = rxn->runReactant(mol, 0);
TEST_ASSERT(!product_sets.empty());
for (const auto &products : product_sets) {
TEST_ASSERT(products.size() == 1);
for (const Bond *bond : products[0]->bonds()) {
TEST_ASSERT(Bond::BondType::SINGLE == bond->getBondType());
TEST_ASSERT(Bond::BondStereo::STEREONONE == bond->getStereo());
}
}
// and if we don't strip direction?
auto lmol = RWMOL_SPTR(SmilesToMol(R"(C/C=C/[Br])"));
auto product_sets2 = rxn->runReactant(lmol, 0);
TEST_ASSERT(!product_sets2.empty());
auto osmi = MolToSmiles(*product_sets2[0][0]);
TEST_ASSERT(osmi == "CCCBr");
}
{ // Reaction explicitly destroys stereochemistry
// (no directed bonds enclosing the double bond)
const std::string reaction(
R"([C:1]/[C:2]=[C:3]/[Br:4]>>[C:1][C:2]=[C:3]-[Br:4])");
std::unique_ptr<ChemicalReaction> rxn{
RxnSmartsToChemicalReaction(reaction)};
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
const auto product_sets = rxn->runReactant(mol, 0);
TEST_ASSERT(!product_sets.empty());
for (const auto &products : product_sets) {
TEST_ASSERT(products.size() == 1);
for (const Bond *bond : products[0]->bonds()) {
TEST_ASSERT(Bond::BondStereo::STEREONONE == bond->getStereo());
// Make sure the temporary mark set in the reaction has been removed.
TEST_ASSERT(!bond->hasProp("_UnknownStereoRxnBond"));
if (bond->getIdx() == 1) {
TEST_ASSERT(Bond::BondType::DOUBLE == bond->getBondType());
} else {
TEST_ASSERT(Bond::BondType::SINGLE == bond->getBondType());
}
}
}
// and if we don't strip direction?
auto lmol = RWMOL_SPTR(SmilesToMol(R"(C/C=C/[Br])"));
auto product_sets2 = rxn->runReactant(lmol, 0);
TEST_ASSERT(!product_sets.empty());
auto osmi = MolToSmiles(*product_sets2[0][0]);
TEST_ASSERT(osmi == "CC=CBr");
}
{ // Reaction with 2 product sets
const std::string reaction(R"([C:1]=[C:2]>>[Si:1]=[C:2])");
std::unique_ptr<ChemicalReaction> rxn{
RxnSmartsToChemicalReaction(reaction)};
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
rxn->initReactantMatchers();
const auto product_sets = rxn->runReactant(mol, 0);
TEST_ASSERT(product_sets.size() == 2);
for (const auto &products : product_sets) {
TEST_ASSERT(products.size() == 1);
TEST_ASSERT(check_bond_stereo(products[0], 0, 2, 3,
Bond::BondStereo::STEREOTRANS));
}
// and if we don't strip direction?
auto lmol = RWMOL_SPTR(SmilesToMol(R"(C/C=C/[Br])"));
auto product_sets2 = rxn->runReactant(lmol, 0);
TEST_ASSERT(!product_sets2.empty());
auto osmi = MolToSmiles(*product_sets2[0][0]);
TEST_ASSERT(osmi == "C/[SiH]=C/Br");
osmi = MolToSmiles(*product_sets2[1][0]);
TEST_ASSERT(osmi == "C/C=[SiH]/Br");
}
{ // Reactant stereo propagated by (stereoatom, anti-stereoatom) pair
auto mol2 = RWMOL_SPTR(SmilesToMol(R"(Cl/C(C)=C(/Br)F)"));
strip_bond_directions(mol2);
TEST_ASSERT(check_bond_stereo(mol2, 2, 0, 4, Bond::BondStereo::STEREOE));
const std::string reaction(R"([C:1]=[C:2][Br:3]>>[C:1]=[C:2].[Br:3])");
std::unique_ptr<ChemicalReaction> rxn{
RxnSmartsToChemicalReaction(reaction)};
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
rxn->initReactantMatchers();
auto product_sets = rxn->runReactant(mol2, 0);
TEST_ASSERT(product_sets.size() == 1);
TEST_ASSERT(product_sets[0].size() == 2);
// We are only interested in the product that keeps the double bond
TEST_ASSERT(check_bond_stereo(product_sets[0][0], 0, 2, 4,
Bond::BondStereo::STEREOCIS));
// and if we don't strip direction?
auto lmol = RWMOL_SPTR(SmilesToMol(R"(Cl/C(C)=C(/Br)F)"));
auto product_sets2 = rxn->runReactant(lmol, 0);
TEST_ASSERT(!product_sets2.empty());
auto osmi = MolToSmiles(*product_sets2[0][0]);
TEST_ASSERT(osmi == "C/C(Cl)=C/F");
}
{ // Reactant stereo propagated by anti-stereoatoms pair
auto mol2 = RWMOL_SPTR(SmilesToMol(R"(Cl/C(C)=C(/Br)F)"));
strip_bond_directions(mol2);
TEST_ASSERT(check_bond_stereo(mol2, 2, 0, 4, Bond::BondStereo::STEREOE));
const std::string reaction(
R"([Cl:4][C:1]=[C:2][Br:3]>>[C:1]=[C:2].[Br:3].[Cl:4])");
std::unique_ptr<ChemicalReaction> rxn{
RxnSmartsToChemicalReaction(reaction)};
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 3);
rxn->initReactantMatchers();
auto product_sets = rxn->runReactant(mol2, 0);
TEST_ASSERT(product_sets.size() == 1);
TEST_ASSERT(product_sets[0].size() == 3);
// We are only interested in the product that keeps the double bond
TEST_ASSERT(check_bond_stereo(product_sets[0][0], 0, 2, 3,
Bond::BondStereo::STEREOTRANS));
// and if we don't strip direction?
auto lmol = RWMOL_SPTR(SmilesToMol(R"(Cl/C(C)=C(/Br)F)"));
auto product_sets2 = rxn->runReactant(lmol, 0);
TEST_ASSERT(!product_sets2.empty());
auto osmi = MolToSmiles(*product_sets2[0][0]);
TEST_ASSERT(osmi == "C/C=C/F");
}
}
void testGithub2547() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing Github #2547: Check kekulization issues in mdl rxn files"
<< std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/kekule_reaction.rxn";
BOOST_LOG(rdInfoLog) << "--- reading file" << std::endl;
std::unique_ptr<ChemicalReaction> rxn(RxnFileToChemicalReaction(fName));
BOOST_LOG(rdInfoLog) << "--- read file" << std::endl;
ROMOL_SPTR mol("c1ccccc1"_smiles);
rxn->initReactantMatchers();
std::vector<ROMOL_SPTR> v{mol};
auto prods = rxn->runReactants(v);
TEST_ASSERT(prods.size() == 0);
RxnOps::sanitizeRxn(*rxn);
prods = rxn->runReactants(v);
TEST_ASSERT(prods.size() > 1);
}
void testDblBondCrash() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Testing double bond stereo vanishing during a reaction" << std::endl;
{
const std::string reaction(R"([N;!H0:1]>>[N:1])");
std::unique_ptr<ChemicalReaction> rxn(
RxnSmartsToChemicalReaction(reaction));
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
{
auto mol = RWMOL_SPTR(SmilesToMol("C/C=C(/C)CN"));
std::vector<ROMOL_SPTR> v{mol};
auto prods = rxn->runReactants(v);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(RWMol *)prods[0][0].get());
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "C/C=C(/C)CN");
}
{
// create an artificial situation in the molecule where bond stereo is
// set, but neither stereoatoms nor CIP ranks are there (this can happen
// with serialized molecules from old RDKit versions)
auto mol = RWMOL_SPTR(SmilesToMol("C/C=C(/C)CN"));
mol->getBondWithIdx(1)->getStereoAtoms().clear();
for (auto atom : mol->atoms()) {
if (atom->hasProp(common_properties::_CIPRank)) {
atom->clearProp(common_properties::_CIPRank);
}
}
std::vector<ROMOL_SPTR> v{mol};
auto prods = rxn->runReactants(v);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(RWMol *)prods[0][0].get());
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "CC=C(C)CN");
}
{
SmilesParserParams ps;
ps.sanitize = true;
auto mol = RWMOL_SPTR(SmilesToMol("CC(=O)/N=C(\\C)c1nonc1N", ps));
std::vector<ROMOL_SPTR> v{mol};
auto prods = rxn->runReactants(v);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(RWMol *)prods[0][0].get());
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "CC(=O)/N=C(\\C)c1nonc1N");
}
{
SmilesParserParams ps;
ps.sanitize = true;
auto mol = RWMOL_SPTR(SmilesToMol("CC(=O)/N=C(\\C)c1nonc1N", ps));
// make sure that sanitizing again doesn't screw things up.
MolOps::sanitizeMol(*mol);
std::vector<ROMOL_SPTR> v{mol};
auto prods = rxn->runReactants(v);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(RWMol *)prods[0][0].get());
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "CC(=O)/N=C(\\C)c1nonc1N");
}
{
// make sure that sanitizing afterwards doesn't screw things up:
SmilesParserParams ps;
ps.sanitize = false;
auto mol = RWMOL_SPTR(SmilesToMol("CC(=O)/N=C(\\C)c1nonc1N", ps));
MolOps::sanitizeMol(*mol);
std::vector<ROMOL_SPTR> v{mol};
auto prods = rxn->runReactants(v);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(RWMol *)prods[0][0].get());
TEST_ASSERT(MolToSmiles(*prods[0][0]) == "CC(=O)/N=C(\\C)c1nonc1N");
}
{
// another example
const std::string reaction2(R"([N;!H0;$(N-c):1]>>[N:1]-c1cncnn1)");
std::unique_ptr<ChemicalReaction> rxn2(
RxnSmartsToChemicalReaction(reaction2));
TEST_ASSERT(rxn2);
rxn2->initReactantMatchers();
auto mol = RWMOL_SPTR(SmilesToMol("CC(=O)/C=C(\\N)c1nonc1N"));
std::vector<ROMOL_SPTR> v{mol};
auto prods = rxn2->runReactants(v);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
MolOps::sanitizeMol(*(RWMol *)prods[0][0].get());
TEST_ASSERT(MolToSmiles(*prods[0][0]) ==
"CC(=O)/C=C(\\N)c1nonc1Nc1cncnn1");
}
}
}
void testGithub3097() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github issue # 3097" << std::endl;
std::string smi =
"[c:6][n:7][c:8].[N:14]#[N:15]>>[C:6].[C:8][N:7]=[N+:14]=[N-:15]";
std::unique_ptr<ChemicalReaction> rxn{RxnSmartsToChemicalReaction(smi)};
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
auto mol1 = RWMOL_SPTR(SmilesToMol("c1cc[nH]c1"));
auto mol2 = RWMOL_SPTR(SmilesToMol("N#N"));
std::vector<ROMOL_SPTR> v{mol1, mol2};
auto prods = rxn->runReactants(v);
// if products are not empty this is already a success
TEST_ASSERT(prods.size() > 0);
}
void testRxnBlockRemoveHs() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing removing explicit Hs from RxnBlock"
<< std::endl;
std::string rxnB = R"RXN($RXN
Dummy 0
Dummy 0123456789
1 1
$MOL
Dummy 01234567892D
10 10 0 0 0 0 999 V2000
7.0222 -11.1783 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
8.0615 -11.7783 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
7.0222 -9.6783 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0
5.7231 -8.9283 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0
5.7231 -7.7283 0.0000 A 0 0 0 0 0 0 0 0 0 5 0 0
4.4242 -9.6783 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0
4.4242 -11.1783 0.0000 C 0 0 0 0 0 0 0 0 0 7 0 0
3.3849 -11.7783 0.0000 A 0 0 0 0 0 0 0 0 0 8 0 0
5.7231 -11.9283 0.0000 N 0 0 0 0 0 0 0 0 0 9 0 0
5.7231 -13.1094 0.0000 H 0 0
1 2 2 0 0 0 8
1 3 1 0 0 0 8
3 4 2 0 0 0 8
4 5 1 0 0 0 2
4 6 1 0 0 0 8
6 7 2 0 0 0 8
7 8 1 0 0 0 2
7 9 1 0 0 0 8
9 1 1 0 0 0 8
9 10 1 0
M SUB 1 9 2
M END
$MOL
Dummy 01234567892D
9 9 0 0 0 0 999 V2000
17.0447 -11.1783 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
18.0840 -11.7783 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
17.0447 -9.6783 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0
15.7457 -8.9283 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0
15.7457 -7.7283 0.0000 A 0 0 0 0 0 0 0 0 0 5 0 0
14.4467 -9.6783 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0
14.4467 -11.1783 0.0000 C 0 0 0 0 0 0 0 0 0 7 0 0
13.4074 -11.7783 0.0000 A 0 0 0 0 0 0 0 0 0 8 0 0
15.7457 -11.9283 0.0000 N 0 0 0 0 0 0 0 0 0 9 0 0
1 2 1 0 0 0 8
1 3 1 0 0 0 8
3 4 2 0 0 0 8
4 5 1 0 0 0 2
4 6 1 0 0 0 8
6 7 2 0 0 0 8
7 8 1 0 0 0 2
7 9 1 0 0 0 8
9 1 2 0 0 0 8
M END
)RXN";
ROMOL_SPTR mol(
static_cast<ROMol *>(SmilesToMol("c1(=O)nc([Cl])cc([F])[nH]1")));
std::vector<ROMOL_SPTR> v{mol};
{
std::unique_ptr<ChemicalReaction> rxn(RxnBlockToChemicalReaction(rxnB));
TEST_ASSERT(rxn.get());
rxn->initReactantMatchers();
auto prods = rxn->runReactants(v);
// if the explicit hydrogen is not removed and the reactant template
// is not sanitized, the reactant template is not aromatic and our
// aromatic reactant won't match
TEST_ASSERT(prods.size() == 0);
}
{
std::unique_ptr<ChemicalReaction> rxn(
RxnBlockToChemicalReaction(rxnB, true, true));
TEST_ASSERT(rxn.get());
rxn->initReactantMatchers();
auto prods = rxn->runReactants(v);
TEST_ASSERT(prods.size() == 2);
}
}
void testGithub3078() {
BOOST_LOG(rdInfoLog) << "--------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog)
<< "Reaction-edge stereo bonds should default to STEREONONE" << std::endl;
const std::string reaction(
R"([C:1][C:2]1[C:3][N:4]1>>[C:1][C:2]1=[C:3][N:4]1)");
std::unique_ptr<ChemicalReaction> rxn(RxnSmartsToChemicalReaction(reaction));
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
std::vector<ROMOL_SPTR> reactant{"CC1CN1"_smiles};
auto prods = rxn->runReactants(reactant);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
const auto bond = prods[0][0]->getBondWithIdx(1);
TEST_ASSERT(bond->getBondType() == Bond::DOUBLE);
TEST_ASSERT(bond->getStereo() == Bond::STEREONONE);
// Make sure the temporary mark set in the reaction has been removed.
TEST_ASSERT(!bond->hasProp("_UnknownStereoRxnBond"));
}
void testGithub4162() {
const std::string reaction(
R"([C:1](=[O:2])-[OD1].[N!H0:3]>>[C:1](=[O:2])[N:3])");
std::unique_ptr<ChemicalReaction> rxn(RxnSmartsToChemicalReaction(reaction));
std::unique_ptr<ChemicalReaction> rxnCopy(new ChemicalReaction(*rxn));
RxnOps::sanitizeRxn(*rxn);
RxnOps::sanitizeRxn(*rxnCopy);
std::string pkl;
ReactionPickler::pickleReaction(*rxn, pkl);
std::unique_ptr<ChemicalReaction> rxnFromPickle(new ChemicalReaction(pkl));
RxnOps::sanitizeRxn(*rxnFromPickle);
ReactionPickler::pickleReaction(*rxnFromPickle, pkl);
rxnFromPickle.reset(new ChemicalReaction(pkl));
RxnOps::sanitizeRxn(*rxnFromPickle);
}
void testGithub4114() {
BOOST_LOG(rdInfoLog) << "--------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Reactions don't propagate bond properties"
<< std::endl;
const std::string DUMMY_PROP{"dummy_prop"};
std::vector<ROMOL_SPTR> mol{"ClC(N=O)=C=C=C=C(Br)N=S"_smiles};
// React the left side of the mol
const std::string reaction(
R"([Cl:1][C:2]([N:3]=[O:4])=[C:5]=[C:6]>>[F:1][Si:2]([P:3]~[S:4])(~[Si:5]=[Si:6]))");
std::unique_ptr<ChemicalReaction> rxn(RxnSmartsToChemicalReaction(reaction));
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
// Set dummy properties on all bonds; mark the central double bonds
// as EITHERDOUBLE
for (unsigned int i = 0; i < mol[0]->getNumBonds(); ++i) {
auto bnd = mol[0]->getBondWithIdx(i);
bnd->setProp(DUMMY_PROP, i);
if (i >= 3 && i <= 6) {
TEST_ASSERT(bnd->getBondType() == Bond::DOUBLE);
bnd->setBondDir(Bond::EITHERDOUBLE);
}
}
auto prods = rxn->runReactants(mol);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
// Make sure the reaction did not alter the graph
for (const auto &at : prods[0][0]->atoms()) {
auto mapno = at->getProp<unsigned int>(common_properties::reactantAtomIdx);
TEST_ASSERT(mapno == at->getIdx());
}
for (const auto &rBnd : mol[0]->bonds()) {
auto pBnd = prods[0][0]->getBondBetweenAtoms(rBnd->getBeginAtomIdx(),
rBnd->getEndAtomIdx());
// Bonds 0, 1 and 4 are overridden in the product template, and should
// therefore override the properties.
// Bonds 2 and 3 are "null bonds", and should get properties copied over.
// Bonds > 4 are reactant bonds, and should keep their properties.
auto rBndIdx = rBnd->getIdx();
if (rBndIdx == 0 || rBndIdx == 1 || rBndIdx == 4) {
TEST_ASSERT(!pBnd->hasProp(DUMMY_PROP));
} else {
unsigned int dummy_prop;
TEST_ASSERT(pBnd->getPropIfPresent(DUMMY_PROP, dummy_prop));
TEST_ASSERT(dummy_prop == rBndIdx);
}
// Bond 3 is a "null bond", and should preserve EITHERDOUBLE.
// Bond 4 is specified in the reaction, and should not preserve
// EITHERDOUBLE. Bonds 5 & 6 are not included in the reaction, so they
// should keep EITHERDOUBLE dir.
if (rBndIdx == 3 || rBndIdx == 5 || rBndIdx == 6) {
TEST_ASSERT(pBnd->getBondType() == Bond::DOUBLE);
TEST_ASSERT(pBnd->getBondDir() == Bond::EITHERDOUBLE);
} else {
TEST_ASSERT(pBnd->getBondDir() == Bond::NONE);
}
}
}
void testGithub4183() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github #4183: Reading a rxn file in v3000 "
"format that contains agents"
<< std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/v3k_with_agents.rxn";
ChemicalReaction *rxn = RxnFileToChemicalReaction(fName);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 3);
delete rxn;
}
void testGithub4410() {
BOOST_LOG(rdInfoLog) << "--------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Github #4410: wrong double bond stereochemistry"
<< std::endl;
const std::string reaction(
R"([N:4][C:6](/[Cl:9])=[C:7](\[Cl:10])[C:11]>>[Br:4][CX3:6](\[Cl:9])=[CX3:7](/[Cl:10])[C:11])");
std::unique_ptr<ChemicalReaction> rxn(RxnSmartsToChemicalReaction(reaction));
TEST_ASSERT(rxn);
rxn->initReactantMatchers();
std::vector<ROMOL_SPTR> mol{R"(C\C(Cl)=C(\N)Cl)"_smiles};
auto prods = rxn->runReactants(mol);
TEST_ASSERT(prods.size() == 1);
TEST_ASSERT(prods[0].size() == 1);
auto dblBnd = prods[0][0]->getBondBetweenAtoms(1, 3);
TEST_ASSERT(dblBnd->getBondType() == Bond::DOUBLE);
TEST_ASSERT(dblBnd->getStereoAtoms() == std::vector<int>({2, 4}));
TEST_ASSERT(dblBnd->getStereo() == Bond::STEREOTRANS);
TEST_ASSERT(MolToSmiles(*prods[0][0]) == R"(C/C(Cl)=C(\Cl)Br)");
}
void testMultiTemplateRxnQueries() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing multi-template isMoleculeXOfReaction queries"
<< std::endl;
std::string rxn_smarts =
"[S;v1&H0,v2&H1:1].[S;v2;H0,H1:2][S;v2;H0,H1:3]>>[S:3].[S:1][S:2]";
ChemicalReaction *rxn = RxnSmartsToChemicalReaction(rxn_smarts);
TEST_ASSERT(rxn->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn->getNumProductTemplates() == 2);
rxn->initReactantMatchers();
unsigned int nWarn, nError;
TEST_ASSERT(rxn->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0 && nError == 0);
ROMol *reactant = SmilesToMol("SC1=CC(CSSCC2=CC=CC=C2)=CC=C1");
ROMol *product = reactant;
ROMol *neither = SmilesToMol("c1ccccc1");
std::vector<unsigned int> which;
bool is_reactant = isMoleculeReactantOfReaction(*rxn, *reactant, which);
TEST_ASSERT(is_reactant);
TEST_ASSERT(which == std::vector<unsigned int>({0, 1}));
unsigned int first_match;
is_reactant = isMoleculeReactantOfReaction(*rxn, *reactant, first_match);
TEST_ASSERT(is_reactant);
TEST_ASSERT(first_match == 0);
is_reactant = isMoleculeReactantOfReaction(*rxn, *reactant);
TEST_ASSERT(is_reactant);
is_reactant = isMoleculeReactantOfReaction(*rxn, *neither, which);
TEST_ASSERT(!is_reactant);
TEST_ASSERT(which.empty());
is_reactant = isMoleculeReactantOfReaction(*rxn, *neither, first_match);
TEST_ASSERT(!is_reactant);
TEST_ASSERT(first_match == 2);
is_reactant = isMoleculeReactantOfReaction(*rxn, *neither);
TEST_ASSERT(!is_reactant);
bool is_product = isMoleculeProductOfReaction(*rxn, *product, which);
TEST_ASSERT(is_product);
TEST_ASSERT(which == std::vector<unsigned int>({0, 1}));
is_product = isMoleculeProductOfReaction(*rxn, *product, first_match);
TEST_ASSERT(is_product);
TEST_ASSERT(first_match == 0);
is_product = isMoleculeProductOfReaction(*rxn, *product);
TEST_ASSERT(is_product);
is_product = isMoleculeProductOfReaction(*rxn, *neither, which);
TEST_ASSERT(!is_product);
TEST_ASSERT(which.empty());
is_product = isMoleculeProductOfReaction(*rxn, *neither, first_match);
TEST_ASSERT(!is_product);
TEST_ASSERT(first_match == 2);
is_product = isMoleculeProductOfReaction(*rxn, *neither);
TEST_ASSERT(!is_product);
delete reactant;
delete neither;
delete rxn;
}
void testChemicalReactionCopyAssignment() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing ChemicalReaction copy assignment operator"
<< std::endl;
std::string rxn_smarts1 =
"[C;$(C=O):1][OH1].[N;$(N[#6]);!$(N=*);!$([N-]);!$(N#*);!$([ND3]);!$([ND4]);!$(N[O,N]);!$(N[C,S]=[S,O,N]):2]>>[C:1][N+0:2]";
ChemicalReaction *rxn1 = RxnSmartsToChemicalReaction(rxn_smarts1);
rxn1->setImplicitPropertiesFlag(true);
rxn1->initReactantMatchers();
unsigned int nWarn, nError;
TEST_ASSERT(rxn1->validate(nWarn, nError, false));
TEST_ASSERT(nWarn == 0 && nError == 0);
std::string rxn_smarts2 = "[O:1]>>[N:1]";
ChemicalReaction *rxn2 = RxnSmartsToChemicalReaction(rxn_smarts2);
*rxn2 = *rxn1;
// Check we copied the base class members
TEST_ASSERT(rxn2->getPropList() == rxn1->getPropList());
// Check we copied the flags
TEST_ASSERT(rxn2->getImplicitPropertiesFlag());
TEST_ASSERT(rxn2->isInitialized());
// Check we copied the reactant/product templates
TEST_ASSERT(rxn2->getNumReactantTemplates() == 2);
TEST_ASSERT(rxn2->getNumProductTemplates() == 1);
MOL_SPTR_VECT::const_iterator it1 = rxn1->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator it2 = rxn2->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator end_it1 = rxn1->endReactantTemplates();
while (it1 != end_it1) {
TEST_ASSERT(MolToSmiles(**it1) == MolToSmiles(**it2));
++it1;
++it2;
}
it1 = rxn1->beginProductTemplates();
it2 = rxn2->beginProductTemplates();
end_it1 = rxn1->endProductTemplates();
while (it1 != end_it1) {
TEST_ASSERT(MolToSmiles(**it1) == MolToSmiles(**it2));
++it1;
++it2;
}
// Check that the reactions don't share resources
const RWMol &rxn1_reactant = *rxn1->getReactants().at(0);
const_cast<RWMol &>(rxn1_reactant).clear();
ROMOL_SPTR rxn2_reactant = rxn2->getReactants().at(0);
TEST_ASSERT(rxn2_reactant->getNumAtoms() > 0);
// Check the reaction works
MOL_SPTR_VECT reactants;
reactants.emplace_back(SmilesToMol("CC(=O)O"));
reactants.emplace_back(SmilesToMol("CCN"));
std::vector<MOL_SPTR_VECT> products = rxn2->runReactants(reactants);
TEST_ASSERT(MolToSmiles(*products[0][0]) == "CCNC(C)=O");
delete rxn1;
delete rxn2;
}
void testGithub6138() {
// Pickling reactions removed some of their properties set after reaction
// initialization
auto rxn_smarts = "[c:1]:[n&H1&+0&D2:3]:[n:2]>>[c:1]:[3n&H0&+0&D3:3]:[2n:2]";
std::unique_ptr<ChemicalReaction> rxn(
RxnSmartsToChemicalReaction(rxn_smarts));
ROMOL_SPTR mol("c1cn[nH]c1"_smiles);
rxn->initReactantMatchers();
MOL_SPTR_VECT reacts;
reacts.push_back(mol);
auto prods = rxn->runReactants(reacts);
std::string pkl;
ReactionPickler::pickleReaction(*rxn, pkl);
std::unique_ptr<ChemicalReaction> lrxn(new ChemicalReaction());
ReactionPickler::reactionFromPickle(pkl, lrxn.get());
auto prods2 = lrxn->runReactants(reacts);
auto s1 = MolToSmiles(*prods[0][0]);
auto s2 = MolToSmiles(*prods2[0][0]);
TEST_ASSERT(s1 == s2);
}
void testReactionWithChiralAgent() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing introduction of new atoms with chirality"
<< std::endl;
{ // a reaction with a chiral agent - v3000
std::string rdbase = getenv("RDBASE");
std::string fName;
fName =
rdbase +
"/Code/GraphMol/ChemReactions/testData/testRXNChiralityAgentV3000.rxn";
ChemicalReaction *rxn =
RxnFileToChemicalReaction(fName, false, false, false);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 1);
auto outputRxn = ChemicalReactionToRxnSmiles(*rxn);
TEST_ASSERT(
outputRxn ==
"[CH:1]([F:2])([CH3:3])[CH2:4][CH2:5][Br:6]>CC[C@H](C)Cl>[CH:1]([F:2])([CH3:3])[CH2:4][CH2:5][CH2:7][CH:8]([CH3:9])[Cl:10]");
BOOST_LOG(rdInfoLog) << ChemicalReactionToRxnSmiles(*rxn) << std::endl;
delete rxn;
}
{ // a reaction with a chiral agent - v2000
std::string rdbase = getenv("RDBASE");
std::string fName;
fName =
rdbase +
"/Code/GraphMol/ChemReactions/testData/testRXNChiralityAgentV2000.rxn";
ChemicalReaction *rxn =
RxnFileToChemicalReaction(fName, false, false, false);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxn->getNumAgentTemplates() == 1);
auto outputRxn = ChemicalReactionToRxnSmiles(*rxn);
TEST_ASSERT(
outputRxn ==
"[CH:1]([F:2])([CH3:3])[CH2:4][CH2:5][Br:6]>CC[C@H](C)Cl>[CH:1]([F:2])([CH3:3])[CH2:4][CH2:5][CH2:7][CH:8]([CH3:9])[Cl:10]");
BOOST_LOG(rdInfoLog) << ChemicalReactionToRxnSmiles(*rxn) << std::endl;
delete rxn;
}
}
void testGithub5890() {
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Github Issue 5890: Testing reaction with radicals"
<< std::endl;
{
std::string rdbase = getenv("RDBASE");
std::string fName;
fName = rdbase + "/Code/GraphMol/ChemReactions/testData/v3k.radicals.rxn";
ChemicalReaction *rxn =
RxnFileToChemicalReaction(fName, false, false, false);
TEST_ASSERT(rxn);
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
std::string pkl;
ReactionPickler::pickleReaction(rxn, pkl);
delete rxn;
rxn = new ChemicalReaction();
ReactionPickler::reactionFromPickle(pkl, rxn);
auto outputRxn = ChemicalReactionToRxnSmiles(*rxn);
BOOST_LOG(rdInfoLog) << outputRxn << std::endl;
TEST_ASSERT(outputRxn == "[CH]1[CH][CH]1>>C");
delete rxn;
}
}
int main() {
RDLog::InitLogs();
BOOST_LOG(rdInfoLog)
<< "********************************************************\n";
BOOST_LOG(rdInfoLog) << "Testing Chemical Reactions \n";
test1Basics();
test2SimpleReactions();
test3RingFormation();
test4MultipleProducts();
test5Salts();
test6DaylightParser();
test7MDLParser();
test8Validation();
test9ProductQueries();
test10ChiralityDaylight();
test11ChiralityRxn();
test12DoubleBondStereochem();
test13Issue1748846();
test14Issue1804420();
test15Issue1882749();
test16Exceptions();
test17Issue1920627();
test18PropertyTransfer();
test19Issue2050085();
test20BondQueriesInProduct();
test21Issue2540021();
test22DotsToRemoveBonds();
test23Pickling();
test24AtomFlags();
test25Conformers();
test26V3000MDLParser();
test27SmartsWriter();
test28RxnDepictor();
test29RxnWriter();
test30ReactProdQueries();
test31Issue3140490();
test32Replacements();
test33ReactingAtoms1();
test34ReactingAtoms2();
test35ParensInReactants1();
test36ParensInReactants2();
test37ProtectOption();
test38AddRecursiveQueriesToReaction();
test39InnocentChiralityLoss();
test40AgentsInSmarts();
test41Github233();
test42ReactionSmiles();
test44Github290();
test45SmilesWriter();
test46Agents();
test47TestReactionMoleculeConversion();
test48ParensInProducts1();
test49ParensInProducts2();
test50RNXFileParserWithEmptyAgentColumn();
test51RNXSmilesFromPatentData();
test52RedundantProductMappingNumbersAndRunReactants();
test53ReactionSubstructureMatching();
test54RedundantProductMappingNumbersAndRSChirality();
test55RedundantProductMappingNumbersAndEZStereochemistry();
test56TestOldPickleVersion();
test57IntroductionOfNewChiralCenters();
test58MolFileValueRoundTrip();
test59ReactionCanonicalization();
test60RunSingleReactant();
test61Github685();
test62Github975();
test63CopyConstructor();
test43Github243();
test64Github1266();
test65SanitizeUnmappedHs();
test66SanitizeMappedHs();
test67SanitizeMappedHsInReactantAndProd();
test68MappedHToHeavy();
test69Github1387();
test70Github1544();
testSanitizeException();
testReactionProperties();
testGithub1950();
testGithub1869();
testGithub1269();
testGithub1868();
testBondStereoGistExamples();
testStereoBondIsomerization();
testOtherBondStereo();
testGithub2547();
testGithub3097();
testDblBondCrash();
testRxnBlockRemoveHs();
testGithub3078();
testGithub4162();
testGithub4114();
testGithub4183();
testGithub4410();
testMultiTemplateRxnQueries();
testChemicalReactionCopyAssignment();
testGithub6138();
testReactionWithChiralAgent();
testGithub5890();
BOOST_LOG(rdInfoLog)
<< "*******************************************************\n";
return (0);
}
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