void OBStereoFacade::InitMaps()
{
if (m_perceive && !m_mol->HasChiralityPerceived())
PerceiveStereo(m_mol);
std::vector<OBGenericData *> stereoData = m_mol->GetAllData(OBGenericDataType::StereoData);
std::vector<OBGenericData*>::iterator data;
for (data = stereoData.begin(); data != stereoData.end(); ++data) {
OBStereo::Type type = ((OBStereoBase*)*data)->GetType();
if (type == OBStereo::Tetrahedral) {
OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(*data);
OBTetrahedralStereo::Config config = ts->GetConfig();
if (config.center == OBStereo::NoRef)
continue;
m_tetrahedralMap[config.center] = ts;
} else
if (type == OBStereo::SquarePlanar) {
OBSquarePlanarStereo *sp = dynamic_cast<OBSquarePlanarStereo*>(*data);
OBSquarePlanarStereo::Config config = sp->GetConfig();
if (config.center == OBStereo::NoRef)
continue;
m_squarePlanarMap[config.center] = sp;
} else
if (type == OBStereo::CisTrans) {
OBCisTransStereo *ct = dynamic_cast<OBCisTransStereo*>(*data);
OBCisTransStereo::Config config = ct->GetConfig();
// find the bond id from begin & end atom ids
unsigned long id = OBStereo::NoRef;
OBAtom *a = m_mol->GetAtomById(config.begin);
if (!a)
continue;
FOR_BONDS_OF_ATOM (bond, a) {
unsigned long beginId = bond->GetBeginAtom()->GetId();
unsigned long endId = bond->GetEndAtom()->GetId();
if ((beginId == config.begin && endId == config.end) ||
(beginId == config.end && endId == config.begin)) {
id = bond->GetId();
break;
}
}
if (id == OBStereo::NoRef)
continue;
m_cistransMap[id] = ct;
}
bool OBCisTransStereo::operator==(const OBCisTransStereo &other) const
{
if (!IsValid() || !other.IsValid())
return false;
Config u = OBTetraPlanarStereo::ToConfig(other.GetConfig(),
m_cfg.refs.at(0), OBStereo::ShapeU);
unsigned long a1 = u.refs.at(0);
unsigned long b1 = u.refs.at(2);
if ((a1 == OBStereo::ImplicitRef) && (b1 == OBStereo::ImplicitRef)) {
a1 = u.refs.at(1);
b1 = u.refs.at(3);
}
if (b1 != OBStereo::ImplicitRef)
if (a1 == GetTransRef(b1))
return true;
if (a1 != OBStereo::ImplicitRef)
if (b1 == GetTransRef(a1))
return true;
return false;
}
void genericSmilesCanonicalTest(const std::string &smiles)
{
cout << "Testing generic smiles <-> canonical smiles" << endl;
// read a smiles string
OBMol mol;
OBConversion conv;
OB_REQUIRE( conv.SetInFormat("smi") );
OB_REQUIRE( conv.SetOutFormat("can") );
cout << "smiles: " << smiles << endl;
// read a smiles string
OB_REQUIRE( conv.ReadString(&mol, smiles) );
// store the stereo data for the smiles string using unique symmetry ids
std::vector<OBTetrahedralStereo::Config> tetrahedral1;
std::vector<OBCisTransStereo::Config> cistrans1;
std::vector<OBSquarePlanarStereo::Config> squareplanar1;
// get the stereo data
OB_ASSERT( mol.HasData(OBGenericDataType::StereoData) );
std::vector<OBGenericData *> stereoData = mol.GetAllData(OBGenericDataType::StereoData);
std::vector<unsigned int> canlbls;
std::vector<unsigned int> symclasses;
OBGraphSym gs1(&mol);
gs1.GetSymmetry(symclasses);
CanonicalLabels(&mol, symclasses, canlbls);
cout << "mol.NumAtoms = " << mol.NumAtoms() << endl;
for (std::vector<OBGenericData*>::iterator data = stereoData.begin(); data != stereoData.end(); ++data) {
if (((OBStereoBase*)*data)->GetType() == OBStereo::Tetrahedral) {
// convert to tetrahedral data
OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(*data);
OB_REQUIRE( ts );
OB_ASSERT( ts->IsValid() );
if (!ts->IsValid())
continue;
OBTetrahedralStereo::Config config = ts->GetConfig();
// convert atom ids to symmetry ids
if (mol.GetAtomById(config.center))
config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
if (mol.GetAtomById(config.from))
config.from = canlbls.at( mol.GetAtomById(config.from)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
tetrahedral1.push_back(config);
} else
if (((OBStereoBase*)*data)->GetType() == OBStereo::CisTrans) {
// convert to tetrahedral data
OBCisTransStereo *ct = dynamic_cast<OBCisTransStereo*>(*data);
OB_REQUIRE( ct );
OB_ASSERT( ct->IsValid() );
OBCisTransStereo::Config config = ct->GetConfig();
// convert atom ids to symmetry ids
config.begin = canlbls.at( mol.GetAtomById(config.begin)->GetIdx() - 1 );
config.end = canlbls.at( mol.GetAtomById(config.end)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[3]))
config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
cistrans1.push_back(config);
} else
if (((OBStereoBase*)*data)->GetType() == OBStereo::SquarePlanar) {
// convert to tetrahedral data
OBSquarePlanarStereo *sp = dynamic_cast<OBSquarePlanarStereo*>(*data);
OB_REQUIRE( sp );
OB_ASSERT( sp->IsValid() );
if (!sp->IsValid())
continue;
OBSquarePlanarStereo::Config config = sp->GetConfig();
// convert atom ids to symmetry ids
if (mol.GetAtomById(config.center))
config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[3]))
config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
squareplanar1.push_back(config);
}
}
// write to can smiles
std::string canSmiles = conv.WriteString(&mol);
cout << "canSmiles: " << canSmiles;
// read can smiles in again
OB_REQUIRE( conv.ReadString(&mol, canSmiles) );
// store the stereo data for the smiles string using unique symmetry ids
std::vector<OBTetrahedralStereo::Config> tetrahedral2;
std::vector<OBCisTransStereo::Config> cistrans2;
std::vector<OBSquarePlanarStereo::Config> squareplanar2;
// get the stereo data
OB_ASSERT( mol.HasData(OBGenericDataType::StereoData) );
stereoData = mol.GetAllData(OBGenericDataType::StereoData);
OBGraphSym gs2(&mol);
gs2.GetSymmetry(symclasses);
CanonicalLabels(&mol, symclasses, canlbls);
cout << "mol.NumAtoms = " << mol.NumAtoms() << endl;
for (std::vector<OBGenericData*>::iterator data = stereoData.begin(); data != stereoData.end(); ++data) {
if (((OBStereoBase*)*data)->GetType() == OBStereo::Tetrahedral) {
// convert to tetrahedral data
OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(*data);
OB_REQUIRE( ts );
OB_ASSERT( ts->IsValid() );
OBTetrahedralStereo::Config config = ts->GetConfig();
// convert atom ids to symmetry ids
if (mol.GetAtomById(config.center))
config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
if (mol.GetAtomById(config.from))
config.from = canlbls.at( mol.GetAtomById(config.from)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
tetrahedral2.push_back(config);
}
if (((OBStereoBase*)*data)->GetType() == OBStereo::CisTrans) {
// convert to tetrahedral data
OBCisTransStereo *ct = dynamic_cast<OBCisTransStereo*>(*data);
OB_REQUIRE( ct );
OB_ASSERT( ct->IsValid() );
OBCisTransStereo::Config config = ct->GetConfig();
// convert atom ids to symmetry ids
config.begin = canlbls.at( mol.GetAtomById(config.begin)->GetIdx() - 1 );
config.end = canlbls.at( mol.GetAtomById(config.end)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[3]))
config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
cistrans2.push_back(config);
} else
if (((OBStereoBase*)*data)->GetType() == OBStereo::SquarePlanar) {
// convert to tetrahedral data
OBSquarePlanarStereo *sp = dynamic_cast<OBSquarePlanarStereo*>(*data);
OB_REQUIRE( sp );
OB_ASSERT( sp->IsValid() );
OBSquarePlanarStereo::Config config = sp->GetConfig();
// convert atom ids to symmetry ids
if (mol.GetAtomById(config.center))
config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[3]))
config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
squareplanar2.push_back(config);
}
}
// compare the tetrahedral structs
OB_ASSERT( tetrahedral1.size() == tetrahedral2.size() );
for (unsigned int i = 0; i < tetrahedral1.size(); ++i) {
for (unsigned int j = 0; j < tetrahedral2.size(); ++j) {
if (tetrahedral1[i].center == tetrahedral2[j].center)
OB_ASSERT( tetrahedral1[i] == tetrahedral2[j] );
if ( tetrahedral1[i] != tetrahedral2[j] ) {
cout << "1 = " << tetrahedral1[i] << endl;
cout << "2 = " << tetrahedral2[j] << endl;
}
}
}
// compare the cistrans structs
OB_ASSERT( cistrans1.size() == cistrans2.size() );
for (unsigned int i = 0; i < cistrans1.size(); ++i) {
for (unsigned int j = 0; j < cistrans2.size(); ++j) {
if ((cistrans1[i].begin == cistrans2[j].begin) && (cistrans1[i].end == cistrans2[j].end))
OB_ASSERT( cistrans1[i] == cistrans2[j] );
if ((cistrans1[i].begin == cistrans2[j].end) && (cistrans1[i].end == cistrans2[j].begin))
OB_ASSERT( cistrans1[i] == cistrans2[j] );
}
}
// compare the square-planar structs
OB_ASSERT( squareplanar1.size() == squareplanar2.size() );
for (unsigned int i = 0; i < squareplanar1.size(); ++i) {
for (unsigned int j = 0; j < squareplanar2.size(); ++j) {
if (squareplanar1[i].center == squareplanar2[j].center)
OB_ASSERT( squareplanar1[i] == squareplanar2[j] );
if ( squareplanar1[i] != squareplanar2[j] ) {
cout << "1 = " << squareplanar1[i] << endl;
cout << "2 = " << squareplanar2[j] << endl;
}
}
}
cout << "." << endl << endl;
}
OBGenericData* OBCisTransStereo::Clone(OBBase *mol) const
{
OBCisTransStereo *data = new OBCisTransStereo(static_cast<OBMol*>(mol));
data->SetConfig(m_cfg);
return data;
}
