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rdkit/Code/GraphMol/testChirality.cpp

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// $Id$
//
// Copyright (C) 2007, 2008 Greg Landrum
//
// @@ All Rights Reserved @@
//
//
// 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/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir2a.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
fName = rdbase+"/Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir2b.mol";
m = MolFileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
smi=MolToSmiles(*m,true);
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#if 1
smi=MolToSmiles(*m,true);
BOOST_LOG(rdInfoLog)<<"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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#if 1
smi=MolToSmiles(*m,true);
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#if 1
smi=MolToSmiles(*m,true);
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#if 1
smi=MolToSmiles(*m,true);
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
#if 1
smi=MolToSmiles(*m,true);
delete m;
m=SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
MolOps::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPCode"));
m->getAtomWithIdx(3)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp("_CIPCode"));
m->getAtomWithIdx(5)->getProp("_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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPCode"));
m->getAtomWithIdx(3)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp("_CIPCode"));
m->getAtomWithIdx(5)->getProp("_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::assignAtomChiralCodes(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPCode"));
m->getAtomWithIdx(3)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp("_CIPCode"));
mol->getAtomWithIdx(0)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
mol->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp("_CIPCode"));
mol->getAtomWithIdx(0)->getProp("_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_CW);
MolOps::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp("_CIPCode"));
mol->getAtomWithIdx(0)->getProp("_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_CW);
MolOps::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp("_CIPCode"));
mol->getAtomWithIdx(0)->getProp("_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_CW);
MolOps::assignAtomChiralCodes(*mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->hasProp("_CIPCode"));
mol->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete mol;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testChiralityCleanup(){
ROMol *mol;
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);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignAtomChiralCodes(*mol,true);
TEST_ASSERT(!mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete mol;
smi = "F[C@+](C)(Cl)(Br)I";
mol = SmilesToMol(smi);
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
MolOps::assignAtomChiralCodes(*mol,true);
TEST_ASSERT(!mol->getAtomWithIdx(1)->hasProp("_CIPCode"));
TEST_ASSERT(mol->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete mol;
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::assignAtomChiralCodes(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
m->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
m->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
m->getAtomWithIdx(0)->getProp("_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::assignAtomChiralCodes(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
m->getAtomWithIdx(0)->getProp("_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::assignAtomChiralCodes(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_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::assignAtomChiralCodes(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
int main(){
RDLog::InitLogs();
//boost::logging::enable_logs("rdApp.debug");
testSmiles1();
testMol1();
testMol2();
testRoundTrip();
testChiralityCleanup();
testChiralityFrom3D();
return 0;
}
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