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rdkit/Code/GraphMol/testPickler.cpp
Greg Landrum ed84596422 fix and test issue 285
2013-02-01 04:12:41 +00:00

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// $Id$
//
// Copyright (C) 2004-2011 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDGeneral/RDLog.h>
#include <stdlib.h>
#include <ctime>
#include <iostream>
#include <fstream>
#include <boost/algorithm/string.hpp>
using namespace RDKit;
void test1(bool doLong=0){
std::string fName = getenv("RDBASE");
fName += "/Code/GraphMol/test_data/canonSmiles.smi";
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing String Pickle Roundtrips." << std::endl;
SmilesMolSupplier suppl(fName,"\t",0,1,false);
int count = 0;
while(!suppl.atEnd()){
ROMol *m = suppl.next();
TEST_ASSERT(m);
std::string pickle;
MolPickler::pickleMol(*m,pickle);
TEST_ASSERT(pickle.size());
ROMol m2;
MolPickler::molFromPickle(pickle,m2);
std::string smi1=MolToSmiles(*m);
//BOOST_LOG(rdInfoLog) << smi << " " << smi1 << std::endl;
std::string smi2=MolToSmiles(m2);
if(smi1!=smi2){
BOOST_LOG(rdInfoLog) << "Line: " << count << "\n " << smi1 << "\n != \n " << smi2 << std::endl;
}
TEST_ASSERT(smi1==smi2);
delete m;
count++;
if(!doLong && count >= 100) break;
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void _createPickleFile(){
std::string smiName = getenv("RDBASE");
smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
std::string pklName = getenv("RDBASE");
#ifdef OLD_PICKLE
pklName += "/Code/GraphMol/test_data/canonSmiles.v1.pkl";
#else
pklName += "/Code/GraphMol/test_data/canonSmiles.v2.pkl";
#endif
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "creating pickle file." << std::endl;
SmilesMolSupplier suppl(smiName,"\t",0,1,false);
std::ofstream outStream(pklName.c_str(),std::ios_base::binary);
int count = 0;
while(!suppl.atEnd()){
ROMol *m = suppl.next();
TEST_ASSERT(m);
std::string pickle;
MolPickler::pickleMol(*m,outStream);
delete m;
count++;
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void test2(bool doLong=0){
std::string smiName = getenv("RDBASE");
smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
std::string pklName = getenv("RDBASE");
pklName += "/Code/GraphMol/test_data/canonSmiles.v1.pkl";
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing reading existing pickle file (v1)." << std::endl;
SmilesMolSupplier suppl(smiName,"\t",0,1,false);
std::ifstream inStream(pklName.c_str(),std::ios_base::binary);
int count = 0;
while(!suppl.atEnd()){
ROMol *m1 = suppl.next();
TEST_ASSERT(m1);
ROMol m2;
MolPickler::molFromPickle(inStream,m2);
std::string smi1=MolToSmiles(*m1);
std::string smi2=MolToSmiles(m2);
if(smi1!=smi2){
BOOST_LOG(rdInfoLog) << "Line: " << count << "\n " << smi1 << "\n != \n " << smi2 << std::endl;
}
TEST_ASSERT(smi1==smi2);
delete m1;
count++;
if(!doLong && count >= 100) break;
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void test3(bool doLong=0){
std::string smiName = getenv("RDBASE");
smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
std::string pklName = getenv("RDBASE");
pklName += "/Code/GraphMol/test_data/canonSmiles.v2.pkl";
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing reading existing pickle file (v2)." << std::endl;
SmilesMolSupplier suppl(smiName,"\t",0,1,false);
std::ifstream inStream(pklName.c_str(),std::ios_base::binary);
int count = 0;
while(!suppl.atEnd()){
ROMol *m1 = suppl.next();
TEST_ASSERT(m1);
ROMol m2;
MolPickler::molFromPickle(inStream,m2);
std::string smi1=MolToSmiles(*m1,1);
std::string smi2=MolToSmiles(m2,1);
if(smi1!=smi2){
BOOST_LOG(rdInfoLog) << "Line: " << count << "\n " << smi1 << "\n != \n " << smi2 << std::endl;
}
TEST_ASSERT(smi1==smi2);
delete m1;
count++;
if(!doLong && count >= 100) break;
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void timeTest(bool doLong=0){
time_t t1,t2;
std::string smiName = getenv("RDBASE");
smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
std::string pklName = getenv("RDBASE");
pklName += "/Code/GraphMol/test_data/canonSmiles.v2.pkl";
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Timing reads." << std::endl;
t1 = std::time(0);
SmilesMolSupplier suppl(smiName,"\t",0,1,false);
int count = 0;
while(!suppl.atEnd()){
ROMol *m1 = suppl.next();
TEST_ASSERT(m1);
count++;
if(!doLong && count >= 100) break;
delete m1;
}
t2 = std::time(0);
BOOST_LOG(rdInfoLog) << " Smiles time: " << std::difftime(t2,t1) << std::endl;;
std::ifstream inStream(pklName.c_str(),std::ios_base::binary);
t1 = std::time(0);
while(count>0){
ROMol m2;
MolPickler::molFromPickle(inStream,m2);
count--;
if(!doLong && count >= 100) break;
}
t2 = std::time(0);
BOOST_LOG(rdInfoLog) << " Pickle time: " << std::difftime(t2,t1) << std::endl;;
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void test4(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing combining molecules using pickles." << std::endl;
ROMol *m1 = SmilesToMol("C1CC1");
TEST_ASSERT(m1);
ROMol *m2 = SmilesToMol("C1COC1");
TEST_ASSERT(m2);
ROMol m3;
std::string pickle;
MolPickler::pickleMol(*m1,pickle);
MolPickler::molFromPickle(pickle,m3);
MolPickler::pickleMol(*m2,pickle);
MolPickler::molFromPickle(pickle,m3);
m3.debugMol(std::cout);
TEST_ASSERT(m3.getNumAtoms()==7);
TEST_ASSERT(m3.getNumBonds()==7);
TEST_ASSERT(m3.getRingInfo()->numRings()==2);
TEST_ASSERT(m3.getRingInfo()->isAtomInRingOfSize(0,3));
TEST_ASSERT(!m3.getRingInfo()->isAtomInRingOfSize(0,4));
TEST_ASSERT(!m3.getRingInfo()->isAtomInRingOfSize(4,3));
TEST_ASSERT(m3.getRingInfo()->isAtomInRingOfSize(4,4));
TEST_ASSERT(m3.getRingInfo()->isBondInRingOfSize(0,3));
TEST_ASSERT(!m3.getRingInfo()->isBondInRingOfSize(0,4));
TEST_ASSERT(!m3.getRingInfo()->isBondInRingOfSize(4,3));
TEST_ASSERT(m3.getRingInfo()->isBondInRingOfSize(4,4));
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testIssue164(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Issue164: Roundtrip Pickle Failure." << std::endl;
std::string smi="NCCCCC(NC(C(C(C)C)NC(=O)C1CCCN1C(C(N)CCCNC(=N)N)=O)=O)C(NC(C(C)C)C(NC(Cc2ccc(O)cc2)C(=O)N6C(C(NC(CC(N)=O)C(NCC(NC(C)C(NC(CCC(O)=O)C(NC(CC(O)=O)C(NC(C(NC(CO)C(NC(C)C(NC(CCC(O)=O)C(NC(C)C(NC(Cc3ccccc3)C(=O)N5C(C(NC(CC(C)C)C(NC(C(NC(C(O)=O)Cc4ccccc4)=O)CCC(O)=O)=O)=O)CCC5)=O)=O)=O)=O)=O)CCC(O)=O)=O)=O)=O)=O)=O)=O)CCC6)=O)=O";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
std::string pickle;
ROMol m2;
MolPickler::pickleMol(*m1,pickle);
MolPickler::molFromPickle(pickle,m2);
TEST_ASSERT(m1->getNumAtoms()==m2.getNumAtoms());
// the issue had to do with number of atoms, so let's make an enormous
// molecule and try again:
RWMol *m3 = static_cast<RWMol *>(SmilesToMol(smi));
m3->insertMol(*m1);
m3->insertMol(*m1);
MolOps::sanitizeMol(*m3);
MolPickler::pickleMol(*m3,pickle);
ROMol m4;
MolPickler::molFromPickle(pickle,m4);
TEST_ASSERT(m3->getNumAtoms()==m4.getNumAtoms());
TEST_ASSERT(m3->getNumBonds()==m4.getNumBonds());
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testIssue219(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Issue219: Pickle Failure with Conformations." << std::endl;
std::string smi="CC";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
std::string pickle;
ROMol *m2;
MolPickler::pickleMol(*m1,pickle);
m2 = new ROMol();
MolPickler::molFromPickle(pickle,*m2);
TEST_ASSERT(m1->getNumAtoms()==m2->getNumAtoms());
Conformer *conf = new Conformer(2);
conf->setId(23);
m1->addConformer(conf);
MolPickler::pickleMol(*m1,pickle);
delete m2;
m2 = new ROMol();
MolPickler::molFromPickle(pickle,*m2);
TEST_ASSERT(m1->getNumAtoms()==m2->getNumAtoms());
TEST_ASSERT(m2->getConformer().getId()==23);
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testIssue220(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Issue220: Pickle problems with bond stereochemistry." << std::endl;
std::string smi="N/N=C/C";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondWithIdx(1)->getStereo()!=Bond::STEREONONE);
std::string pickle;
ROMol *m2;
MolPickler::pickleMol(*m1,pickle);
m2 = new ROMol();
MolPickler::molFromPickle(pickle,*m2);
TEST_ASSERT(m1->getNumAtoms()==m2->getNumAtoms());
TEST_ASSERT(m1->getNumBonds()==m2->getNumBonds());
TEST_ASSERT(m2->getBondWithIdx(1)->getStereo()!=Bond::STEREONONE);
for(unsigned int i=0;i<m1->getNumBonds();++i){
TEST_ASSERT(m1->getBondWithIdx(i)->getStereo() ==
m2->getBondWithIdx(i)->getStereo());
TEST_ASSERT(m1->getBondWithIdx(i)->getStereoAtoms() ==
m2->getBondWithIdx(i)->getStereoAtoms());
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testQueries(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing query serialization." << std::endl;
std::string smi,pickle,smi2;
int tmpInt;
ROMol *m1,*m2;
MatchVectType matchV;
// start simple : atom map numbers
smi="C";
m1= SmilesToMol(smi);
TEST_ASSERT(m1);
m1->getAtomWithIdx(0)->setProp("molAtomMapNumber",1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==1);
TEST_ASSERT(m1->getAtomWithIdx(0)->hasProp("molAtomMapNumber"));
m1->getAtomWithIdx(0)->getProp("molAtomMapNumber",tmpInt);
TEST_ASSERT(tmpInt==1);
delete m1;
// now a basic query:
smi="C";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==1);
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomAnd");
// query should be for aliphatic C:
smi="C";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="O";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="c1ccccc1";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m1;
// atom lists:
smi="[C,N,O]";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==1);
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomOr");
smi="C";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="O";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="N";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="F";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="c1nocc1";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(1)));
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(2)));
delete m1;
// more complex atom queries:
smi="[C&D2,N&D1]";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==1);
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomOr");
smi="C";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="CC";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="C(C)C";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="C(C)(C)C";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="N";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="NC";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="N(C)C";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
// basic recursive queries:
smi="[$([#6])]";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==1);
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="RecursiveStructure");
smi="C";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="N";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="c1ccccc1";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
delete m1;
smi="[R2]";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==1);
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomInNRings");
smi="C1CCC1";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
delete m2;
smi="C12(CCC2)CCC1";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(1)));
delete m2;
// basic bond queries:
smi="[#6][#6]";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==2);
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getAtomWithIdx(1)->hasQuery());
TEST_ASSERT(m1->getBondWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getBondWithIdx(0)->getQuery()->getDescription()=="BondOr");
smi="CC";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="C=C";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="CN";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="c1ccccc1";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="[#6]-[#6]";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==2);
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getAtomWithIdx(1)->hasQuery());
TEST_ASSERT(m1->getBondWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getBondWithIdx(0)->getQuery()->getDescription()=="BondOrder");
smi="CC";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="C=C";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="CN";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="c1ccccc1";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="C=C";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==2);
smi=MolToSmarts(*m1);
TEST_ASSERT(smi=="C=C");
smi="C=[$(C=O)]";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==2);
smi=MolToSmarts(*m1);
BOOST_LOG(rdErrorLog)<<smi<<std::endl;
TEST_ASSERT(smi=="C=[$(C=O)]");
smi="S(=O)(=O)-[C;H2]([F,Br,I,Cl])";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
smi=MolToSmarts(*m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
smi2=MolToSmarts(*m1);
BOOST_LOG(rdErrorLog)<<smi<<" "<<smi2<<std::endl;
TEST_ASSERT(smi==smi2);
// more complex recursive queries:
smi="[$(C)]";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==1);
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="RecursiveStructure");
smi="C";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="N";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="c1ccccc1";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
delete m1;
// more complex recursive queries:
smi="[$(C=O);$(C-N)]";
m1= SmartsToMol(smi);
TEST_ASSERT(m1);
MolPickler::pickleMol(*m1,pickle);
delete m1;
m1 = new ROMol();
MolPickler::molFromPickle(pickle,*m1);
TEST_ASSERT(m1->getNumAtoms()==1);
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomAnd");
smi="NCO";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
delete m2;
smi="CNC(=O)";
m2= SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
delete m2;
delete m1;
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testRadicals(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing radical handling in pickles." << std::endl;
std::string smi="C[CH]C";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getAtomWithIdx(1)->getNumRadicalElectrons()==1);
std::string pickle;
ROMol *m2;
MolPickler::pickleMol(*m1,pickle);
m2 = new ROMol();
MolPickler::molFromPickle(pickle,*m2);
TEST_ASSERT(m1->getNumAtoms()==m2->getNumAtoms());
TEST_ASSERT(m1->getNumBonds()==m2->getNumBonds());
TEST_ASSERT(m2->getAtomWithIdx(1)->getNumRadicalElectrons()==1);
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testIssue2788233(bool doLong=0){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 2788233." << std::endl;
{
std::string fName = getenv("RDBASE");
fName += "/Code/GraphMol/test_data/Issue2788233.mol";
RWMol *m=MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==2);
TEST_ASSERT(m->getNumBonds()==0);
std::string pickle;
MolPickler::pickleMol(*m,pickle);
RWMol *m2 = new RWMol();
MolPickler::molFromPickle(pickle,*m2);
TEST_ASSERT(m2->getNumAtoms()==2);
TEST_ASSERT(m2->getNumBonds()==0);
delete m;
delete m2;
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testIssue3202580(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 3202580." << std::endl;
{
ROMol *m1 = SmilesToMol("C");
TEST_ASSERT(m1);
TEST_ASSERT(feq(m1->getAtomWithIdx(0)->getMass(),12.011,.001));
std::string pickle;
MolPickler::pickleMol(*m1,pickle);
RWMol *m2 = new RWMol();
MolPickler::molFromPickle(pickle,*m2);
TEST_ASSERT(feq(m2->getAtomWithIdx(0)->getMass(),12.011,.001));
delete m1;
delete m2;
}
{
ROMol *m1 = SmilesToMol("[12CH4]");
TEST_ASSERT(m1);
TEST_ASSERT(feq(m1->getAtomWithIdx(0)->getMass(),12.000,.001));
std::string pickle;
MolPickler::pickleMol(*m1,pickle);
RWMol *m2 = new RWMol();
MolPickler::molFromPickle(pickle,*m2);
TEST_ASSERT(feq(m2->getAtomWithIdx(0)->getMass(),12.000,.001));
delete m1;
delete m2;
}
{
ROMol *m1 = SmilesToMol("[13CH4]");
TEST_ASSERT(m1);
TEST_ASSERT(m1->getAtomWithIdx(0)->getIsotope()==13);
std::cerr<<" mass! "<<m1->getAtomWithIdx(0)->getMass()<<std::endl;
TEST_ASSERT(feq(m1->getAtomWithIdx(0)->getMass(),13.003,.001));
std::string pickle;
MolPickler::pickleMol(*m1,pickle);
RWMol *m2 = new RWMol();
MolPickler::molFromPickle(pickle,*m2);
TEST_ASSERT(feq(m2->getAtomWithIdx(0)->getMass(),13.003,.001));
delete m1;
delete m2;
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testIssue3316407(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 3316407." << std::endl;
{
std::string fName = getenv("RDBASE");
fName += "/Code/GraphMol/FileParsers/test_data/rgroups1.mol";
RWMol *m=MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
std::string pickle;
MolPickler::pickleMol(*m,pickle);
RWMol *m2 = new RWMol();
MolPickler::molFromPickle(pickle,*m2);
TEST_ASSERT(m2->getNumAtoms()==5);
for(unsigned int i=0;i<m->getNumAtoms();++i){
TEST_ASSERT(m->getAtomWithIdx(i)->getExplicitValence()==m2->getAtomWithIdx(i)->getExplicitValence());
TEST_ASSERT(m->getAtomWithIdx(i)->getImplicitValence()==m2->getAtomWithIdx(i)->getImplicitValence());
}
// part of sf.net issue 285:
TEST_ASSERT(m2->getAtomWithIdx(3)->hasProp("dummyLabel"));
TEST_ASSERT(m2->getAtomWithIdx(4)->hasProp("dummyLabel"));
delete m;
delete m2;
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testIssue3496759(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 3496759." << std::endl;
{
ROMol *m1 = SmartsToMol("c1ncncn1");
TEST_ASSERT(m1);
std::string smi1=MolToSmiles(*m1,1);
TEST_ASSERT(smi1=="c1ncncn1");
std::string pickle;
MolPickler::pickleMol(*m1,pickle);
RWMol *m2 = new RWMol(pickle);
TEST_ASSERT(m2);
std::string smi2=MolToSmiles(*m2,1);
TEST_ASSERT(smi2=="c1ncncn1");
delete m1;
delete m2;
}
{
std::string fName = getenv("RDBASE");
fName += "/Data/SmartsLib/RLewis_smarts.txt";
std::ifstream inf(fName.c_str());
while(!inf.eof()){
std::string inl;
std::getline(inf,inl);
if(inl[0]=='#'||inl.size()<2) continue;
std::vector<std::string> tokens;
boost::split(tokens,inl,boost::is_any_of(" \t"));
//std::cerr<<"smarts: "<<tokens[0]<<std::endl;
ROMol *m1 = SmartsToMol(tokens[0]);
TEST_ASSERT(m1);
std::string smi1=MolToSmiles(*m1,1);
std::string sma1=MolToSmarts(*m1);
std::string pickle;
MolPickler::pickleMol(*m1,pickle);
RWMol *m2 = new RWMol(pickle);
TEST_ASSERT(m2);
std::string smi2=MolToSmiles(*m2,1);
std::string sma2=MolToSmarts(*m2);
//std::cerr<<"smi match: "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
//std::cerr<<"sma match: "<<sma1<<" "<<sma2<<std::endl;
TEST_ASSERT(sma1==sma2);
delete m1;
delete m2;
}
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testIssue280(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 280." << std::endl;
{
ROMol *m1 = SmilesToMol("CCC");
TEST_ASSERT(m1);
std::string v="1";
m1->getAtomWithIdx(0)->setProp("molAtomMapNumber",v);
// ints still work
m1->getAtomWithIdx(1)->setProp("molAtomMapNumber",2);
std::string pickle;
MolPickler::pickleMol(*m1,pickle);
RWMol *m2 = new RWMol(pickle);
TEST_ASSERT(m2);
TEST_ASSERT(m2->getAtomWithIdx(0)->hasProp("molAtomMapNumber"));
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("molAtomMapNumber"));
int iv;
m2->getAtomWithIdx(0)->getProp("molAtomMapNumber",iv);
TEST_ASSERT(iv==1);
m2->getAtomWithIdx(1)->getProp("molAtomMapNumber",iv);
TEST_ASSERT(iv==2);
delete m1;
delete m2;
}
{ // but bogus values are not propagated:
ROMol *m1 = SmilesToMol("CC");
TEST_ASSERT(m1);
std::string v="foo";
m1->getAtomWithIdx(0)->setProp("molAtomMapNumber",v);
std::string pickle;
MolPickler::pickleMol(*m1,pickle);
RWMol *m2 = new RWMol(pickle);
TEST_ASSERT(m2);
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp("molAtomMapNumber"));
delete m1;
delete m2;
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
void testIssue285(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 285." << std::endl;
{
ROMol *m1 = SmilesToMol("*C");
TEST_ASSERT(m1);
std::string v="R";
m1->getAtomWithIdx(0)->setProp("dummyLabel",v);
std::string pickle;
MolPickler::pickleMol(*m1,pickle);
RWMol *m2 = new RWMol(pickle);
TEST_ASSERT(m2);
TEST_ASSERT(m2->getAtomWithIdx(0)->hasProp("dummyLabel"));
m2->getAtomWithIdx(0)->getProp("dummyLabel",v);
TEST_ASSERT(v=="R");
delete m1;
delete m2;
}
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
}
int main(int argc, char *argv[]) {
RDLog::InitLogs();
bool doLong=false;
if(argc>1) {
if(!strncmp(argv[1],"-l",2)){
doLong=true;
}
}
//_createPickleFile();
#if 1
test1(doLong);
//test2(doLong);
test3(doLong);
test4();
testIssue164();
testIssue219();
testIssue220();
//timeTest(doLong);
testQueries();
testRadicals();
#endif
testIssue2788233();
testIssue3202580();
testIssue3316407();
testIssue3496759();
testIssue280();
testIssue285();
return 0;
}
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