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rdkit/Code/GraphMol/SmilesParse/test.cpp

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// $Id$
//
// Copyright (C) 2003-2014 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 <iostream>
#include <string>
#include <GraphMol/RDKitBase.h>
#include "SmilesParse.h"
#include "SmilesWrite.h"
#include "SmartsWrite.h"
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/RDLog.h>
//#include <boost/log/functions.hpp>
using namespace RDKit;
using namespace std;
typedef ROMol Mol;
void testPass(){
int i = 0;
ROMol *mol,*mol2;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing molecules which should parse." << std::endl;
string smis[]={
#if 1
"C1CC2C1CC2",
"c1cccn(=O)c1",
"C",
"CC",
"C-C",
"C=C",
"[CH2+]C[CH+2]",
"C1CC1",
"C1CC=1",
"C=1CC1",
"C=C-O",
"C1CC1",
"C1NC1",
"C1=CC1",
"C1CCC1",
"CC(C)CC",
"CC(=O)O",
"C1C(=O)C1",
"C1C(N)C1",
"CC(O)C",
"OC=CCC",
"CC([O-])O",
"C1CC2C1CC2",
"Cl/C=C/Cl",
"Cl/C=C\\Cl",
"Cl/C=C/Cl",
"Cl/C=C\\Cl",
"Cl/C=C\\\\Cl",
"C1CC.CC1",
"C1C(C2CC2).C2CC2C1",
"[Na+].[Cl-].[NH4+].[Cl-]",
"C[35Cl]",
"C%10CC%10",
"[H][H]",
"[H+]",
"C[N+](=O)[O-]",
"N1C(=N)SC=C1",
"[O-][N+](=O)C1=CNC(=N)S1",
"CN(=O)=O",
"C1=CC=C[N+]([O-])=C1",
"C1=CC=CN(=O)=C1",
// test whitespace tolerance:
" C1=CC=CN(=O)=C1",
"C1=CC=CN(=O)=C1 ",
" C1=CC=CN(=O)=C1 ",
"\tC1=CC=CN(=O)=C1\r\n",
#endif
// test dummy atoms:
"c1ccccc1[*]",
"c1ccccc1[1*]",
"S1cccc1",
"*1ccccc1",
"C1=CC=CC=C1",
"*1=CC=CC=C1",
"*1*cccc1",
"*1**ccc1",
// test aromatic se and te:
"c1ccc[se]1",
"c1ccc[te]1",
// test zeros as ring indices, issue 2690982:
"C0CC0",
// test canonization error, issue 3018558:
"C/C(/C=C2\\Sc1ccc(cc1N\\2C))=C5\\SC4=NccN4C\\5=O",
// "the most common molecule in the universe",
// expressed in an ugly way:
"[HH]",
"[2HH]",
"[HH2-]",// issue 3535669
"[2HH2-]",// issue 3535669
// problems handling aromatic boron, issue 3480481
"b1ccccc1",
"C[Rf]C", // issue 3535668
"[C:1]",
"[C:0]", // issue 3525776
"[si]1cccc[si]1", // aromatic Si (github issue 5)
"EOS"};
while( smis[i] != "EOS" ){
string smi = smis[i];
//BOOST_LOG(rdInfoLog)<< "***: " << smi << std::endl;
mol = SmilesToMol(smi);
CHECK_INVARIANT(mol,smi);
if (mol) {
unsigned int nAts = mol->getNumAtoms();
CHECK_INVARIANT(nAts!=0,smi.c_str());
smi=MolToSmiles(*mol);
//BOOST_LOG(rdInfoLog)<< " > " << smi << std::endl;
mol2 = SmilesToMol(smi);
CHECK_INVARIANT(mol2->getNumAtoms()==nAts,smi.c_str())
delete mol;
delete mol2;
}
i++;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testFail(){
int i = 0;
Mol *mol;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing molecules which should fail to parse/sanitize." << std::endl;
// alternate good and bad smiles here to ensure that the parser can resume parsing
// on good input:
string smis[]={
"CC=(CO)C",
"CC(=CO)C",
"C1CC",
"C1CC1",
"Ccc",
"CCC",
"fff", // tests the situation where the parser cannot do anything at all
"CCC",
"N(=O)(=O)=O", // bad sanitization failure
"C1CC1",
"C=0", // part of sf.net issue 2525792
"C1CC1",
"C0", // part of sf.net issue 2525792
"C1CC1",
"C-0", // part of sf.net issue 2525792
"C1CC1",
"C+0", // part of sf.net issue 2525792
"C1CC1",
"[H2H]",
"C1CC1",
"[HH2]",
"C1CC1",
"EOS"};
// turn off the error log temporarily:
while( smis[i] != "EOS" ){
string smi = smis[i];
boost::logging::disable_logs("rdApp.error");
try {
mol = SmilesToMol(smi);
} catch (MolSanitizeException) {
mol = (Mol *)0;
}
boost::logging::enable_logs("rdApp.error");
if(!(i%2)) {
CHECK_INVARIANT(!mol,smi);
}
else{
CHECK_INVARIANT(mol,smi);
}
i++;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testDetails(){
Mol *mol;
Atom *a;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing details" << std::endl;
// implicit/explicit H handling
smi = "OC([OH])C[O-]";
mol = SmilesToMol(smi);
CHECK_INVARIANT(mol,smi);
CHECK_INVARIANT(mol->getNumAtoms()==5,"");
a = mol->getAtomWithIdx(0);
CHECK_INVARIANT(a->getImplicitValence()==1,"");
CHECK_INVARIANT(a->getExplicitValence()==1,"");
CHECK_INVARIANT(a->getNoImplicit()==0,"");
CHECK_INVARIANT(a->getFormalCharge()==0,"");
a = mol->getAtomWithIdx(2);
CHECK_INVARIANT(a->getImplicitValence()==0,"");
CHECK_INVARIANT(a->getExplicitValence()==2,"");
CHECK_INVARIANT(a->getNoImplicit()==1,"");
CHECK_INVARIANT(a->getFormalCharge()==0,"");
a = mol->getAtomWithIdx(4);
CHECK_INVARIANT(a->getImplicitValence()==0,"");
CHECK_INVARIANT(a->getExplicitValence()==1,"");
CHECK_INVARIANT(a->getNoImplicit()==1,"");
CHECK_INVARIANT(a->getFormalCharge()==-1,"");
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testProblems(){
Mol *mol;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing smiles that were previously problems" << std::endl;
// ring closure handling with branches/fragments
VECT_INT_VECT rings;
smi = "C1(CC1CC1CC1)";
mol = SmilesToMol(smi);
CHECK_INVARIANT(mol,smi);
int ringCount=MolOps::findSSSR(*mol,rings);
CHECK_INVARIANT(ringCount==2,"");
CHECK_INVARIANT(rings.size()==2,"");
CHECK_INVARIANT(rings[0].size()==3,"");
CHECK_INVARIANT(rings[1].size()==3,"");
// this is truly pathological, but both daylight
// and chemdraw parse it properly
smi = "C1.C1CC1CC1";
delete mol;
mol = SmilesToMol(smi);
CHECK_INVARIANT(mol,smi);
ringCount=MolOps::findSSSR(*mol,rings);
CHECK_INVARIANT(ringCount==1,"");
CHECK_INVARIANT(rings.size()==1,"");
CHECK_INVARIANT(rings[0].size()==3,"");
// here's another stupid case that we need to handle:
delete mol;
smi = "C1CC11CC1";
mol = SmilesToMol(smi);
CHECK_INVARIANT(mol,smi);
ringCount=MolOps::findSSSR(*mol,rings);
CHECK_INVARIANT(ringCount==2,"");
CHECK_INVARIANT(rings.size()==2,"");
CHECK_INVARIANT(rings[0].size()==3,"");
CHECK_INVARIANT(rings[1].size()==3,"");
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testBasicCanon(){
Mol *mol;
std::string smi,refSmi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing basic SMILES canonicalization" << std::endl;
#if 1
smi = "C1OCCCC1";
mol = SmilesToMol(smi);
refSmi = MolToSmiles(*mol);
delete mol;
smi = "C1COCCC1";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "O1CCCCC1";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "OC=CC";
mol = SmilesToMol(smi);
refSmi = MolToSmiles(*mol);
delete mol;
smi = "CC=CO";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "C(C)=CO";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "C(O)=CC";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol);
TEST_ASSERT(refSmi==smi);
// --- These are related to Issue 109
delete mol;
smi = "C([H])Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getNumAtoms()==2);
refSmi = MolToSmiles(*mol);
delete mol;
smi = "CCl";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol);
TEST_ASSERT(refSmi==smi);
delete mol;
#endif
// -- Issue 131
smi = "P#[Ga]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getNumAtoms()==2);
refSmi = MolToSmiles(*mol);
delete mol;
mol = SmilesToMol(refSmi);
smi = MolToSmiles(*mol);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "O=[Ba]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getNumAtoms()==2);
refSmi = MolToSmiles(*mol);
delete mol;
mol = SmilesToMol(refSmi);
smi = MolToSmiles(*mol);
TEST_ASSERT(refSmi==smi);
// make sure empty molecules return empty SMILES:
delete mol;
mol = new ROMol();
smi = MolToSmiles(*mol);
TEST_ASSERT(smi=="");
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testLeak(){
int i = 0;
Mol *mol;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing a leak" << std::endl;
smi = "C1CC1";
for(i=0;i<1000000;i++){
mol = SmilesToMol(smi,0,1);
if(!(i%1000)){
BOOST_LOG(rdInfoLog) << i << std::endl;
}
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testStereochem(){
Mol *mol;
std::string smi,refSmi,cip;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing handling of stereochemical smiles" << std::endl;
smi = "F[C@](Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
refSmi = MolToSmiles(*mol,1);
delete mol;
smi = "F[C@](Br)(I)Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "F[C@](I)(Cl)Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "Cl[C@](Br)(F)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "Cl[C@](F)(I)Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "I[C@](F)(Br)Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "I[C@](Br)(Cl)F";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "F[C@@](Br)(Cl)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "F[C@@](Cl)(I)Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "Cl[C@@](Br)(I)F";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "Cl[C@@](F)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "[C@@](Cl)(F)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "F[C@H](Cl)Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
refSmi = MolToSmiles(*mol,1);
delete mol;
smi = "Br[C@H](F)Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
smi = MolToSmiles(*mol,1);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "Br[C@]([H])(F)Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "Br[C@](F)(Cl)[H]";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "Br[C@]1(F)(Cl).[H]1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "Br[C@H]1Cl.F1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "Br[C@]12Cl.F2.[H]1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "Br[C@]21Cl.F1.[H]2";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "[C@@H](Br)(F)Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
delete mol;
smi = "[H][C@@](Br)(F)Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi = MolToSmiles(*mol,1);
TEST_ASSERT(smi==refSmi);
// an additional set of test cases from the Chirality notes document.
// one can never have too many tests of this stuff.
delete mol;
smi = "F[C@]([H])(O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete mol;
smi = "F[C@]1([H])OC1";
mol = SmilesToMol(smi);
//TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete mol;
smi = "F[C@H](O)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete mol;
smi = "F[C@@H]1OC1";
mol = SmilesToMol(smi);
//TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete mol;
smi = "[C@](F)([H])(O)C";
mol = SmilesToMol(smi);
//TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete mol;
smi = "[C@@]1(F)([H])OC1";
mol = SmilesToMol(smi);
//TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete mol;
smi = "[C@@H](F)(O)C";
mol = SmilesToMol(smi);
//TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="C[C@@H](O)F")
smi = MolToSmiles(*mol,true,false,0);
TEST_ASSERT(smi=="[C@H](C)(O)F")
delete mol;
smi = "[C@@H]1(F)OC1";
mol = SmilesToMol(smi);
//TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="F[C@H]1CO1")
smi = MolToSmiles(*mol,true,false,0);
TEST_ASSERT(smi=="[C@H]1(F)CO1")
delete mol;
smi = "C1O[C@H]1F";
mol = SmilesToMol(smi);
//TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(2)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete mol;
smi = "C1O[C@@]1([H])F";
mol = SmilesToMol(smi);
//TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(2)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
// -----------------------------------
// test some double-bond containing molecules:
//-- cis --
delete mol;
smi = "F\\C=C/Br";
mol = SmilesToMol(smi);
refSmi = MolToSmiles(*mol,1);
delete mol;
mol = SmilesToMol(refSmi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "Br\\C=C/F";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "Br/C=C\\F";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "F/C=C\\Br";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
//-- trans --
delete mol;
smi = "F\\C=C\\Br";
mol = SmilesToMol(smi);
refSmi = MolToSmiles(*mol,1);
delete mol;
mol = SmilesToMol(refSmi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "Br\\C=C\\F";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "Br/C=C/F";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "F/C=C/Br";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
//-- more complex --
delete mol;
smi = "F\\C=C(/Cl)\\Br";
mol = SmilesToMol(smi);
refSmi = MolToSmiles(*mol,1);
delete mol;
mol = SmilesToMol(refSmi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "F/C=C(\\Cl)/Br";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "F/C=C(\\Cl)Br";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "F/C=C(Cl)/Br";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
//-- combine chirality with cis/trans --
delete mol;
smi = "F[C@H](Cl)\\C=C(/F)";
mol = SmilesToMol(smi);
refSmi = MolToSmiles(*mol,1);
delete mol;
mol = SmilesToMol(refSmi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "F[C@H](Cl)/C=C(\\F)";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
smi = "Cl[C@@H](F)/C=C(\\F)";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
smi = "Cl[C@@H](F)\\C=C(/F)";
mol = SmilesToMol(smi);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue127(){
Mol *mol,*mol2;
std::string smi,refSmi,tempStr;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 127 (chiral smiles with fused rings)" << std::endl;
smi = "Cl[C@]12[Si]C(C2)O1";
mol = SmilesToMol(smi);
//mol->debugMol(std::cout);
TEST_ASSERT(mol);
#if 1
// first roundtrip the non-chiral SMILES:
refSmi = MolToSmiles(*mol);
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
tempStr=MolToSmiles(*mol2);
TEST_ASSERT(refSmi==tempStr);
delete mol2;
#endif
// now do the true SMILES:
refSmi = MolToSmiles(*mol,1);
mol2 = SmilesToMol(refSmi);
//mol2->debugMol(std::cout);
TEST_ASSERT(mol2);
tempStr=MolToSmiles(*mol2,1);
//std::cout << refSmi << " : " << tempStr << std::endl;
TEST_ASSERT(refSmi==tempStr);
delete mol2;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue143(){
Mol *mol;
std::string smi,refSmi,tempStr;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 143 (removing chiral tags for non-chiral centers)" << std::endl;
smi = "C[C@](C)(C)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
refSmi = MolToSmiles(*mol,true);
TEST_ASSERT(refSmi=="CC(C)(C)C");
delete mol;
smi = "CC[C@](C)(C)C=O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
refSmi = MolToSmiles(*mol,true);
TEST_ASSERT(refSmi=="CCC(C)(C)C=O");
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue151(){
Mol *mol,*mol2;
std::string smi,refSmi,tempStr;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 151 (Chiral centers in rings with hydrogen on them not handled correctly)" << std::endl;
smi = "C1S[C@H]1O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
refSmi = MolToSmiles(*mol,true);
TEST_ASSERT(refSmi=="O[C@H]1CS1");
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(refSmi==smi);
delete mol;
delete mol2;
smi = "F[C@@H]1O[C@H](Cl)S1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(4)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(mol->getAtomWithIdx(3)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
refSmi = MolToSmiles(*mol,true);
TEST_ASSERT(refSmi=="F[C@@H]1O[C@H](Cl)S1");
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(refSmi==smi);
delete mol;
delete mol2;
smi = "Cl[C@@H]1S[C@@H](O1)F";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(4)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(mol->getAtomWithIdx(3)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
refSmi = MolToSmiles(*mol,true);
TEST_ASSERT(refSmi=="F[C@@H]1O[C@H](Cl)S1");
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(refSmi==smi);
delete mol;
delete mol2;
smi = "Cl[C@@H]1O[C@H](F)S1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(4)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(mol->getAtomWithIdx(3)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
refSmi = MolToSmiles(*mol,true);
TEST_ASSERT(refSmi=="F[C@H]1O[C@@H](Cl)S1");
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(refSmi==smi);
delete mol;
delete mol2;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue153(){
std::string code;
Mol *mol,*mol2;
std::string smi,refSmi,tempStr;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 153 (Incorrect order of ring-closure bonds from SMILES)" << std::endl;
smi = "C1(O[C@H]12)S2";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(2)->getProp(common_properties::_CIPCode,code);
TEST_ASSERT(code=="S");
refSmi = MolToSmiles(*mol,true);
TEST_ASSERT(refSmi=="O1C2S[C@H]12");
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(refSmi==smi);
delete mol;
delete mol2;
smi = "C1(O[C@H]21)S2";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(2)->getProp(common_properties::_CIPCode,code);
TEST_ASSERT(code=="R");
refSmi = MolToSmiles(*mol,true);
TEST_ASSERT(refSmi=="O1C2S[C@@H]12");
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(refSmi==smi);
delete mol;
delete mol2;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue157(){
std::string code;
Mol *mol,*mol2;
std::string smi,refSmi,tempStr;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 157 (Symmetric molecules with multiple chiral centers badly canonicalized)" << std::endl;
#if 1
smi = "O[C@](C)(Cl)[C@@](O)(Cl)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(mol->getAtomWithIdx(4)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,code);
TEST_ASSERT(code=="R");
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(4)->getProp(common_properties::_CIPCode,code);
TEST_ASSERT(code=="S");
refSmi = MolToSmiles(*mol,true);
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(refSmi==smi);
delete mol;
delete mol2;
smi = "Cl[C@@](C)1CC[C@@](C)(C1)Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
refSmi = MolToSmiles(*mol,true);
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(refSmi==smi);
delete mol;
delete mol2;
BOOST_LOG(rdInfoLog)<<"-**-**---------------------------------------"<<std::endl;
smi = "[H][C@@]12CC(CO1)CN2";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,smi);
TEST_ASSERT(smi=="S");
refSmi = MolToSmiles(*mol,true);
BOOST_LOG(rdInfoLog)<<refSmi<<std::endl;
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
BOOST_LOG(rdInfoLog)<<refSmi<<std::endl;
BOOST_LOG(rdInfoLog)<<smi<<std::endl;
TEST_ASSERT(refSmi==smi);
delete mol;
delete mol2;
#endif
smi = "[H][C@@]12C[14C@@](C=C1)(C3C2C(NC3=O)=O)[H]";
//smi="C1=C[C@@H]2C[C@H]1C1C(=O)NC(=O)C21";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
mol->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,smi);
TEST_ASSERT(smi=="R");
mol->getAtomWithIdx(2)->getProp(common_properties::_CIPCode,smi);
TEST_ASSERT(smi=="S");
//mol->debugMol(std::cout);
refSmi = MolToSmiles(*mol,true);
mol2 = SmilesToMol(refSmi);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
BOOST_LOG(rdInfoLog)<<refSmi<<std::endl;
BOOST_LOG(rdInfoLog)<<smi<<std::endl;
TEST_ASSERT(refSmi==smi);
delete mol;
delete mol2;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue159(){
Mol *mol;
std::string smi,refSmi,tempStr;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 159 (cis/trans wrong in some branched systems)" << std::endl;
smi = "C/C=C/O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
refSmi = MolToSmiles(*mol,1);
delete mol;
smi = "C(\\C)=C/O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "C(\\\\C)=C/O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "C(=C/O)\\C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOE);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
delete mol;
smi = "C(\\C/C=C/Cl)=C/O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(2)->getStereo() == Bond::STEREOE);
delete mol;
smi = "O=C\\C=C/F";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(0)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
TEST_ASSERT(mol->getBondWithIdx(2)->getStereo() == Bond::STEREOZ);
delete mol;
smi = "C(/C=O)=C/F";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
TEST_ASSERT(mol->getBondWithIdx(2)->getStereo() == Bond::STEREOZ);
delete mol;
smi = "C(=C/F)/C=O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOZ);
TEST_ASSERT(mol->getBondWithIdx(3)->getStereo() == Bond::STEREONONE);
delete mol;
smi = "C(=O)\\C=C/Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(2)->getStereo() == Bond::STEREOZ);
TEST_ASSERT(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
delete mol;
smi = "CC(=O)\\C=C/Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOZ);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
delete mol;
smi = "C(=O)\\N=C\\Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(2)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
delete mol;
smi = "CC(=O)\\N=C\\Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
delete mol;
smi = "C(/Br)(=C/Cl)Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOZ);
delete mol;
smi = "C(=C/Cl)(/Br)Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOZ);
delete mol;
smi = "Cl\\C=C(\\Br)";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
delete mol;
smi = "Cl\\C(=C\\Br)";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
delete mol;
smi = "C(/C=C/C)";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
delete mol;
smi = "C(/C)=C/C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOZ);
// ---------
// These next few molecules test propagation of bond flips:
// ---------
delete mol;
smi = "Cl/C=C(/C=C/C)\\C=C\\Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOZ);
TEST_ASSERT(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(6)->getStereo() == Bond::STEREOE);
delete mol;
smi = "C(/C=C/C)(\\C=C\\Br)=C\\Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(6)->getStereo() == Bond::STEREOZ);
delete mol;
smi = "Br/C=C/C(/C=C/C)=C\\Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(6)->getStereo() == Bond::STEREOZ);
delete mol;
smi = "Cl/C=C(/C=C/C=C\\F)\\C=C\\Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOZ);
TEST_ASSERT(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(5)->getStereo() == Bond::STEREOZ);
TEST_ASSERT(mol->getBondWithIdx(8)->getStereo() == Bond::STEREOE);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue175(){
Mol *mol;
std::string smi,refSmi,tempStr;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 175 (cis/trans wrong on ring closures)" << std::endl;
smi = "Cl\\C=C1.F/1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
delete mol;
smi = "Cl\\C=C1CN/1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
smi = "C/1=C/F.F1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOZ);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue176(){
Mol *mol;
std::string smi,refSmi,tempStr;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 176 (problems with 'mol BOND ring_number')" << std::endl;
smi = "C1CC1C1CC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumBonds()==7);
delete mol;
smi = "C1CC1C1CC-1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumBonds()==7);
delete mol;
smi = "C1CC1C1CC=1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumBonds()==7);
delete mol;
smi = "C1CC1C=1CC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumBonds()==7);
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue180(){
Mol *mol;
std::string smi,refSmi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 180: Z/E problems" << std::endl;
smi = "Cl/C(=N\\O)/C(=N\\O)Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOZ);
TEST_ASSERT(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOE);
refSmi = MolToSmiles(*mol,1);
delete mol;
smi="Cl/C(/C(Br)=N\\O)=N\\O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(5)->getStereo() == Bond::STEREOZ);
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue184(){
Mol *mol;
std::string smi,refSmi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 184: Cis/Trans incorrect on ring-closure bonds" << std::endl;
smi = "C1NC(Cl)C(=N\\O)/C1=N\\O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
//mol->debugMol(std::cout);
TEST_ASSERT(mol->getBondWithIdx(4)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOZ);
TEST_ASSERT(mol->getBondWithIdx(7)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(mol->getBondWithIdx(7)->getStereo() == Bond::STEREOZ);
refSmi = MolToSmiles(*mol,1);
delete mol;
mol = SmilesToMol(refSmi);
TEST_ASSERT(mol);
for(RWMol::BondIterator bondIt=mol->beginBonds();
bondIt!=mol->endBonds();
bondIt++){
if((*bondIt)->getBondType()==Bond::DOUBLE){
TEST_ASSERT((*bondIt)->getStereo()==Bond::STEREOZ);
}
}
smi = MolToSmiles(*mol,1);
TEST_ASSERT(refSmi==smi);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue185(){
Mol *mol;
std::string smi,refSmi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 185: Cis/Trans incorrect on writing branches" << std::endl;
// start with a simple E/Z handling case with branches:
smi ="C(/C)=N/O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOZ);
refSmi = MolToSmiles(*mol,1,0,0);
BOOST_LOG(rdInfoLog)<<refSmi<<std::endl;
TEST_ASSERT(refSmi=="C(\\C)=N\\O");
delete mol;
// make sure we can round-trip:
mol = SmilesToMol(refSmi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOZ);
delete mol;
// now make it more complex
smi ="CC(=N\\O)/C=P/N";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
TEST_ASSERT(mol->getBondWithIdx(4)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOE);
refSmi = MolToSmiles(*mol,1);
BOOST_LOG(rdInfoLog)<<refSmi<<std::endl;
delete mol;
mol = SmilesToMol(refSmi);
TEST_ASSERT(mol);
for(RWMol::BondIterator bondIt=mol->beginBonds();
bondIt!=mol->endBonds();
bondIt++){
if((*bondIt)->getBondType()==Bond::DOUBLE){
TEST_ASSERT((*bondIt)->getStereo()==Bond::STEREOE);
}
}
smi = MolToSmiles(*mol,1);
//std::cout << "ref: " << refSmi << " -> " << smi << std::endl;
TEST_ASSERT(refSmi==smi);
// now repeat that experiment, but this time root the SMILES so that
// we go in a "sensible" order:
delete mol;
smi ="CC(=N\\O)/C=P/N";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
refSmi = MolToSmiles(*mol,true,false,6);
BOOST_LOG(rdInfoLog)<<refSmi<<std::endl;
TEST_ASSERT(refSmi=="N/P=C/C(C)=N/O");
delete mol;
mol = SmilesToMol(refSmi);
TEST_ASSERT(mol);
for(RWMol::BondIterator bondIt=mol->beginBonds();
bondIt!=mol->endBonds();
bondIt++){
if((*bondIt)->getBondType()==Bond::DOUBLE){
TEST_ASSERT((*bondIt)->getStereo()==Bond::STEREOE);
}
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue191(){
Mol *mol;
std::string smi,refSmi;
int numE=0;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 191: Bad bond directions in a branch" << std::endl;
smi ="C2=NNC(N=C2)=N\\N=C\\c1ccccc1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getBondWithIdx(7)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(mol->getBondWithIdx(7)->getStereo() == Bond::STEREOE);
refSmi = MolToSmiles(*mol,1);
delete mol;
//std::cout << "ref: " << refSmi << std::endl;
mol = SmilesToMol(refSmi);
TEST_ASSERT(mol);
//mol->debugMol(std::cout);
numE = 0;
for(RWMol::BondIterator bondIt=mol->beginBonds();
bondIt!=mol->endBonds();
bondIt++){
if((*bondIt)->getBondType()==Bond::DOUBLE){
TEST_ASSERT((*bondIt)->getStereo()!=Bond::STEREOZ);
if((*bondIt)->getStereo()==Bond::STEREOE){
numE++;
}
}
}
TEST_ASSERT(numE==1);
smi = MolToSmiles(*mol,1);
//std::cout << "ref: " << refSmi << " -> " << smi << std::endl;
TEST_ASSERT(refSmi==smi);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue256(){
Mol *mol;
Bond *bond;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 256: SMILES yields incorrect structure" << std::endl;
smi ="C1CC[C+]1=1CCC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
bond=mol->getBondBetweenAtoms(3,0);
TEST_ASSERT(bond)
TEST_ASSERT(bond->getBondType()==Bond::SINGLE);
bond=mol->getBondBetweenAtoms(3,6);
TEST_ASSERT(bond)
TEST_ASSERT(bond->getBondType()==Bond::DOUBLE);
delete mol;
smi ="C1CC[C+]=11CCC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
bond=mol->getBondBetweenAtoms(3,0);
TEST_ASSERT(bond)
TEST_ASSERT(bond->getBondType()==Bond::DOUBLE);
bond=mol->getBondBetweenAtoms(3,6);
TEST_ASSERT(bond)
TEST_ASSERT(bond->getBondType()==Bond::SINGLE);
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue266(){
RWMol *mol;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Issue 266: kekulized SMILES output" << std::endl;
smi ="c1ccccc1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol);
TEST_ASSERT(smi=="c1ccccc1");
MolOps::Kekulize(*mol);
smi = MolToSmiles(*mol);
TEST_ASSERT(smi=="C1=CC=CC=C1");
delete mol;
smi ="c1ccccc1c1ccccc1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol);
TEST_ASSERT(smi=="c1ccc(-c2ccccc2)cc1");
MolOps::Kekulize(*mol);
smi = MolToSmiles(*mol);
TEST_ASSERT(smi=="C1=CC=C(C2=CC=CC=C2)C=C1");
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testRootedAt(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing rootedAtAtom functionality" << std::endl;
{
RWMol *mol;
std::string smi;
smi ="CN(C)C";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false,false,-1);
TEST_ASSERT(smi=="CN(C)C");
smi = MolToSmiles(*mol,false,false,1);
TEST_ASSERT(smi=="N(C)(C)C");
smi = MolToSmiles(*mol,false,false,2);
TEST_ASSERT(smi=="CN(C)C");
delete mol;
}
{
// This was github issue #182:
RWMol mol;
std::string smi;
smi = MolToSmiles(mol);
TEST_ASSERT(smi=="");
smi = MolToSmiles(mol,false,false,0);
TEST_ASSERT(smi=="");
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIsotopes(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing isotope handling" << std::endl;
{
std::string smi ="C[13C](C)(C)C";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(feq(mol->getAtomWithIdx(1)->getMass(),13.0034));
smi = MolToSmiles(*mol,false);
TEST_ASSERT(smi=="CC(C)(C)C");
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="C[13C](C)(C)C");
delete mol;
}
{
std::string smi ="C[12C](C)(C)C";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->getMass()==12.0);
smi = MolToSmiles(*mol,false);
TEST_ASSERT(smi=="CC(C)(C)C");
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="C[12C](C)(C)C");
delete mol;
}
{
std::string smi ="CC[U]";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false);
TEST_ASSERT(smi=="CC[U]");
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="CC[U]");
delete mol;
}
{
std::string smi ="CC[238U]";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false);
TEST_ASSERT(smi=="CC[U]");
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="CC[238U]");
delete mol;
}
{
// issue 3526814
std::string smi ="CCCCS(=[18O])(=O)CCCCl";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false);
TEST_ASSERT(smi=="CCCCS(=O)(=O)CCCCl");
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="CCCCS(=O)(=[18O])CCCCl");
delete mol;
}
{
// issue 3526814
std::string smi ="CCCCS(=[24O])(=O)CCCCl";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false);
TEST_ASSERT(smi=="CCCCS(=O)(=O)CCCCl");
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="CCCCS(=O)(=[24O])CCCCl");
delete mol;
}
{
// issue 3526814
std::string smi ="CCCCS(=O)(=[24O])CCCCl";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false);
TEST_ASSERT(smi=="CCCCS(=O)(=O)CCCCl");
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="CCCCS(=O)(=[24O])CCCCl");
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testBug1670149(){
RWMol *mol;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing SF.net bug 1670149" << std::endl;
smi ="C1[NH2+]CCC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false,false,-1);
TEST_ASSERT(smi=="C1CC[NH2+]C1");
mol->getAtomWithIdx(1)->setNumExplicitHs(0);
mol->getAtomWithIdx(1)->setNoImplicit(false);
mol->getAtomWithIdx(1)->updatePropertyCache();
TEST_ASSERT(mol->getAtomWithIdx(1)->getNumImplicitHs()==2);
smi = MolToSmiles(*mol,false,false,-1);
TEST_ASSERT(smi=="C1CC[NH2+]C1");
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testBug1719046(){
RWMol *mol;
std::string smi;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing SF.net bug 1719046: explicit Hs in canonical smiles" << std::endl;
smi ="Cl[CH]1CCCCC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false,false,-1);
std::cerr<<"smi: "<<smi<<std::endl;
TEST_ASSERT(smi=="ClC1CCCCC1");
delete mol;
smi ="Cl[C@H]1CCCCC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false,false,-1);
std::cerr<<"smi: "<<smi<<std::endl;
TEST_ASSERT(smi=="ClC1CCCCC1");
delete mol;
smi ="Cl[C@H]1C(Br)CCCC1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false,false,-1);
std::cerr<<"smi: "<<smi<<std::endl;
TEST_ASSERT(smi=="ClC1CCCCC1Br");
delete mol;
smi ="[CH]1=[CH][CH]=[CH][CH]=[CH]1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false,false,-1);
std::cerr<<"smi: "<<smi<<std::endl;
TEST_ASSERT(smi=="c1ccccc1");
delete mol;
smi ="c1ccccn1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false,false,-1);
std::cerr<<"smi: "<<smi<<std::endl;
TEST_ASSERT(smi=="c1ccncc1");
delete mol;
smi ="C1=CNC=C1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false,false,-1);
std::cerr<<"smi: "<<smi<<std::endl;
TEST_ASSERT(smi=="c1cc[nH]c1");
delete mol;
smi ="[CH]1=[CH][NH][CH]=[CH]1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false,false,-1);
std::cerr<<"smi: "<<smi<<std::endl;
TEST_ASSERT(smi=="c1cc[nH]c1");
delete mol;
// this was Issue 35525671
smi="P1C=CC=C1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,false,false,-1);
std::cerr<<"smi: "<<smi<<std::endl;
TEST_ASSERT(smi=="c1cc[pH]c1");
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testBug1842174(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing SF.net bug 1842174: bad bond dirs in branches" << std::endl;
RWMol *mol;
std::string smi;
smi ="F/C=N/Cl";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,true,false,-1);
BOOST_LOG(rdInfoLog) << smi << std::endl;
TEST_ASSERT(smi=="F/C=N/Cl");
smi = MolToSmiles(*mol,true,false,1);
BOOST_LOG(rdInfoLog) << smi << std::endl;
TEST_ASSERT(smi=="C(\\F)=N/Cl");
delete mol;
smi ="C(\\C=C\\F)=C(/Cl)Br";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,true,false,-1);
BOOST_LOG(rdInfoLog) << smi << std::endl;
TEST_ASSERT(smi=="F/C=C/C=C(/Cl)Br");
smi = MolToSmiles(*mol,true,false,0);
BOOST_LOG(rdInfoLog) << smi << std::endl;
TEST_ASSERT(smi=="C(/C=C/F)=C(\\Cl)Br");
delete mol;
smi ="O=NC1=NOC(=N\\O)/C1=N\\O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,true,false,-1);
BOOST_LOG(rdInfoLog) << smi << std::endl;
TEST_ASSERT(smi=="O=NC1=NOC(=N\\O)/C1=N\\O");
// ----------------------
// the next two examples are a pair:
// vvvvvvvvvvvvvvvvvvvvvv
delete mol;
smi ="O/N=C/1COCC1=N\\O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,true,false,-1);
BOOST_LOG(rdInfoLog) << smi << std::endl;
TEST_ASSERT(smi=="O/N=C1\\COC\\C1=N\\O");
// this time the algorithm is forced to set
// the directionality on the ring closure bond:
delete mol;
smi ="O/N=C/1COC[N+]1=N\\O";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi = MolToSmiles(*mol,true,false,-1);
BOOST_LOG(rdInfoLog) << smi << std::endl;
TEST_ASSERT(smi=="O/N=C1\\COC\\[N+]1=N\\O");
// ^^^^^^^^^^^^^^^^^^^^^^
// end of the pair
// ----------------------
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testBug1844617(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing SF.net bug 1844617: oscillating chirality in canonical smiles" << std::endl;
RWMol *mol;
std::string smi,smi2;
std::string label;
#if 0
smi ="O=C1C2OCC[C@@]22C(CC1)CNCC2";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
//mol->debugMol(std::cout);
TEST_ASSERT(mol->getAtomWithIdx(6)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(6)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
smi = MolToSmiles(*mol,true);
BOOST_LOG(rdInfoLog) << smi << std::endl;
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi2 = MolToSmiles(*mol,true);
BOOST_LOG(rdInfoLog) << smi2 << std::endl;
TEST_ASSERT(smi==smi2);
delete mol;
#endif
smi ="O=C1CC[C@@]2(O)[C@@H]3N(C)CC[C@]22[C@H]1OC[C@H]2CC3";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
//mol->debugMol(std::cout);
MolOps::assignStereochemistry(*mol);
//mol->debugMol(std::cout);
TEST_ASSERT(mol->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(4)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
TEST_ASSERT(mol->getAtomWithIdx(6)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(6)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
TEST_ASSERT(mol->getAtomWithIdx(11)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(11)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
TEST_ASSERT(mol->getAtomWithIdx(12)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(12)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
TEST_ASSERT(mol->getAtomWithIdx(15)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(15)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
#if 1
smi = MolToSmiles(*mol,true);
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
//mol->debugMol(std::cout);
smi2 = MolToSmiles(*mol,true);
BOOST_LOG(rdInfoLog) << smi << std::endl;
BOOST_LOG(rdInfoLog) << smi2 << std::endl;
TEST_ASSERT(smi==smi2);
#endif
delete mol;
smi ="O=C1CC[C@@]2(O)[C@@H]3N(C)CC[C@]22[C@H]1OC[C@H]2CC3";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
//mol->debugMol(std::cout);
MolOps::assignStereochemistry(*mol);
//mol->debugMol(std::cout);
TEST_ASSERT(mol->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(4)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
TEST_ASSERT(mol->getAtomWithIdx(6)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(6)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
TEST_ASSERT(mol->getAtomWithIdx(11)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(11)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
TEST_ASSERT(mol->getAtomWithIdx(12)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(12)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
TEST_ASSERT(mol->getAtomWithIdx(15)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(15)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
#if 1
smi = MolToSmiles(*mol,true,false,0);
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
//mol->debugMol(std::cout);
smi2 = MolToSmiles(*mol,true,false,0);
BOOST_LOG(rdInfoLog) << smi << std::endl;
BOOST_LOG(rdInfoLog) << smi2 << std::endl;
TEST_ASSERT(smi==smi2);
#endif
delete mol;
smi ="O=C1CC[C@@]2(O)[C@@H]3N(CC4CC4)CC[C@]22[C@H]1OC[C@H]2CC3";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
//mol->debugMol(std::cout);
TEST_ASSERT(mol->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(4)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
TEST_ASSERT(mol->getAtomWithIdx(6)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(6)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
TEST_ASSERT(mol->getAtomWithIdx(14)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(14)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
TEST_ASSERT(mol->getAtomWithIdx(15)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(15)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
TEST_ASSERT(mol->getAtomWithIdx(18)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(18)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
#if 1
smi = MolToSmiles(*mol,true);
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
smi2 = MolToSmiles(*mol,true);
BOOST_LOG(rdInfoLog) << smi << std::endl;
BOOST_LOG(rdInfoLog) << smi2 << std::endl;
TEST_ASSERT(smi==smi2);
#endif
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testBug1844959(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing SF.net bug 1844959: bad handling of Hs in chiral smiles" << std::endl;
RWMol *mol;
std::string smi,smi2;
std::string label;
// ----------------------
// the next examples are a set:
// (this is the part that was originally working):
// vvvvvvvvvvvvvvvvvvvvvv
smi ="C[C@]12CNOC2.F1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
smi = MolToSmiles(*mol,true);
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
smi2 = MolToSmiles(*mol,true);
TEST_ASSERT(smi==smi2);
// swap the order and make sure the chirality swaps with it:
delete mol;
smi ="C[C@]12CNOC1.F2";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
smi = MolToSmiles(*mol,true);
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
smi2 = MolToSmiles(*mol,true);
TEST_ASSERT(smi==smi2);
// now make sure it works with a reversed chiral tag:
smi ="C[C@@]12CNOC2.F1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
smi = MolToSmiles(*mol,true);
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
smi2 = MolToSmiles(*mol,true);
TEST_ASSERT(smi==smi2);
delete mol;
smi ="C[C@@]12CNOC1.F2";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
smi = MolToSmiles(*mol,true);
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
smi2 = MolToSmiles(*mol,true);
TEST_ASSERT(smi==smi2);
// ^^^^^^^^^^^^^^^^^^^^^^
// end of the set
// ----------------------
// ----------------------
// the next examples are a set:
// (this is the part that was originally failing):
// vvvvvvvvvvvvvvvvvvvvvv
BOOST_LOG(rdInfoLog)<<"--------------------------------------------"<<std::endl;
smi ="C[C@]12CNOC2.[H]1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
//mol->debugMol(std::cerr);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
smi = MolToSmiles(*mol,true);
BOOST_LOG(rdInfoLog)<<smi<<std::endl;
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
//mol->debugMol(std::cerr);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
smi2 = MolToSmiles(*mol,true);
TEST_ASSERT(smi==smi2);
// swap the order and make sure the chirality swaps with it:
delete mol;
smi ="C[C@]12CNOC1.[H]2";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
smi = MolToSmiles(*mol,true);
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
smi2 = MolToSmiles(*mol,true);
TEST_ASSERT(smi==smi2);
// now make sure it works with a reversed chiral tag:
smi ="C[C@@]12CNOC2.[H]1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
smi = MolToSmiles(*mol,true);
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="R");
smi2 = MolToSmiles(*mol,true);
TEST_ASSERT(smi==smi2);
delete mol;
smi ="C[C@@]12CNOC1.[H]2";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
smi = MolToSmiles(*mol,true);
delete mol;
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
MolOps::assignStereochemistry(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
mol->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,label);
TEST_ASSERT(label=="S");
smi2 = MolToSmiles(*mol,true);
TEST_ASSERT(smi==smi2);
// ^^^^^^^^^^^^^^^^^^^^^^
// end of the set
// ----------------------
delete mol;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testBug1942220(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing sf.net bug 1942220" << std::endl;
RWMol *m;
std::string smi;
smi="[C](Cl)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==3);
TEST_ASSERT(m->getNumAtoms(false)==3);
smi = MolToSmiles(*m);
TEST_ASSERT(smi=="Cl[C]Br");
delete m;
smi="[CH2](Cl)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==3);
TEST_ASSERT(m->getNumAtoms(false)==5);
smi = MolToSmiles(*m);
TEST_ASSERT(smi=="ClCBr");
delete m;
smi="C(Cl)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==3);
TEST_ASSERT(m->getNumAtoms(false)==5);
smi = MolToSmiles(*m);
TEST_ASSERT(smi=="ClCBr");
delete m;
smi="OS(=O)=O";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
//TEST_ASSERT(m->getNumAtoms(false)==5);
smi = MolToSmiles(*m);
TEST_ASSERT(smi=="O=[SH](=O)O");
delete m;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testRingStereochemReporting(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing error reporting with ring stereochem" << std::endl;
RWMol *m;
std::string smi;
smi="C[C@H]1CC[C@@H](C)CC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==8);
smi = MolToSmiles(*m,true);
TEST_ASSERT(m->hasProp(common_properties::_ringStereoWarning));
smi = MolToSmiles(*m,false);
TEST_ASSERT((!m->hasProp(common_properties::_ringStereoWarning)));
delete m;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testBug3127883()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 3127883 (kekulization failing) " << std::endl;
{
ROMol *m;
std::string smi;
smi = "c(:c:c:1):c:c:c:1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
delete m;
}
{
ROMol *m;
std::string smi;
smi = "c1(:c(:c(:c(-C(-c2:c(:c(:c(:c(:c:2)))))=C):c(:c:1))))";
m = SmilesToMol(smi);
TEST_ASSERT(m);
delete m;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testBug3139534(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3139534: stereochemistry in larger rings" << std::endl;
// the parsing part of this is in ../testChirality.cpp, here we look at
// smiles generation
{
RWMol *m;
std::string smiles="C1COC/C=C\\CCC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(4)->getStereo()==Bond::STEREOZ);
smiles = MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog) << "smiles: " << smiles<< std::endl;
TEST_ASSERT(smiles=="C1=C\\COCCCCC/1");
delete m;
}
{
RWMol *m;
std::string smiles="C1COC/C=C/CCC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(4)->getStereo()==Bond::STEREOE);
smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="C1=C/COCCCCC/1");
delete m;
}
{
RWMol *m;
std::string smiles="C1CC/C=C/C=C/CCC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles = MolToSmiles(*m,true,false,-1,false);
//TEST_ASSERT(smiles=="C1CC/C=C/C=C/CCC1");
TEST_ASSERT(smiles=="C1CC/C=C/C=C/CCC1");
smiles = MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog) << "smiles: " << smiles<< std::endl;
TEST_ASSERT(smiles=="C1=C/CCCCCC/C=C/1");
delete m;
}
{
RWMol *m;
std::string smiles="C/1=C/C=C/CCCCCC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles = MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog) << "smiles: " << smiles<< std::endl;
TEST_ASSERT(smiles=="C1=C\\CCCCCC/C=C/1");
delete m;
}
{
RWMol *m;
std::string smiles="C1COC/C=C/C=C/C1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(4)->getStereo()==Bond::STEREOE);
smiles = MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog) << "smiles: " << smiles<< std::endl;
TEST_ASSERT(smiles=="C1=C/CCCOC/C=C/1");
delete m;
}
{
RWMol *m;
std::string smiles="C1=C/OCC/C=C\\CC\\1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondWithIdx(5)->getStereo()==Bond::STEREOZ);
delete m;
}
{
RWMol *m;
std::string smiles="C1CCCCN/C=C/1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles = MolToSmiles(*m,true,false,7,false);
BOOST_LOG(rdInfoLog) << "smiles: " << smiles<< std::endl;
TEST_ASSERT(smiles=="C1=C/NCCCCC/1");
smiles = MolToSmiles(*m,true,false,0,false);
BOOST_LOG(rdInfoLog) << "smiles: " << smiles<< std::endl;
TEST_ASSERT(smiles=="C1CCCCN/C=C/1");
delete m;
}
{
RWMol *m;
std::string smiles="CCC/[N+]/1=C/c2ccccc2OC(=O)/C=C1/O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(3)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondWithIdx(14)->getStereo()==Bond::STEREOE);
smiles = MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog) << "smiles: " << smiles<< std::endl;
TEST_ASSERT(smiles=="CCC/[N+]1=C/c2ccccc2OC(=O)\\C=C/1O");
delete m;
}
// some torture tests with natural products (thanks to James Davidson for the examples)
{
RWMol *m;
std::string smiles="NC(=O)O[C@H]1C(/C)=C/[C@H](C)[C@@H](O)[C@@H](OC)C[C@H](C)C\\C2=C(/OC)C(=O)\\C=C(\\NC(=O)C(\\C)=C\\C=C/[C@@H]1OC)C2=O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondBetweenAtoms(30,32)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondBetweenAtoms(33,34)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondBetweenAtoms(5,7)->getStereo()==Bond::STEREOE);
std::string csmiles=MolToSmiles(*m,true);
RWMol *m2;
for(unsigned int i=0;i<m->getNumAtoms();++i){
std::string nsmiles=MolToSmiles(*m,true,false,i,false);
m2 = SmilesToMol(nsmiles);
TEST_ASSERT(m2);
std::string ncsmiles = MolToSmiles(*m2,true);
if(ncsmiles!=csmiles){
std::cerr<<" failed in iteration: "<<i<<"\n"<<csmiles<<"\n != \n"<<ncsmiles<<"\n starting from:\n"<<nsmiles<<"\n";
m2->debugMol(std::cerr);
TEST_ASSERT(ncsmiles==csmiles);
}
delete m2;
}
delete m;
}
{
RWMol *m;
std::string smiles="CC(O[C@@H]1C=C(C)[C@H]2[C@H]([C@H]3O[C@@H]2C/C(C)=C\\CC[C@@]3(C)OC(C)=O)[C@H]1C(OC(C)=O)(C)C)=O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondBetweenAtoms(13,15)->getStereo()==Bond::STEREOZ);
std::string csmiles=MolToSmiles(*m,true);
RWMol *m2;
for(unsigned int i=0;i<m->getNumAtoms();++i){
std::string nsmiles=MolToSmiles(*m,true,false,i,false);
m2 = SmilesToMol(nsmiles);
TEST_ASSERT(m2);
std::string ncsmiles = MolToSmiles(*m2,true);
if(ncsmiles!=csmiles){
std::cerr<<" failed in iteration: "<<i<<"\n"<<csmiles<<"\n != \n"<<ncsmiles<<"\n starting from:\n"<<nsmiles<<"\n";
m2->debugMol(std::cerr);
TEST_ASSERT(ncsmiles==csmiles);
}
delete m2;
}
delete m;
}
{
RWMol *m;
std::string smiles="CC(O[C@@H]1C=C(C)[C@H]2[C@H]([C@H]3O[C@@H]2C/C(C)=C/CC[C@@]3(C)OC(C)=O)[C@H]1C(OC(C)=O)(C)C)=O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondBetweenAtoms(13,15)->getStereo()==Bond::STEREOE);
std::string csmiles=MolToSmiles(*m,true);
RWMol *m2;
for(unsigned int i=0;i<m->getNumAtoms();++i){
std::string nsmiles=MolToSmiles(*m,true,false,i,false);
m2 = SmilesToMol(nsmiles);
TEST_ASSERT(m2);
std::string ncsmiles = MolToSmiles(*m2,true);
if(ncsmiles!=csmiles){
std::cerr<<" failed in iteration: "<<i<<"\n"<<csmiles<<"\n != \n"<<ncsmiles<<"\n starting from:\n"<<nsmiles<<"\n";
m2->debugMol(std::cerr);
TEST_ASSERT(ncsmiles==csmiles);
}
delete m2;
}
delete m;
}
{
RWMol *m;
std::string smiles="CC(=O)[C@@H]1CC=C(C)[C@@H]2[C@@H]3O[C@@H]([C@@H](O)C/C=C\\CC3)[C@@H]12";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondBetweenAtoms(15,16 )->getStereo()==Bond::STEREOZ);
std::string csmiles=MolToSmiles(*m,true);
RWMol *m2;
for(unsigned int i=0;i<m->getNumAtoms();++i){
std::string nsmiles=MolToSmiles(*m,true,false,i,false);
m2 = SmilesToMol(nsmiles);
TEST_ASSERT(m2);
std::string ncsmiles = MolToSmiles(*m2,true);
if(ncsmiles!=csmiles){
std::cerr<<" failed in iteration: "<<i<<"\n"<<csmiles<<"\n != \n"<<ncsmiles<<"\n starting from:\n"<<nsmiles<<"\n";
m2->debugMol(std::cerr);
TEST_ASSERT(ncsmiles==csmiles);
}
delete m2;
}
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testAtomMaps(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "test adding atom-map information" << std::endl;
{
RWMol *m;
std::string smiles="[*:1]CCC([C:200])C";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::molAtomMapNumber));
//changed: smiles does not need to be canonical
smiles = MolToSmiles(*m,true,false,-1,false);
TEST_ASSERT(smiles=="[*:1]CCC([C:200])C");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBug3145697(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3145697 repeated ring labels in disconnected structures" << std::endl;
{
RWMol *m;
std::string smiles="C1.C11.C1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="CCC");
delete m;
smiles="C1.C11.C";
m = SmilesToMol(smiles);
TEST_ASSERT(!m);
delete m;
}
{
RWMol *m;
std::string smiles="C1.C11.O1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="CCO");
delete m;
smiles="C1.C1=1.O1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="CC=O");
delete m;
smiles="C1.C=11.O1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="C=CO");
delete m;
}
{
RWMol *m;
std::string smiles="C1C.CC11CCC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="CCC1(C)CCC1");
delete m;
smiles="C1C.CC11CCC";
m = SmilesToMol(smiles);
TEST_ASSERT(!m);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBug3152751(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3152751 cannot roundtrip charged aromatic Se and Te" << std::endl;
{
RWMol *m;
std::string smiles="c1cccc[te+]1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
smiles = MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
}
{
RWMol *m;
std::string smiles="c1cccc[se+]1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
smiles = MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
}
{
RWMol *m;
std::string smiles="c1ccc[te]1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
smiles = MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
}
{
RWMol *m;
std::string smiles="c1ccc[se]1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
smiles = MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testReplacementPatterns(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing use of replacement patterns in input" << std::endl;
{
std::string smi ="C{cycloprop}C";
std::map<std::string,std::string> repls;
repls["{cycloprop}"]="C1(CC1)";
RWMol *mol = SmilesToMol(smi,0,true,&repls);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==5);
TEST_ASSERT(mol->getAtomWithIdx(1)->getDegree()==4);
delete mol;
}
{
std::string smi ="C{cycloprop}C";
std::map<std::string,std::string> repls;
repls["{cycloprop}"]="C1(C({acid})C1)";
repls["{acid}"]="C(=O)O";
RWMol *mol = SmilesToMol(smi,0,true,&repls);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==8);
TEST_ASSERT(mol->getAtomWithIdx(1)->getDegree()==4);
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testAllBondsExplicit(){
BOOST_LOG(rdInfoLog)<< "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing forcing explicit bonds in the output SMILES" << std::endl;
{
std::string smi ="CCC";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==3);
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="CCC");
smi = MolToSmiles(*mol,true,false,-1,true,true);
TEST_ASSERT(smi=="C-C-C");
delete mol;
}
{
std::string smi ="C1CC1";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==3);
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="C1CC1");
smi = MolToSmiles(*mol,true,false,-1,true,true);
TEST_ASSERT(smi=="C1-C-C-1");
delete mol;
}
{
std::string smi ="c1ccccc1";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==6);
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="c1ccccc1");
smi = MolToSmiles(*mol,true,false,-1,true,true);
TEST_ASSERT(smi=="c1:c:c:c:c:c:1");
delete mol;
}
{
std::string smi ="c1ccccc1c1ccccc1";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==12);
smi = MolToSmiles(*mol,true);
TEST_ASSERT(smi=="c1ccc(-c2ccccc2)cc1");
smi = MolToSmiles(*mol,true,false,-1,true,true);
TEST_ASSERT(smi=="c1:c:c:c(-c2:c:c:c:c:c:2):c:c:1");
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testBug3525799(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3525799: bad smiles for r groups" << std::endl;
{
RWMol *m;
std::string smiles="CC*";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="[*]CC");
m->getAtomWithIdx(2)->setProp(common_properties::dummyLabel,"foo");
smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="[*]CC");
delete m;
}
{
RWMol *m;
std::string smiles="CC*";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="[*]CC");
m->getAtomWithIdx(2)->setProp(common_properties::smilesSymbol,"Xa");
smiles = MolToSmiles(*m,true);
TEST_ASSERT(smiles=="[Xa]CC");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBug3526810(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3526810: canonical smiles failure in symmetric heterocycles" << std::endl;
{
RWMol *m;
std::string smiles="C1SCCSCCCSCCSCC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles1 = MolToSmiles(*m,true);
delete m;
std::string smiles2="C1CSCCSCCCSCCSC1";
m = SmilesToMol(smiles2);
TEST_ASSERT(m);
std::string csmiles2 = MolToSmiles(*m,true);
delete m;
//std::cerr<<"csmi1: "<<csmiles1<<std::endl;
//std::cerr<<"csmi2: "<<csmiles2<<std::endl;
TEST_ASSERT(csmiles1==csmiles2);
}
{
RWMol *m;
std::string smiles="C1NCCNCCCNCCNCC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles1 = MolToSmiles(*m,true);
delete m;
std::string smiles2="C1CNCCNCCCNCCNC1";
m = SmilesToMol(smiles2);
TEST_ASSERT(m);
std::string csmiles2 = MolToSmiles(*m,true);
delete m;
//std::cerr<<"csmi1: "<<csmiles1<<std::endl;
//std::cerr<<"csmi2: "<<csmiles2<<std::endl;
TEST_ASSERT(csmiles1==csmiles2);
}
{
RWMol *m;
std::string smiles="C1CNCCCNCCNCCCNC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles1 = MolToSmiles(*m,true);
delete m;
std::string smiles2="C1CCNCCCNCCNCCCN1";
m = SmilesToMol(smiles2);
TEST_ASSERT(m);
std::string csmiles2 = MolToSmiles(*m,true);
delete m;
//std::cerr<<"csmi1: "<<csmiles1<<std::endl;
//std::cerr<<"csmi2: "<<csmiles2<<std::endl;
TEST_ASSERT(csmiles1==csmiles2);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBug3526815(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3526815: canonical smiles failure in many symmetric fragments" << std::endl;
{
RWMol *m;
std::string smiles="O.O.O.O.O.O.O.O.O.[Pd].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[O-]S(=O)(=O)c1cccc(c1)P(c1cccc(c1)S(=O)(=O)[O-])c1cccc(c1)S(=O)(=O)[O-].[O-]S(=O)(=O)c1cccc(c1)P(c1cccc(c1)S(=O)(=O)[O-])c1cccc(c1)S(=O)(=O)[O-].[O-]S(=O)(=O)c1cccc(c1)P(c1cccc(c1)S(=O)(=O)[O-])c1cccc(c1)S(=O)(=O)[O-]";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles1 = MolToSmiles(*m,true);
delete m;
std::string smiles2="O.O.O.O.O.O.O.O.O.[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[O-]S(c1cccc(P(c2cccc(S([O-])(=O)=O)c2)c2cccc(S([O-])(=O)=O)c2)c1)(=O)=O.[Pd].[O-]S(=O)(=O)c1cccc(P(c2cccc(S([O-])(=O)=O)c2)c2cccc(S([O-])(=O)=O)c2)c1.[O-]S(=O)(=O)c1cccc(P(c2cccc(S([O-])(=O)=O)c2)c2cccc(S([O-])(=O)=O)c2)c1";
m = SmilesToMol(smiles2);
TEST_ASSERT(m);
std::string csmiles2 = MolToSmiles(*m,true);
delete m;
//std::cerr<<"csmi1: "<<csmiles1<<std::endl;
//std::cerr<<"csmi2: "<<csmiles2<<std::endl;
TEST_ASSERT(csmiles1==csmiles2);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testFragmentSmiles(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Fragment Smiles" << std::endl;
{
RWMol *m;
std::string smiles="OCCCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse);
TEST_ASSERT(csmiles=="CCO");
delete m;
}
{
RWMol *m;
std::string smiles="OCCCCCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2,3};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse);
TEST_ASSERT(csmiles=="CCCO");
delete m;
}
{
RWMol *m;
std::string smiles="OC1CC1CCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={1,2,3};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse);
TEST_ASSERT(csmiles=="C1CC1");
delete m;
}
{
RWMol *m;
std::string smiles="OC1CC1CCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={1,2,3};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
int bs[]={1,2,6};
std::vector<int> bondsToUse(bs,bs+sizeof(bs)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,&bondsToUse);
TEST_ASSERT(csmiles=="C1CC1");
delete m;
}
{
RWMol *m;
std::string smiles="OC1CC1CCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={1,2,3};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
int bs[]={1,2};
std::vector<int> bondsToUse(bs,bs+sizeof(bs)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,&bondsToUse);
TEST_ASSERT(csmiles=="CCC");
delete m;
}
{
RWMol *m;
std::string smiles="OC1CCCCC1N";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={1,2,3,4,5,6};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse);
TEST_ASSERT(csmiles=="C1CCCCC1");
delete m;
}
{
RWMol *m;
std::string smiles="OCCCCCCN";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={1,2,3,4,5,6};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse);
TEST_ASSERT(csmiles=="CCCCCC");
delete m;
}
{
RWMol *m;
std::string smiles="OCCCCCCN";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={1,2,3,4,5,6};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
int bs[]={1,2,3,4,5};
std::vector<int> bondsToUse(bs,bs+sizeof(bs)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,&bondsToUse);
TEST_ASSERT(csmiles=="CCCCCC");
delete m;
}
{
RWMol *m;
std::string smiles="OC1CCCCC1N";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={1,2,3,4,5,6};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
int bs[]={1,2,3,4,5};
std::vector<int> bondsToUse(bs,bs+sizeof(bs)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,&bondsToUse);
TEST_ASSERT(csmiles=="CCCCCC");
delete m;
}
{
RWMol *m;
std::string smiles="Oc1ccccc1N";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={1,2,3,4,5,6};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse);
TEST_ASSERT(csmiles=="c1ccccc1");
delete m;
}
{
RWMol *m;
std::string smiles="Oc1ccccc1N";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={1,2,3,4,5,6};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
int bs[]={1,2,3,4,5};
std::vector<int> bondsToUse(bs,bs+sizeof(bs)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,&bondsToUse);
TEST_ASSERT(csmiles=="cccccc");
delete m;
}
{
RWMol *m;
std::string smiles="OCCCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string labels[5]={"[A]","[B]","[B]","",""};
std::vector<std::string> atomLabels(labels,labels+5);
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,0,&atomLabels);
TEST_ASSERT(csmiles=="[A][B][B]");
delete m;
}
{
RWMol *m;
std::string smiles="CCCCO";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={2,3,4};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string labels[5]={"","","[B]","[B]","[A]"};
std::vector<std::string> atomLabels(labels,labels+5);
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,0,&atomLabels);
TEST_ASSERT(csmiles=="[A][B][B]");
delete m;
}
{
RWMol *m;
std::string smiles="CCCCO";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={2,3,4};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string labels[5]={"","","[B]","[A]","[B]"};
std::vector<std::string> atomLabels(labels,labels+5);
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,0,&atomLabels);
TEST_ASSERT(csmiles=="[B][A][B]");
delete m;
}
{
RWMol *m;
std::string smiles="CC(=O)OCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2,3};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,0,0,0);
TEST_ASSERT(csmiles=="CC(O)=O");
delete m;
}
{
RWMol *m;
std::string smiles="CC(=O)OCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2,3};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string labels[5]={"-","=","-","",""};
std::vector<std::string> bondLabels(labels,labels+5);
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,0,0,&bondLabels);
TEST_ASSERT(csmiles=="C-C(-O)=O");
delete m;
}
{
RWMol *m;
std::string smiles="CC(=O)OCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2,3};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string labels[5]={"a","b","a","",""};
std::vector<std::string> bondLabels(labels,labels+5);
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,0,0,&bondLabels);
TEST_ASSERT(csmiles=="CaC(aO)bO");
delete m;
}
{
RWMol *m;
std::string smiles="CC(=CC)CCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2,4};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse);
TEST_ASSERT(csmiles=="C=C(C)C");
delete m;
}
{
RWMol *m;
std::string smiles="CC(=CC)CCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2,4};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string labels[6]={"a","b","","a","",""};
std::vector<std::string> bondLabels(labels,labels+6);
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,0,0,&bondLabels);
std::cerr<<csmiles<<std::endl;
TEST_ASSERT(csmiles=="CbC(aC)aC");
delete m;
}
{
RWMol *m;
std::string smiles="CC(=CC)CCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2,4};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string labels[6]={"b","a","","a","",""};
std::vector<std::string> bondLabels(labels,labels+6);
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,0,0,&bondLabels);
std::cerr<<csmiles<<std::endl;
TEST_ASSERT(csmiles=="CaC(aC)bC" );
delete m;
}
{
RWMol *m;
std::string smiles="CC(=CC)CCC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2,4};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string labels[6]={"b","b","","a","",""};
std::vector<std::string> bondLabels(labels,labels+6);
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,0,0,&bondLabels);
std::cerr<<csmiles<<std::endl;
TEST_ASSERT(csmiles=="CaC(bC)bC" || csmiles=="CbC(aC)bC");
delete m;
}
{
RWMol *m;
std::string smiles="OC1CC1CC";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,4};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string csmiles = MolFragmentToSmiles(*m,atomsToUse,0,0,0,false,false,-1,false);
std::cerr<<csmiles<<std::endl;
TEST_ASSERT(csmiles=="O.C");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBug3528556(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3528556: canonical smiles failure in cycle" << std::endl;
{
RWMol *m;
std::string smiles="N12.N13.C24.C35.C46.C56";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles1 = MolToSmiles(*m,true);
delete m;
std::string smiles2="N1NCCCC1";
m = SmilesToMol(smiles2);
TEST_ASSERT(m);
std::string csmiles2 = MolToSmiles(*m,true);
delete m;
TEST_ASSERT(csmiles1==csmiles2);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBug253(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "do not repeat ring closure digits on the same atom" << std::endl;
{
RWMol *m;
std::string smiles="C1CCCC1CCC1CCCCC11CCCCC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles1 = MolToSmiles(*m,true);
std::cerr<<"--"<<csmiles1<<std::endl;
TEST_ASSERT(csmiles1=="C1CCC2(CC1)CCCCC2CCC1CCCC1");
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBug257(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 257: unrecognized bonds are in SMILES as ?s" << std::endl;
{
RWMol *m;
std::string smiles="CCO";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
m->getBondWithIdx(1)->setBondType(Bond::UNSPECIFIED);
std::string csmiles = MolToSmiles(*m);
TEST_ASSERT(csmiles=="CC~O");
delete m;
m = SmilesToMol(csmiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType()==Bond::UNSPECIFIED);
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub12(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github 12: non-canonical fragment smiles" << std::endl;
{
RWMol *m;
std::string smiles="c1c(C)cccc1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int as[]={0,1,2};
std::vector<int> atomsToUse(as,as+sizeof(as)/sizeof(int));
std::string csmiles1 = MolFragmentToSmiles(*m,atomsToUse);
int as2[]={1,2,3};
std::vector<int> atomsToUse2(as2,as2+sizeof(as2)/sizeof(int));
std::string csmiles2 = MolFragmentToSmiles(*m,atomsToUse2);
TEST_ASSERT(csmiles1==csmiles2);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testRingStereochem(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing handling of ring stereochemistry" << std::endl;
{
// examples from TJ O'Donnell
std::string inSmiles[]={
"N#Cc1ccc2[nH]cc([C@H]3CC[C@@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1",
"N#Cc1ccc2[nH]cc([C@@H]3CC[C@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1",
"N#Cc1ccc2[nH]cc([C@@H]3CC[C@@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1",
"N#Cc1ccc2[nH]cc([C@H]3CC[C@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1",
"N#Cc1ccc2[nH]cc([C@@H]3CC[C@@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1",
"N#Cc1ccc2[nH]cc([C@H]3CC[C@H](N4CCN(c5cccc6nccnc65)CC4)CC3)c2c1",
"O=C(N[C@@H]1CC[C@@H](CCN2CCN(c3cccc(Cl)c3Cl)CC2)CC1)c1cccs1",
"O=C(N[C@H]1CC[C@H](CCN2CCN(c3cccc(Cl)c3Cl)CC2)CC1)c1cccs1",
"Cn1ccc2ccc3c4[nH]c5c(cccc5CCN[C@H]5CC[C@H](O)CC5)c4c4c(c3c21)C(=O)NC4=O",
"Cn1ccc2ccc3c4[nH]c5c(cccc5CCN[C@@H]5CC[C@@H](O)CC5)c4c4c(c3c21)C(=O)NC4=O",
"N=C(N)Nc1ccc(CNC(=O)N2CCN(C(=O)O[C@@H]3CCC[C@H](OC(=O)N4CCN(C(=O)CCCCn5ccnc5)CC4)CCC3)CC2)cc1",
"N=C(N)Nc1ccc(CNC(=O)N2CCN(C(=O)O[C@H]3CCC[C@@H](OC(=O)N4CCN(C(=O)CCCCn5ccnc5)CC4)CCC3)CC2)cc1",
"CC(C)c1cc(C(C)C)c(S(=O)(=O)NC[C@H]2CC[C@H](C(=O)NNC(=O)c3cc4ccccc4s3)CC2)c(C(C)C)c1",
"CC(C)c1cc(C(C)C)c(S(=O)(=O)NC[C@@H]2CC[C@@H](C(=O)NNC(=O)c3cc4ccccc4s3)CC2)c(C(C)C)c1",
"O=C(CCC[C@@H]1OO[C@H](CCCC(=O)c2ccccc2)OO1)c1ccccc1",
"O=C(CCC[C@@H]1OO[C@H](CCCC(=O)c2ccccc2)OO1)c1ccccc1",
"O=C(CCC[C@@H]1OO[C@@H](CCCC(=O)c2ccccc2)OO1)c1ccccc1",
"O=C(CCC[C@H]1OO[C@H](CCCC(=O)c2ccccc2)OO1)c1ccccc1",
"CCCn1c2[nH]c([C@@H]3CC[C@@H](CNC(C)=O)CC3)nc2c(=O)n(CCC)c1=O",
"CCCn1c2[nH]c([C@H]3CC[C@H](CNC(C)=O)CC3)nc2c(=O)n(CCC)c1=O",
"c1cc2c(cccc2N2CCN([C@H]3CC[C@@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1",
"c1cc2c(cccc2N2CCN([C@@H]3CC[C@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1",
"c1cc2c(cccc2N2CCN([C@H]3CC[C@@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1",
"c1cc2c(cccc2N2CCN([C@@H]3CC[C@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1",
"c1cc2c(cccc2N2CCN([C@@H]3CC[C@@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1",
"c1cc2c(cccc2N2CCN([C@H]3CC[C@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1",
"c1cc2c(cccc2N2CCN([C@@H]3CC[C@@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1",
"c1cc2c(cccc2N2CCN([C@H]3CC[C@H](c4c[nH]c5ccccc54)CC3)CC2)[nH]1",
"CCCCC(=O)N[C@@]1(C(=O)N[C@H](Cc2ccccc2)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)NCC(N)=O)CC[C@@H](c2ccc(C)cc2)CC1",
"CCCCC(=O)N[C@]1(C(=O)N[C@H](Cc2ccccc2)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(=O)NCC(N)=O)CC[C@H](c2ccc(C)cc2)CC1",
"CC(C)Oc1ccccc1N1CCN([C@H]2CC[C@@H](NS(=O)(=O)c3cnc(Cl)c(Br)c3)CC2)CC1",
"CC(C)Oc1ccccc1N1CCN([C@@H]2CC[C@H](NS(=O)(=O)c3cnc(Cl)c(Br)c3)CC2)CC1",
"CC(C)Oc1ccccc1N1CCN([C@H]2CC[C@@H](NS(=O)(=O)c3cnc(Cl)c(Br)c3)CC2)CC1",
"CC(C)Oc1ccccc1N1CCN([C@@H]2CC[C@H](NS(=O)(=O)c3cnc(Cl)c(Br)c3)CC2)CC1",
"EOS"
};
unsigned int idx=0;
while(inSmiles[idx]!="EOS"){
std::string smi1=inSmiles[idx++];
std::string smi2=inSmiles[idx++];
RWMol *m1= SmilesToMol(smi1);;
TEST_ASSERT(m1);
RWMol *m2= SmilesToMol(smi2);;
TEST_ASSERT(m2);
TEST_ASSERT(m1->getNumAtoms()==m2->getNumAtoms());
TEST_ASSERT(m1->getNumBonds()==m2->getNumBonds());
std::string csmiles1 = MolToSmiles(*m1,true);
std::string csmiles2 = MolToSmiles(*m2,true);
if(csmiles1!=csmiles2){
std::cerr<<"---------\n"<<csmiles1<<"\n"<<csmiles2<<std::endl;
}
TEST_ASSERT(csmiles1==csmiles2);
delete m1;
delete m2;
}
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub45(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github 45: stereochemistry information influencing non-stereo SMILES" << std::endl;
{
RWMol *m;
std::string smiles="CC1CCC[13C]2(C)C1CC[14CH]2C(C)=O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles1a = MolToSmiles(*m);
std::string csmiles1b = MolToSmiles(*m,true);
std::string smiles2="CC1CCC[C]2(C)C1CC[CH]2C(C)=O";
delete m;
m = SmilesToMol(smiles2);
TEST_ASSERT(m);
std::string csmiles2a = MolToSmiles(*m);
std::string csmiles2b = MolToSmiles(*m,true);
TEST_ASSERT(csmiles1a==csmiles2a);
TEST_ASSERT(csmiles1b!=csmiles2b);
delete m;
}
{
RWMol *m;
std::string smiles="CC1CCC[C@@]2(C)C1CC[C@@H]2C(C)=O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles1a = MolToSmiles(*m);
std::string csmiles1b = MolToSmiles(*m,true);
std::string smiles2="CC1CCC[C]2(C)C1CC[CH]2C(C)=O";
delete m;
m = SmilesToMol(smiles2);
TEST_ASSERT(m);
std::string csmiles2a = MolToSmiles(*m);
std::string csmiles2b = MolToSmiles(*m,true);
TEST_ASSERT(csmiles1a==csmiles2a);
TEST_ASSERT(csmiles1b!=csmiles2b);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub206(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github 206: Problems round-tripping P" << std::endl;
{
RWMol *m;
std::string smiles="O=[PH3]";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles = MolToSmiles(*m,true);
TEST_ASSERT(csmiles=="O=[PH3]");
delete m;
}
{
RWMol *m;
std::string smiles="O=P";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles = MolToSmiles(*m,true);
TEST_ASSERT(csmiles=="O=P");
delete m;
}
{
RWMol *m;
std::string smiles="O=[PH]";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles = MolToSmiles(*m,true);
TEST_ASSERT(csmiles=="O=P");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub210(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github 210: flag possible stereocenters when calling assignStereochemistry()" << std::endl;
{
RWMol *m;
std::string smiles="O[C@H](F)CC(F)(Cl)I";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp(common_properties::_ChiralityPossible));
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub298(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github 298: cannot generate smiles for ChEBI_50252" << std::endl;
{
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/test_data/ChEBI_50252.mol";
RWMol *m = MolFileToMol(fName,false,false);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==80);
TEST_ASSERT(m->getNumBonds()==210);
m->updatePropertyCache(false);
MolOps::fastFindRings(*m);
std::string csmiles=MolToSmiles(*m);
TEST_ASSERT(csmiles!="");
TEST_ASSERT(csmiles.find("%100")==std::string::npos);
delete m;
m = SmilesToMol(csmiles,0,false);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==80);
TEST_ASSERT(m->getNumBonds()==210);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub378(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github 378: SMILES parser doing the wrong thing for odd dot-disconnected construct" << std::endl;
{
RWMol *m;
std::string smiles="C1.C1CO1.N1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondBetweenAtoms(0,1));
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondType()==Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(3,4));
TEST_ASSERT(m->getBondBetweenAtoms(3,4)->getBondType()==Bond::SINGLE);
TEST_ASSERT(!m->getBondBetweenAtoms(1,3));
delete m;
}
{
RWMol *m;
std::string smiles="C1(O.C1)CO1.N1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondBetweenAtoms(0,2));
TEST_ASSERT(m->getBondBetweenAtoms(0,2)->getBondType()==Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(0,3));
TEST_ASSERT(m->getBondBetweenAtoms(0,3)->getBondType()==Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(5,4));
TEST_ASSERT(m->getBondBetweenAtoms(5,4)->getBondType()==Bond::SINGLE);
TEST_ASSERT(!m->getBondBetweenAtoms(2,3));
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub389(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing Github 389: Add option to SmilesWriter to allow writing of all explicit hydrogens" << std::endl;
{
RWMol *m;
std::string smiles="CCO";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::string csmiles=MolToSmiles(*m,true,false,-1,true,false,true);
TEST_ASSERT(csmiles!="");
TEST_ASSERT(csmiles.find("[CH3]")!=std::string::npos);
TEST_ASSERT(csmiles.find("[CH2]")!=std::string::npos);
TEST_ASSERT(csmiles.find("[OH]")!=std::string::npos);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testEmptyStrings(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing handling of empty SMILES/SMARTS strings" << std::endl;
{
RWMol *m;
std::string smiles="";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==0);
std::string csmiles=MolToSmiles(*m);
TEST_ASSERT(csmiles=="");
delete m;
}
{
RWMol *m;
std::string smiles="";
m = SmartsToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==0);
std::string csmiles=MolToSmarts(*m);
TEST_ASSERT(csmiles=="");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testSmilesWriteForModifiedMolecules(){
BOOST_LOG(rdInfoLog) << "testing smiles writing/canonicalization for modified molecules." << std::endl;
{
std::string smiles="c1ccccc1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
m->getAtomWithIdx(0)->setAtomicNum(8);
std::string smi = MolToSmiles(*m, true);
//std::cerr<< smi <<std::endl;
TEST_ASSERT(smi=="c1ccocc1");
delete m;
}
}
int
main(int argc, char *argv[])
{
RDLog::InitLogs();
//boost::logging::enable_logs("rdApp.debug");
#if 1
testPass();
testFail();
testDetails();
testProblems();
//testLeak();
testBasicCanon();
testIssue127();
testIssue143();
testIssue151();
testIssue153();
testIssue175();
testIssue176();
testIssue180();
testIssue159();
testIssue184();
testIssue185();
testIssue191();
testIssue256();
testIssue266();
testRootedAt();
testIsotopes();
testBug1670149();
testBug1842174();
testBug1844959();
testIssue157();
testStereochem();
testBug1942220();
testBug3127883();
testAtomMaps();
testBug3145697();
testBug3152751();
testReplacementPatterns();
testAllBondsExplicit();
testBug3139534();
testBug3526815();
testBug3525799();
testBug3526810();
testBug3528556();
testBug253();
testBug257();
testRingStereochem();
testGithub45();
testGithub206();
testGithub210();
testGithub378();
testGithub389();
testBug1719046();
#endif
testBug1844617();
#if 1 // POSTPONED during canonicalization rewrite
//testGithub298();
testFragmentSmiles();
testGithub12();
#endif
testSmilesWriteForModifiedMolecules();
}
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