Update the Open Babel API in Avogadro

avogadro/src/mainwindow.cpp

@@ -74,6 +74,7 @@
 #include <avogadro/color.h>
 
 #include <openbabel/obconversion.h>
+#include <openbabel/elements.h>
 #include <openbabel/mol.h>
 #include <openbabel/builder.h>
 #include <openbabel/forcefield.h>
@@ -1999,7 +2000,7 @@ class XMLEventSource : public pqEventSource
 
   int GetAtomicNum(string name, int &iso)
   {
-    int n = OpenBabel::etab.GetAtomicNum(name.c_str(), iso);
+    int n = OpenBabel::OBElements::GetAtomicNum(name.c_str());
     if (iso != 0)
       return 0;  // "D" ot "T"
     if (n != 0)
@@ -2012,8 +2013,10 @@ class XMLEventSource : public pqEventSource
       if (name == (*i)->GetSymbol())
       return((*i)->GetAtomicNum());*/
 
-    for (unsigned int i=0; i<etab.GetNumberOfElements(); i++)
-      if (!QString::compare(name.c_str(), etab.GetName(i).c_str(), Qt::CaseInsensitive))
+    // 118 elements right now in Open Babel. We can change in the future if
+    // needed
+    for (unsigned int i=0; i < 118; i++)
+      if (!QString::compare(name.c_str(), OBElements::GetName(i), Qt::CaseInsensitive))
 	      return i;
 
     if (!QString::compare(name.c_str(), "Deuterium", Qt::CaseInsensitive))
@@ -2271,7 +2274,7 @@ class XMLEventSource : public pqEventSource
     QStringList ids;
     for (QList<Atom*>::const_iterator it = atoms.constBegin(),
            it_end = atoms.constEnd(); it != it_end; ++it) {
-      ids << OpenBabel::etab.GetSymbol((*it)->atomicNumber());
+      ids << OpenBabel::OBElements::GetSymbol((*it)->atomicNumber());
     }
 
     // Fractional coordinates

avogadro/src/primitiveitemmodel.cpp

@@ -34,6 +34,7 @@
 #include <avogadro/molecule.h>
 #include <avogadro/engine.h>
 
+#include <openbabel/elements.h>
 #include <openbabel/mol.h>
 
 namespace Avogadro {
@@ -263,7 +264,7 @@ namespace Avogadro {
         }
         else if(type == Primitive::AtomType) {
           Atom *atom = static_cast<Atom*>(primitive);
-          str = QString(OpenBabel::etab.GetSymbol(atom->atomicNumber())) + ' '
+          str = QString(OpenBabel::OBElements::GetSymbol(atom->atomicNumber())) + ' '
                 + QString::number(atom->index()+1);
         }
         else if(type == Primitive::BondType){

avogadro/src/projectdelegates/atomdelegate.cpp

@@ -25,6 +25,7 @@
 #include <avogadro/molecule.h>
 #include <avogadro/atom.h>
 
+#include <openbabel/elements.h>
 #include <openbabel/mol.h>
 
 #include <QDebug>
@@ -39,11 +40,11 @@ namespace Avogadro
   AtomDelegate::AtomDelegate(ProjectTreeModel *model) : ProjectTreeModelDelegate(model), m_label(0), m_widget(0)
   {
   }
- 
+
   AtomDelegate::~AtomDelegate()
   {
   }
-    
+
   void AtomDelegate::initStructure(GLWidget *widget, ProjectTreeItem *parent)
   {
     // save the widget
@@ -58,7 +59,7 @@ namespace Avogadro
   {
     // the user has expanded our label, we now initialize the bond items
     // and keep track of the using the signals...
-    
+
     Molecule *molecule = m_widget->molecule();
     disconnect(molecule, 0, this, 0);
     // connect some signals to keep track of changes
@@ -77,11 +78,11 @@ namespace Avogadro
     if (m_label->childCount())
       model()->removeRows(m_label, 0, m_label->childCount());
 
-    // add the atoms...  
+    // add the atoms...
     model()->insertRows(m_label, 0, molecule->numAtoms());
     for (int i = 0; i < m_label->childCount(); ++i) {
       ProjectTreeItem *item = m_label->child(i);
-      item->setData(0, QString(OpenBabel::etab.GetSymbol(molecule->atom(i)->atomicNumber())));
+      item->setData(0, QString(OpenBabel::OBElements::GetSymbol(molecule->atom(i)->atomicNumber())));
       item->setData(1, QString("%1").arg(i));
       // set the primitive
       PrimitiveList primitives;
@@ -90,45 +91,45 @@ namespace Avogadro
     }
 
   }
-  
+
   void AtomDelegate::primitiveAdded(Primitive *primitive)
   {
     if (primitive->type() != Primitive::AtomType)
       return;
-    
+
     Atom *atom = static_cast<Atom*>(primitive);
-    
+
     // add the new primitive to the end
     model()->insertRows(m_label, m_label->childCount(), 1);
     ProjectTreeItem *item = m_label->child(m_label->childCount() - 1);
-    item->setData(0, QString(OpenBabel::etab.GetSymbol(atom->atomicNumber())));
-    item->setData(1, QString("%1").arg(primitive->index())); 
+    item->setData(0, QString(OpenBabel::OBElements::GetSymbol(atom->atomicNumber())));
+    item->setData(1, QString("%1").arg(primitive->index()));
     // set the primitive
     PrimitiveList primitives;
     primitives.append(primitive);
     item->setPrimitives(primitives);
   }
- 
+
   void AtomDelegate::primitiveUpdated(Primitive *primitive)
   {
     if (primitive->type() == Primitive::MoleculeType) {
       initialize();
       return;
     }
 
-    if (primitive->type() != Primitive::AtomType) 
+    if (primitive->type() != Primitive::AtomType)
       return;
 
     Atom *atom = static_cast<Atom*>(primitive);
-    
+
     ProjectTreeItem *item = m_label->child(primitive->index());
-    item->setData(0, QString(OpenBabel::etab.GetSymbol(atom->atomicNumber())));
-    item->setData(1, QString("%1").arg(primitive->index())); 
- 
+    item->setData(0, QString(OpenBabel::OBElements::GetSymbol(atom->atomicNumber())));
+    item->setData(1, QString("%1").arg(primitive->index()));
+
 
     model()->emitDataChanged(m_label, primitive->index());
   }
- 
+
   void AtomDelegate::primitiveRemoved(Primitive *primitive)
   {
     if (primitive->type() != Primitive::AtomType)
@@ -145,12 +146,12 @@ namespace Avogadro
       }
     }
   }
- 
+
   void AtomDelegate::writeSettings(QSettings &settings) const
   {
     ProjectTreeModelDelegate::writeSettings(settings);
   }
-  
+
   void AtomDelegate::readSettings(QSettings &settings)
   {
     ProjectTreeModelDelegate::readSettings(settings);

libavogadro/src/colors/elementcolor.cpp

@@ -28,6 +28,7 @@
 #include <avogadro/atom.h>
 #include <QtPlugin>
 
+#include <openbabel/elements.h>
 #include <openbabel/mol.h>
 
 namespace Avogadro {
@@ -48,10 +49,11 @@ namespace Avogadro {
     const Atom *atom = static_cast<const Atom*>(p);
 
     if (atom->atomicNumber()) {
-      std::vector<double> rgb = OpenBabel::etab.GetRGB(atom->atomicNumber());
-      m_channels[0] = rgb[0];
-      m_channels[1] = rgb[1];
-      m_channels[2] = rgb[2];
+      double r, g, b;
+      OpenBabel::OBElements::GetRGB(atom->atomicNumber(), &r, &g, &b);
+      m_channels[0] = r;
+      m_channels[1] = g;
+      m_channels[2] = b;
     } else {
       m_channels[0] = 0.2;
       m_channels[1] = 0.2;

libavogadro/src/colors/residuecolor.cpp

@@ -29,6 +29,7 @@
 #include <avogadro/residue.h>
 #include <avogadro/atom.h>
 
+#include <openbabel/elements.h>
 #include <openbabel/mol.h>
 #include <openbabel/atom.h>
 #include <openbabel/residue.h>
@@ -169,20 +170,21 @@ namespace Avogadro {
         residue = atom->residue();
 
       // default is to color by element if no residue is specified
-      std::vector<double> rgb = OpenBabel::etab.GetRGB( atom->atomicNumber() );
+      double r, g, b;
+      OpenBabel::OBElements::GetRGB(atom->atomicNumber(), &r, &g, &b);
 
       if (!residue) {
-        m_channels[0] = rgb[0];
-        m_channels[1] = rgb[1];
-        m_channels[2] = rgb[2];
+        m_channels[0] = r;
+        m_channels[1] = g;
+        m_channels[2] = b;
         m_channels[3] = 1.0;
         return;
       }
       residueName = residue->name();
       if (residueName.compare("UNK", Qt::CaseInsensitive) == 0) {
-        m_channels[0] = rgb[0];
-        m_channels[1] = rgb[1];
-        m_channels[2] = rgb[2];
+        m_channels[0] = r;
+        m_channels[1] = g;
+        m_channels[2] = b;
         m_channels[3] = 1.0;
         return;
       }

libavogadro/src/colors/smartscolor.cpp

@@ -29,6 +29,7 @@
 #include <avogadro/atom.h>
 #include <avogadro/colorbutton.h>
 
+#include <openbabel/elements.h>
 #include <openbabel/mol.h>
 #include <openbabel/atom.h>
 #include <openbabel/parsmart.h>
@@ -45,14 +46,14 @@ namespace Avogadro {
 
   /// Constructor
   SmartsColor::SmartsColor() : _highlightColor(255, 0, 128), _settingsWidget(NULL)
-  { 
+  {
     _pattern = new OBSmartsPattern;
     _smartsString.clear();
   }
 
   /// Destructor
   SmartsColor::~SmartsColor()
-  { 
+  {
     if (_pattern) {
       delete _pattern;
       _pattern = NULL;
@@ -132,8 +133,9 @@ namespace Avogadro {
     // Start with the default "element color"
     QColor newcolor;
     if (atom->atomicNumber()) {
-      std::vector<double> rgb = OpenBabel::etab.GetRGB(atom->atomicNumber());
-      newcolor.setRgbF(rgb[0], rgb[1], rgb[2]);
+      double r, g, b;
+      OpenBabel::OBElements::GetRGB(atom->atomicNumber(), &r, &g, &b);
+      newcolor.setRgbF(r, g, b);
     } else {
       newcolor.setRgbF(0.2f, 0.2f, 0.2f);
     }
@@ -160,7 +162,7 @@ namespace Avogadro {
           if (matched)
             break; // no need to check other matches
         } // matches
-        
+
       } // matched molecule
     } // finite, valid SMARTS
 

libavogadro/src/elementdetail_p.cpp

@@ -27,6 +27,7 @@
 #include "elementdetail_p.h"
 #include "elementtranslator.h"
 
+#include <openbabel/elements.h>
 #include <openbabel/mol.h>
 
 #include <QGraphicsSceneMouseEvent>
@@ -65,13 +66,14 @@ namespace Avogadro{
     QFontMetrics fm(font);
     int pixelHeight = fm.height();
 
-    QString symbol = OpenBabel::etab.GetSymbol(m_element);
+    QString symbol = OpenBabel::OBElements::GetSymbol(m_element);
     QString name(ElementTranslator::name(m_element));
-    QString mass = QString("%L1").arg(OpenBabel::etab.GetMass(m_element), 0, 'f', 3);
+    QString mass = QString("%L1").arg(OpenBabel::OBElements::GetMass(m_element), 0, 'f', 3);
 
-    std::vector<double> color = OpenBabel::etab.GetRGB(m_element);
+    double r, g, b;
+    OpenBabel::OBElements::GetRGB(m_element, &r, &g, &b);
     QColor m_color;
-    m_color.setRgbF(color[0], color[1], color[2]);
+    m_color.setRgbF(r, g, b);
 
     // Draw the element detail border and fill with the element colour
     painter->setBrush(m_color);

libavogadro/src/elementitem_p.cpp

@@ -28,6 +28,7 @@
 #include "elementitem_p.h"
 #include "elementtranslator.h"
 
+#include <openbabel/elements.h>
 #include <openbabel/mol.h>
 
 #include <QGraphicsSceneMouseEvent>
@@ -45,12 +46,13 @@ namespace Avogadro{
     // Want these items to be selectable
     setFlags(QGraphicsItem::ItemIsSelectable);
 
-    m_symbol = OpenBabel::etab.GetSymbol(m_element);
+    m_symbol = OpenBabel::OBElements::GetSymbol(m_element);
     if(!m_symbol.isEmpty())
       m_valid = true;
-    std::vector<double> color = OpenBabel::etab.GetRGB(m_element);
+    double r, g, b;
+    OpenBabel::OBElements::GetRGB(m_element, &r, &g, &b);
     m_color = new QColor();
-    m_color->setRgbF(color[0], color[1], color[2]);
+    m_color->setRgbF(r, g, b);
     // Set some custom data to make it easy to figure out which element we are
     setData(0, m_element);
   }

libavogadro/src/engines/bsdyengine.cpp

@@ -36,6 +36,7 @@
 #include <QGLWidget> // for OpenGL bits
 #include <QDebug>
 
+#include <openbabel/elements.h>
 #include <openbabel/mol.h>
 
 using namespace std;
@@ -91,12 +92,12 @@ namespace Avogadro
   {
     double radiusCovalent(const Atom *atom)
     {
-      return OpenBabel::etab.GetCovalentRad(atom->atomicNumber());
+      return OpenBabel::OBElements::GetCovalentRad(atom->atomicNumber());
     }
 
     double radiusVdW(const Atom *atom)
     {
-      return OpenBabel::etab.GetVdwRad(atom->atomicNumber());
+      return OpenBabel::OBElements::GetVdwRad(atom->atomicNumber());
     }
   } // End of anonymous namespace
 

libavogadro/src/engines/labelengine.cpp

@@ -42,6 +42,7 @@
 #include <QtGui/QFontDialog>
 //#include <QtGui/QPainter>
 
+#include <openbabel/elements.h>
 #include <openbabel/mol.h>
 
 using namespace std;
@@ -134,19 +135,19 @@ namespace Avogadro {
         str = QString("%L1").arg(a->index() + 1);
         break;
       case 2: // Element Symbol
-        str = QString(OpenBabel::etab.GetSymbol(a->atomicNumber()));
+        str = QString(OpenBabel::OBElements::GetSymbol(a->atomicNumber()));
         break;
       case 3: // Symbol & Number in Group
         gi = a->groupIndex();
         if (gi != 0) {
-          str = QString(OpenBabel::etab.GetSymbol(a->atomicNumber())) + QString("%L1").arg(gi);
+          str = QString(OpenBabel::OBElements::GetSymbol(a->atomicNumber())) + QString("%L1").arg(gi);
         }
         else {
-          str = QString(OpenBabel::etab.GetSymbol(a->atomicNumber()));
+          str = QString(OpenBabel::OBElements::GetSymbol(a->atomicNumber()));
         }
         break;
       case 4: // Symbol & Atom Number
-        str = QString(OpenBabel::etab.GetSymbol(a->atomicNumber())) + QString("%L1").arg(a->index() + 1);
+        str = QString(OpenBabel::OBElements::GetSymbol(a->atomicNumber())) + QString("%L1").arg(a->index() + 1);
         break;
       case 5: // Formal charge
         if (a->formalCharge())
@@ -174,7 +175,7 @@ namespace Avogadro {
         QList<QByteArray> propertyNames = a->dynamicPropertyNames();
         // If this is a strange offset, use the element symbol
         if ( customIndex < 0 || customIndex >= propertyNames.size())
-          str = QString(OpenBabel::etab.GetSymbol(a->atomicNumber()));
+          str = QString(OpenBabel::OBElements::GetSymbol(a->atomicNumber()));
         else
           str = a->property(propertyNames[customIndex].data()).toString();
      }