pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-06 22:39:55 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
61b05af6fcb9c8d7e3b580f74b4e1585cdab5697
rdkit/Code/GraphMol/FileParsers/test1.cpp
Greg Landrum 61b05af6fc Modify suppliers and parsers so that they don't throw 
exceptions into python when reading a bad molecule. (Feature
request 1932875)

Modify constructors for both suppliers and parsers so that 
throw BadFileExceptions if they cannot open the file. (Feature
request 1938303)
2008-04-09 03:33:49 +00:00

1360 lines
34 KiB
C++
Executable File
Raw Blame History

// $Id$
//
// Copyright (C) 2002-2008 Greg Landrum and Rational Discovery LLC
// All Rights Reserved
//
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include "FileParsers.h"
#include "MolFileStereochem.h"
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <string>
using namespace RDKit;
void test1(){
BOOST_LOG(rdInfoLog) << "testing atom query parsing" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/list-query.mol";
RWMol *m = MolFileToMol(fName,false);
//MolOps::sanitizeMol(*m);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==6);
std::string smi = MolToSmiles(*m);
//TEST_ASSERT(smi=="[*]1ccccc1");
TEST_ASSERT(smi=="[*]1=CC=CC=C1");
smi = "C1=CC=CC=C1";
RWMol *m2 = SmilesToMol(smi,false,false);
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==6);
// sanitize it, which will aromatize the bonds... we will not match:
MolOps::sanitizeMol(*m2);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "N1=CC=CC=C1";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==6);
delete m2;
smi = "S1=CC=CC=C1";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "P1=CC=CC=C1";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==6);
delete m2;
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/not-list-query.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC(=C)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "CC(=O)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smi = "CC(=N)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smi = "CC(=O)C(=C)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "C(=C)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
// make sure new-style atom lists override old-style atom lists:
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/conflicting-list-query.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC(=C)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "CC(=O)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test2(){
BOOST_LOG(rdInfoLog) << "testing bond query parsing" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/bond-query.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getNumAtoms()==5);
std::string smi = MolToSmiles(*m);
TEST_ASSERT(smi=="C=CC?CC");
smi = "C1=CC=CC=C1";
RWMol *m2 = SmilesToMol(smi,false,false);
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==5);
// sanitize it (making bonds aromatic) ... we will not match:
MolOps::sanitizeMol(*m2);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C=CC=CC=C";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==5);
delete m2;
smi = "C=CCCC=C";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==5);
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/RingBondQuery.mol";
delete m;
m = MolFileToMol(fName);
TEST_ASSERT(m->getNumAtoms()==5);
delete m2;
smi = "C1CCC1C";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smi = "C1CC2C1C2";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==5);
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ChainBondQuery.mol";
delete m;
m = MolFileToMol(fName);
TEST_ASSERT(m->getNumAtoms()==5);
delete m2;
smi = "C1CCC1C";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==5);
delete m2;
smi = "C1CC2C1C2";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test4(){
// basic writing test
BOOST_LOG(rdInfoLog) << " ----------> Test4 "<< std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/";
std::string fName = rdbase + "test_data/mol1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
std::string smi=MolToSmiles(*m);
CHECK_INVARIANT(smi=="c1cc[cH-]c1",smi);
TEST_ASSERT(m->getConformer().is3D()==false);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
smi = MolToSmiles(*m);
CHECK_INVARIANT(smi=="c1cc[cH-]c1",smi);
TEST_ASSERT(m->getConformer().is3D()==false);
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void test5(){
// formerly problematic molecules
BOOST_LOG(rdInfoLog) << " ----------> Test5 "<< std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/";
std::string fName = rdbase + "test_data/issue123.mol";
RWMol *m = MolFileToMol(fName);
CHECK_INVARIANT(m,"");
TEST_ASSERT(m->getNumAtoms()==23);
TEST_ASSERT(m->getConformer().is3D()==true);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==23);
TEST_ASSERT(m->getConformer().is3D()==true);
delete m;
// now try without removing the Hs:
m = MolFileToMol(fName,true,false);
CHECK_INVARIANT(m,"");
TEST_ASSERT(m->getNumAtoms()==39);
}
void test6(){
BOOST_LOG(rdInfoLog) << "testing chirality parsing" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/";
std::string fName = rdbase + "test_data/chiral1.mol";
RWMol *m;
std::string smi,cip;
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@](F)(Cl)Br");
delete m;
fName = rdbase+"test_data/chiral1a.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@](F)(Cl)Br");
delete m;
fName = rdbase+"test_data/chiral2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@@](F)(Cl)Br");
delete m;
fName = rdbase+"test_data/chiral2a.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@@](F)(Cl)Br");
delete m;
fName = rdbase+"test_data/chiral3.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#if 1
smi = MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog) << " smi: " << smi << std::endl;
TEST_ASSERT(smi=="C[C@H](F)Cl");
#endif
delete m;
fName = rdbase+"test_data/chiral3a.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#if 1
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@H](F)Cl");
#endif
delete m;
fName = rdbase+"test_data/chiral4.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
#if 1
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@@H](F)Cl");
#endif
delete m;
fName = rdbase+"test_data/chiral4a.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
#if 1
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@@H](F)Cl");
#endif
delete m;
fName = rdbase+"test_data/chiral5.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp("_CIPCode"));
#if 1
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="CC(C)(Cl)Br");
#endif
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test7(){
BOOST_LOG(rdInfoLog) << "testing roundtrip chirality parsing" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/";
RWMol *m,*m2;
std::string fName;
std::string smi,molBlock,smi2,cip;
fName = rdbase+"test_data/chiral1.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@](F)(Cl)Br");
molBlock=MolToMolBlock(*m);
m2=MolBlockToMol(molBlock);
TEST_ASSERT(m2)
smi2 = MolToSmiles(*m2,true);
TEST_ASSERT(smi==smi2);
delete m;
delete m2;
fName = rdbase+"test_data/chiral2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@@](F)(Cl)Br");
molBlock=MolToMolBlock(*m);
m2=MolBlockToMol(molBlock);
TEST_ASSERT(m2)
smi2 = MolToSmiles(*m2,true);
TEST_ASSERT(smi==smi2);
delete m;
delete m2;
fName = rdbase+"test_data/chiral3.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#if 1
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@H](F)Cl");
molBlock=MolToMolBlock(*m);
BOOST_LOG(rdInfoLog) << molBlock << std::endl;
m2=MolBlockToMol(molBlock);
TEST_ASSERT(m2)
MolOps::assignAtomChiralCodes(*m2);
TEST_ASSERT(m2->getAtomWithIdx(0)->hasProp("_CIPCode"));
m2->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
smi2 = MolToSmiles(*m2,true);
TEST_ASSERT(smi==smi2);
delete m2;
#endif
delete m;
fName = rdbase+"test_data/chiral4.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
#if 1
smi = MolToSmiles(*m,true);
TEST_ASSERT(smi=="C[C@@H](F)Cl");
molBlock=MolToMolBlock(*m);
//BOOST_LOG(rdInfoLog) << molBlock << std::endl;
m2=MolBlockToMol(molBlock);
TEST_ASSERT(m2)
MolOps::assignAtomChiralCodes(*m2);
TEST_ASSERT(m2->getAtomWithIdx(0)->hasProp("_CIPCode"));
m2->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
//smi2 = MolToSmiles(*m2,true);
//TEST_ASSERT(smi==smi2);
delete m2;
#endif
delete m;
fName = rdbase+"test_data/Issue142d.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#if 1
smi = MolToSmiles(*m,true);
m2=SmilesToMol(smi);
smi2 = MolToSmiles(*m2,true);
if(smi!=smi2){
BOOST_LOG(rdInfoLog) << "\n " << smi << "\n !=\n " << smi2 << std::endl;
}
TEST_ASSERT(smi==smi2);
delete m2;
//BOOST_LOG(rdInfoLog) << "SMI: "<< smi << std::endl;
molBlock=MolToMolBlock(*m);
BOOST_LOG(rdInfoLog) << molBlock << std::endl;
m2=MolBlockToMol(molBlock);
TEST_ASSERT(m2)
smi2 = MolToSmiles(*m2,true);
if(smi!=smi2){
BOOST_LOG(rdInfoLog) << "\n " << smi << "\n !=\n " << smi2 << std::endl;
}
TEST_ASSERT(smi==smi2);
delete m2;
#endif
delete m;
fName = rdbase+"test_data/Issue142b.mol";
m = MolFileToMol(fName);
BOOST_LOG(rdInfoLog) << m->getNumAtoms() << "\n";
BOOST_LOG(rdInfoLog) << "-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-" << std::endl;
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPCode"));
m->getAtomWithIdx(3)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#if 1
smi = MolToSmiles(*m,true);
m2=SmilesToMol(smi);
smi2 = MolToSmiles(*m2,true);
if(smi!=smi2){
BOOST_LOG(rdInfoLog) << "\n " << smi << "\n !=\n " << smi2 << std::endl;
}
TEST_ASSERT(smi==smi2);
delete m2;
//BOOST_LOG(rdInfoLog) << "SMI: "<< smi << std::endl;
BOOST_LOG(rdInfoLog) << m->getNumAtoms() << " " << m->getConformer().getNumAtoms() << "\n";
molBlock=MolToMolBlock(*m);
BOOST_LOG(rdInfoLog) << molBlock << std::endl;
m2=MolBlockToMol(molBlock);
TEST_ASSERT(m2)
smi2 = MolToSmiles(*m2,true);
if(smi!=smi2){
BOOST_LOG(rdInfoLog) << "\n " << smi << "\n !=\n " << smi2 << std::endl;
}
TEST_ASSERT(smi==smi2);
delete m2;
#endif
delete m;
fName = rdbase+"test_data/issue142a.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==28);
#if 1
smi = MolToSmiles(*m,true);
m2=SmilesToMol(smi);
smi2 = MolToSmiles(*m2,true);
if(smi!=smi2){
BOOST_LOG(rdInfoLog) << "\n " << smi << "\n !=\n " << smi2 << std::endl;
}
TEST_ASSERT(smi==smi2);
delete m2;
molBlock=MolToMolBlock(*m);
BOOST_LOG(rdInfoLog) << molBlock << std::endl;
m2=MolBlockToMol(molBlock);
TEST_ASSERT(m2)
smi2 = MolToSmiles(*m2,true);
if(smi!=smi2){
BOOST_LOG(rdInfoLog) << "\n " << smi << "\n !=\n " << smi2 << std::endl;
}
TEST_ASSERT(smi==smi2);
delete m2;
#endif
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test8(){
BOOST_LOG(rdInfoLog) << "testing reading without sanitization" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/";
RWMol *m;
std::string fName;
std::string smi,molBlock,smi2;
// in this case the test means to not remove Hs:
fName = rdbase+"test_data/unsanitary.mol";
m = MolFileToMol(fName,false);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==6);
delete m;
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==3);
delete m;
fName = rdbase+"test_data/unsanitary2.mol";
m = MolFileToMol(fName,false);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue145(){
BOOST_LOG(rdInfoLog) << "testing Issue145:\n Mol parsing: molecule yields non-canonical smiles from mol block" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/";
RWMol *m,*m2;
std::string fName;
std::string smi,molBlock,smi2;
fName = rdbase+"test_data/issue145.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==19);
smi = MolToSmiles(*m,true);
m2=SmilesToMol(smi);
smi2 = MolToSmiles(*m2,true);
if(smi!=smi2){
BOOST_LOG(rdInfoLog) << "\n " << smi << "\n !=\n " << smi2 << std::endl;
}
TEST_ASSERT(smi==smi2);
delete m2;
molBlock=MolToMolBlock(*m);
m2=MolBlockToMol(molBlock);
TEST_ASSERT(m2)
smi2 = MolToSmiles(*m2,true);
if(smi!=smi2){
BOOST_LOG(rdInfoLog) << "\n " << smi << "\n !=\n " << smi2 << std::endl;
}
TEST_ASSERT(smi==smi2);
delete m;
delete m2;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue148(){
BOOST_LOG(rdInfoLog) << "testing Issue148:\n Mol files containing mis-drawn nitro groups not properly parsed" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/";
RWMol *m;
std::string fName;
std::string smi,molBlock,smi2;
fName = rdbase+"test_data/issue148.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge()==1);
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue180(){
BOOST_LOG(rdInfoLog) << "testing Issue180: bad Z/E assignments" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/";
RWMol *m;
std::string fName;
std::string code;
Bond *bond;
fName = rdbase+"test_data/Issue180.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
bond = m->getBondWithIdx(2);
TEST_ASSERT(bond->getBondType()==Bond::DOUBLE);
TEST_ASSERT(bond->getStereo()==Bond::STEREOZ);
bond = m->getBondWithIdx(5);
TEST_ASSERT(bond->getBondType()==Bond::DOUBLE);
TEST_ASSERT(bond->getStereo()==Bond::STEREOE);
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue264(){
BOOST_LOG(rdInfoLog) << "testing Issue264: bad stereochemistry from mol files" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/";
RWMol *m1,*m2;
std::string smi1,smi2;
std::string fName;
fName = rdbase+"test_data/Issue264-1.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
fName = rdbase+"test_data/Issue264-2.mol";
m2 = MolFileToMol(fName);
TEST_ASSERT(m2);
smi1 = MolToSmiles(*m1,false);
smi2 = MolToSmiles(*m2,false);
TEST_ASSERT(smi1==smi2);
smi1 = MolToSmiles(*m1,true);
smi2 = MolToSmiles(*m2,true);
BOOST_LOG(rdInfoLog) << smi1 << std::endl;
BOOST_LOG(rdInfoLog) << smi2 << std::endl;
TEST_ASSERT(smi1!=smi2);
delete m1;
delete m2;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue399(){
BOOST_LOG(rdInfoLog) << "testing Issue399: bond wedging cleanup" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/test_data/";
RWMol *m1;
std::string smi1,smi2;
std::string fName;
fName = rdbase+"Issue399a.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
#if 1
smi1 = MolToSmiles(*m1,true);
TEST_ASSERT(smi1=="C[C@H]1CO1");
#endif
MolOps::assignAtomChiralCodes(*m1);
TEST_ASSERT(m1->getAtomWithIdx(1)->hasProp("_CIPCode"));
m1->getAtomWithIdx(1)->getProp("_CIPCode",smi2);
TEST_ASSERT(smi2=="S");
#if 1
WedgeMolBonds(*m1,&m1->getConformer());
TEST_ASSERT(m1->getBondWithIdx(0)->getBondDir()==Bond::BEGINWEDGE);
TEST_ASSERT(m1->getBondWithIdx(1)->getBondDir()==Bond::NONE);
TEST_ASSERT(m1->getBondWithIdx(2)->getBondDir()==Bond::NONE);
TEST_ASSERT(m1->getBondWithIdx(3)->getBondDir()==Bond::NONE);
#endif
delete m1;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testMolFileChgLines(){
BOOST_LOG(rdInfoLog) << "testing SF.Net Issue1603923: problems with multiple chg lines" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/test_data/";
RWMol *m1;
std::string fName;
fName = rdbase+"MolFileChgBug.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getAtomWithIdx(24)->getFormalCharge()==-1);
TEST_ASSERT(m1->getAtomWithIdx(25)->getFormalCharge()==-1);
delete m1;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testSymmetricDblBondStereochem(){
// this was sf.net issue 1718794:
// http://sourceforge.net/tracker/index.php?func=detail&aid=1718794&group_id=160139&atid=814650)
BOOST_LOG(rdInfoLog) << "testing double bonds with symmetric substituents" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/test_data/";
RWMol *m1;
std::string fName,smi;
fName = rdbase+"cistrans.1a.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi=="C/C=C/Cl");
fName = rdbase+"cistrans.2a.mol";
delete m1;
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi=="C/C=C\\Cl");
fName = rdbase+"cistrans.1.mol";
delete m1;
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi=="C/C=C/C");
fName = rdbase+"cistrans.2.mol";
delete m1;
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi=="C/C=C\\C");
fName = rdbase+"cistrans.3.mol";
delete m1;
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi=="CC=CC");
delete m1;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testRingDblBondStereochem(){
// this was sf.net issue 1725068:
// http://sourceforge.net/tracker/index.php?func=detail&aid=1725068&group_id=160139&atid=814650
BOOST_LOG(rdInfoLog) << "testing double bonds in rings with stereochem specifications" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/test_data/";
RWMol *m1;
std::string fName,smi;
fName = rdbase+"badringstereochem3.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi.find("/",0)==std::string::npos);
TEST_ASSERT(smi.find("\\",0)==std::string::npos);
delete m1;
fName = rdbase+"badringstereochem2.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi.find("/",0)==std::string::npos);
TEST_ASSERT(smi.find("\\",0)==std::string::npos);
delete m1;
fName = rdbase+"badringstereochem.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi.find("/",0)==std::string::npos);
TEST_ASSERT(smi.find("\\",0)==std::string::npos);
delete m1;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testMolFileRGroups(){
BOOST_LOG(rdInfoLog) << "testing mol file R-group parsing" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/rgroups1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
unsigned int idx;
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_MolFileRLabel"));
m->getAtomWithIdx(3)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==2);
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_MolFileRLabel"));
m->getAtomWithIdx(4)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==1);
RWMol *m2;
MatchVectType mv;
std::string smi;
smi = "C1C(O)C1C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==5);
delete m2;
smi = "C1CC(O)C1C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smi = "C1C(CO)C1CC";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==5);
delete m2;
smi = "CC(=O)CC";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/rgroups2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_MolFileRLabel"));
m->getAtomWithIdx(3)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==1);
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_MolFileRLabel"));
m->getAtomWithIdx(4)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==1);
smi = "C1C(O)C1C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==5);
delete m2;
smi = "C1CC(O)C1C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smi = "C1C(CO)C1CC";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==5);
delete m2;
smi = "CC(=O)CC";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testMolFileDegreeQueries(){
BOOST_LOG(rdInfoLog) << "testing mol file degree queries" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/subst1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
RWMol *m2;
MatchVectType mv;
std::string smi;
smi = "CC(=O)O";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "CC(=O)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "CC(=O)";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/subst2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC(=O)O";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "CC(=O)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "CC(O)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "CC(O)";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smi = "CC(O)(C)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/subst3.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC(=O)O";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==3);
delete m2;
smi = "CC(=O)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==3);
delete m2;
smi = "CC(O)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
smi = "CC(O)";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smi = "CC(O)(C)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/subst4.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC(=O)O";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testMolFileRBCQueries(){
BOOST_LOG(rdInfoLog) << "testing mol file ring-bond count queries" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
RWMol *m;
RWMol *m2;
MatchVectType mv;
std::string smi;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C1CCC1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==2);
delete m2;
smi = "C12C3C4C1C5C2C3C45";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_3.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C1CCC1";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C12C3C4C1C5C2C3C45";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==2);
delete m2;
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_0.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==2);
delete m2;
smi = "C1CCC1";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_4.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C1CCC1";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C12C3C4C1C5C2C3C45";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C1CS234C5CC2CC13CC4C5";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==2);
delete m2;
smi = "C1C2CC3CC4CC1S234";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==2);
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_star.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==2);
delete m2;
smi = "C1CCC1";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_star2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C1CCC1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "C1CC2C1CC2";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "C12C3C4C1C5C2C3C45";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_star3.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C1CCC1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "C1CC2C1CC2";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C12C3C4C1C5C2C3C45";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testMolFileUnsaturationQueries(){
BOOST_LOG(rdInfoLog) << "testing mol file unsaturation queries" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
RWMol *m;
RWMol *m2;
MatchVectType mv;
std::string smi;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/unsaturation.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CO";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C=O";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==2);
delete m2;
smi = "CCO";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==0);
delete m2;
smi = "C=CO";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==2);
delete m2;
smi = "C#CO";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==2);
delete m2;
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testMolFileQueryToSmarts(){
BOOST_LOG(rdInfoLog) << "testing mol file queries -> SMARTS " << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
RWMol *m;
std::string sma;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
sma = MolToSmarts(*m,true);
TEST_ASSERT(sma=="[#6&$(*(@*)@*)&!$(*(@*)(@*)@*)]-[#6]")
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_3.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
sma = MolToSmarts(*m,true);
TEST_ASSERT(sma=="[#6&$(*(@*)(@*)@*)&!$(*(@*)(@*)(@*)@*)]-[#6]")
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_0.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
sma = MolToSmarts(*m,true);
TEST_ASSERT(sma=="[#6&!$(*@*)]-[#6]")
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_4.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
sma = MolToSmarts(*m,true);
TEST_ASSERT(sma=="[#16&$(*(@*)(@*)(@*)@*)&!$(*(@*)(@*)(@*)(@*)@*)]-[#6]")
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_star.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
sma = MolToSmarts(*m,true);
TEST_ASSERT(sma=="[#6&!$(*@*)]-[#6]")
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/ringcount_star2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
sma = MolToSmarts(*m,true);
TEST_ASSERT(sma.find("[#6&$(*(@*)@*)&!$(*(@*)(@*)@*)]")!=std::string::npos);
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/unsaturation.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
sma = MolToSmarts(*m,true);
TEST_ASSERT(sma=="[#6;$(*=,:,#*)]~[#8]")
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testMissingFiles(){
BOOST_LOG(rdInfoLog) << "testing handling of missing files" << std::endl;
std::string fName;
bool ok;
RWMol *m;
fName = "bogus_file.mol";
ok=false;
try{
m = MolFileToMol(fName);
} catch (BadFileException &e){
ok=true;
}
TEST_ASSERT(ok);
ok=false;
try{
m = TPLFileToMol(fName);
} catch (BadFileException &e){
ok=true;
}
TEST_ASSERT(ok);
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
int main(int argc,char *argv[]){
RDLog::InitLogs();
#if 1
test1();
test2();
test4();
test5();
test6();
testIssue145();
testIssue148();
test7();
test8();
testIssue180();
testIssue264();
testIssue399();
testMolFileChgLines();
testSymmetricDblBondStereochem();
testRingDblBondStereochem();
testMolFileRGroups();
#endif
testMolFileDegreeQueries();
testMolFileRBCQueries();
testMolFileUnsaturationQueries();
testMolFileQueryToSmarts();
testMissingFiles();
//testCrash();
return 0;
}
Reference in New Issue View Git Blame Copy Permalink