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47dbaf2304c857bafa33213df4ced317c827e447
rdkit/Code/GraphMol/testChirality.cpp
Nadine Schneider 47dbaf2304 Fix: ring stereo chemistry was swapped incorrectly
2015-02-11 18:21:15 +01:00

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// $Id$
//
// Copyright (C) 2007-2010 Greg Landrum
//
// @@ 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.
//
//
// There are chirality test cases spread all over the place. Many of the
// tests here are repeats, but it's good to have everything in one place.
#include <RDGeneral/utils.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
//#include <boost/log/functions.hpp>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Canon.h>
#include <GraphMol/new_canon.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include <iostream>
using namespace RDKit;
using namespace std;
void testMol1(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "CIP codes from a mol file (1)" << std::endl;
std::string rdbase = getenv("RDBASE");
RWMol *m;
std::string fName,smi;
std::string cip;
// start with SMILES:
BOOST_LOG(rdInfoLog) << " >>>>>>>>>>>>> smiles 1 <<<<<<<<<<<<<< " << std::endl;
smi="O[C@@H](N)I";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi="[C@H](O)(N)I";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
MolOps::removeStereochemistry(*m);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
BOOST_LOG(rdInfoLog) << " >>>>>>>>>>>>> mol file <<<<<<<<<<<<<< " << std::endl;
delete m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir1a.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir1b.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
MolOps::removeStereochemistry(*m);
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
delete m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir2a.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
MolOps::removeStereochemistry(*m);
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
delete m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir2b.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
MolOps::removeStereochemistry(*m);
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
BOOST_LOG(rdInfoLog) << "done" << std::endl;
};
void testRoundTrip(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "CIP codes from a mol->smiles conversion (1)" << std::endl;
std::string rdbase = getenv("RDBASE");
RWMol *m;
std::string fName,smi,smi2;
std::string cip;
// start with SMILES:
smi="O[C@@H](N)I";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi=MolToSmiles(*m,true);
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi2=MolToSmiles(*m,true);
TEST_ASSERT(smi==smi2);
smi="[C@H](O)(N)I";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
#if 1
smi=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<"smiout: "<<smi<<std::endl;
TEST_ASSERT(smi=="N[C@H](O)I");
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi2=MolToSmiles(*m,true);
TEST_ASSERT(smi==smi2);
#endif
BOOST_LOG(rdInfoLog) << " >>>>>>>>>>>>> mol file <<<<<<<<<<<<<< " << std::endl;
delete m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir1a.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
#if 1
smi=MolToSmiles(*m,true);
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi2=MolToSmiles(*m,true);
TEST_ASSERT(smi==smi2);
#endif
delete m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir1b.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
#if 1
smi=MolToSmiles(*m,true);
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi2=MolToSmiles(*m,true);
TEST_ASSERT(smi==smi2);
#endif
delete m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir2a.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
#if 1
smi=MolToSmiles(*m,true);
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi2=MolToSmiles(*m,true);
TEST_ASSERT(smi==smi2);
#endif
delete m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir2b.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
#if 1
smi=MolToSmiles(*m,true);
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
smi2=MolToSmiles(*m,true);
TEST_ASSERT(smi==smi2);
#endif
BOOST_LOG(rdInfoLog) << "done" << std::endl;
};
void testMol2(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "CIP codes from a mol file (2)" << std::endl;
std::string rdbase = getenv("RDBASE");
RWMol *m;
std::string fName,smi;
std::string cip;
// start with SMILES:
BOOST_LOG(rdInfoLog) << " >>>>>>>>>>>>> smiles 1 <<<<<<<<<<<<<< " << std::endl;
smi="[C@]1(SC[C@@]([H])(F)[C@]1(Br)O)([I])[H]";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(5)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
// same molecule, H combined with the first atom (reproduces
// exact situation in upcoming mol file)
BOOST_LOG(rdInfoLog) << " >>>>>>>>>>>>> smiles 2 <<<<<<<<<<<<<< " << std::endl;
delete m;
smi="[C@@H]1(SC[C@@]([H])(F)[C@]1(Br)O)([I])";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(5)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
BOOST_LOG(rdInfoLog) << " >>>>>>>>>>>>> mol file <<<<<<<<<<<<<< " << std::endl;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/Issue142b.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
BOOST_LOG(rdInfoLog) << "done" << std::endl;
};
void testSmiles1(){
ROMol *mol;
std::string smi,cip;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "CIP codes from 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");
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");
delete mol;
smi = "F[C@](I)(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=="S");
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");
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");
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");
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");
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");
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");
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");
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");
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");
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");
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");
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");
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");
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");
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");
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");
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");
delete mol;
smi = "Br[C@]12Cl.F1.[H]2";
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 = "[C@@](C)(Br)(F)Cl";
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=="R");
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");
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");
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");
delete mol;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testChiralityCleanup(){
ROMol *mol,*mol2;
std::string smi,cip;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "chirality cleanup" << std::endl;
smi = "F[C@H+](Cl)(Br)I";
mol = SmilesToMol(smi,false,false);
mol2 = MolOps::removeHs(*mol,false,false);
delete mol;
mol=mol2;
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol,true);
TEST_ASSERT(!mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete mol;
smi = "F[C@+](C)(Cl)(Br)I";
mol = SmilesToMol(smi,false,false);
mol2 = MolOps::removeHs(*mol,false,false);
delete mol;
mol=mol2;
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol,true);
TEST_ASSERT(!mol->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete mol;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testRingStereochemistry(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "test ring stereochemistry " << std::endl;
// NOTE: this test is for correctness, not canonicality
{
std::string smi = "B[C@H]1CC[C@H](C)CC1";
RWMol *m = SmilesToMol(smi);
std::string smi1=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi<<" "<<smi1<<std::endl;
TEST_ASSERT(smi1=="B[C@H]1CC[C@H](C)CC1");
delete m;
#if 0
smi="B[C@@H]1CC[C@@H](C)CC1";
m = SmilesToMol(smi);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
TEST_ASSERT(smi2==smi);
delete m;
#endif
}
{
std::string smi = "C1[C@@H](B)CC[C@H](C)C1";
RWMol *m = SmilesToMol(smi);
std::string smi1=MolToSmiles(*m,true);
smi = "B[C@H]1CC[C@H](C)CC1";
BOOST_LOG(rdInfoLog)<<" : "<<smi<<" "<<smi1<<std::endl;
TEST_ASSERT(smi1==smi);
delete m;
#if 0
smi="C1[C@H](B)CC[C@@H](C)C1";
m = SmilesToMol(smi);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
TEST_ASSERT(smi2==smi1);
delete m;
#endif
}
{
std::string smi = "C[C@H]1CC[C@H](F)CC1";
RWMol *m = SmilesToMol(smi);
std::string smi1=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi<<" "<<smi1<<std::endl;
TEST_ASSERT(smi1=="C[C@H]1CC[C@H](F)CC1");
delete m;
#if 0
smi="C[C@@H]1CC[C@@H](F)CC1";
m = SmilesToMol(smi);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
TEST_ASSERT(smi2==smi1);
delete m;
#endif
}
{
std::string smi = "F[C@H]1CC[C@H](C)CC1";
RWMol *m = SmilesToMol(smi);
std::string smi1=MolToSmiles(*m,true);
delete m;
#if 0
smi="F[C@@H]1CC[C@@H](C)CC1";
m = SmilesToMol(smi);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
TEST_ASSERT(smi2==smi1);
delete m;
#endif
}
{
std::string smi = "F[C@H]1CC[C@](C)(C)CC1";
RWMol *m = SmilesToMol(smi);
std::string smi1=MolToSmiles(*m,true);
delete m;
smi="FC1CCC(C)(C)CC1";
m = SmilesToMol(smi);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
TEST_ASSERT(smi2==smi1);
delete m;
}
{
std::string smi = "C1C[C@H]2CC[C@@H]1CC2";
RWMol *m = SmilesToMol(smi);
std::string smi1=MolToSmiles(*m,true);
delete m;
smi="C1CC2CCC1CC2";
m = SmilesToMol(smi);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
TEST_ASSERT(smi2==smi1);
delete m;
}
{
std::string smi = "C[C@]12CC[C@](C)(CC1)CC2";
RWMol *m = SmilesToMol(smi);
std::string smi1=MolToSmiles(*m,true);
delete m;
smi="CC12CCC(C)(CC1)CC2";
m = SmilesToMol(smi);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
TEST_ASSERT(smi2==smi1);
delete m;
}
{
// make sure we aren't removing stereochem that should still be there
std::string smi = "C[C@@]12CC[C@@](C)(NC1)OC2";
RWMol *m = SmilesToMol(smi);
std::string smi1=MolToSmiles(*m,true);
delete m;
smi="CC12CCC(C)(NC1)OC2";
m = SmilesToMol(smi);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi2<<" "<<smi1<<std::endl;
TEST_ASSERT(smi2!=smi1);
delete m;
}
#if 0
// FIX : these tests do not pass
{
std::string smi = "C[C@H]1CC[C@H](C)CC1";
RWMol *m = SmilesToMol(smi);
std::string smi1=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi<<" "<<smi1<<std::endl;
TEST_ASSERT(smi1==smi);
delete m;
}
{
std::string smi = "C1[C@@H](C)CC[C@H](C)C1";
RWMol *m = SmilesToMol(smi);
m->debugMol(std::cerr);
std::string smi1=MolToSmiles(*m,true);
smi = "C[C@H]1CC[C@H](C)CC1";
BOOST_LOG(rdInfoLog)<<" : "<<smi<<" "<<smi1<<std::endl;
m->debugMol(std::cerr);
TEST_ASSERT(smi1==smi);
delete m;
}
#endif
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testChiralityFrom3D(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "chirality perception from 3D coordinates: " << std::endl;
std::string rdbase = getenv("RDBASE");
RWMol *m;
std::string fName,smi;
std::string cip;
fName = rdbase+"/Code/GraphMol/test_data/chi3d_r1.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
MolOps::assignChiralTypesFrom3D(*m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
fName = rdbase+"/Code/GraphMol/test_data/chi3d_s1.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
MolOps::assignChiralTypesFrom3D(*m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete m;
fName = rdbase+"/Code/GraphMol/test_data/chi3d_r2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignChiralTypesFrom3D(*m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
fName = rdbase+"/Code/GraphMol/test_data/chi3d_s2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignChiralTypesFrom3D(*m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete m;
fName = rdbase+"/Code/GraphMol/test_data/chi3d_r1_bad.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
// this molecule starts out with incorrect stereochemistry (e.g. the bond wedging
// does not match the 3D structure. Start by verifying that the start position is bad:
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
// now assign the stereochem based on the 3D structure and check that we get it
// right:
MolOps::assignChiralTypesFrom3D(*m,-1,true);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIterativeChirality(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "iterative chirality (sf.net issue 1931470): " << std::endl;
std::string rdbase = getenv("RDBASE");
// unless otherwise noted, the R/S and Z/E assignments here
// match Marvin and ChemDraw.
#if 1
{ // atom-chirality -> atom-chirality
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi1a.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(5)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // atom-chirality -> atom-chirality
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi1b.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(5)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // atom-chirality -> atom-chirality
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi1c.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(5)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
#if 1 // this fails due to sf.net bug 1896935
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
#endif
delete m;
}
{ // atom-chirality -> atom-chirality
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi1d.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(5)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
#if 1 // this fails due to sf.net bug 1896935
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
#endif
delete m;
}
{ // atom-chirality -> atom-chirality
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi1e.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(!m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(!m->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(!m->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
#if 0 // this fails due to sf.net bug 1896935
std::cerr<<"m pre -----"<<std::endl;
m->debugMol(std::cerr);
std::cerr<<"-----"<<std::endl;
std::string smi1=MolToSmiles(*m,true);
std::cerr<<"m post -----"<<std::endl;
m->debugMol(std::cerr);
std::cerr<<"-----"<<std::endl;
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::cerr<<"m2 pre -----"<<std::endl;
m->debugMol(std::cerr);
std::cerr<<"-----"<<std::endl;
std::string smi2=MolToSmiles(*m,true);
std::cerr<<"m post -----"<<std::endl;
m->debugMol(std::cerr);
std::cerr<<"-----"<<std::endl;
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
#endif
delete m;
}
{ // bond-stereochem -> atom-chirality
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi2a.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==8);
TEST_ASSERT(m->getBondBetweenAtoms(2,5)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondBetweenAtoms(0,4)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S"); // this value is from ChemDraw, Marvin doesn't tag it.
std::string smi1=MolToSmiles(*m,true);
MolOps::removeStereochemistry(*m);
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getBondBetweenAtoms(0,4)->getStereo()==Bond::STEREONONE);
TEST_ASSERT(m->getBondBetweenAtoms(2,5)->getStereo()==Bond::STEREONONE);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // bond-stereochem -> atom-chirality
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi2b.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==8);
TEST_ASSERT(m->getBondBetweenAtoms(2,5)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondBetweenAtoms(0,4)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R"); // this value is from ChemDraw, Marvin doesn't tag it.
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // bond-stereochem -> atom-chirality
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi2c.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==8);
TEST_ASSERT(m->getBondBetweenAtoms(2,5)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondBetweenAtoms(0,4)->getStereo()==Bond::STEREOE);
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // bond-stereochem -> atom-chirality
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi2d.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==8);
TEST_ASSERT(m->getBondBetweenAtoms(2,5)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondBetweenAtoms(0,4)->getStereo()==Bond::STEREOANY);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R"); // this value is from ChemDraw, Marvin doesn't tag it.
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // bond-stereochem -> atom-chirality
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi2e.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==8);
TEST_ASSERT(m->getBondBetweenAtoms(2,5)->getStereo()==Bond::STEREOANY);
TEST_ASSERT(m->getBondBetweenAtoms(0,4)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S"); // this value is from ChemDraw, Marvin doesn't tag it.
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // atom chirality -> bond stereochemistry
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi3a.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==11);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(7)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(7)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getBondBetweenAtoms(1,2)->getStereo()==Bond::STEREOZ); // this value is from ChemDraw, Marvin doesn't tag it.
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // atom chirality -> bond stereochemistry
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi3b.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==11);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(7)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(7)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getBondBetweenAtoms(1,2)->getStereo()==Bond::STEREOE); // this value is from ChemDraw, Marvin doesn't tag it.
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // atom chirality -> bond stereochemistry
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi3c.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==11);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(7)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(7)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getBondBetweenAtoms(1,2)->getStereo()==Bond::STEREONONE);
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
#endif
{ // bond stereochemistry -> bond stereochemistry
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi4a.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(m->getBondBetweenAtoms(4,5)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondBetweenAtoms(3,7)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getStereo()==Bond::STEREOE);
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // bond stereochemistry -> bond stereochemistry
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi4b.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(m->getBondBetweenAtoms(4,5)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondBetweenAtoms(3,7)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getStereo()==Bond::STEREOZ);
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // bond stereochemistry -> bond stereochemistry
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi4c.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(m->getBondBetweenAtoms(4,5)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondBetweenAtoms(3,7)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getStereo()==Bond::STEREONONE);
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
{ // bond stereochemistry -> bond stereochemistry
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/iChi4d.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==9);
TEST_ASSERT(m->getBondBetweenAtoms(4,5)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondBetweenAtoms(3,7)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getStereo()==Bond::STEREONONE);
std::string smi1=MolToSmiles(*m,true);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testBondDirRemoval(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing that the removal of bond directions is correct: " << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string cip;
std::string fName = rdbase+"/Code/GraphMol/test_data/stereoOrder1.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==7);
TEST_ASSERT(m->getBondBetweenAtoms(1,2)->getStereo()==Bond::STEREOZ);
TEST_ASSERT(m->getBondBetweenAtoms(4,5)->getStereo()==Bond::STEREOE);
// on input all the single bonds are in the same direction:
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondDir()==m->getBondBetweenAtoms(1,4)->getBondDir());
TEST_ASSERT(m->getBondBetweenAtoms(2,3)->getBondDir()==m->getBondBetweenAtoms(1,4)->getBondDir());
TEST_ASSERT(m->getBondBetweenAtoms(5,6)->getBondDir()==m->getBondBetweenAtoms(1,4)->getBondDir());
std::string smi1=MolToSmiles(*m,true);
// check removal of redundant bond direction information:
std::vector<unsigned int> oranks(m->getNumAtoms(),0);
Canon::rankMolAtoms(*m,oranks);
std::vector<Canon::AtomColors> colors(m->getNumAtoms());
Canon::MolStack stack;
std::vector<unsigned int> ranks(oranks.size());
for(unsigned int i=0;i<ranks.size();++i) ranks[i]=oranks[i];
Canon::canonicalizeFragment(*m,0,colors,ranks,stack);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondDir()==Bond::NONE);
TEST_ASSERT(m->getBondBetweenAtoms(2,3)->getBondDir()==m->getBondBetweenAtoms(1,4)->getBondDir());
TEST_ASSERT(m->getBondBetweenAtoms(5,6)->getBondDir()==m->getBondBetweenAtoms(1,4)->getBondDir());
std::string smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
m = SmilesToMol(smi1);
TEST_ASSERT(m);
smi2=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<" : "<<smi1<<" "<<smi2<<std::endl;
TEST_ASSERT(smi1==smi2);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue2705543(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 2705543: " << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName;
RWMol *m;
std::string cip;
{
fName = rdbase+"/Code/GraphMol/test_data/Issue2705543.1h.mol";
m = MolFileToMol(fName,true,false);
TEST_ASSERT(m);
MolOps::assignChiralTypesFrom3D(*m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(2)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(4)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
}
{
fName = rdbase+"/Code/GraphMol/test_data/Issue2705543.1.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==13);
MolOps::assignChiralTypesFrom3D(*m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(2)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(4)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
}
{
fName = rdbase+"/Code/GraphMol/test_data/Issue2705543.2h.mol";
m = MolFileToMol(fName,true,false);
TEST_ASSERT(m);
MolOps::assignChiralTypesFrom3D(*m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
m->getAtomWithIdx(2)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(4)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
m->getAtomWithIdx(4)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
}
{
fName = rdbase+"/Code/GraphMol/test_data/Issue2705543.2.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==13);
MolOps::assignChiralTypesFrom3D(*m);
MolOps::assignStereochemistry(*m,true);
#if 0
for(unsigned int i=0;i<m->getNumAtoms();++i){
if(m->getAtomWithIdx(i)->hasProp(common_properties::_CIPCode)){
m->getAtomWithIdx(i)->getProp(common_properties::_CIPCode,cip);
std::cerr<<" >> "<<i<<" "<<cip<<std::endl;
}
}
#endif
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
m->getAtomWithIdx(2)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(m->getAtomWithIdx(4)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
m->getAtomWithIdx(4)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue2762917(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 2762917: chirality swap on addHs()" << std::endl;
std::string rdbase = getenv("RDBASE");
{
RWMol *m;
std::string cip;
std::string smiles="[C@@H](C)(Cl)O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete m;
}
{
RWMol *m;
std::string cip;
std::string smiles="CCC.[C@@H](C)(Cl)O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
MolOps::addHs(*m);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete m;
}
{
RWMol *m;
std::string cip;
std::string smiles="[C@@H]([C@H](C)O)(C)O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
MolOps::addHs(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(0)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete m;
}
{
RWMol *m;
std::string cip;
std::string smiles="C1CC.[C@@H]1(Cl)O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
MolOps::addHs(*m);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(3)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue3009911(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3009911: bad atom priorities" << std::endl;
{
RWMol *m;
std::string smiles="F[C@](O)(c1ccccc1)C(=C)CO";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int *ranks;
ranks = new int[m->getNumAtoms()];
MolOps::assignStereochemistry(*m,true);
for(unsigned int i=0;i<m->getNumAtoms();++i){
unsigned int rank;
TEST_ASSERT(m->getAtomWithIdx(i)->hasProp(common_properties::_CIPRank))
m->getAtomWithIdx(i)->getProp(common_properties::_CIPRank,rank);
ranks[i]=rank;
}
// basics:
TEST_ASSERT(ranks[0]>ranks[1]);
TEST_ASSERT(ranks[2]>ranks[1]);
TEST_ASSERT(ranks[0]>ranks[2]);
// now the key point:
TEST_ASSERT(ranks[3]<ranks[9]);
std::string cip;
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
delete [] ranks;
}
{
RWMol *m;
std::string smiles="COC(C)(OC)[C@](O)(F)C(C)=O";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
int *ranks;
ranks = new int[m->getNumAtoms()];
MolOps::assignStereochemistry(*m,true);
for(unsigned int i=0;i<m->getNumAtoms();++i){
unsigned int rank;
TEST_ASSERT(m->getAtomWithIdx(i)->hasProp(common_properties::_CIPRank))
m->getAtomWithIdx(i)->getProp(common_properties::_CIPRank,rank);
ranks[i]=rank;
}
// basics:
TEST_ASSERT(ranks[8]>ranks[7]);
TEST_ASSERT(ranks[7]>ranks[9]);
TEST_ASSERT(ranks[7]>ranks[2]);
// FIX: these are the key points, but at the moment they are not handled correctly
// due to a weakness in the CIP-ranking algorithm.
//TEST_ASSERT(ranks[2]>ranks[9]);
std::string cip;
TEST_ASSERT(m->getAtomWithIdx(6)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(6)->getProp(common_properties::_CIPCode,cip);
//TEST_ASSERT(cip=="R");
delete m;
delete [] ranks;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue3139534(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3139534: stereochemistry in larger rings" << std::endl;
// the smiles generation part of this is in SmilesParse/test.cpp
// tests that the creation and assignment are correct:
{
RWMol *m;
std::string smiles="C1COCC/C=C\\CC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(5)->getStereo()==Bond::STEREOZ);
delete m;
}
{
RWMol *m;
std::string smiles="C1COCC/C=C/CC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(5)->getStereo()==Bond::STEREOE);
delete m;
}
{
RWMol *m;
std::string smiles="C/1=C/OCCC=CCC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo()==Bond::STEREOZ);
delete m;
}
{
RWMol *m;
std::string smiles="C1=C/OCCC=CCC\\1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo()==Bond::STEREOZ);
delete m;
}
{
RWMol *m;
std::string smiles="C\\1=C/OCCC=CCC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo()==Bond::STEREOE);
delete m;
}
{
RWMol *m;
std::string smiles="C1=C/OCCC=CCC/1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo()==Bond::STEREOE);
delete m;
}
{
RWMol *m;
std::string smiles="C/1=C/OCC/C=C\\CC1";
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="C\\1=C/OCC/C=C\\CC1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondWithIdx(5)->getStereo()==Bond::STEREOZ);
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="C1=C/OCC/C=C\\CC/1";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m->getBondWithIdx(5)->getStereo()==Bond::STEREOZ);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testFindChiralAtoms(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Test findChiralAtoms." << std::endl;
{
// by default the chirality possible flag is not assigned:
RWMol *m;
std::string smiles="F[C@H](Cl)C(Cl)(Br)C(F)(F)F";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(!(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode)));
TEST_ASSERT(!(m->getAtomWithIdx(6)->hasProp(common_properties::_CIPCode)));
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp(common_properties::_ChiralityPossible));
TEST_ASSERT(!m->getAtomWithIdx(3)->hasProp(common_properties::_ChiralityPossible));
TEST_ASSERT(!(m->getAtomWithIdx(6)->hasProp(common_properties::_ChiralityPossible)));
// but we can force it:
MolOps::assignStereochemistry(*m,true,true,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
TEST_ASSERT(!(m->getAtomWithIdx(3)->hasProp(common_properties::_CIPCode)));
TEST_ASSERT(!(m->getAtomWithIdx(6)->hasProp(common_properties::_CIPCode)));
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_ChiralityPossible));
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp(common_properties::_ChiralityPossible));
TEST_ASSERT(!(m->getAtomWithIdx(6)->hasProp(common_properties::_ChiralityPossible)));
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testIssue3453172(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Issue 3453172: stereochemistry at three-coordinate S and Se" << std::endl;
{
RWMol *m;
std::string smiles="C=[S@](F)Br";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
}
{
RWMol *m;
std::string smiles="C[S@+](F)Br";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
}
{
RWMol *m;
std::string smiles="C=[Se@](F)Br";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
}
{
RWMol *m;
std::string smiles="C[Se@+](F)Br";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
}
{
RWMol *m;
std::string smiles="C=[S@](Br)Br";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete m;
}
{
RWMol *m;
std::string smiles="C[S@+](Br)Br";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete m;
}
{
RWMol *m;
std::string smiles="C=[Se@](Br)Br";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete m;
}
{
RWMol *m;
std::string smiles="C[Se@+](Br)Br";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete m;
}
{
// this was issue 254
RWMol *m;
std::string smiles="O=[S@](c1ccccc1)C";
m = SmilesToMol(smiles);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub87(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing github issue 87: removal of bond wedging" << std::endl;
std::string rdbase = getenv("RDBASE");
{
std::string fName = rdbase+"/Code/GraphMol/test_data/github87.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
WedgeMolBonds(*m,&m->getConformer());
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondDir()==Bond::BEGINWEDGE);
m->getAtomWithIdx(0)->setChiralTag(Atom::CHI_UNSPECIFIED);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondDir()==Bond::NONE);
delete m;
}
{
std::string fName = rdbase+"/Code/GraphMol/test_data/github87.2.mol";
RWMol *m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
WedgeMolBonds(*m,&m->getConformer());
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondDir()==Bond::BEGINDASH);
m->getAtomWithIdx(0)->setChiralTag(Atom::CHI_UNSPECIFIED);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondDir()==Bond::NONE);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub90(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing github issue 90: isotopes and chirality" << std::endl;
{
std::string smi="C[C@@H](F)[13CH3]";
ROMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
MolOps::assignStereochemistry(*m,true,true);
std::string cip;
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="R");
delete m;
}
{
std::string smi="[13CH3][C@@H](F)C";
ROMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
MolOps::assignStereochemistry(*m,true,true);
std::string cip;
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
m->getAtomWithIdx(1)->getProp(common_properties::_CIPCode,cip);
TEST_ASSERT(cip=="S");
delete m;
}
{
std::string smi="[CH3][C@@H](F)C";
ROMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(!m->getAtomWithIdx(1)->hasProp(common_properties::_CIPCode));
delete m;
}
{
std::string smi="C\\C([13CH3])=C(/C)[13CH3]";
ROMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==6);
TEST_ASSERT(m->getBondWithIdx(2)->getStereo()==Bond::STEREOZ);
delete m;
}
{
std::string smi="C\\C([CH3])=C(/C)[13CH3]";
ROMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==6);
TEST_ASSERT(m->getBondWithIdx(2)->getStereo()==Bond::STEREONONE);
delete m;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
int main(){
RDLog::InitLogs();
//boost::logging::enable_logs("rdApp.debug");
#if 1
testSmiles1();
testMol1();
testMol2();
testRoundTrip();
testChiralityCleanup();
testChiralityFrom3D();
testIterativeChirality();
testBondDirRemoval();
testIssue2762917();
testIssue3009911();
testIssue3139534();
testFindChiralAtoms();
testIssue3453172();
testRingStereochemistry();
testGithub87();
testGithub90();
#endif
testIssue2705543();
return 0;
}
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