void ReadFileThread::detectConformers(unsigned int c,
const OpenBabel::OBMol &first,
const OpenBabel::OBMol ¤t)
{
if (!c) {
// this is the first molecule read
m_moleculeFile->setConformerFile(true);
addConformer(current);
return;
}
if (!m_moleculeFile->isConformerFile())
return;
// as long as we are not sure if this really is a
// conformer/trajectory file, add the conformers
addConformer(current);
// performance: check only certain molecule 1-10,20,50
switch (c) {
case 1:
case 2:
case 3:
case 4:
case 5:
case 6:
case 7:
case 8:
case 9:
case 10:
case 20:
case 50:
break;
default:
return;
}
if (first.NumAtoms() != current.NumAtoms()) {
m_moleculeFile->setConformerFile(false);
m_moleculeFile->m_conformers.clear();
return;
}
for (unsigned int i = 0; i < first.NumAtoms(); ++i) {
OpenBabel::OBAtom *firstAtom = first.GetAtom(i+1);
OpenBabel::OBAtom *currentAtom = current.GetAtom(i+1);
if (firstAtom->GetAtomicNum() != currentAtom->GetAtomicNum()) {
m_moleculeFile->setConformerFile(false);
m_moleculeFile->m_conformers.clear();
return;
}
}
}
// Helper function -- handle SMARTS selections
// Called by performAction()
void SelectExtension::selectSMARTS(GLWidget *widget)
{
bool ok;
QString pattern = QInputDialog::getText(qobject_cast<QWidget*>(parent()),
tr("SMARTS Selection"),
tr("SMARTS pattern to select"),
QLineEdit::Normal,
"", &ok);
if (ok && !pattern.isEmpty()) {
OBSmartsPattern smarts;
smarts.Init(pattern.toStdString());
OpenBabel::OBMol obmol = m_molecule->OBMol();
smarts.Match(obmol);
// if we have matches, select them
if(smarts.NumMatches() != 0) {
QList<Primitive *> matchedAtoms;
vector< vector <int> > mapList = smarts.GetUMapList();
vector< vector <int> >::iterator i; // a set of matching atoms
vector<int>::iterator j; // atom ids in each match
for (i = mapList.begin(); i != mapList.end(); ++i) {
for (j = i->begin(); j != i->end(); ++j) {
matchedAtoms.append(m_molecule->atom(obmol.GetAtom(*j)->GetIdx()-1));
}
}
widget->clearSelected();
widget->setSelected(matchedAtoms, true);
widget->update();
} // end matches
}
return;
}
void Molecule::addHydrogens(Atom *a,
const QList<unsigned long> &atomIds,
const QList<unsigned long> &bondIds)
{
if (atomIds.size() != bondIds.size()) {
qDebug() << "Error, addHydrogens called with atom & bond id lists of different size!";
}
// Construct an OBMol, call AddHydrogens and translate the changes
OpenBabel::OBMol obmol = OBMol();
if (a) {
OpenBabel::OBAtom *obatom = obmol.GetAtom(a->index()+1);
// Set implicit valence for unusual elements not handled by OpenBabel
// PR#2803076
switch (obatom->GetAtomicNum()) {
case 3:
case 11:
case 19:
case 37:
case 55:
case 85:
case 87:
obatom->SetImplicitValence(1);
obatom->SetHyb(1);
obmol.SetImplicitValencePerceived();
break;
case 4:
case 12:
case 20:
case 38:
case 56:
case 88:
obatom->SetImplicitValence(2);
obatom->SetHyb(2);
obmol.SetImplicitValencePerceived();
break;
case 84: // Po
obatom->SetImplicitValence(2);
obatom->SetHyb(3);
obmol.SetImplicitValencePerceived();
break;
default: // do nothing
break;
}
obmol.AddHydrogens(obatom);
}
else
obmol.AddHydrogens();
// All new atoms in the OBMol must be the additional hydrogens
unsigned int numberAtoms = numAtoms();
int j = 0;
for (unsigned int i = numberAtoms+1; i <= obmol.NumAtoms(); ++i, ++j) {
if (obmol.GetAtom(i)->IsHydrogen()) {
OpenBabel::OBAtom *obatom = obmol.GetAtom(i);
Atom *atom;
if (atomIds.isEmpty())
atom = addAtom();
else if (j < atomIds.size())
atom = addAtom(atomIds.at(j));
else {
qDebug() << "Error - not enough unique ids in addHydrogens.";
break;
}
atom->setOBAtom(obatom);
// Get the neighbor atom
OpenBabel::OBBondIterator iter;
OpenBabel::OBAtom *next = obatom->BeginNbrAtom(iter);
Bond *bond;
if (bondIds.isEmpty())
bond = addBond();
else // Already confirmed by atom ids
bond = addBond(bondIds.at(j));
bond->setEnd(Molecule::atom(atom->index()));
bond->setBegin(Molecule::atom(next->GetIdx()-1));
}
}
for (unsigned int i = 1; i <= numberAtoms; ++i) {
// Warning -- OB atom index off-by-one here
atom(i-1)->setPartialCharge(obmol.GetAtom(i)->GetPartialCharge());
}
}
//--
bool DataProperty::Satisfy(OpenBabel::OBRing* pRing,
const std::string& refTo,
std::vector<Class*>& vecSatisfiedClasses,
std::string& refValue)
{
//bool bSatisfied = false;
int iPosition = -1;
// [rad] if we are default, we automatically satisfy
if(!IsDefault())
{
if(!SatisfyCommon(vecSatisfiedClasses, iPosition))
{
// [rad] this property does not apply
refValue = "";
return(false);
}
}
// [rad] go through possible data types..
if(!refTo.compare("RING_SIZE"))
{
ConvertInt(pRing->Size(), refValue);
}
else if(!refTo.compare("RING_IS_AROMATIC"))
{
ConvertBool(pRing->IsAromatic(), refValue);
}
else if(!refTo.compare("RING_IS_HOMOCYCLIC"))
{
OpenBabel::OBMol* pMolecule = pRing->GetParent();
OpenBabel::OBAtom* pAtom;
bool bHomoCyclic = true;
std::vector<int>::iterator iter_path = pRing->_path.begin();
while(iter_path != pRing->_path.end())
{
pAtom = pMolecule->GetAtom((*iter_path));
if(pAtom)
{
if(6 != pAtom->GetAtomicNum())
{
bHomoCyclic = false;
break;
}
}
iter_path++;
}
ConvertBool(bHomoCyclic, refValue);
}
else if(!refTo.compare("RING_IS_HETEROCYCLIC"))
{
OpenBabel::OBMol* pMolecule = pRing->GetParent();
OpenBabel::OBAtom* pAtom;
bool bHeteroCyclic = false;
std::vector<int>::iterator iter_path = pRing->_path.begin();
while(iter_path != pRing->_path.end())
{
pAtom = pMolecule->GetAtom((*iter_path));
if(pAtom)
{
if(6 != pAtom->GetAtomicNum())
{
bHeteroCyclic = true;
break;
}
}
iter_path++;
}
ConvertBool(bHeteroCyclic, refValue);
}
else
{
// [rad] unknown datatype?
refValue = "";
return(false);
}
return(true);
}