Support more molecular properties

avogadro/qtplugins/applycolors/applycolors.cpp

@@ -12,10 +12,12 @@
 #include <avogadro/core/vector.h>
 #include <avogadro/qtgui/molecule.h>
 
-#include <QStringList>
 #include <QAction>
 #include <QColorDialog>
 #include <QInputDialog>
+#include <QStringList>
+
+#include <QDebug>
 
 using namespace tinycolormap;
 
@@ -248,14 +250,14 @@ void ApplyColors::applyChargeColors()
 
   // populate the dialog to choose the model and colormap
   ChargeColorDialog dialog;
-  for (const auto &model : identifiers) {
+  for (const auto& model : identifiers) {
     auto name = Calc::ChargeManager::instance().nameForModel(model);
     dialog.modelCombo->addItem(name.c_str(), model.c_str());
   }
   dialog.exec();
   if (dialog.result() != QDialog::Accepted)
     return;
-  
+
   // get the model and colormap
   const auto model = dialog.modelCombo->currentData().toString().toStdString();
   const auto colormapName = dialog.colorMapCombo->currentText();
@@ -267,6 +269,12 @@ void ApplyColors::applyChargeColors()
   float maxCharge = 0.0f;
   auto charges =
     Calc::ChargeManager::instance().partialCharges(model, *m_molecule);
+  // check if the model string is already a partial charge type
+  if (m_molecule->partialChargeTypes().find(model) !=
+      m_molecule->partialChargeTypes().end()) {
+    charges = m_molecule->partialCharges(model);
+  }
+
   for (Index i = 0; i < numAtoms; ++i) {
     float charge = charges(i, 0);
     minCharge = std::min(minCharge, charge);
@@ -568,4 +576,4 @@ void ApplyColors::applyShapelyColors()
   m_molecule->emitChanged(QtGui::Molecule::Atoms);
 }
 
-} // namespace Avogadro
+} // namespace Avogadro::QtPlugins

avogadro/qtplugins/molecularproperties/molecularmodel.cpp

@@ -197,6 +197,16 @@ QString formatFormula(Molecule* molecule)
   return formula;
 }
 
+QString formatPointGroup(std::string pointgroup)
+{
+  // first character is in capital
+  // then everything else is in subscript using <sub>...</sub>
+  QString formatted = QString::fromStdString(pointgroup);
+  QString output = formatted.at(0).toUpper();
+  output += QString("<sub>%1</sub>").arg(formatted.mid(1));
+  return output;
+}
+
 // Qt calls this for multiple "roles" across row / columns in the index
 //   we also combine multiple types into this class, so lots of special cases
 QVariant MolecularModel::data(const QModelIndex& index, int role) const
@@ -247,6 +257,8 @@ QVariant MolecularModel::data(const QModelIndex& index, int role) const
   else if (key == " 9totalSpinMultiplicity")
     return QVariant::fromValue(
       static_cast<int>(m_molecule->totalSpinMultiplicity()));
+  else if (key == "pointgroup")
+    return formatPointGroup(it->second.toString());
 
   return QString::fromStdString(it->second.toString());
 }
@@ -317,6 +329,8 @@ QVariant MolecularModel::headerData(int section, Qt::Orientation orientation,
       return tr("Entropy (kcal/mol•K)");
     else if (it->first == "gibbs")
       return tr("Gibbs Free Energy (kcal/mol)");
+    else if (it->first == "pointgroup")
+      return tr("Point Group", "point group symmetry");
     else if (it != map.end())
       return QString::fromStdString(it->first);
 

avogadro/qtplugins/symmetry/symmetrywidget.cpp

@@ -301,6 +301,7 @@ void SymmetryWidget::setCenterOfMass(double cm[3])
 void SymmetryWidget::setPointGroupSymbol(QString pg)
 {
   m_ui->pointGroupLabel->setText(pg);
+  m_molecule->setData("pointgroup", pg.toStdString());
 }
 
 void SymmetryWidget::setSymmetryOperations(

avogadro/quantumio/orca.cpp

@@ -60,14 +60,6 @@ bool ORCAOutput::read(std::istream& in, Core::Molecule& molecule)
     return false;
   }
 
-  // add the partial charges
-  if (m_partialCharges.size() > 0) {
-    for (auto it = m_partialCharges.begin(); it != m_partialCharges.end();
-         ++it) {
-      molecule.setPartialCharges(it->first, it->second);
-    }
-  }
-
   if (m_frequencies.size() > 0 &&
       m_frequencies.size() == m_vibDisplacements.size() &&
       m_frequencies.size() == m_IRintensities.size()) {
@@ -143,6 +135,17 @@ bool ORCAOutput::read(std::istream& in, Core::Molecule& molecule)
   basis->setMolecule(&molecule);
   load(basis);
 
+  // we have to do a few things *after* any modifications to bonds / atoms
+  // because those automatically clear partial charges and data
+
+  // add the partial charges
+  if (m_partialCharges.size() > 0) {
+    for (auto it = m_partialCharges.begin(); it != m_partialCharges.end();
+         ++it) {
+      molecule.setPartialCharges(it->first, it->second);
+    }
+  }
+
   molecule.setData("totalCharge", m_charge);
   molecule.setData("totalSpinMultiplicity", m_spin);
   molecule.setData("dipoleMoment", m_dipoleMoment);
@@ -273,6 +276,11 @@ void ORCAOutput::processLine(std::istream& in, GaussianSet* basis)
   } else if (Core::contains(key, "MOLECULAR ORBITALS")) {
     m_currentMode = MO;
     getline(in, key); //------------
+  } else if (Core::contains(key, "HIRSHFELD ANALYSIS")) {
+    m_currentMode = HirshfeldCharges;
+    for (unsigned int i = 0; i < 6; ++i) {
+      getline(in, key); // skip header
+    }
   } else if (Core::contains(key, "ATOMIC CHARGES")) {
     m_currentMode = Charges;
     // figure out what type of charges we have
@@ -352,6 +360,34 @@ void ORCAOutput::processLine(std::istream& in, GaussianSet* basis)
         m_currentMode = NotParsing;
         break;
       }
+      case HirshfeldCharges: {
+        // should start at the first atom
+        if (key.empty())
+          break;
+
+        Eigen::MatrixXd charges(m_atomNums.size(), 1);
+        charges.setZero();
+
+        list = Core::split(key, ' ');
+        while (!key.empty()) {
+          if (list.size() != 4) {
+            break;
+          }
+          // e.g. index atom charge spin
+          // e.g. 0 O   -0.714286   0.000
+          int atomIndex = Core::lexicalCast<int>(list[0]);
+          double charge = Core::lexicalCast<double>(list[2]);
+          charges(atomIndex, 0) = charge;
+
+          getline(in, key);
+          key = Core::trimmed(key);
+          list = Core::split(key, ' ');
+        }
+
+        m_partialCharges["Hirshfeld"] = charges;
+        m_currentMode = NotParsing;
+        break;
+      }
       case Charges: {
         // should start at the first atom
         if (key.empty())

avogadro/quantumio/orca.h

@@ -83,6 +83,7 @@ class AVOGADROQUANTUMIO_EXPORT ORCAOutput : public Io::FileFormat
     MO,
     OrbitalEnergies,
     Charges,
+    HirshfeldCharges,
     Frequencies,
     VibrationalModes,
     IR,