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rdkit/Code/GraphMol/SLNParse/test.cpp
Greg Landrum 772ef9199b fix and test sf.net issue 277;
2013-01-06 11:04:01 +00:00

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// $Id$
//
// Copyright (c) 2008, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior
// written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Created by Greg Landrum September, 2006
//
#include <iostream>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SLNParse/SLNParse.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDGeneral/RDLog.h>
using namespace std;
void test1(){
RDKit::RWMol *mol;
std::string sln;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test1 " << std::endl;
sln = "CH4";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
delete mol;
sln = "CH3CH3";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==2);
TEST_ASSERT(mol->getRingInfo()->numRings()==0);
delete mol;
sln = "C[1]H2CH2CH2@1";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==3);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
delete mol;
sln = "C[2]H2CH2CH2@2";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==3);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
delete mol;
sln = "C[200]H2CH2CH2@200";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==3);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
delete mol;
sln = "C[1:foo]H2CH2CH2@1";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==3);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
delete mol;
sln = "C[foo;bar=1;baz=bletch]H4";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getRingInfo()->numRings()==0);
delete mol;
sln = "CH3CH(CH3)OCH3";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==5);
TEST_ASSERT(mol->getRingInfo()->numRings()==0);
TEST_ASSERT(mol->getAtomWithIdx(0)->getDegree()==1);
TEST_ASSERT(mol->getAtomWithIdx(1)->getDegree()==3);
TEST_ASSERT(mol->getAtomWithIdx(2)->getDegree()==1);
TEST_ASSERT(mol->getAtomWithIdx(3)->getDegree()==2);
delete mol;
sln = "CH3CH(CH3)OCH3.Cl";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==6);
TEST_ASSERT(mol->getRingInfo()->numRings()==0);
TEST_ASSERT(mol->getAtomWithIdx(0)->getDegree()==1);
TEST_ASSERT(mol->getAtomWithIdx(1)->getDegree()==3);
TEST_ASSERT(mol->getAtomWithIdx(2)->getDegree()==1);
TEST_ASSERT(mol->getAtomWithIdx(3)->getDegree()==2);
TEST_ASSERT(mol->getAtomWithIdx(4)->getDegree()==1);
TEST_ASSERT(mol->getAtomWithIdx(5)->getDegree()==0);
delete mol;
sln = "H-O-H";
mol=RDKit::SLNToMol(sln,false);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==3);
TEST_ASSERT(mol->getAtomWithIdx(0)->getAtomicNum()==1);
TEST_ASSERT(mol->getAtomWithIdx(1)->getAtomicNum()==8);
TEST_ASSERT(mol->getAtomWithIdx(2)->getAtomicNum()==1);
delete mol;
sln = "HC(F)(Cl)Br";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
delete mol;
sln = "CH3C(=O)H";
mol=RDKit::SLNToMol(sln,false);//,1);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==7);
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test2(){
RDKit::RWMol *mol;
std::string sln;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test2: bond orders " << std::endl;
sln = "CH3CH3";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==2);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::SINGLE);
delete mol;
sln = "CH2-CH2";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==2);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::SINGLE);
delete mol;
sln = "CH2=CH2";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==2);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::DOUBLE);
delete mol;
sln = "CH#CH";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==2);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::TRIPLE);
delete mol;
sln = "C[1]H-CH2-CH2-CH2-CH2-CH=@1";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==6);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(1,2)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,3)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(3,4)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(4,5)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(5,0)->getBondType()==RDKit::Bond::DOUBLE);
delete mol;
sln = "C[1]H:CH:CH:CH:CH:CH:@1";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==6);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::AROMATIC);
TEST_ASSERT(mol->getBondBetweenAtoms(1,2)->getBondType()==RDKit::Bond::AROMATIC);
TEST_ASSERT(mol->getBondBetweenAtoms(2,3)->getBondType()==RDKit::Bond::AROMATIC);
TEST_ASSERT(mol->getBondBetweenAtoms(3,4)->getBondType()==RDKit::Bond::AROMATIC);
TEST_ASSERT(mol->getBondBetweenAtoms(4,5)->getBondType()==RDKit::Bond::AROMATIC);
TEST_ASSERT(mol->getBondBetweenAtoms(5,0)->getBondType()==RDKit::Bond::AROMATIC);
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test3(){
std::string pval;
RDKit::RWMol *mol;
std::string sln;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test3: atom properties " << std::endl;
sln = "C[-]H3";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getFormalCharge()==-1);
delete mol;
sln = "C[charge=-]H3";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getFormalCharge()==-1);
delete mol;
sln = "C[charge=-1]H3";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getFormalCharge()==-1);
delete mol;
sln = "C[CHARGE=-1]H3";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getFormalCharge()==-1);
delete mol;
sln = "C[chARgE=-1]H3";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getFormalCharge()==-1);
delete mol;
sln = "C[1:-2]H2";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getFormalCharge()==-2);
delete mol;
sln = "C[1:+]H5";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getFormalCharge()==1);
delete mol;
sln = "C[1:+2]H6";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getFormalCharge()==2);
delete mol;
sln = "C[1:foo;bar=baz]H4";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp("foo"));
mol->getAtomWithIdx(0)->getProp("foo",pval);
TEST_ASSERT(pval=="");
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp("bar"));
mol->getAtomWithIdx(0)->getProp("bar",pval);
TEST_ASSERT(pval=="baz");
TEST_ASSERT(!mol->getAtomWithIdx(0)->hasProp("baz"));
delete mol;
sln = "H[I=2]-C(-H[I=2])(F)F";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==5);
TEST_ASSERT(mol->getAtomWithIdx(0)->getIsotope()==2);
TEST_ASSERT(mol->getAtomWithIdx(2)->getIsotope()==2);
delete mol;
sln = "C[*]H3";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNumExplicitHs()==3);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNumImplicitHs()==0);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNoImplicit());
TEST_ASSERT(mol->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
#if 1
// FIX: this should be accepted
delete mol;
sln = "CH[I=2]";
mol=RDKit::SLNToMol(sln);//,true,1);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==2);
#endif
// but this should not be accepted:
delete mol;
sln = "CH4[I=13]";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(!mol);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test4(){
RDKit::RWMol *mol;
std::string sln;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test4: hydrogen handling " << std::endl;
sln = "CH4";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNumExplicitHs()==4);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNumImplicitHs()==0);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNoImplicit());
delete mol;
sln = "C[-]H3";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNumExplicitHs()==3);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNumImplicitHs()==0);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNoImplicit());
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test5(){
std::string pval;
RDKit::RWMol *patt,*mol;
std::vector<RDKit::MatchVectType> mV;
std::string sln,smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test5: basic queries " << std::endl;
#if 1
sln = "C[charge=+1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(patt->getAtomWithIdx(0)->getNumExplicitHs()==0);
TEST_ASSERT(patt->getAtomWithIdx(0)->getNoImplicit());
TEST_ASSERT(patt->getAtomWithIdx(0)->getNumImplicitHs()==0);
smi = "C[CH2+](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete mol;
smi = "C[CH](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!RDKit::SubstructMatch(*mol,*patt,mV));
delete mol;
smi = "C[CH3+2](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!RDKit::SubstructMatch(*mol,*patt,mV));
delete mol;
smi = "C(=O)OC";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
delete patt;
sln = "AnyAny";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
delete patt;
sln = "Any-Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
delete patt;
sln = "Any=Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
sln = "Any#Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete patt;
sln = "Any:Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete patt;
sln = "Any~Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
delete patt;
sln = "C[charge=+1|charge=+2]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C[CH2+](C)[CH+2]";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
delete mol;
smi = "C[CH2+](C)[N+2]";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete mol;
smi = "C[N+](C)[CH+2]";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
sln = "C[charge=+1;HC=2]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C[CH2+](CC)[NH+]";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV[0][0].second==1);
delete patt;
sln = "Any[charge=+1;HC=2]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C[CH2+](CC)[NH+]";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV[0][0].second==1);
delete patt;
sln = "Any[charge=+1;!HC=2]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C[CH2+](CC)[NH+]";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV[0][0].second==4);
delete mol;
smi = "[H]CC[H]";
mol=RDKit::SmilesToMol(smi,0,false);
TEST_ASSERT(mol);
RDKit::MolOps::sanitizeMol(*mol);
TEST_ASSERT(mol->getNumAtoms()==4);
delete patt;
sln = "AnyAny";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
delete patt;
sln = "HevHev";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
sln = "AnyHev";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
delete patt;
delete mol;
smi = "FC(Cl)(Br)CI";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
RDKit::MolOps::sanitizeMol(*mol);
TEST_ASSERT(mol->getNumAtoms()==6);
sln = "HalC";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==4);
delete patt;
#endif
delete mol;
smi = "CO[2H]";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
RDKit::MolOps::sanitizeMol(*mol);
TEST_ASSERT(mol->getNumAtoms()==3);
sln = "H";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
sln = "H[i=1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete patt;
sln = "H[i=2]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
sln = "Het";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test6(){
std::string pval;
RDKit::RWMol *patt,*mol;
std::vector<RDKit::MatchVectType> mV;
std::string sln,smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test6: ring queries " << std::endl;
sln = "C[rbc=2]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(!patt->getAtomWithIdx(0)->hasProp("rbc"));
smi = "C1CC1";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
delete mol;
smi = "C1C2C1C2";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
delete mol;
smi = "CCC";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!RDKit::SubstructMatch(*mol,*patt,mV));
delete patt;
sln = "C[rbc=1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C1CC1";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!RDKit::SubstructMatch(*mol,*patt,mV));
delete mol;
smi = "CCC";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!RDKit::SubstructMatch(*mol,*patt,mV));
delete patt;
sln = "C[rbc=3]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C1CC1";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!RDKit::SubstructMatch(*mol,*patt,mV));
delete mol;
smi = "C1C2C1C2";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
// test case sensitivity, just because we should:
delete patt;
sln = "C[rBC=2]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(!patt->getAtomWithIdx(0)->hasProp("rbc"));
delete mol;
smi = "C1CC1C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
delete patt;
sln = "C[r]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C1CC1C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
delete patt;
sln = "C[1:rbc=f]CCC@1";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==4);
delete mol;
smi = "C1CCC1";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete mol;
smi = "C1CC2C1CC2";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
delete patt;
sln = "C[1:rbc=f]C[rbc=f]CC@1";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==4);
delete mol;
smi = "C1CCC1";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV));
delete mol;
smi = "C1CC2C1CC2";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
delete patt;
sln = "C[1:rbc=f]C[rbc=f]C[rbc=f]C@1";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==4);
delete mol;
smi = "C1CCC1";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete mol;
smi = "C1CC2C1CC2";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(!RDKit::SubstructMatch(*mol,*patt,mV));
delete patt;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test7(){
std::string pval;
RDKit::RWMol *patt,*mol;
std::vector<RDKit::MatchVectType> mV;
std::string sln,smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test7: qualified queries " << std::endl;
sln = "C[charge=+1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
smi = "C[CH2+](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
sln = "C[charge<1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C[CH2+](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
delete mol;
smi = "C[CH](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==4);
delete mol;
smi = "C[CH3+2](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
delete patt;
sln = "C[charge<=1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
smi = "C[CH2+](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==4);
delete mol;
smi = "C[CH](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==4);
delete mol;
smi = "C[CH3+2](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
delete patt;
sln = "C[charge>=1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
smi = "C[CH2+](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete mol;
smi = "C[CH](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete mol;
smi = "C[CH3+2](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
sln = "C[charge>1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
smi = "C[CH2+](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete mol;
smi = "C[CH](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete mol;
smi = "C[CH3+2](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
sln = "C[charge!=0]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
smi = "C[CH2+](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete mol;
smi = "C[CH](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete mol;
smi = "C[CH3+2](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
sln = "C[charge!=1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
smi = "C[CH2+](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
delete mol;
smi = "C[CH](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==4);
delete mol;
smi = "C[CH3+2](C)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==4);
delete patt;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test8(){
std::string pval;
RDKit::RWMol *patt,*mol;
std::vector<RDKit::MatchVectType> mV;
std::string sln,smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test8: more complex atom properties " << std::endl;
sln = "Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
smi = "C(=O)OC";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==4);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[1][0].second==1);
TEST_ASSERT(mV[2][0].second==2);
TEST_ASSERT(mV[3][0].second==3);
delete patt;
sln = "CO[F]C";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==3);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[0][1].second==2);
delete patt;
sln = "Any[TBO=4]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
// CHECK: should TBO really match both Cs here or only atom 3 (i.e. should it be degree or valence)?
TEST_ASSERT(mV.size()==2);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[1][0].second==3);
delete patt;
sln = "Any[TAC=2]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0][0].second==2);
delete patt;
sln = "Any[TAC>2]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV.size()==2);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[1][0].second==3);
delete patt;
sln = "Any[HC=1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0][0].second==0);
delete patt;
sln = "Any[HC=0]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV.size()==2);
TEST_ASSERT(mV[0][0].second==1);
TEST_ASSERT(mV[1][0].second==2);
delete patt;
sln = "Any[HC=F]H3";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0][0].second==3);
delete patt;
sln = "Any[HAC>1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV.size()==2);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[1][0].second==2);
delete patt;
sln = "Any[HAC=1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV.size()==2);
TEST_ASSERT(mV[0][0].second==1);
TEST_ASSERT(mV[1][0].second==3);
delete patt;
sln = "Any[HAC=F]~Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV.size()==2);
TEST_ASSERT(mV[0][0].second==1);
TEST_ASSERT(mV[1][0].second==3);
delete patt;
sln = "AnyAny[TAC=F]Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==3);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0][1].second==2);
delete mol;
smi = "CCC=C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete patt;
sln = "CC";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
delete patt;
sln = "CC[F]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete patt;
sln = "CC[F]H3";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
delete patt;
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test9(){
std::string pval;
RDKit::RWMol *patt,*mol;
std::vector<RDKit::MatchVectType> mV;
std::string sln,smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test9: recursive SLNs " << std::endl;
sln = "Any[is=Cl,Br,I]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
smi = "C(=O)Cl";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==2);
delete mol;
smi = "C(=O)Br";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==2);
delete mol;
smi = "C(=O)I";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==2);
delete mol;
smi = "C(=O)C";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete patt;
sln = "C[is=C=O]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C(=O)OC";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==0);
delete patt;
sln = "Any[is=C,O;charge=-1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C(=O)OC";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==0);
delete mol;
smi = "C(=O)[O-]";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==2);
delete patt;
// make sure we aren't case sensitive:
sln = "Any[Is=C,O;charge=-1]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "[C-](=O)O";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==0);
delete patt;
// check handling of 'not':
sln = "Any[not=N,O]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C(=O)OCN";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV.size()==2);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[1].size()==1);
TEST_ASSERT(mV[1][0].second==3);
delete patt;
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test10(){
std::string pval;
RDKit::RWMol *patt,*mol;
std::vector<RDKit::MatchVectType> mV;
std::string sln,smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test10: nested recursive SLNs " << std::endl;
// do recursions in the 'is':
sln = "Any[is=C[is=Any=O],O]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
smi = "C(=O)OC";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==3);
TEST_ASSERT(mV.size()==3);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[1].size()==1);
TEST_ASSERT(mV[1][0].second==1);
TEST_ASSERT(mV[2].size()==1);
TEST_ASSERT(mV[2][0].second==2);
// do recursions in the 'not':
delete patt;
sln = "Any[not=C[is=Any=O],O]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C(=O)OC";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==3);
delete patt;
// move the anchor:
sln = "C[is=C=O]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
delete mol;
smi = "C(=O)OC";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==0);
delete patt;
sln = "C[is=O=C*]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==0);
delete patt;
sln = "C[is=O=C]";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(!RDKit::SubstructMatch(*mol,*patt,mV));
delete patt;
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test11(){
std::string pval,cip;
RDKit::RWMol *mol;
std::vector<RDKit::MatchVectType> mV;
std::string sln,smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test11: chiral SLNs " << std::endl;
sln = "CH(Cl)(F)Br";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==RDKit::Atom::CHI_UNSPECIFIED);
delete mol;
sln = "C[s=N]H(Cl)(F)Br";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
std::cerr << sln << " -> " << MolToSmiles(*mol,true) << " " << mol->getNumAtoms() << std::endl;
smi = MolToSmiles(*mol,true);
//TEST_ASSERT(smi=="F[C@@H](Cl)Br");
delete mol;
sln = "ClC[s=i]H(F)Br";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
//mol->debugMol(std::cerr);
#if 0
RDKit::MolOps::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#endif
std::cerr << sln << " -> " << MolToSmiles(*mol,true) << " " << mol->getNumAtoms() << std::endl;
smi = MolToSmiles(*mol,true);
//TEST_ASSERT(smi=="F[C@@H](Cl)Br");
delete mol;
sln = "FC[s=N]H(Cl)Br";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
std::cerr << sln << " -> " << MolToSmiles(*mol,true) << " " << mol->getNumAtoms() << std::endl;
smi = MolToSmiles(*mol,true);
//TEST_ASSERT(smi=="F[C@@H](Cl)Br");
delete mol;
sln = "FC[s=N]H(Br)Cl";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
std::cerr << sln << " -> " << MolToSmiles(*mol,true) << " " << mol->getNumAtoms() << std::endl;
smi = MolToSmiles(*mol,true);
//TEST_ASSERT(smi=="F[C@H](Cl)Br");
delete mol;
sln = "HC[s=N](Cl)(F)Br";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
std::cerr << sln << " -> " << MolToSmiles(*mol,true) << " " << mol->getNumAtoms() << std::endl;
smi = MolToSmiles(*mol,true);
//TEST_ASSERT(smi=="F[C@@H](Cl)Br");
delete mol;
sln = "C[s=i]H(Cl)(F)Br";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
smi = MolToSmiles(*mol,true);
std::cerr << sln << " -> " << MolToSmiles(*mol,true) << " " << mol->getNumAtoms() << std::endl;
//TEST_ASSERT(smi=="F[C@H](Cl)Br");
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test12(){
RDKit::RWMol *patt,*mol;
std::vector<RDKit::MatchVectType> mV;
std::string sln,smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test12: bond queries and properties " << std::endl;
sln = "Any-Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
smi = "C=CN";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==2);
TEST_ASSERT(mV[0][0].second==1);
TEST_ASSERT(mV[0][1].second==2);
delete patt;
sln = "Any~Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV[0].size()==2);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[0][1].second==1);
TEST_ASSERT(mV[1].size()==2);
TEST_ASSERT(mV[1][0].second==1);
TEST_ASSERT(mV[1][1].second==2);
delete patt;
sln = "Any-=Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV[0].size()==2);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[0][1].second==1);
TEST_ASSERT(mV[1].size()==2);
TEST_ASSERT(mV[1][0].second==1);
TEST_ASSERT(mV[1][1].second==2);
delete patt;
sln = "Any=-Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV[0].size()==2);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[0][1].second==1);
TEST_ASSERT(mV[1].size()==2);
TEST_ASSERT(mV[1][0].second==1);
TEST_ASSERT(mV[1][1].second==2);
delete patt;
sln = "Any-:Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV[0].size()==2);
TEST_ASSERT(mV[0][0].second==1);
TEST_ASSERT(mV[0][1].second==2);
sln = "Any-[type=2]Any";
delete patt;
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV[0].size()==2);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[0][1].second==1);
delete patt;
sln = "Any-[type=2|type=1]Any";
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV[0].size()==2);
TEST_ASSERT(mV[0][0].second==0);
TEST_ASSERT(mV[0][1].second==1);
TEST_ASSERT(mV[1].size()==2);
TEST_ASSERT(mV[1][0].second==1);
TEST_ASSERT(mV[1][1].second==2);
sln = "O~[r]C";
delete patt;
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
delete mol;
smi = "O=CC1COC1";
mol=RDKit::SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==2);
TEST_ASSERT(mV[0].size()==2);
TEST_ASSERT(mV[0][0].second==4);
TEST_ASSERT(mV[1][0].second==4);
sln = "O~[!r]C";
delete patt;
patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==2);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV[0].size()==2);
TEST_ASSERT(mV[0][0].second==0);
delete mol;
delete patt;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test13(){
RDKit::RWMol *mol;
std::string sln;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test13: ring closure details " << std::endl;
sln = "C[1]H2CH2CH2CH2CH2CH2@1";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==6);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
TEST_ASSERT(mol->getRingInfo()->atomRings()[0].size()==6);
delete mol;
sln = "C[1]H2CH2(CH2CH2CH2CH2@1)";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==6);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
TEST_ASSERT(mol->getRingInfo()->atomRings()[0].size()==6);
delete mol;
sln = "CH2(C[1]H2)CH2(CH2CH2CH2@1)";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==6);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
TEST_ASSERT(mol->getRingInfo()->atomRings()[0].size()==6);
delete mol;
sln = "C[1]H2CH2CH2CH2C[2]HCH@1CH2CH2@2";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==8);
TEST_ASSERT(mol->getRingInfo()->numRings()==2);
TEST_ASSERT(mol->getRingInfo()->atomRings()[0].size()==6);
TEST_ASSERT(mol->getRingInfo()->atomRings()[1].size()==4);
delete mol;
sln = "C[1]H2(CH2(CH2(CH2(C[2]H(CH@1(CH2(CH2@2)))))))";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==8);
TEST_ASSERT(mol->getRingInfo()->numRings()==2);
TEST_ASSERT(mol->getRingInfo()->atomRings()[0].size()==6);
TEST_ASSERT(mol->getRingInfo()->atomRings()[1].size()==4);
delete mol;
sln = "C[1](CH2CH2CH(CH2CH2@1)CH2CH2@1)Cl";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==9);
TEST_ASSERT(mol->getRingInfo()->numRings()==3);
TEST_ASSERT(mol->getRingInfo()->atomRings()[0].size()==6);
TEST_ASSERT(mol->getRingInfo()->atomRings()[1].size()==6);
TEST_ASSERT(mol->getRingInfo()->atomRings()[2].size()==6);
delete mol;
sln = "CH2(CH2@1)CH2(C[1]H2)";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(!mol);
sln = "CH2(CH2@1)";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(!mol);
delete mol;
sln = "C[1]H-CH2-C(@1)=O";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(1,2)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,0)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,3)->getBondType()==RDKit::Bond::DOUBLE);
delete mol;
sln = "C[1]H-CH2-CH(@1)O";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(1,2)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,0)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,3)->getBondType()==RDKit::Bond::SINGLE);
delete mol;
sln = "C[1]H-CH2-C(=@1)O";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(1,2)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,0)->getBondType()==RDKit::Bond::DOUBLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,3)->getBondType()==RDKit::Bond::SINGLE);
delete mol;
sln = "C[1]H-CH2-C(O)=@1";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(1,2)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,0)->getBondType()==RDKit::Bond::DOUBLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,3)->getBondType()==RDKit::Bond::SINGLE);
delete mol;
sln = "C[1]H-CH2-C(O)(=@1)";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
TEST_ASSERT(mol->getRingInfo()->numRings()==1);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(1,2)->getBondType()==RDKit::Bond::SINGLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,0)->getBondType()==RDKit::Bond::DOUBLE);
TEST_ASSERT(mol->getBondBetweenAtoms(2,3)->getBondType()==RDKit::Bond::SINGLE);
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test14(){
RDKit::RWMol *mol;
std::string sln;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test14: error catching " << std::endl;
sln = "CH2(C@1H2)CH2(CH2CH2C[1]H2)";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(!mol);
sln = "CH2(CH2[1])CH2(CH2CH2CH2@1)";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(!mol);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test15(){
RDKit::RWMol *mol;
std::string sln;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test15: CTAB properties " << std::endl;
{
sln = "CH4<blah>";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("blah"));
delete mol;
}
{
sln = "CH4<name=methane>";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("_Name"));
std::string sval;
mol->getProp("_Name",sval);
TEST_ASSERT(sval=="methane");
delete mol;
}
{
sln = "CH4<blah;foo=\"1\">";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("blah"));
TEST_ASSERT(mol->hasProp("foo"));
std::string sval;
mol->getProp("foo",sval);
TEST_ASSERT(sval=="1");
delete mol;
}
{
sln = "CH4<blah;foo=1>";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("blah"));
TEST_ASSERT(mol->hasProp("foo"));
std::string sval;
mol->getProp("foo",sval);
TEST_ASSERT(sval=="1");
delete mol;
}
{
sln = "CH4<name=\"methane\";blah;coord2d=(1,0);too.small;test=lots and-lots of special,characters all at once.>";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("blah"));
std::string sval;
mol->getProp("_Name",sval);
TEST_ASSERT(sval=="methane");
mol->getProp("coord2d",sval);
TEST_ASSERT(sval=="(1,0)");
TEST_ASSERT(mol->hasProp("too.small"));
TEST_ASSERT(mol->hasProp("test"));
mol->getProp("test",sval);
TEST_ASSERT(sval=="lots and-lots of special,characters all at once.");
delete mol;
}
{
// Though it isn't part of the spec,
// sometimes we have multiple ctab property blocks:
sln = "CH4<foo=1><bar=2>";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("foo"));
TEST_ASSERT(mol->hasProp("bar"));
std::string sval;
mol->getProp("foo",sval);
TEST_ASSERT(sval=="1");
mol->getProp("bar",sval);
TEST_ASSERT(sval=="2");
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void test16(){
RDKit::RWMol *mol;
std::string sln;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test16: simple macro atoms " << std::endl;
{
sln = "CH3ZCH3{Z:O}";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==3);
TEST_ASSERT(mol->getAtomWithIdx(1)->getAtomicNum()==8);
delete mol;
}
{
sln = "CH3ZGCH3{Z:O}{G:N}";
mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==4);
TEST_ASSERT(mol->getAtomWithIdx(1)->getAtomicNum()==8);
TEST_ASSERT(mol->getAtomWithIdx(2)->getAtomicNum()==7);
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue278(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test issue278: handling of 'not' and 'is' queries on Any" << std::endl;
{
std::string sln = "Any[IS=C(=O)]";
RDKit::RWMol *mol=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasQuery());
delete mol;
}
{
std::string sln = "Any[NOT=C(=O)]";
RDKit::RWMol *mol=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasQuery());
delete mol;
}
{
std::string sln = "Any[IS=C(=O)]";
RDKit::RWMol *mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasQuery());
delete mol;
}
{
std::string sln = "Any[NOT=C(=O)]";
RDKit::RWMol *mol=RDKit::SLNToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasQuery());
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue277(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test issue277: parse error with & " << std::endl;
{
std::string sln = "Any[NOT=C,IS=O]";
RDKit::RWMol *mol=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasQuery());
delete mol;
}
{
std::string sln = "Any[NOT=C;IS=O]";
RDKit::RWMol *mol=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasQuery());
delete mol;
}
{
std::string sln = "Any[NOT=C&IS=O]";
RDKit::RWMol *mol=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasQuery());
delete mol;
}
{
std::string sln = "Any[NOT=C,N&IS=O,S]";
RDKit::RWMol *mol=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==1);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasQuery());
delete mol;
}
{
std::string sln = "Hev[!r;NOT=N]";
RDKit::RWMol *patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(patt->getAtomWithIdx(0)->hasQuery());
std::string smi = "CC1CC1N";
RDKit::RWMol *mol=RDKit::SmilesToMol(smi);
std::vector<RDKit::MatchVectType> mV;
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==0);
delete mol;
delete patt;
}
{
std::string sln = "Hev[!r&NOT=N]";
RDKit::RWMol *patt=RDKit::SLNQueryToMol(sln);
TEST_ASSERT(patt);
TEST_ASSERT(patt->getNumAtoms()==1);
TEST_ASSERT(patt->getAtomWithIdx(0)->hasQuery());
std::string smi = "CC1CC1N";
RDKit::RWMol *mol=RDKit::SmilesToMol(smi);
std::vector<RDKit::MatchVectType> mV;
TEST_ASSERT(mol);
TEST_ASSERT(RDKit::SubstructMatch(*mol,*patt,mV)==1);
TEST_ASSERT(mV.size()==1);
TEST_ASSERT(mV[0].size()==1);
TEST_ASSERT(mV[0][0].second==0);
delete mol;
delete patt;
}
{
// examples from Pat Walters, taken from http://pubs.acs.org/doi/abs/10.1021/ci300461a
std::string slns[]={
"HetC(=O)O-[!R]C[8]:Hev(Any[NOT=O,S[TAC=2],C[TAC=4],N[TAC=3]]):Hev:Hev(Any[IS=Hal,C#N,C(F)(F)F,S(=O)=O,C(=O)&NOT=C(=O)OH]):Hev:Hev(Any[NOT=O,S[TAC=2],C[TAC=4],N[TAC=3]]):@8",
"HetC(=O)O-[!R]C[8]:Hev(Any[IS=Hal,C#N,C(F)(F)F,S(=O)=O,C(=O)&NOT=C(=O)OH]):Hev:Hev(Any[NOT=O,S[TAC=2],C[TAC=4],N[TAC=3]]):Hev:Hev(Any[NOT=O,S[TAC=2],C[TAC=4],N[TAC=3]]):@8",
"CCH=[!R]C(Any[IS=H,C])Any[IS=C#N,C(=O)&NOT=C(=O)Any[IS=N,O]]",
"Any[IS=C,O]CH=[!R]C(Any[IS=C(=O),S(=O),C#N,Hal,C(Hal)(Hal)Hal&NOT=C(=O)OH])Any[IS=C(=O),S(=O),C#N&NOT=C(=O)OH]",
"C[1](C(=O)OC[5]:C:C:C:C:C:@5CH=@1)Any[IS=C(=O),C(=S),S(=O),C#N,Hal,C(Hal)(Hal)Hal&NOT=C(=O)OH]",
"C[1](=CHOC[5]:C:C:C:C:C:@5C@1=O)Any[IS=C(=O),C(=S),S(=O),C#N,Hal,C(Hal)(Hal)Hal&NOT=C(=O)OH]",
"C[1]:N:Any(Any[IS=Hal,S(=O)(=O)C]):Any:Any(Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):Any:@1",
"C[1]:N:Any(Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):Any:Any(Any[IS=Hal,S(=O)(=O)C]):Any:@1",
"C[1]:N:Any(Any[IS=Hal,S(=O)(=O)C]):Any(Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):Any:Any:@1",
"C[1]:N:Any(Any[IS=Hal,S(=O)(=O)C]):Any:Any:Any(Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):@1",
"C[1](Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):N:Any(Any[IS=Hal,S(=O)(=O)C]):Any(Any[NOT=N]):Any(Any[NOT=N]):Any:@1",
"C[1]:N:Any:Any(Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):Any(Any[IS=Hal,S(=O)(=O)C]):Any:@1",
"C[1](Any[NOT=N,O]):C(Any[IS=Hal,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):C(Any[IS=Hal,S(=O)(=O)C,C[r](=O)NC]):C(Any[NOT=N,O]):C(Any[NOT=N,O]):C(Any[IS=Hal,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):@1",
"C[1](Any[IS=Hal,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):C(Any[IS=Hal,S(=O)(=O)C,C[r](=O)NC]):C(Any[IS=Hal,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):C(Any[NOT=N,O]):C(Any[NOT=N,O]):C(Any[NOT=N,O]):@1",
"N(Any[IS=H,C[TAC=4]&NOT=C[TAC=4]-[R]C[TAC=4]N])(Any[IS=H,C[TAC=4]&NOT=C[TAC=4]-[R]C[TAC=4]N])(Any[IS=H,C[TAC=4]&NOT=C[TAC=4]-[R]C[TAC=4]N])<max=1>",
"Any[IS=H,C&NOT=C=O]N[!r](Any[IS=H,C&NOT=C=O])C(=O)C<max=2>",
"Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]",
"Hev[!r&NOT=C=O,S(=O)(=O),N*S(=O),N*(C=O)]Hev[!r&NOT=C=O,S(=O)(=O),N*S(=O),N*(C=O)]Hev[!r&NOT=C=O,S(=O)(=O),N*S(=O),N*(C=O)]Hev[!r&NOT=C=O,S(=O)(=O),N*S(=O),N*(C=O)]Hev[!r&NOT=C=O,S(=O)(=O)]Any[IS=CH3,OH,NH2,N(CH3)CH3]",
"EOF"
};
unsigned int i=0;
while(slns[i]!="EOF"){
RDKit::RWMol *mol=RDKit::SLNQueryToMol(slns[i++]);
TEST_ASSERT(mol);
}
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
int
main(int argc, char *argv[])
{
RDLog::InitLogs();
// FIX: need a test for handling Hs in the SLN itself. This should be done for
// both normal and query SLNs and must be done after the SLN parser handles
// that case (errr, duh)
#if 1
test1();
test2();
test3();
test4();
test5();
test6();
test7();
test8();
test9();
test10();
//test11();
test12();
test13();
test14();
test15();
test16();
#endif
testIssue277();
testIssue278();
}
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