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rdkit/Code/GraphMol/FileParsers/test1.cpp
Greg Landrum cfc14230e1 fix issues 3525799 and 3526810 
this changes some canonical SMILES
and removes support for "[Xa]" dummy atoms in SMILES
2012-05-18 05:56:45 +00:00

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// $Id$
//
// Copyright (C) 2002-2011 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/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Canon.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>
#include <fstream>
#include <boost/lexical_cast.hpp>
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=="C1=CC=CC=C1");
m->updatePropertyCache();
smi = MolToSmarts(*m);
TEST_ASSERT(smi=="[#6]1=[#6]-[#6]=[#6]-[#6]=[#6,#7,#15]-1");
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;
// longer list queries, this was issue 2413431:
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/list-query-long.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(14)->hasQuery());
smi = "C1COC2=CC3=CC4=C(C=CC=C4)C=C3C=C2C1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smi = "C1C[Se]C2=CC3=CC4=C(C=CC=C4)C=C3C=C2C1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smi = "C1C[Te]C2=CC3=CC4=C(C=CC=C4)C=C3C=C2C1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smi = "C1C[As]C2=CC3=CC4=C(C=CC=C4)C=C3C=C2C1";
m2 = SmilesToMol(smi);
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::assignStereochemistry(*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::assignStereochemistry(*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::assignStereochemistry(*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::assignStereochemistry(*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::assignStereochemistry(*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::assignStereochemistry(*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);
m2=MolBlockToMol(molBlock);
TEST_ASSERT(m2)
MolOps::assignStereochemistry(*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::assignStereochemistry(*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::assignStereochemistry(*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::assignStereochemistry(*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::assignStereochemistry(*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::assignStereochemistry(*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 handling of charge lines" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/test_data/";
// SF.Net Issue1603923: problems with multiple chg lines
{
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;
}
// many charges in one molecule:
{
RWMol *m1;
std::string fName;
fName = rdbase+"manycharges.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getAtomWithIdx(0)->getFormalCharge()==-1);
TEST_ASSERT(m1->getAtomWithIdx(13)->getFormalCharge()==-1);
std::string molBlock = MolToMolBlock(*m1);
//std::cerr<<molBlock<<std::endl;
delete m1;
m1 = MolBlockToMol(molBlock);
//m1->debugMol(std::cerr);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getAtomWithIdx(0)->getFormalCharge()==-1);
TEST_ASSERT(m1->getAtomWithIdx(13)->getFormalCharge()==-1);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testDblBondStereochem(){
BOOST_LOG(rdInfoLog) << "testing basic double bond stereochemistry" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/test_data/";
{
RWMol *m1;
std::string fName=rdbase+"simple_z.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondWithIdx(0)->getStereo()==Bond::STEREOZ);
delete m1;
}
{
RWMol *m1;
std::string fName=rdbase+"simple_e.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondWithIdx(0)->getStereo()==Bond::STEREOE);
delete m1;
}
{
RWMol *m1;
std::string fName=rdbase+"simple_either.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondWithIdx(0)->getStereo()==Bond::STEREOANY);
TEST_ASSERT(m1->getBondWithIdx(0)->getBondDir()==Bond::EITHERDOUBLE);
delete m1;
}
// the next group for sf.net issue 3009836
BOOST_LOG(rdInfoLog) << " sub-test for issue 3099836"<<std::endl;
{
RWMol *m1;
std::string fName=rdbase+"Issue3009836.1.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondBetweenAtoms(3,4)->getStereo()==Bond::STEREOZ);
delete m1;
}
{
RWMol *m1;
std::string fName=rdbase+"Issue3009836.2.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondBetweenAtoms(3,4)->getStereo()==Bond::STEREOZ);
delete m1;
}
{
RWMol *m1;
std::string fName=rdbase+"Issue3009836.3.mol";
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondBetweenAtoms(6,7)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m1->getBondBetweenAtoms(10,11)->getStereo()==Bond::STEREOZ);
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);
TEST_ASSERT(m1->getBondWithIdx(0)->getStereo()==Bond::STEREOE);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi=="C/C=C/Cl");
fName = rdbase+"cistrans.2a.mol";
delete m1;
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondWithIdx(0)->getStereo()==Bond::STEREOZ);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi=="C/C=C\\Cl");
fName = rdbase+"cistrans.1.mol";
delete m1;
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondWithIdx(0)->getStereo()==Bond::STEREOE);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi=="C/C=C/C");
fName = rdbase+"cistrans.2.mol";
delete m1;
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondWithIdx(0)->getStereo()==Bond::STEREOZ);
smi = MolToSmiles(*m1,true);
TEST_ASSERT(smi=="C/C=C\\C");
fName = rdbase+"cistrans.3.mol";
delete m1;
m1 = MolFileToMol(fName);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getBondWithIdx(0)->getStereo()==Bond::STEREOANY);
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;
std::string label;
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_MolFileRLabel"));
m->getAtomWithIdx(3)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==2);
TEST_ASSERT(m->getAtomWithIdx(3)->getAtomicNum()==0);
TEST_ASSERT(feq(m->getAtomWithIdx(3)->getMass(),2));
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_MolFileRLabel"));
m->getAtomWithIdx(4)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==1);
TEST_ASSERT(m->getAtomWithIdx(4)->getAtomicNum()==0);
TEST_ASSERT(feq(m->getAtomWithIdx(4)->getMass(),1));
// test sf.net issue 3316600:
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("dummyLabel"));
m->getAtomWithIdx(3)->getProp("dummyLabel",label);
TEST_ASSERT(label=="R2");
TEST_ASSERT(m->getAtomWithIdx(3)->getSymbol()=="R2");
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("dummyLabel"));
m->getAtomWithIdx(4)->getProp("dummyLabel",label);
TEST_ASSERT(label=="R1");
TEST_ASSERT(m->getAtomWithIdx(4)->getSymbol()=="R1");
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(3)->getAtomicNum()==0);
TEST_ASSERT(feq(m->getAtomWithIdx(3)->getMass(),1));
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_MolFileRLabel"));
m->getAtomWithIdx(4)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==1);
TEST_ASSERT(m->getAtomWithIdx(4)->getAtomicNum()==0);
TEST_ASSERT(feq(m->getAtomWithIdx(4)->getMass(),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;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/rgroups3.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_MolFileRLabel"));
m->getAtomWithIdx(3)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==11);
TEST_ASSERT(m->getAtomWithIdx(3)->getAtomicNum()==0);
TEST_ASSERT(feq(m->getAtomWithIdx(3)->getMass(),11));
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_MolFileRLabel"));
m->getAtomWithIdx(4)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==503);
TEST_ASSERT(m->getAtomWithIdx(4)->getAtomicNum()==0);
TEST_ASSERT(feq(m->getAtomWithIdx(4)->getMass(),503));
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;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/combined.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
smi = "CC(=O)[CH-]C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==4);
delete m2;
smi = "CC(=O)[C-](C)C";
m2 = SmilesToMol(smi,false,false);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
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 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;
}
void testIssue1965035(){
BOOST_LOG(rdInfoLog) << "testing issue Issue1965035: problems with WedgeMolBonds " << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
RWMol *m;
std::string sma;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue1965035.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
// the mol file parser removes bond wedging info:
TEST_ASSERT(m->getBondWithIdx(4)->getBondDir()==Bond::NONE);
// but a chiral tag is assigned:
TEST_ASSERT(m->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
WedgeMolBonds(*m,&m->getConformer());
TEST_ASSERT(m->getBondWithIdx(4)->getBondDir()==Bond::BEGINDASH);
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testRadicals(){
BOOST_LOG(rdInfoLog) << "testing handling of radicals " << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
RWMol *m;
std::string smiles;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/radical.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
TEST_ASSERT(m->getAtomWithIdx(1)->getNumRadicalElectrons()==1);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
TEST_ASSERT(m->getAtomWithIdx(1)->getNumRadicalElectrons()==1);
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBadBondOrders(){
BOOST_LOG(rdInfoLog) << "testing handling of bogus bond orders (issue 2337369)" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
RWMol *m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/bondorder0.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondType()==Bond::UNSPECIFIED);
TEST_ASSERT(!m->getBondBetweenAtoms(0,1)->hasQuery());
delete m;
fName = rdbase + "/Code/GraphMol/FileParsers/test_data/bondorder9.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->hasQuery());
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getQuery()->getDescription()=="BondNull");
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testAtomParity(){
BOOST_LOG(rdInfoLog) << "testing handling of atom stereo parity flags" << std::endl;
std::string rdbase = getenv("RDBASE");
{
int parity;
std::string fName= rdbase + "/Code/GraphMol/FileParsers/test_data/parity.simple1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("molParity"));
m->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==1);
// if we don't perceive the stereochem first, no parity
// flags end up in the output:
std::string molBlock = MolToMolBlock(*m);
RWMol *m2 = MolBlockToMol(molBlock);
TEST_ASSERT(m2);
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(!m2->getAtomWithIdx(1)->hasProp("molParity"));
delete m2;
// now perceive stereochem, then look for the parity
// flags:
MolOps::assignChiralTypesFrom3D(*m);
molBlock = MolToMolBlock(*m);
m2 = MolBlockToMol(molBlock);
TEST_ASSERT(m2);
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("molParity"));
m2->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==1);
delete m2;
delete m;
}
{
int parity;
std::string fName= rdbase + "/Code/GraphMol/FileParsers/test_data/parity.simple2.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("molParity"));
m->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==2);
MolOps::assignChiralTypesFrom3D(*m);
std::string molBlock = MolToMolBlock(*m);
RWMol *m2 = MolBlockToMol(molBlock);
TEST_ASSERT(m2);
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("molParity"));
m2->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==2);
delete m2;
delete m;
}
{
// a case with an H on the chiral center:
int parity;
std::string fName= rdbase + "/Code/GraphMol/FileParsers/test_data/parity.simpleH1.mol";
RWMol *m = MolFileToMol(fName,true,false);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("molParity"));
m->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==1);
MolOps::assignChiralTypesFrom3D(*m);
std::string molBlock = MolToMolBlock(*m);
RWMol *m2 = MolBlockToMol(molBlock,true,false);
TEST_ASSERT(m2);
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("molParity"));
m2->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==1);
delete m2;
// if we remove the H and write things out, we should
// still get the right answer back:
m2 = (RWMol *)MolOps::removeHs(*((ROMol *)m));
molBlock = MolToMolBlock(*m2);
delete m2;
m2 = MolBlockToMol(molBlock);
TEST_ASSERT(m2);
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("molParity"));
m2->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==1);
delete m2;
delete m;
}
{
// a case with an H on the chiral center:
int parity;
std::string fName= rdbase + "/Code/GraphMol/FileParsers/test_data/parity.simpleH2.mol";
RWMol *m = MolFileToMol(fName,true,false);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("molParity"));
m->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==2);
MolOps::assignChiralTypesFrom3D(*m);
std::string molBlock = MolToMolBlock(*m);
RWMol *m2 = MolBlockToMol(molBlock,true,false);
TEST_ASSERT(m2);
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("molParity"));
m2->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==2);
delete m2;
m2 = (RWMol *)MolOps::removeHs(*((ROMol *)m));
molBlock = MolToMolBlock(*m2);
delete m2;
m2 = MolBlockToMol(molBlock);
TEST_ASSERT(m2);
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("molParity"));
m2->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==2);
delete m2;
delete m;
}
{
// a case with an N as the "chiral" center
int parity;
std::string fName= rdbase + "/Code/GraphMol/FileParsers/test_data/parity.nitrogen.mol";
RWMol *m = MolFileToMol(fName,true,false);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("molParity"));
m->getAtomWithIdx(1)->getProp("molParity",parity);
TEST_ASSERT(parity==1);
MolOps::assignChiralTypesFrom3D(*m);
std::string molBlock = MolToMolBlock(*m);
RWMol *m2 = MolBlockToMol(molBlock,true,false);
TEST_ASSERT(m2);
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(!m2->getAtomWithIdx(1)->hasProp("molParity"));
delete m2;
delete m;
}
{
// a case with two Hs on the chiral center:
std::string fName= rdbase + "/Code/GraphMol/FileParsers/test_data/parity.twoHs.mol";
RWMol *m = MolFileToMol(fName,true,false);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp("molParity"));
// add a bogus chiral spec:
m->getAtomWithIdx(0)->setChiralTag(Atom::CHI_TETRAHEDRAL_CW);
std::string molBlock = MolToMolBlock(*m);
RWMol *m2 = (RWMol *)MolOps::removeHs(*((ROMol *)m));
molBlock = MolToMolBlock(*m2);
delete m2;
m2 = MolBlockToMol(molBlock,true,false);
TEST_ASSERT(m2);
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp("molParity"));
TEST_ASSERT(!m2->getAtomWithIdx(1)->hasProp("molParity"));
delete m2;
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue2692246(){
// basic writing test
BOOST_LOG(rdInfoLog) << " Testing issue 2692246 "<< std::endl;
std::string smiles(120,'C');
smiles += "[CH3+]";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==121);
TEST_ASSERT(m->getAtomWithIdx(120)->getFormalCharge()==1);
delete m;
BOOST_LOG(rdInfoLog) << " done"<< std::endl;
}
void testKekulizationSkip(){
// basic writing test
BOOST_LOG(rdInfoLog) << " Testing mol blocks without kekulization "<< std::endl;
std::string smiles("c1ccccc1");
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string molBlock = MolToMolBlock(*m,true,-1,false);
TEST_ASSERT(molBlock.find("1 2 4")!=std::string::npos);
TEST_ASSERT(molBlock.find("2 3 4")!=std::string::npos);
TEST_ASSERT(molBlock.find("3 4 4")!=std::string::npos);
molBlock = MolToMolBlock(*m);
TEST_ASSERT(molBlock.find("1 2 4")==std::string::npos);
TEST_ASSERT(molBlock.find("2 3 4")==std::string::npos);
TEST_ASSERT(molBlock.find("3 4 4")==std::string::npos);
delete m;
BOOST_LOG(rdInfoLog) << " done"<< std::endl;
}
void testMolFileAtomValues(){
BOOST_LOG(rdInfoLog) << "testing atom values in mol files" << std::endl;
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/";
{
RWMol *m;
std::string fName,val;
fName = rdbase+"test_data/AtomProps1.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp("molFileValue"));
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("molFileValue"));
m->getAtomWithIdx(1)->getProp("molFileValue",val);
TEST_ASSERT(val=="acidchloride");
delete m;
}
{
RWMol *m;
std::string fName,val;
fName = rdbase+"test_data/AtomProps2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp("molFileValue"));
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("molFileValue"));
m->getAtomWithIdx(1)->getProp("molFileValue",val);
TEST_ASSERT(val=="acidchloride");
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("molFileValue"));
m->getAtomWithIdx(2)->getProp("molFileValue",val);
TEST_ASSERT(val=="testing");
TEST_ASSERT(m->getAtomWithIdx(3)->getFormalCharge()==-1);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testMolFileAtomQueries(){
BOOST_LOG(rdInfoLog) << "testing handling of A, Q, and * in mol files" << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/query_star.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
RWMol *m2;
MatchVectType mv;
std::string smi;
smi = "[H]c1ccccc1";
m2 = SmilesToMol(smi,false,false);
MolOps::sanitizeMol(*m2);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==7);
delete m2;
smi = "Cc1ccccc1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==7);
delete m2;
smi = "Clc1ccccc1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==7);
delete m2;
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/query_A.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
RWMol *m2;
MatchVectType mv;
std::string smi;
smi = "[H]c1ccccc1";
m2 = SmilesToMol(smi,false,false);
MolOps::sanitizeMol(*m2);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smi = "Cc1ccccc1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==7);
delete m2;
smi = "Clc1ccccc1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==7);
delete m2;
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/query_Q.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
RWMol *m2;
MatchVectType mv;
std::string smi;
smi = "[H]c1ccccc1";
m2 = SmilesToMol(smi,false,false);
MolOps::sanitizeMol(*m2);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smi = "Cc1ccccc1";
m2 = SmilesToMol(smi);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smi = "Clc1ccccc1";
m2 = SmilesToMol(smi);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==7);
delete m2;
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testListsAndValues(){
BOOST_LOG(rdInfoLog) << "testing handling of mol files with atom lists and values" << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/lists_plus_values.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
std::string value;
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("molFileValue"));
m->getAtomWithIdx(1)->getProp("molFileValue",value);
TEST_ASSERT(value=="halogen");
TEST_ASSERT(m->getAtomWithIdx(1)->hasQuery());
TEST_ASSERT(m->getAtomWithIdx(1)->getQuery()->getDescription()=="AtomOr");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test1V3K(){
BOOST_LOG(rdInfoLog) << "testing basic handling of v3000 mol files" << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==8);
TEST_ASSERT(m->getNumBonds()==8);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.3.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(m->getNumBonds()==9);
TEST_ASSERT(m->getAtomWithIdx(4)->getFormalCharge()==-1);
TEST_ASSERT(m->getAtomWithIdx(4)->getMass()==17.0);
//m->debugMol(std::cerr);
//TEST_ASSERT(m->getBondWithIdx(8)->getBondDir()==Bond::BEGINWEDGE);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.5a.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
TEST_ASSERT(m->getNumBonds()==4);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.5b.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
TEST_ASSERT(m->getNumBonds()==4);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.6a.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getNumBonds()==3);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo()==Bond::STEREOE);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.6b.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getNumBonds()==3);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo()==Bond::STEREOANY);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.crash1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==7);
TEST_ASSERT(m->getNumBonds()==7);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test2V3K(){
BOOST_LOG(rdInfoLog) << "testing more queries from v3000 mol files" << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.2.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==8);
TEST_ASSERT(m->getNumBonds()==8);
std::string smiles="O=C(O)C1OCCC1";
RWMol *m2 = SmilesToMol(smiles);
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smiles="O=C(O)C1OCCC1";
m2 = SmilesToMol(smiles);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smiles="O=C(O)C1SCCS1";
m2 = SmilesToMol(smiles);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smiles="O=C(O)C1OCCN1";
m2 = SmilesToMol(smiles);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smiles="O=C(O)C1OCCO1";
m2 = SmilesToMol(smiles);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.4a.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==2);
TEST_ASSERT(m->getNumBonds()==1);
std::string smiles="OC1OCC1";
RWMol *m2 = SmilesToMol(smiles);
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smiles="C1OCC1";
m2 = SmilesToMol(smiles);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smiles="COCC";
m2 = SmilesToMol(smiles);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.4b.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==2);
TEST_ASSERT(m->getNumBonds()==1);
std::string smiles="OC1OCC1";
RWMol *m2 = SmilesToMol(smiles);
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smiles="C1OCC1";
m2 = SmilesToMol(smiles);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smiles="COCC";
m2 = SmilesToMol(smiles);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/v3k.rbc.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==3);
TEST_ASSERT(m->getNumBonds()==2);
std::string smiles="C1CC1";
RWMol *m2 = SmilesToMol(smiles);
TEST_ASSERT(m2);
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
delete m2;
smiles="CCC";
m2 = SmilesToMol(smiles);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
smiles="N1NC2NNC12";
m2 = SmilesToMol(smiles);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue2963522(){
BOOST_LOG(rdInfoLog) << " Testing issue 2963522 "<< std::endl;
{
std::string smiles="CC=CC";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREONONE);
Conformer *conf=new Conformer(m->getNumAtoms());
conf->setAtomPos(0,RDGeom::Point3D(-1,1,0));
conf->setAtomPos(1,RDGeom::Point3D(0,1,0));
conf->setAtomPos(2,RDGeom::Point3D(0,-1,0));
conf->setAtomPos(3,RDGeom::Point3D(1,-1,0));
m->addConformer(conf,true);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREOANY);
delete m;
}
{
std::string smiles="C/C=C\\C";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREOZ);
Conformer *conf=new Conformer(m->getNumAtoms());
conf->setAtomPos(0,RDGeom::Point3D(-1,1,0));
conf->setAtomPos(1,RDGeom::Point3D(0,1,0));
conf->setAtomPos(2,RDGeom::Point3D(0,-1,0));
conf->setAtomPos(3,RDGeom::Point3D(-1,-1,0));
m->addConformer(conf,true);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREOZ);
delete m;
}
{
std::string smiles="C/C=C/C";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREOE);
Conformer *conf=new Conformer(m->getNumAtoms());
conf->setAtomPos(0,RDGeom::Point3D(-1,1,0));
conf->setAtomPos(1,RDGeom::Point3D(0,1,0));
conf->setAtomPos(2,RDGeom::Point3D(0,-1,0));
conf->setAtomPos(3,RDGeom::Point3D(1,-1,0));
m->addConformer(conf,true);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREOE);
delete m;
}
{
std::string smiles="C1C=CC1";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREONONE);
Conformer *conf=new Conformer(m->getNumAtoms());
conf->setAtomPos(0,RDGeom::Point3D(-1,1,0));
conf->setAtomPos(1,RDGeom::Point3D(0,1,0));
conf->setAtomPos(2,RDGeom::Point3D(0,-1,0));
conf->setAtomPos(3,RDGeom::Point3D(-1,-1,0));
m->addConformer(conf,true);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREONONE);
delete m;
}
{
// this was issue 3009756:
std::string smiles="CC(=O)C";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREONONE);
Conformer *conf=new Conformer(m->getNumAtoms());
conf->setAtomPos(0,RDGeom::Point3D(-1,0,0));
conf->setAtomPos(1,RDGeom::Point3D(0,0,0));
conf->setAtomPos(2,RDGeom::Point3D(0,1,0));
conf->setAtomPos(3,RDGeom::Point3D(1,0,0));
m->addConformer(conf,true);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREONONE);
delete m;
}
{
// this was issue 3009756:
std::string smiles="CC(=C)Cl";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREONONE);
Conformer *conf=new Conformer(m->getNumAtoms());
conf->setAtomPos(0,RDGeom::Point3D(-1,0,0));
conf->setAtomPos(1,RDGeom::Point3D(0,0,0));
conf->setAtomPos(2,RDGeom::Point3D(0,1,0));
conf->setAtomPos(3,RDGeom::Point3D(1,0,0));
m->addConformer(conf,true);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREONONE);
delete m;
}
BOOST_LOG(rdInfoLog) << " done"<< std::endl;
}
void testIssue3073163(){
BOOST_LOG(rdInfoLog) << " Testing issue 3073163 "<< std::endl;
{
std::string smiles="C[2H]";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles="[2#1]";
RWMol *p = SmartsToMol(smiles);
TEST_ASSERT(p);
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*m,*p,mv));
std::string mb=MolToMolBlock(*m);
std::cerr<<"mb:\n"<<mb<<"----\n";
RWMol *m2=MolBlockToMol(mb);
TEST_ASSERT(m2);
std::cerr<<" mol: "<<MolToSmiles(*m,true)<<std::endl;
std::cerr<<" mol2: "<<MolToSmiles(*m2,true)<<std::endl;
TEST_ASSERT(SubstructMatch(*m2,*p,mv));
delete m2;
delete m;
delete p;
}
BOOST_LOG(rdInfoLog) << " done"<< std::endl;
}
void testIssue3154208(){
BOOST_LOG(rdInfoLog) << " Testing Issue3154208 (a large mol failure)"<< std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/largemol.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==476);
TEST_ASSERT(m->getNumBonds()==531);
std::cerr<<"generating smiles"<<std::endl;
std::string smiles=MolToSmiles(*m,false,false,-1,false);
std::cerr<<"smiles: "<<smiles<<std::endl;
std::cerr<<"converting back"<<std::endl;
RWMol *m2 = SmilesToMol(smiles);
TEST_ASSERT(m2);
TEST_ASSERT(m2->getNumAtoms()==476);
TEST_ASSERT(m2->getNumBonds()==531);
MatchVectType mv;
std::cerr<<"check isomorphism"<<std::endl;
TEST_ASSERT(SubstructMatch(*m,*m2,mv));
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
#if 1
BOOST_LOG(rdInfoLog)<<"Large molecule canonical smiles test"<<std::endl;
std::string csmiles=MolToSmiles(*m);
for(unsigned int i=0;i<50;++i){
if(!(i%10)) BOOST_LOG(rdInfoLog)<<"Iteration: "<<i+1<<" of 50"<<std::endl;
std::string nsmiles = MolToSmiles(*m,false,false,2*i,false);
RWMol *nm=SmilesToMol(nsmiles);
TEST_ASSERT(nm);
TEST_ASSERT(nm->getNumAtoms()==476);
TEST_ASSERT(nm->getNumBonds()==531);
nsmiles=MolToSmiles(*m);
if(nsmiles!=csmiles){
std::cerr<<"MISMATCH:\n"<<nsmiles<<"\n"<<csmiles<<"\n";
}
TEST_ASSERT(nsmiles==csmiles);
delete nm;
}
#endif
delete m;
}
BOOST_LOG(rdInfoLog) << " done"<< std::endl;
}
void testIssue3228150(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3228150: round-trip stereochemistry failure" << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName;
RWMol *m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/Issue3228150.sdf";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondWithIdx(2)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(2)->getStereo()==Bond::STEREOZ);
std::string smi1=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<std::endl;
m->clearComputedProps();
m->updatePropertyCache();
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{
std::string fName;
RWMol *m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/Issue3228150.full.sdf";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(2)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(2)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondWithIdx(4)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(4)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondWithIdx(6)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(6)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondWithIdx(8)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(8)->getStereo()==Bond::STEREOZ);
std::string smi1=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<std::endl;
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getBondWithIdx(2)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(2)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondWithIdx(4)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(4)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondWithIdx(6)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(6)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondWithIdx(8)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(8)->getStereo()==Bond::STEREOZ);
std::string smi2=MolToSmiles(*m,true);
smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue3313540(){
BOOST_LOG(rdInfoLog) << "testing writing mol file R-groups (issue 3313540)" << 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);
std::string mb=MolToMolBlock(*m);
RWMol *m2=MolBlockToMol(mb);
TEST_ASSERT(m2);
TEST_ASSERT(m2->getAtomWithIdx(3)->hasProp("_MolFileRLabel"));
m2->getAtomWithIdx(3)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==2);
TEST_ASSERT(m2->getAtomWithIdx(4)->hasProp("_MolFileRLabel"));
m2->getAtomWithIdx(4)->getProp("_MolFileRLabel",idx);
TEST_ASSERT(idx==1);
delete m;
delete m2;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue3359739(){
// basic writing test
BOOST_LOG(rdInfoLog) << " ----------> Test issue 3359739 "<< std::endl;
std::string smi="[C]C";
RWMol *m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==3);
std::string molBlock = MolToMolBlock(*m);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
// NOTE: the following is correct according to the current
// state of the code and what the CTAB format supports,
// but it's definitely not chemically correct
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testIssue3374639(){
// basic writing test
BOOST_LOG(rdInfoLog) << " ----------> Test issue 3374639 "<< std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3374639.2.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
std::string cip;
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3374639.1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
std::string cip;
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3374639.full.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getAtomWithIdx(16)->hasProp("_CIPCode"));
std::string cip;
m->getAtomWithIdx(16)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
}
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testThreeCoordinateChirality(){
// basic writing test
BOOST_LOG(rdInfoLog) << " ----------> Test three-coordinate chirality "<< std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
std::string cip;
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.2.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
std::string cip;
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.3.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp("_CIPCode"));
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.4.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp("_CIPCode"));
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.5.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
std::string cip;
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.6.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
std::string cip;
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
}
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testIssue3375647(){
// basic writing test
BOOST_LOG(rdInfoLog) << " ----------> Test issue 3375647 "<< std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3375647.1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getBondBetweenAtoms(2,11)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondBetweenAtoms(2,11)->getBondDir()!=Bond::EITHERDOUBLE);
TEST_ASSERT(m->getBondBetweenAtoms(2,11)->getStereo()==Bond::STEREOZ);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3375647.2.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getBondBetweenAtoms(2,11)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondBetweenAtoms(2,11)->getBondDir()!=Bond::EITHERDOUBLE);
TEST_ASSERT(m->getBondBetweenAtoms(2,11)->getStereo()==Bond::STEREOE);
delete m;
}
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testIssue3375684(){
// basic writing test
BOOST_LOG(rdInfoLog) << " ----------> Test issue 3375684 "<< std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3375684.1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getBondBetweenAtoms(6,7)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondBetweenAtoms(6,7)->getBondDir()==Bond::EITHERDOUBLE);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3375684.2.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m->getBondBetweenAtoms(3,9)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondBetweenAtoms(3,9)->getBondDir()!=Bond::EITHERDOUBLE);
TEST_ASSERT(m->getBondBetweenAtoms(3,9)->getStereo()==Bond::STEREOE);
delete m;
}
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testChiralPhosphorous(){
// basic writing test
BOOST_LOG(rdInfoLog) << " ----------> Test handling of chiral phosphorous "<< std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chiral_phosphorous.1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp("_CIPCode"));
std::string cip;
m->getAtomWithIdx(5)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chiral_phosphorous.2.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp("_CIPCode"));
std::string cip;
m->getAtomWithIdx(5)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chiral_phosphorous.3.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(5)->hasProp("_CIPCode"));
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chiral_phosphorous.4.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(5)->hasProp("_CIPCode"));
delete m;
}
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testIssue3392107(){
// basic writing test
BOOST_LOG(rdInfoLog) << " ----------> Test issue 3392107 "<< std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3392107.1.mol";
RWMol *m = MolFileToMol(fName);
std::string smi;
MatchVectType mv;
RWMol *m2;
smi = "C1CCCCC1";
m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==6);
delete m2;
smi = "C1CCCCN1";
m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==6);
delete m2;
smi = "C1CCNCN1";
m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(SubstructMatch(*m2,*m,mv));
TEST_ASSERT(mv.size()==6);
delete m2;
smi = "C1NCNCN1";
m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(!SubstructMatch(*m2,*m,mv));
delete m2;
delete m;
}
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testIssue3432136(){
BOOST_LOG(rdInfoLog) << " ----------> Test issue 3432136 "<< std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3432136_1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(!m);
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3432136_1.v3k.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(!m);
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3432136_2.v3k.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3432136_2.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
}
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testIssue3477283(){
BOOST_LOG(rdInfoLog) << " ----------> Test issue 3477283 "<< std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3477283.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
}
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testIssue3484552(){
BOOST_LOG(rdInfoLog) << " ----------> Test issue 3484552 "<< std::endl;
{
std::string smi = "C[13CH3]";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getMass()>12.999);
std::string molBlock = MolToMolBlock(*m);
TEST_ASSERT(molBlock.find("M ISO")!=std::string::npos);
delete m;
m = MolBlockToMol(molBlock);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getMass()>12.999);
delete m;
}
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testIssue3514824(){
BOOST_LOG(rdInfoLog) << " ----------> Test issue 3514824 "<< std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3514824.2.mol";
RWMol *m = MolFileToMol(fName,false);
TEST_ASSERT(m);
m->updatePropertyCache();
MolOps::findSSSR(*m);
TEST_ASSERT(m->getRingInfo());
TEST_ASSERT(m->getRingInfo()->isInitialized());
TEST_ASSERT(m->getRingInfo()->numRings()==6);
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3514824.mol";
RWMol *m = MolFileToMol(fName,false);
TEST_ASSERT(m);
m->updatePropertyCache();
MolOps::findSSSR(*m);
TEST_ASSERT(m->getRingInfo());
TEST_ASSERT(m->getRingInfo()->isInitialized());
TEST_ASSERT(m->getRingInfo()->numRings()==8);
}
BOOST_LOG(rdInfoLog) << " Finished <---------- "<< std::endl;
}
void testIssue3525799(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3525799: bad smiles for r groups" << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3525799.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
std::string smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="[*]c1oc2c([*])c([*])c([*])c([*])c2c(=O)c1-c1c([*])c([*])c([*])c([*])c1[*]");
}
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();
testDblBondStereochem();
testSymmetricDblBondStereochem();
testRingDblBondStereochem();
testMolFileRGroups();
testMolFileDegreeQueries();
testMolFileRBCQueries();
testMolFileUnsaturationQueries();
testMolFileQueryToSmarts();
testMissingFiles();
testIssue1965035();
testRadicals();
testBadBondOrders();
testAtomParity();
testIssue2692246();
testKekulizationSkip();
testMolFileAtomValues();
testMolFileAtomQueries();
testListsAndValues();
//testCrash();
test1V3K();
test2V3K();
testIssue2963522();
testIssue3073163();
testIssue3154208();
testIssue3228150();
testIssue3313540();
testIssue3359739();
testIssue3374639();
testThreeCoordinateChirality();
testIssue3375647();
testIssue3375684();
testChiralPhosphorous();
testIssue3392107();
testIssue3432136();
testIssue3477283();
#endif
testIssue3484552();
testIssue3514824();
testIssue3525799();
return 0;
}
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