File avogadro-port-to-eigen3.patch of Package avogadro-qt4

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File avogadro-port-to-eigen3.patch of Package avogadro-qt4 (Revision d63f207da5f9f58050f6f1efee56d70f)

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From 43af3c117b0b3220b15c2fe2895b94bbd83d3a60 Mon Sep 17 00:00:00 2001
From: Claudio Fernandes <claudiosf.claudio@gmail.com>
Date: Sun, 15 Jan 2017 21:23:39 -0200
Subject: [PATCH] Adapt Avogadro to Eigen 3.3

---
 CMakeLists.txt                                |  9 +-----
 avogadro/src/mainwindow.cpp                   |  5 ++--
 libavogadro/src/camera.cpp                    | 10 +++----
 libavogadro/src/camera.h                      | 14 +++++-----
 libavogadro/src/engines/wireengine.cpp        |  4 +--
 .../crystallographyextension.cpp              |  2 +-
 .../ui/ceviewoptionswidget.cpp                |  2 +-
 .../src/extensions/orca/orcaanalysedialog.cpp |  1 -
 .../src/extensions/orca/orcainputdialog.cpp   |  1 -
 .../extensions/qtaim/qtaimmathutilities.cpp   |  1 +
 .../qtaim/qtaimwavefunctionevaluator.cpp      | 28 +++++++++----------
 .../surfaces/openqube/gamessukout.cpp         |  1 +
 .../surfaces/openqube/slaterset.cpp           |  6 ++--
 libavogadro/src/glpainter_p.cpp               | 14 +++++-----
 libavogadro/src/glwidget.cpp                  |  4 +--
 libavogadro/src/molecule.cpp                  | 26 +++++++++++++++--
 libavogadro/src/navigate.cpp                  |  2 +-
 libavogadro/src/tools/bondcentrictool.cpp     | 28 +++++++++----------
 libavogadro/src/tools/manipulatetool.cpp      | 17 ++++++-----
 libavogadro/src/tools/navigatetool.cpp        |  3 +-
 libavogadro/src/tools/skeletontree.cpp        |  7 +++--
 libavogadro/src/tools/skeletontree.h          |  2 +-
 22 files changed, 102 insertions(+), 85 deletions(-)

Index: avogadro-1.2.0/CMakeLists.txt
===================================================================
--- avogadro-1.2.0.orig/CMakeLists.txt
+++ avogadro-1.2.0/CMakeLists.txt
@@ -231,14 +231,7 @@ if(NOT Linguist_FOUND)
   message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
 endif()
 
-find_package(Eigen3) # find and setup Eigen3 if available
-if(NOT EIGEN3_FOUND)
-   message(STATUS "Cannot find Eigen3, trying Eigen2")
-   find_package(Eigen2 REQUIRED) # Some version is required
-else()
-# Use Stage10 Eigen3 support
-   set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
-endif()
+find_package(Eigen3 REQUIRED) # find and setup Eigen3 if available
 
 find_package(ZLIB REQUIRED)
 find_package(OpenBabel2 REQUIRED) # find and setup OpenBabel
Index: avogadro-1.2.0/avogadro/src/mainwindow.cpp
===================================================================
--- avogadro-1.2.0.orig/avogadro/src/mainwindow.cpp
+++ avogadro-1.2.0/avogadro/src/mainwindow.cpp
@@ -115,7 +115,6 @@
 #include <QDebug>
 
 #include <Eigen/Geometry>
-#include <Eigen/Array>
 #define USEQUAT
 // This is a "hidden" exported Qt function on the Mac for Qt-4.x.
 #ifdef Q_WS_MAC
@@ -2775,7 +2774,7 @@ protected:
     linearGoal.row(1) = linearGoal.row(2).cross(linearGoal.row(0));
 
     // calculate the translation matrix
-    Transform3d goal(linearGoal);
+    Projective3d goal(linearGoal);
 
     goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
 
@@ -2840,7 +2839,7 @@ protected:
     Matrix3d linearGoal = Matrix3d::Identity();
 
     // calculate the translation matrix
-    Transform3d goal(linearGoal);
+    Projective3d goal(linearGoal);
 
     goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
 
Index: avogadro-1.2.0/libavogadro/src/camera.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/camera.cpp
+++ avogadro-1.2.0/libavogadro/src/camera.cpp
@@ -47,7 +47,7 @@ namespace Avogadro
 
       CameraPrivate() {};
 
-      Eigen::Transform3d modelview, projection;
+      Eigen::Projective3d modelview, projection;
       const GLWidget *parent;
       double angleOfViewY;
       double orthoScale;
@@ -169,20 +169,20 @@ namespace Avogadro
 
   double Camera::distance(const Eigen::Vector3d & point) const
   {
-    return ( d->modelview * point ).norm();
+    return ( d->modelview * point.homogeneous() ).head<3>().norm();
   }
 
-  void Camera::setModelview(const Eigen::Transform3d &matrix)
+  void Camera::setModelview(const Eigen::Projective3d &matrix)
   {
     d->modelview = matrix;
   }
 
-  const Eigen::Transform3d & Camera::modelview() const
+  const Eigen::Projective3d & Camera::modelview() const
   {
     return d->modelview;
   }
 
-  Eigen::Transform3d & Camera::modelview()
+  Eigen::Projective3d & Camera::modelview()
   {
     return d->modelview;
   }
Index: avogadro-1.2.0/libavogadro/src/camera.h
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/camera.h
+++ avogadro-1.2.0/libavogadro/src/camera.h
@@ -101,16 +101,16 @@ namespace Avogadro {
       double angleOfViewY() const;
       /** Sets 4x4 "modelview" matrix representing the camera orientation and position.
         * @param matrix the matrix to copy from
-        * @sa Eigen::Transform3d & modelview(), applyModelview() */
-      void setModelview(const Eigen::Transform3d &matrix);
+        * @sa Eigen::Projective3d & modelview(), applyModelview() */
+      void setModelview(const Eigen::Projective3d &matrix);
       /** @return a constant reference to the 4x4 "modelview" matrix representing
         *         the camera orientation and position
-        * @sa setModelview(), Eigen::Transform3d & modelview() */
-      const Eigen::Transform3d & modelview() const;
+        * @sa setModelview(), Eigen::Projective3d & modelview() */
+      const Eigen::Projective3d & modelview() const;
       /** @return a non-constant reference to the 4x4 "modelview" matrix representing
         *         the camera orientation and position
-        * @sa setModelview(), const Eigen::Transform3d & modelview() const */
-      Eigen::Transform3d & modelview();
+        * @sa setModelview(), const Eigen::Projective3d & modelview() const */
+      Eigen::Projective3d & modelview();
       /** Calls gluPerspective() or glOrtho() with parameters automatically chosen
         * for rendering the GLWidget's molecule with this camera. Should be called
         * only in GL_PROJECTION matrix mode. Example code is given
@@ -342,7 +342,7 @@ namespace Avogadro {
        * @return {x/w, y/w, z/w} vector
        */
       Eigen::Vector3d V4toV3DivW(const Eigen::Vector4d & v4) {
-        return v4.start<3>()/v4.w();
+        return v4.head<3>()/v4.w();
       }
   };
 
Index: avogadro-1.2.0/libavogadro/src/engines/wireengine.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/engines/wireengine.cpp
+++ avogadro-1.2.0/libavogadro/src/engines/wireengine.cpp
@@ -109,7 +109,7 @@ namespace Avogadro {
     const Camera *camera = pd->camera();
 
     // perform a rough form of frustum culling
-    Eigen::Vector3d transformedPos = pd->camera()->modelview() * v;
+    Eigen::Vector3d transformedPos = (pd->camera()->modelview() * v.homogeneous()).head<3>();
     double dot = transformedPos.z() / transformedPos.norm();
     if(dot > -0.8)
       return true;
@@ -167,7 +167,7 @@ namespace Avogadro {
       map = pd->colorMap(); // fall back to global color map
 
     // perform a rough form of frustum culling
-    Eigen::Vector3d transformedEnd1 = pd->camera()->modelview() * v1;
+    Eigen::Vector3d transformedEnd1 = (pd->camera()->modelview() * v1.homogeneous()).head<3>();
     double dot = transformedEnd1.z() / transformedEnd1.norm();
     if(dot > -0.8)
       return true; // i.e., don't bother rendering
Index: avogadro-1.2.0/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
@@ -1989,7 +1989,7 @@ namespace Avogadro
     // fix coordinates
     // Apply COB matrix:
     Eigen::Matrix3d invCob;
-    cob.computeInverse(&invCob);
+    invCob = cob.inverse();
     for (QList<Eigen::Vector3d>::iterator
            it = fcoords.begin(),
            it_end = fcoords.end();
Index: avogadro-1.2.0/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
@@ -139,7 +139,7 @@ namespace Avogadro
   {
     // View into a Miller plane
     Camera *camera = m_glWidget->camera();
-    Eigen::Transform3d modelView;
+    Eigen::Projective3d modelView;
     modelView.setIdentity();
 
     // OK, so we want to rotate to look along the normal at the plane
Index: avogadro-1.2.0/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
@@ -41,7 +41,6 @@
 #include <openbabel/mol.h>
 
 #include <Eigen/Geometry>
-#include <Eigen/LeastSquares>
 
 #include <vector>
 
Index: avogadro-1.2.0/libavogadro/src/extensions/orca/orcainputdialog.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/orca/orcainputdialog.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/orca/orcainputdialog.cpp
@@ -33,7 +33,6 @@
 #include <openbabel/mol.h>
 
 #include <Eigen/Geometry>
-#include <Eigen/LeastSquares>
 
 #include <vector>
 
Index: avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
@@ -28,6 +28,7 @@
 
 #include <cmath>
 #include <Eigen/QR>
+#include <Eigen/Eigenvalues>
 
 namespace Avogadro {
   namespace QTAIMMathUtilities {
Index: avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
@@ -35,21 +35,21 @@ namespace Avogadro
     m_nprim=wfn.numberOfGaussianPrimitives();
     m_nnuc=wfn.numberOfNuclei();
 
-    m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.xNuclearCoordinates(),m_nnuc);
-    m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(wfn.yNuclearCoordinates(),m_nnuc);
-    m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.zNuclearCoordinates(),m_nnuc);
-    m_nucz=Map<Matrix<qint64,Dynamic,1> >(wfn.nuclearCharges(),m_nnuc);
-    m_X0=Map<Matrix<qreal,Dynamic,1> >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1);
-    m_Y0=Map<Matrix<qreal,Dynamic,1> >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1);
-    m_Z0=Map<Matrix<qreal,Dynamic,1> >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1);
-    m_xamom=Map<Matrix<qint64,Dynamic,1> >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1);
-    m_yamom=Map<Matrix<qint64,Dynamic,1> >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1);
-    m_zamom=Map<Matrix<qint64,Dynamic,1> >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1);
-    m_alpha=Map<Matrix<qreal,Dynamic,1> >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1);
+    m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xNuclearCoordinates()),m_nnuc);
+    m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yNuclearCoordinates()),m_nnuc);
+    m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zNuclearCoordinates()),m_nnuc);
+    m_nucz=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.nuclearCharges()),m_nnuc);
+    m_X0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xGaussianPrimitiveCenterCoordinates()),m_nprim,1);
+    m_Y0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yGaussianPrimitiveCenterCoordinates()),m_nprim,1);
+    m_Z0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zGaussianPrimitiveCenterCoordinates()),m_nprim,1);
+    m_xamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.xGaussianPrimitiveAngularMomenta()),m_nprim,1);
+    m_yamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.yGaussianPrimitiveAngularMomenta()),m_nprim,1);
+    m_zamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.zGaussianPrimitiveAngularMomenta()),m_nprim,1);
+    m_alpha=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.gaussianPrimitiveExponentCoefficients()),m_nprim,1);
     // TODO Implement screening for unoccupied molecular orbitals.
-    m_occno=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1);
-    m_orbe=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalEigenvalues(),m_nmo,1);
-    m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim);
+    m_occno=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalOccupationNumbers()),m_nmo,1);
+    m_orbe=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalEigenvalues()),m_nmo,1);
+    m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(const_cast<qreal*>(wfn.molecularOrbitalCoefficients()),m_nmo,m_nprim);
     m_totalEnergy=wfn.totalEnergy();
     m_virialRatio=wfn.virialRatio();
 
Index: avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
@@ -19,6 +19,7 @@
 using Eigen::Vector3d;
 using std::vector;
 
+#include <iostream>
 #include <fstream>
 
 namespace OpenQube
Index: avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
+++ avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
@@ -25,9 +25,9 @@
 
 #include "cube.h"
 
-#include <Eigen/Array>
 #include <Eigen/LU>
 #include <Eigen/QR>
+#include <Eigen/Eigenvalues>
 
 #include <cmath>
 
@@ -250,7 +250,9 @@ bool SlaterSet::initialize()
 
   SelfAdjointEigenSolver<MatrixXd> s(m_overlap);
   MatrixXd p = s.eigenvectors();
-  MatrixXd m = p * s.eigenvalues().cwise().inverse().cwise().sqrt().asDiagonal() * p.inverse();
+  // TODO check if this is correct
+  MatrixXd m1 = (s.eigenvalues().array().inverse().sqrt());
+  MatrixXd m = p.array()*(m1.diagonal().array())*p.inverse().array();
   m_normalized = m * m_eigenVectors;
 
   if (!(m_overlap*m*m).isIdentity())
Index: avogadro-1.2.0/libavogadro/src/glpainter_p.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/glpainter_p.cpp
+++ avogadro-1.2.0/libavogadro/src/glpainter_p.cpp
@@ -789,13 +789,13 @@ namespace Avogadro
         } else {
           points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
         }
-        points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
+        points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
       }
 
     // Get vectors representing the points' positions in terms of the model view.
-    Eigen::Vector3d _origin = d->widget->camera()->modelview() * origin;
-    Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin+u);
-    Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin+v);
+    Eigen::Vector3d _origin = (d->widget->camera()->modelview() * origin.homogeneous()).head<3>();
+    Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin+u).homogeneous()).head<3>();
+    Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin+v).homogeneous()).head<3>();
 
     glPushAttrib(GL_ALL_ATTRIB_BITS);
     glPushMatrix();
@@ -880,12 +880,12 @@ namespace Avogadro
         } else {
           points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
         }
-        points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
+        points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
       }
 
     // Get vectors representing the points' positions in terms of the model view.
-    Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin + u);
-    Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin + v);
+    Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin + u).homogeneous()).head<3>();
+    Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin + v).homogeneous()).head<3>();
 
     glPushAttrib(GL_ALL_ATTRIB_BITS);
     glPushMatrix();
Index: avogadro-1.2.0/libavogadro/src/glwidget.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/glwidget.cpp
+++ avogadro-1.2.0/libavogadro/src/glwidget.cpp
@@ -765,7 +765,7 @@ namespace Avogadro {
       GLfloat fogColor[4]= {static_cast<GLfloat>(d->background.redF()), static_cast<GLfloat>(d->background.greenF()),
                             static_cast<GLfloat>(d->background.blueF()), static_cast<GLfloat>(d->background.alphaF())};
       glFogfv(GL_FOG_COLOR, fogColor);
-      Vector3d distance = camera()->modelview() * d->center;
+      Vector3d distance = (camera()->modelview() * d->center.homogeneous()).head<3>();
       double distanceToCenter = distance.norm();
       glFogf(GL_FOG_DENSITY, 1.0);
       glHint(GL_FOG_HINT, GL_NICEST);
@@ -1711,7 +1711,7 @@ namespace Avogadro {
 
       if (d->renderModelViewDebug) {
         // Model view matrix:
-        const Eigen::Transform3d &modelview = d->camera->modelview();
+        const Eigen::Projective3d &modelview = d->camera->modelview();
         y += d->pd->painter()->drawText
             (x, y, tr("ModelView row 1: %L1 %L2 %L3 %L4")
              .arg(modelview(0, 0), 6, 'f', 2, ' ')
Index: avogadro-1.2.0/libavogadro/src/molecule.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/molecule.cpp
+++ avogadro-1.2.0/libavogadro/src/molecule.cpp
@@ -38,7 +38,7 @@
 #include "zmatrix.h"
 
 #include <Eigen/Geometry>
-#include <Eigen/LeastSquares>
+#include <Eigen/Eigenvalues>
 
 #include <vector>
 
@@ -1908,7 +1908,29 @@ namespace Avogadro{
         }
         d->center /= static_cast<double>(nAtoms);
         Eigen::Hyperplane<double, 3> planeCoeffs;
-        Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
+        //Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
+
+        // TODO check if this is OK
+        /************************/
+        typedef Eigen::Matrix<double,3,3> CovMatrixType;
+        typedef Eigen::Vector3d VectorType;
+        
+        VectorType mean = d->center;
+        int size=3;
+        int numPoints=numAtoms();
+        VectorType ** points=atomPositions;
+        CovMatrixType covMat = CovMatrixType::Zero(size, size);
+        VectorType remean = VectorType::Zero(size);
+        for(int i = 0; i < numPoints; ++i)
+        {
+          VectorType diff = (*(points[i]) - mean).conjugate();
+          covMat += diff * diff.adjoint();
+        }
+        Eigen::SelfAdjointEigenSolver<CovMatrixType> eig(covMat);
+        planeCoeffs.normal() = eig.eigenvectors().col(0);
+        /************************/
+
+
         delete[] atomPositions;
         d->normalVector = planeCoeffs.normal();
       }
Index: avogadro-1.2.0/libavogadro/src/navigate.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/navigate.cpp
+++ avogadro-1.2.0/libavogadro/src/navigate.cpp
@@ -40,7 +40,7 @@ namespace Avogadro {
   void Navigate::zoom(GLWidget *widget, const Eigen::Vector3d &goal,
                       double delta)
   {
-    Vector3d transformedGoal = widget->camera()->modelview() * goal;
+    Vector3d transformedGoal = (widget->camera()->modelview() * goal.homogeneous()).head<3>();
     double distanceToGoal = transformedGoal.norm();
 
     double t = ZOOM_SPEED * delta;
Index: avogadro-1.2.0/libavogadro/src/tools/bondcentrictool.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/tools/bondcentrictool.cpp
+++ avogadro-1.2.0/libavogadro/src/tools/bondcentrictool.cpp
@@ -578,8 +578,13 @@ namespace Avogadro {
 
           Vector3d clicked = *m_clickedAtom->pos();
 
-          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
-                (widget->camera()->modelview() * center).z() ? -1 : 1));
+          Eigen::Vector4d otherTransformedHomog = widget->camera()->modelview() * other.homogeneous();
+          Vector3d otherTransformed = otherTransformedHomog.hnormalized();
+          Eigen::Vector4d centerTransformedHomog = (widget->camera()->modelview() * center.homogeneous());
+          Vector3d centerTransformed = centerTransformedHomog.hnormalized();
+
+          Vector3d axis = Vector3d(0, 0, (otherTransformed.z() >=
+                                          centerTransformed.z() ? -1 : 1));
 
           Vector3d centerProj = widget->camera()->project(center);
           centerProj -= Vector3d(0,0,centerProj.z());
@@ -673,8 +678,13 @@ namespace Avogadro {
 
           Vector3d clicked = *m_clickedAtom->pos();
 
-          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
-                (widget->camera()->modelview() * center).z() ? -1 : 1));
+          Eigen::Vector4d otherTransformedHomog = (widget->camera()->modelview() * other.homogeneous());
+          Vector3d otherTransformed = otherTransformedHomog.hnormalized();
+          Eigen::Vector4d centerTransformedHomog = (widget->camera()->modelview() * center.homogeneous());
+          Vector3d centerTransformed = centerTransformedHomog.hnormalized();
+
+          Vector3d axis = Vector3d(0, 0, (otherTransformed.z() >=
+                                          centerTransformed.z() ? -1 : 1));
 
           Vector3d centerProj = widget->camera()->project(center);
           centerProj -= Vector3d(0,0,centerProj.z());
@@ -1362,10 +1372,10 @@ namespace Avogadro {
 
     planeVec = length * (planeVec / planeVec.norm());
 
-    Vector3d topLeft = widget->camera()->modelview() * (left + planeVec);
-    Vector3d topRight = widget->camera()->modelview() * (right + planeVec);
-    Vector3d botRight = widget->camera()->modelview() * (right - planeVec);
-    Vector3d botLeft = widget->camera()->modelview() * (left - planeVec);
+    Vector3d topLeft = (widget->camera()->modelview() * (left + planeVec).homogeneous()).head<3>();
+    Vector3d topRight = (widget->camera()->modelview() * (right + planeVec).homogeneous()).head<3>();
+    Vector3d botRight = (widget->camera()->modelview() * (right - planeVec).homogeneous()).head<3>();
+    Vector3d botLeft = (widget->camera()->modelview() * (left - planeVec).homogeneous()).head<3>();
 
     float alpha = 0.4;
     double lineWidth = 1.5;
@@ -1444,10 +1454,10 @@ namespace Avogadro {
       C = D + ((C-D).normalized() * minWidth);
     }
 
-    Vector3d topLeft = widget->camera()->modelview() * D;
-    Vector3d topRight = widget->camera()->modelview() * C;
-    Vector3d botRight = widget->camera()->modelview() * B;
-    Vector3d botLeft = widget->camera()->modelview() * A;
+    Vector3d topLeft = (widget->camera()->modelview() * D.homogeneous()).head<3>();
+    Vector3d topRight = (widget->camera()->modelview() * C.homogeneous()).head<3>();
+    Vector3d botRight = (widget->camera()->modelview() * B.homogeneous()).head<3>();
+    Vector3d botLeft = (widget->camera()->modelview() * A.homogeneous()).head<3>();
 
     float alpha = 0.4;
     double lineWidth = 1.5;
@@ -1506,12 +1516,12 @@ namespace Avogadro {
       Vector3d positionVector)
   {
     //Rotate skeleton around a particular axis and center point
-    Eigen::Transform3d rotation;
+    Eigen::Projective3d rotation;
     rotation = Eigen::AngleAxisd(angle, rotationVector);
     rotation.pretranslate(centerVector);
     rotation.translate(-centerVector);
 
-    return rotation*positionVector;
+    return (rotation*positionVector.homogeneous()).head<3>();
   }
 
   // ##########  showAnglesChanged  ##########
Index: avogadro-1.2.0/libavogadro/src/tools/manipulatetool.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/tools/manipulatetool.cpp
+++ avogadro-1.2.0/libavogadro/src/tools/manipulatetool.cpp
@@ -40,7 +40,6 @@
 #include <QAbstractButton>
 
 using Eigen::Vector3d;
-using Eigen::Transform3d;
 using Eigen::AngleAxisd;
 
 namespace Avogadro {
@@ -138,7 +137,7 @@ namespace Avogadro {
     double yRotate = m_settingsWidget->yRotateSpinBox->value() * DEG_TO_RAD;
     double zRotate = m_settingsWidget->zRotateSpinBox->value() * DEG_TO_RAD;
 
-    Eigen::Transform3d rotation;
+    Eigen::Projective3d rotation;
     rotation.matrix().setIdentity();
     rotation.translation() = center;
     rotation.rotate(AngleAxisd(xRotate, Vector3d::UnitX())
@@ -152,12 +151,12 @@ namespace Avogadro {
         if (p->type() == Primitive::AtomType) {
           Atom *atom = static_cast<Atom*>(p);
           tempPos = translate + *(atom->pos());
-          atom->setPos(rotation * tempPos);
+          atom->setPos((rotation * tempPos.homogeneous()).head<3>());
         }
     } else {
       foreach(Atom *atom, widget->molecule()->atoms()) {
         tempPos = translate + *(atom->pos());
-        atom->setPos(rotation * tempPos);
+        atom->setPos((rotation * tempPos.homogeneous()).head<3>());
       }
     }
 
@@ -199,7 +198,7 @@ namespace Avogadro {
     widget->setCursor(Qt::SizeVerCursor);
 
     // Move the selected atom(s) in to or out of the screen
-    Vector3d transformedGoal = widget->camera()->modelview() * *goal;
+    Vector3d transformedGoal = (widget->camera()->modelview() * goal->homogeneous()).head<3>();
     double distanceToGoal = transformedGoal.norm();
 
     double t = ZOOM_SPEED * delta;
@@ -255,7 +254,7 @@ namespace Avogadro {
 
     // Rotate the selected atoms about the center
     // rotate only selected primitives
-    Transform3d fragmentRotation;
+    Eigen::Projective3d fragmentRotation;
     fragmentRotation.matrix().setIdentity();
     fragmentRotation.translation() = *center;
     fragmentRotation.rotate(
@@ -266,7 +265,7 @@ namespace Avogadro {
 
     foreach(Primitive *p, widget->selectedPrimitives())
       if (p->type() == Primitive::AtomType)
-        static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
+        static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
     widget->molecule()->update();
   }
 
@@ -274,7 +273,7 @@ namespace Avogadro {
                             double delta) const
   {
     // Tilt the selected atoms about the center
-    Transform3d fragmentRotation;
+    Eigen::Projective3d fragmentRotation;
     fragmentRotation.matrix().setIdentity();
     fragmentRotation.translation() = *center;
     fragmentRotation.rotate(AngleAxisd(delta * ROTATION_SPEED, widget->camera()->backTransformedZAxis()));
@@ -282,7 +281,7 @@ namespace Avogadro {
 
     foreach(Primitive *p, widget->selectedPrimitives())
       if (p->type() == Primitive::AtomType)
-        static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
+        static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
     widget->molecule()->update();
   }
 
Index: avogadro-1.2.0/libavogadro/src/tools/navigatetool.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/tools/navigatetool.cpp
+++ avogadro-1.2.0/libavogadro/src/tools/navigatetool.cpp
@@ -92,7 +92,8 @@ namespace Avogadro {
       double sumOfWeights = 0.;
       QList<Atom*> atoms = widget->molecule()->atoms();
       foreach (Atom *atom, atoms) {
-        Vector3d transformedAtomPos = widget->camera()->modelview() * *atom->pos();
+        Vector3d transformedAtomPos = (widget->camera()->modelview() *
+                                       atom->pos()->homogeneous()).head<3>();
         double atomDistance = transformedAtomPos.norm();
         double dot = transformedAtomPos.z() / atomDistance;
         double weight = exp(-30. * (1. + dot));
Index: avogadro-1.2.0/libavogadro/src/tools/skeletontree.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/tools/skeletontree.cpp
+++ avogadro-1.2.0/libavogadro/src/tools/skeletontree.cpp
@@ -29,6 +29,7 @@
 #include <avogadro/atom.h>
 #include <avogadro/bond.h>
 #include <avogadro/molecule.h>
+#include <iostream>
 
 using namespace Eigen;
 using namespace std;
@@ -221,7 +222,7 @@ namespace Avogadro {
   {
     if (m_rootNode) {
       //Rotate skeleton around a particular axis and center point
-      Eigen::Transform3d rotation;
+      Eigen::Projective3d rotation;
       rotation = Eigen::AngleAxisd(angle, rotationAxis);
       rotation.pretranslate(centerVector);
       rotation.translate(-centerVector);
@@ -248,11 +249,11 @@ namespace Avogadro {
   // ##########  recursiveRotate  ##########
 
   void SkeletonTree::recursiveRotate(Node* n,
-                                     const Eigen::Transform3d &rotationMatrix)
+                                     const Eigen::Projective3d &rotationMatrix)
   {
     // Update the root node with the new position
     Atom* a = n->atom();
-    a->setPos(rotationMatrix * (*a->pos()));
+    a->setPos((rotationMatrix * (*a->pos()).homogeneous()).head<3>());
     a->update();
 
     // Now update the children
Index: avogadro-1.2.0/libavogadro/src/tools/skeletontree.h
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/tools/skeletontree.h
+++ avogadro-1.2.0/libavogadro/src/tools/skeletontree.h
@@ -230,7 +230,7 @@ namespace Avogadro {
        * @param centerVector Center location to rotate around.
        */
       void recursiveRotate(Node* n,
-                           const Eigen::Transform3d &rotationMatrix);
+                           const Eigen::Projective3d &rotationMatrix);
 
   };
 } // End namespace Avogadro
Index: avogadro-1.2.0/libavogadro/src/python/camera.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/python/camera.cpp
+++ avogadro-1.2.0/libavogadro/src/python/camera.cpp
@@ -10,7 +10,7 @@ using namespace Avogadro;
 void export_Camera()
 {
 
-  const Eigen::Transform3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
+  const Eigen::Projective3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
   Eigen::Vector3d (Camera::*unProject_ptr1)(const Eigen::Vector3d&) const = &Camera::unProject;
   Eigen::Vector3d (Camera::*unProject_ptr2)(const QPoint&, const Eigen::Vector3d&) const = &Camera::unProject;
   Eigen::Vector3d (Camera::*unProject_ptr3)(const QPoint&) const = &Camera::unProject;
Index: avogadro-1.2.0/libavogadro/src/python/eigen.cpp
===================================================================
--- avogadro-1.2.0.orig/libavogadro/src/python/eigen.cpp
+++ avogadro-1.2.0/libavogadro/src/python/eigen.cpp
@@ -305,9 +305,9 @@ template <> struct ScalarTraits<double>
     struct innerclass
     {
       //
-      //  Eigen::Transform3d --> python array (4x4)
+      //  Eigen::Projective3d --> python array (4x4)
       //
-      static PyObject* convert(Eigen::Transform3d const &trans)
+      static PyObject* convert(Eigen::Projective3d const &trans)
       {
         npy_intp dims[2] = { 4, 4 };
         PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
@@ -321,9 +321,9 @@ template <> struct ScalarTraits<double>
         return incref(result);
       }
       //
-      //  Eigen::Transform3d* --> python array (4x4)
+      //  Eigen::Projective3d* --> python array (4x4)
       //
-      static PyObject* convert(Eigen::Transform3d *trans)
+      static PyObject* convert(Eigen::Projective3d *trans)
       {
         npy_intp dims[2] = { 4, 4 };
         PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
@@ -337,9 +337,9 @@ template <> struct ScalarTraits<double>
         return incref(result);
       }
       //
-      //  const Eigen::Transform3d* --> python array (4x4)
+      //  const Eigen::Projective3d* --> python array (4x4)
       //
-      static PyObject* convert(const Eigen::Transform3d *trans)
+      static PyObject* convert(const Eigen::Projective3d *trans)
       {
         npy_intp dims[2] = { 4, 4 };
         PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
@@ -358,10 +358,10 @@ template <> struct ScalarTraits<double>
     Transform3d_to_python_array()
     {
       #ifndef WIN32
-      to_python_converter<Eigen::Transform3d, innerclass>();
+      to_python_converter<Eigen::Projective3d, innerclass>();
       #endif
-      to_python_converter<Eigen::Transform3d*, innerclass>();
-      to_python_converter<const Eigen::Transform3d*, innerclass>();
+      to_python_converter<Eigen::Projective3d*, innerclass>();
+      to_python_converter<const Eigen::Projective3d*, innerclass>();
     }
 
   };
@@ -373,17 +373,17 @@ template <> struct ScalarTraits<double>
       // Insert an rvalue from_python converter at the tail of the
       // chain. Used for implicit conversions
       //
-      //  python array --> Eigen::Transform3d
+      //  python array --> Eigen::Projective3d
       //
       // used for:
       //
-      //  void function(Eigen::Transform3d vec)
-      //  void function(Eigen::Transform3d & vec)
-      //  void function(const Eigen::Transform3d & vec)
+      //  void function(Eigen::Projective3d vec)
+      //  void function(Eigen::Projective3d & vec)
+      //  void function(const Eigen::Projective3d & vec)
       //
-      converter::registry::push_back( &convertible, &construct, type_id<Eigen::Transform3d>() );
+      converter::registry::push_back( &convertible, &construct, type_id<Eigen::Projective3d>() );
       
-      converter::registry::insert( &convert, type_id<Eigen::Transform3d>() );
+      converter::registry::insert( &convert, type_id<Eigen::Projective3d>() );
     }
 
     static void* convert(PyObject *obj_ptr)
@@ -401,7 +401,7 @@ template <> struct ScalarTraits<double>
         throw_error_already_set(); // the 1D array does not have exactly 3 elements
 
       double *values = reinterpret_cast<double*>(array->data);
-      Eigen::Transform3d *c_obj = new Eigen::Transform3d();
+      Eigen::Projective3d *c_obj = new Eigen::Projective3d();
       double *dataPtr = c_obj->data();
 
       for (int i = 0; i < 16; ++i)
@@ -432,7 +432,7 @@ template <> struct ScalarTraits<double>
       // I think this is a better way to get at the double array, where is this
       // deleted though? Does Boost::Python do it?
       double *values = reinterpret_cast<double*>(array->data);
-      Eigen::Transform3d *storage = new Eigen::Transform3d();
+      Eigen::Projective3d *storage = new Eigen::Projective3d();
       double *dataPtr = storage->data();
 
       for (int i = 0; i < 16; ++i)
@@ -467,21 +467,21 @@ class EigenUnitTestHelper
     void set_vector3d_ptr(Eigen::Vector3d* vec)                 { m_vector3d = *vec; }
     void set_const_vector3d_ptr(const Eigen::Vector3d* const vec) { m_vector3d = *vec; }
 
-    //Eigen::Transform3d             transform3d()              { return m_transform3d; }
-    //Eigen::Transform3d&            transform3d_ref()          { return m_transform3d; }
-    const Eigen::Transform3d&      const_transform3d_ref()    { return m_transform3d; }
-    Eigen::Transform3d*            transform3d_ptr()          { return &m_transform3d; }
-    const Eigen::Transform3d*      const_transform3d_ptr()    { return &m_transform3d; }
-
-    //void set_transform3d(Eigen::Transform3d vec)                      { m_transform3d = vec; }
-    //void set_transform3d_ref(Eigen::Transform3d& vec)                 { m_transform3d = vec; }
-    void set_const_transform3d_ref(const Eigen::Transform3d& vec)     { m_transform3d = vec; }
-    void set_transform3d_ptr(Eigen::Transform3d* vec)                 { m_transform3d = *vec; }
-    void set_const_transform3d_ptr(const Eigen::Transform3d* const vec) { m_transform3d = *vec; }
+    //Eigen::Projective3d             transform3d()              { return m_transform3d; }
+    //Eigen::Projective3d&            transform3d_ref()          { return m_transform3d; }
+    const Eigen::Projective3d&      const_transform3d_ref()    { return m_transform3d; }
+    Eigen::Projective3d*            transform3d_ptr()          { return &m_transform3d; }
+    const Eigen::Projective3d*      const_transform3d_ptr()    { return &m_transform3d; }
+
+    //void set_transform3d(Eigen::Projective3d vec)                      { m_transform3d = vec; }
+    //void set_transform3d_ref(Eigen::Projective3d& vec)                 { m_transform3d = vec; }
+    void set_const_transform3d_ref(const Eigen::Projective3d& vec)     { m_transform3d = vec; }
+    void set_transform3d_ptr(Eigen::Projective3d* vec)                 { m_transform3d = *vec; }
+    void set_const_transform3d_ptr(const Eigen::Projective3d* const vec) { m_transform3d = *vec; }
  
   private:
     Eigen::Vector3d m_vector3d;
-    Eigen::Transform3d m_transform3d;
+    Eigen::Projective3d m_transform3d;
 
 };
 #endif
@@ -529,7 +529,7 @@ void export_Eigen()
   Vector3x_to_python_array<Eigen::Vector3i>();
   Vector3x_from_python_array<Eigen::Vector3i>();
 
-  // Eigen::Transform3d
+  // Eigen::Projective3d
   Transform3d_to_python_array();
   Transform3d_from_python_array();

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File avogadro-port-to-eigen3.patch of Package avogadro-qt4 (Revision d63f207da5f9f58050f6f1efee56d70f)

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