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Orca: Make sure to update geometry coordinates during parsing #2538

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Orca: Make sure to update geometry coordinates during parsing #2538

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16 changes: 9 additions & 7 deletions src/formats/orcaformat.cpp
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Expand Up @@ -147,6 +147,7 @@ namespace OpenBabel
// Conformer data
bool newMol = false;
double* confCoords;
std::vector<double*> vconf; // index of all frames/conformers

// Unit cell
bool unitCell = false;
Expand Down Expand Up @@ -176,6 +177,7 @@ namespace OpenBabel

if (checkKeywords.find("Geometry Optimization Run") != notFound) {
geoOptRun = true;
// cout << " geom opt run " << endl;
while (ifs.getline(buffer,BUFF_SIZE)) {
string checkNAtoms(buffer);

Expand Down Expand Up @@ -215,6 +217,8 @@ namespace OpenBabel
confCoords[i*3] = x;
confCoords[i*3+1] = y;
confCoords[i*3+2] = z;
atom = mol.GetAtom(i+1);
atom->SetVector(x,y,z);
i++;
} else {
atom->SetVector(x,y,z); //set atom coordinates
Expand All @@ -230,9 +234,7 @@ namespace OpenBabel
// for (int j=0;j<3;j++){
// cout << confCoords[j*3] << " " << confCoords[j*3+1] << " " << confCoords[j*3+2] << endl;
// }

mol.AddConformer(confCoords);
mol.SetConformer(mol.NumConformers());
vconf.push_back(confCoords);
}
} // if "output coordinates"

Expand Down Expand Up @@ -638,16 +640,16 @@ namespace OpenBabel
mol.SetData(etd);
}


if (!pConv->IsOption("b",OBConversion::INOPTIONS))
mol.ConnectTheDots();
if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))
mol.PerceiveBondOrders();

mol.EndModify();

// should provide all the coordinates
mol.SetConformers(vconf);
mol.SetConformer(mol.NumConformers() - 1);

// cout << "num conformers = " << mol.NumConformers() << endl;
// cout << "num conformers = " << mol.NumConformers() << endl;
//cout << "Atom index 0 = " << mol.GetAtom(0)->GetX() << " " << mol.GetAtom(0)->GetY() << " " << mol.GetAtom(0)->GetZ() << endl;
if (hasPartialCharges)
mol.SetPartialChargesPerceived();
Expand Down