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// $Id: test1.cpp 1897 2011-12-23 06:17:39Z glandrum $
//
// Created by Greg Landrum, July 2008
//
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/Invariant.h>
#include <DataStructs/ExplicitBitVect.h>
#include "AvalonTools.h"
#include <string>
using namespace RDKit;
void test1(){
BOOST_LOG(rdInfoLog) << "testing canonical smiles generation" << std::endl;
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ccccc1"));
TEST_ASSERT(m);
std::string smi=AvalonTools::getCanonSmiles(*m);
TEST_ASSERT(smi=="c1ccccc1");
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1cccnc1"));
TEST_ASSERT(m);
std::string smi=AvalonTools::getCanonSmiles(*m);
TEST_ASSERT(smi=="c1ccncc1");
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("n1ccccc1"));
TEST_ASSERT(m);
std::string smi=AvalonTools::getCanonSmiles(*m);
TEST_ASSERT(smi=="c1ccncc1");
delete m;
}
{
std::string smi=AvalonTools::getCanonSmiles("n1ccccc1",true);
TEST_ASSERT(smi=="c1ccncc1");
}
{
std::string smi=AvalonTools::getCanonSmiles("c1cccnc1",true);
TEST_ASSERT(smi=="c1ccncc1");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test2(){
BOOST_LOG(rdInfoLog) << "testing coordinate generation" << std::endl;
#if 0
{
RWMol *m = SmilesToMol("c1cccnc1");
TEST_ASSERT(m);
unsigned int confId=AvalonTools::set2DCoords(*m);
TEST_ASSERT(m->getNumConformers()==1);
TEST_ASSERT(confId==0);
delete m;
}
#endif
{
std::string molb = AvalonTools::set2DCoords("c1cccnc1",true);
TEST_ASSERT(molb!="");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test3(){
BOOST_LOG(rdInfoLog) << "testing fingerprint generation" << std::endl;
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ccccn1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m,bv,512,false,true,0x00006FFF);
BOOST_LOG(rdInfoLog) << "c1ccccn1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==19);
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ccccc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m,bv,512,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1ccccn1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==6);
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1nnccc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m,bv,512,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1nnccc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==27);
delete m;
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1ncncc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP(*m,bv,512,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1ncncc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==27);
delete m;
}
{
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP("c1cccnc1",true,bv,512,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1cccnc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==19);
}
{
ExplicitBitVect bv(512);
AvalonTools::getAvalonFP("c1ccccc1",true,bv,512,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1ccccc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==6);
}
{
ROMol *m = static_cast<ROMol *>(SmilesToMol("c1cccnc1"));
TEST_ASSERT(m);
ExplicitBitVect bv(1024);
AvalonTools::getAvalonFP(*m,bv,1024,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1cccnc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==20);
delete m;
}
{
ExplicitBitVect bv(2048);
AvalonTools::getAvalonFP("c1cocc1",true,bv,2048,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "c1cocc1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==48);
}
{
ExplicitBitVect bv(2048);
AvalonTools::getAvalonFP("C1=COC=C1",true,bv,2048,false,true,0x006FFF);
BOOST_LOG(rdInfoLog) << "C1=COC=C1 " << bv.getNumOnBits() << std::endl;
TEST_ASSERT(bv.getNumOnBits()==48);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testRDK151(){
BOOST_LOG(rdInfoLog) << "testing Jira issue RDK-151: pyAvalonTools not generating chiral smiles from molecules" << std::endl;
{
std::string tSmi="C[C@H](F)Cl";
ROMol *m = static_cast<ROMol *>(SmilesToMol(tSmi));
TEST_ASSERT(m);
std::string smi=AvalonTools::getCanonSmiles(tSmi,true);
CHECK_INVARIANT(smi==tSmi,smi+"!="+tSmi);
smi=AvalonTools::getCanonSmiles(*m);
CHECK_INVARIANT(smi==tSmi,smi+"!="+tSmi);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testSmilesFailures(){
BOOST_LOG(rdInfoLog) << "testing handling of bad smiles strings" << std::endl;
{
std::string tSmi="C1C";
std::string smi=AvalonTools::getCanonSmiles(tSmi,true);
CHECK_INVARIANT(smi=="",smi);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testSubstructFps(){
BOOST_LOG(rdInfoLog) << "testing substructure fingerprints " << std::endl;
{
ExplicitBitVect bv1(512),bv2(512);
AvalonTools::getAvalonFP("c1ccccc1",true,bv1,512,true,true,AvalonTools::avalonSSSBits);
AvalonTools::getAvalonFP("c1ccccc1C(F)(F)F",true,bv2,512);
TEST_ASSERT((bv1&bv2)==bv1);
AvalonTools::getAvalonFP("c1ccccc1C(F)(F)F",true,bv1,512);
TEST_ASSERT((bv1&bv2)==bv1);
AvalonTools::getAvalonFP("c1cccc(C)c1C(F)(F)F",true,bv2,512);
TEST_ASSERT((bv1&bv2)==bv1);
}
{
ExplicitBitVect bv1(512),bv2(512);
AvalonTools::getAvalonFP("c1ccccc1O",true,bv1,512,true,true,AvalonTools::avalonSSSBits);
AvalonTools::getAvalonFP("c1ccccc1OC",true,bv2,512);
TEST_ASSERT((bv1&bv2)==bv1);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testStruChk(){
BOOST_LOG(rdInfoLog) << "testing structure checking " << std::endl;
{
int errs = 0;
RDKit::ROMOL_SPTR m = AvalonTools::checkMol(errs, "c1ccccc1",true);
TEST_ASSERT(errs==0);
m = AvalonTools::checkMol(errs, "c1c(R)cccc1C1(CC-C(C)C1)C",true);
TEST_ASSERT(errs!=0);
}
{
int errs = 0;
std::string res;
boost::tie(res,errs)=AvalonTools::checkMolString("c1ccccc1",true);
TEST_ASSERT(errs==0);
TEST_ASSERT(res!="");
boost::tie(res,errs)=AvalonTools::checkMolString("c1c(R)cccc1C1(CC-C(C)C1)C",true);
TEST_ASSERT(errs==1);
TEST_ASSERT(res=="");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBadMolfile() {
BOOST_LOG(rdInfoLog) << "testing handling bad molecules " << std::endl;
// some tests around dealing with bad mol blocks
{
std::string molb="SNAP007157A\n\
MACCS-II3194121345\n\
\n\
0 0 0 0 0";
std::string smi=AvalonTools::getCanonSmiles(molb,false);
CHECK_INVARIANT(smi=="",smi);
ExplicitBitVect bv(1024);
AvalonTools::getAvalonFP(molb,false,bv,1024);
TEST_ASSERT(bv.getNumOnBits()==0);
std::string oMolb;
AvalonTools::set2DCoords(molb,false);
CHECK_INVARIANT(oMolb=="",oMolb);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
int main(int argc,char *argv[]){
RDLog::InitLogs();
test1();
test2();
test3();
testRDK151();
testSmilesFailures();
testSubstructFps();
testStruChk();
testBadMolfile();
return 0;
}
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