avogadro_eigen3.patch

   1 diff -rupN avogadro-1.2.0/avogadro/src/CMakeLists.txt avogadro-1.2.0-new/avogadro/src/CMakeLists.txt
   2 --- avogadro-1.2.0/avogadro/src/CMakeLists.txt  2016-06-08 16:19:45.000000000 +0200
   3 +++ avogadro-1.2.0-new/avogadro/src/CMakeLists.txt      2018-01-03 14:47:08.649568522 +0100
   4 @@ -22,15 +22,9 @@ include_directories(
   5    ${CMAKE_CURRENT_BINARY_DIR}
   6  )
   7
   8 -if(EIGEN3_FOUND)
   9 -       include_directories(
  10 -               ${EIGEN3_INCLUDE_DIR}
  11 -       )
  12 -elseif(EIGEN2_FOUND)
  13 -       include_directories(
  14 -               ${EIGEN2_INCLUDE_DIR}
  15 -       )
  16 -endif(EIGEN3_FOUND)
  17 +include_directories(
  18 +    ${EIGEN3_INCLUDE_DIR}
  19 +)
  20
  21  if(GLEW_FOUND)
  22    include_directories(${GLEW_INCLUDE_DIR})
  23 diff -rupN avogadro-1.2.0/avogadro/src/mainwindow.cpp avogadro-1.2.0-new/avogadro/src/mainwindow.cpp
  24 --- avogadro-1.2.0/avogadro/src/mainwindow.cpp  2016-06-08 16:19:45.000000000 +0200
  25 +++ avogadro-1.2.0-new/avogadro/src/mainwindow.cpp      2018-01-03 14:45:25.170574246 +0100
  26 @@ -115,7 +115,6 @@
  27  #include <QDebug>
  28
  29  #include <Eigen/Geometry>
  30 -#include <Eigen/Array>
  31  #define USEQUAT
  32  // This is a "hidden" exported Qt function on the Mac for Qt-4.x.
  33  #ifdef Q_WS_MAC
  34 @@ -2775,7 +2774,7 @@ protected:
  35      linearGoal.row(1) = linearGoal.row(2).cross(linearGoal.row(0));
  36
  37      // calculate the translation matrix
  38 -    Transform3d goal(linearGoal);
  39 +    Projective3d goal(linearGoal);
  40
  41      goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
  42
  43 @@ -2840,7 +2839,7 @@ protected:
  44      Matrix3d linearGoal = Matrix3d::Identity();
  45
  46      // calculate the translation matrix
  47 -    Transform3d goal(linearGoal);
  48 +    Projective3d goal(linearGoal);
  49
  50      goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
  51
  52 diff -rupN avogadro-1.2.0/CMakeLists.txt avogadro-1.2.0-new/CMakeLists.txt
  53 --- avogadro-1.2.0/CMakeLists.txt       2016-06-08 16:19:45.000000000 +0200
  54 +++ avogadro-1.2.0-new/CMakeLists.txt   2018-01-03 14:48:31.478563940 +0100
  55 @@ -231,14 +231,7 @@ if(NOT Linguist_FOUND)
  56    message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
  57  endif()
  58
  59 -find_package(Eigen3) # find and setup Eigen3 if available
  60 -if(NOT EIGEN3_FOUND)
  61 -   message(STATUS "Cannot find Eigen3, trying Eigen2")
  62 -   find_package(Eigen2 REQUIRED) # Some version is required
  63 -else()
  64 -# Use Stage10 Eigen3 support
  65 -   set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
  66 -endif()
  67 +find_package(Eigen3 REQUIRED) # find and setup Eigen3
  68
  69  find_package(ZLIB REQUIRED)
  70  find_package(OpenBabel2 REQUIRED) # find and setup OpenBabel
  71 @@ -473,7 +466,6 @@ install(FILES
  72
  73  # Install the find modules we require to be present
  74  install(FILES
  75 -  "${CMAKE_MODULE_PATH}/FindEigen2.cmake"
  76    "${CMAKE_MODULE_PATH}/FindEigen3.cmake"
  77    "${CMAKE_MODULE_PATH}/FindGLEW.cmake"
  78    DESTINATION "${Avogadro_PLUGIN_INSTALL_DIR}/cmake")
  79 diff -rupN avogadro-1.2.0/libavogadro/src/camera.cpp avogadro-1.2.0-new/libavogadro/src/camera.cpp
  80 --- avogadro-1.2.0/libavogadro/src/camera.cpp   2016-06-08 16:19:45.000000000 +0200
  81 +++ avogadro-1.2.0-new/libavogadro/src/camera.cpp       2018-01-03 14:45:25.171574246 +0100
  82 @@ -47,7 +47,7 @@ namespace Avogadro
  83
  84        CameraPrivate() {};
  85
  86 -      Eigen::Transform3d modelview, projection;
  87 +      Eigen::Projective3d modelview, projection;
  88        const GLWidget *parent;
  89        double angleOfViewY;
  90        double orthoScale;
  91 @@ -169,20 +169,20 @@ namespace Avogadro
  92
  93    double Camera::distance(const Eigen::Vector3d & point) const
  94    {
  95 -    return ( d->modelview * point ).norm();
  96 +    return ( d->modelview * point.homogeneous() ).head<3>().norm();
  97    }
  98
  99 -  void Camera::setModelview(const Eigen::Transform3d &matrix)
 100 +  void Camera::setModelview(const Eigen::Projective3d &matrix)
 101    {
 102      d->modelview = matrix;
 103    }
 104
 105 -  const Eigen::Transform3d & Camera::modelview() const
 106 +  const Eigen::Projective3d & Camera::modelview() const
 107    {
 108      return d->modelview;
 109    }
 110
 111 -  Eigen::Transform3d & Camera::modelview()
 112 +  Eigen::Projective3d & Camera::modelview()
 113    {
 114      return d->modelview;
 115    }
 116 diff -rupN avogadro-1.2.0/libavogadro/src/camera.h avogadro-1.2.0-new/libavogadro/src/camera.h
 117 --- avogadro-1.2.0/libavogadro/src/camera.h     2016-06-08 16:19:45.000000000 +0200
 118 +++ avogadro-1.2.0-new/libavogadro/src/camera.h 2018-01-03 14:45:25.171574246 +0100
 119 @@ -101,16 +101,16 @@ namespace Avogadro {
 120        double angleOfViewY() const;
 121        /** Sets 4x4 "modelview" matrix representing the camera orientation and position.
 122          * @param matrix the matrix to copy from
 123 -        * @sa Eigen::Transform3d & modelview(), applyModelview() */
 124 -      void setModelview(const Eigen::Transform3d &matrix);
 125 +        * @sa Eigen::Projective3d & modelview(), applyModelview() */
 126 +      void setModelview(const Eigen::Projective3d &matrix);
 127        /** @return a constant reference to the 4x4 "modelview" matrix representing
 128          *         the camera orientation and position
 129 -        * @sa setModelview(), Eigen::Transform3d & modelview() */
 130 -      const Eigen::Transform3d & modelview() const;
 131 +        * @sa setModelview(), Eigen::Projective3d & modelview() */
 132 +      const Eigen::Projective3d & modelview() const;
 133        /** @return a non-constant reference to the 4x4 "modelview" matrix representing
 134          *         the camera orientation and position
 135 -        * @sa setModelview(), const Eigen::Transform3d & modelview() const */
 136 -      Eigen::Transform3d & modelview();
 137 +        * @sa setModelview(), const Eigen::Projective3d & modelview() const */
 138 +      Eigen::Projective3d & modelview();
 139        /** Calls gluPerspective() or glOrtho() with parameters automatically chosen
 140          * for rendering the GLWidget's molecule with this camera. Should be called
 141          * only in GL_PROJECTION matrix mode. Example code is given
 142 @@ -342,7 +342,7 @@ namespace Avogadro {
 143         * @return {x/w, y/w, z/w} vector
 144         */
 145        Eigen::Vector3d V4toV3DivW(const Eigen::Vector4d & v4) {
 146 -        return v4.start<3>()/v4.w();
 147 +        return v4.head<3>()/v4.w();
 148        }
 149    };
 150
 151 diff -rupN avogadro-1.2.0/libavogadro/src/CMakeLists.txt avogadro-1.2.0-new/libavogadro/src/CMakeLists.txt
 152 --- avogadro-1.2.0/libavogadro/src/CMakeLists.txt       2016-06-08 16:19:45.000000000 +0200
 153 +++ avogadro-1.2.0-new/libavogadro/src/CMakeLists.txt   2018-01-03 14:48:09.786565140 +0100
 154 @@ -14,15 +14,9 @@ include_directories(
 155    ${OPENBABEL2_INCLUDE_DIR}
 156  )
 157
 158 -if(EIGEN3_FOUND)
 159 -       include_directories(
 160 -               ${EIGEN3_INCLUDE_DIR}
 161 -       )
 162 -elseif(EIGEN2_FOUND)
 163 -       include_directories(
 164 -               ${EIGEN2_INCLUDE_DIR}
 165 -       )
 166 -endif(EIGEN3_FOUND)
 167 +include_directories(
 168 +    ${EIGEN3_INCLUDE_DIR}
 169 +)
 170
 171  # I think this is necessary now in order to tell the linker where openbabel is
 172  link_directories(${OPENBABEL2_LIBRARY_DIRS})
 173 diff -rupN avogadro-1.2.0/libavogadro/src/engines/wireengine.cpp avogadro-1.2.0-new/libavogadro/src/engines/wireengine.cpp
 174 --- avogadro-1.2.0/libavogadro/src/engines/wireengine.cpp       2016-06-08 16:19:45.000000000 +0200
 175 +++ avogadro-1.2.0-new/libavogadro/src/engines/wireengine.cpp   2018-01-03 14:45:25.171574246 +0100
 176 @@ -109,7 +109,7 @@ namespace Avogadro {
 177      const Camera *camera = pd->camera();
 178
 179      // perform a rough form of frustum culling
 180 -    Eigen::Vector3d transformedPos = pd->camera()->modelview() * v;
 181 +    Eigen::Vector3d transformedPos = (pd->camera()->modelview() * v.homogeneous()).head<3>();
 182      double dot = transformedPos.z() / transformedPos.norm();
 183      if(dot > -0.8)
 184        return true;
 185 @@ -167,7 +167,7 @@ namespace Avogadro {
 186        map = pd->colorMap(); // fall back to global color map
 187
 188      // perform a rough form of frustum culling
 189 -    Eigen::Vector3d transformedEnd1 = pd->camera()->modelview() * v1;
 190 +    Eigen::Vector3d transformedEnd1 = (pd->camera()->modelview() * v1.homogeneous()).head<3>();
 191      double dot = transformedEnd1.z() / transformedEnd1.norm();
 192      if(dot > -0.8)
 193        return true; // i.e., don't bother rendering
 194 diff -rupN avogadro-1.2.0/libavogadro/src/extensions/crystallography/crystallographyextension.cpp avogadro-1.2.0-new/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
 195 --- avogadro-1.2.0/libavogadro/src/extensions/crystallography/crystallographyextension.cpp      2016-06-08 16:19:45.000000000 +0200
 196 +++ avogadro-1.2.0-new/libavogadro/src/extensions/crystallography/crystallographyextension.cpp  2018-01-03 14:45:25.172574245 +0100
 197 @@ -1989,7 +1989,7 @@ namespace Avogadro
 198      // fix coordinates
 199      // Apply COB matrix:
 200      Eigen::Matrix3d invCob;
 201 -    cob.computeInverse(&invCob);
 202 +    invCob = cob.inverse();
 203      for (QList<Eigen::Vector3d>::iterator
 204             it = fcoords.begin(),
 205             it_end = fcoords.end();
 206 diff -rupN avogadro-1.2.0/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp avogadro-1.2.0-new/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
 207 --- avogadro-1.2.0/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp        2016-06-08 16:19:45.000000000 +0200
 208 +++ avogadro-1.2.0-new/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp    2018-01-03 14:45:25.173574245 +0100
 209 @@ -139,7 +139,7 @@ namespace Avogadro
 210    {
 211      // View into a Miller plane
 212      Camera *camera = m_glWidget->camera();
 213 -    Eigen::Transform3d modelView;
 214 +    Eigen::Projective3d modelView;
 215      modelView.setIdentity();
 216
 217      // OK, so we want to rotate to look along the normal at the plane
 218 diff -rupN avogadro-1.2.0/libavogadro/src/extensions/orca/orcaanalysedialog.cpp avogadro-1.2.0-new/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
 219 --- avogadro-1.2.0/libavogadro/src/extensions/orca/orcaanalysedialog.cpp        2016-06-08 16:19:45.000000000 +0200
 220 +++ avogadro-1.2.0-new/libavogadro/src/extensions/orca/orcaanalysedialog.cpp    2018-01-03 14:45:25.173574245 +0100
 221 @@ -41,7 +41,6 @@
 222  #include <openbabel/mol.h>
 223
 224  #include <Eigen/Geometry>
 225 -#include <Eigen/LeastSquares>
 226
 227  #include <vector>
 228
 229 diff -rupN avogadro-1.2.0/libavogadro/src/extensions/orca/orcainputdialog.cpp avogadro-1.2.0-new/libavogadro/src/extensions/orca/orcainputdialog.cpp
 230 --- avogadro-1.2.0/libavogadro/src/extensions/orca/orcainputdialog.cpp  2016-06-08 16:19:45.000000000 +0200
 231 +++ avogadro-1.2.0-new/libavogadro/src/extensions/orca/orcainputdialog.cpp      2018-01-03 14:45:25.174574245 +0100
 232 @@ -33,7 +33,6 @@
 233  #include <openbabel/mol.h>
 234
 235  #include <Eigen/Geometry>
 236 -#include <Eigen/LeastSquares>
 237
 238  #include <vector>
 239
 240 diff -rupN avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp avogadro-1.2.0-new/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
 241 --- avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp      2016-06-08 16:19:45.000000000 +0200
 242 +++ avogadro-1.2.0-new/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp  2018-01-03 14:45:25.174574245 +0100
 243 @@ -28,6 +28,7 @@
 244
 245  #include <cmath>
 246  #include <Eigen/QR>
 247 +#include <Eigen/Eigenvalues>
 248
 249  namespace Avogadro {
 250    namespace QTAIMMathUtilities {
 251 diff -rupN avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp avogadro-1.2.0-new/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
 252 --- avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp      2016-06-08 16:19:45.000000000 +0200
 253 +++ avogadro-1.2.0-new/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp  2018-01-03 14:45:25.186574245 +0100
 254 @@ -35,21 +35,21 @@ namespace Avogadro
 255      m_nprim=wfn.numberOfGaussianPrimitives();
 256      m_nnuc=wfn.numberOfNuclei();
 257
 258 -    m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.xNuclearCoordinates(),m_nnuc);
 259 -    m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(wfn.yNuclearCoordinates(),m_nnuc);
 260 -    m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.zNuclearCoordinates(),m_nnuc);
 261 -    m_nucz=Map<Matrix<qint64,Dynamic,1> >(wfn.nuclearCharges(),m_nnuc);
 262 -    m_X0=Map<Matrix<qreal,Dynamic,1> >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1);
 263 -    m_Y0=Map<Matrix<qreal,Dynamic,1> >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1);
 264 -    m_Z0=Map<Matrix<qreal,Dynamic,1> >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1);
 265 -    m_xamom=Map<Matrix<qint64,Dynamic,1> >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1);
 266 -    m_yamom=Map<Matrix<qint64,Dynamic,1> >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1);
 267 -    m_zamom=Map<Matrix<qint64,Dynamic,1> >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1);
 268 -    m_alpha=Map<Matrix<qreal,Dynamic,1> >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1);
 269 +    m_nucxcoord=Map<const Matrix<qreal,Dynamic,1> >(wfn.xNuclearCoordinates(),m_nnuc);
 270 +    m_nucycoord=Map<const Matrix<qreal,Dynamic,1> >(wfn.yNuclearCoordinates(),m_nnuc);
 271 +    m_nuczcoord=Map<const Matrix<qreal,Dynamic,1> >(wfn.zNuclearCoordinates(),m_nnuc);
 272 +    m_nucz=Map<const Matrix<qint64,Dynamic,1> >(wfn.nuclearCharges(),m_nnuc);
 273 +    m_X0=Map<const Matrix<qreal,Dynamic,1> >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1);
 274 +    m_Y0=Map<const Matrix<qreal,Dynamic,1> >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1);
 275 +    m_Z0=Map<const Matrix<qreal,Dynamic,1> >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1);
 276 +    m_xamom=Map<const Matrix<qint64,Dynamic,1> >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1);
 277 +    m_yamom=Map<const Matrix<qint64,Dynamic,1> >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1);
 278 +    m_zamom=Map<const Matrix<qint64,Dynamic,1> >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1);
 279 +    m_alpha=Map<const Matrix<qreal,Dynamic,1> >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1);
 280      // TODO Implement screening for unoccupied molecular orbitals.
 281 -    m_occno=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1);
 282 -    m_orbe=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalEigenvalues(),m_nmo,1);
 283 -    m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim);
 284 +    m_occno=Map<const Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1);
 285 +    m_orbe=Map<const Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalEigenvalues(),m_nmo,1);
 286 +    m_coef=Map<const Matrix<qreal,Dynamic,Dynamic,RowMajor> >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim);
 287      m_totalEnergy=wfn.totalEnergy();
 288      m_virialRatio=wfn.virialRatio();
 289
 290 diff -rupN avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt avogadro-1.2.0-new/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt
 291 --- avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt  2016-06-08 16:19:45.000000000 +0200
 292 +++ avogadro-1.2.0-new/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt      2018-01-03 14:47:58.215565780 +0100
 293 @@ -1,13 +1,6 @@
 294  find_package(Qt4 4.6 REQUIRED)
 295 -find_package(Eigen3)
 296 -if(NOT EIGEN3_FOUND)
 297 -  message(STATUS "Cannot find Eigen3, trying Eigen2")
 298 -  find_package(Eigen2 REQUIRED)
 299 -else()
 300 -  set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
 301 -endif()
 302
 303 -include_directories(${QT_INCLUDE_DIR} ${EIGEN2_INCLUDE_DIR})
 304 +include_directories(${QT_INCLUDE_DIR} ${EIGEN3_INCLUDE_DIR})
 305
 306  # Headers for our public API
 307  set(openqube_HDRS
 308 diff -rupN avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp avogadro-1.2.0-new/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
 309 --- avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp 2016-06-08 16:19:45.000000000 +0200
 310 +++ avogadro-1.2.0-new/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp     2018-01-03 14:45:25.176574245 +0100
 311 @@ -19,6 +19,7 @@
 312  using Eigen::Vector3d;
 313  using std::vector;
 314
 315 +#include <iostream>
 316  #include <fstream>
 317
 318  namespace OpenQube
 319 diff -rupN avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp avogadro-1.2.0-new/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
 320 --- avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp   2016-06-08 16:19:45.000000000 +0200
 321 +++ avogadro-1.2.0-new/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp       2018-01-03 14:45:25.187574245 +0100
 322 @@ -25,9 +25,9 @@
 323
 324  #include "cube.h"
 325
 326 -#include <Eigen/Array>
 327  #include <Eigen/LU>
 328  #include <Eigen/QR>
 329 +#include <Eigen/Eigenvalues>
 330
 331  #include <cmath>
 332
 333 @@ -250,7 +250,9 @@ bool SlaterSet::initialize()
 334
 335    SelfAdjointEigenSolver<MatrixXd> s(m_overlap);
 336    MatrixXd p = s.eigenvectors();
 337 -  MatrixXd m = p * s.eigenvalues().cwise().inverse().cwise().sqrt().asDiagonal() * p.inverse();
 338 +
 339 +  MatrixXd m = p * s.eigenvalues().array().inverse().sqrt().matrix().asDiagonal() * p.inverse();
 340 +
 341    m_normalized = m * m_eigenVectors;
 342
 343    if (!(m_overlap*m*m).isIdentity())
 344 diff -rupN avogadro-1.2.0/libavogadro/src/glpainter_p.cpp avogadro-1.2.0-new/libavogadro/src/glpainter_p.cpp
 345 --- avogadro-1.2.0/libavogadro/src/glpainter_p.cpp      2016-06-08 16:19:45.000000000 +0200
 346 +++ avogadro-1.2.0-new/libavogadro/src/glpainter_p.cpp  2018-01-03 14:45:25.177574245 +0100
 347 @@ -789,13 +789,13 @@ namespace Avogadro
 348          } else {
 349            points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
 350          }
 351 -        points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
 352 +        points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
 353        }
 354
 355      // Get vectors representing the points' positions in terms of the model view.
 356 -    Eigen::Vector3d _origin = d->widget->camera()->modelview() * origin;
 357 -    Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin+u);
 358 -    Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin+v);
 359 +    Eigen::Vector3d _origin = (d->widget->camera()->modelview() * origin.homogeneous()).head<3>();
 360 +    Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin+u).homogeneous()).head<3>();
 361 +    Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin+v).homogeneous()).head<3>();
 362
 363      glPushAttrib(GL_ALL_ATTRIB_BITS);
 364      glPushMatrix();
 365 @@ -880,12 +880,12 @@ namespace Avogadro
 366          } else {
 367            points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
 368          }
 369 -        points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
 370 +        points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
 371        }
 372
 373      // Get vectors representing the points' positions in terms of the model view.
 374 -    Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin + u);
 375 -    Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin + v);
 376 +    Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin + u).homogeneous()).head<3>();
 377 +    Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin + v).homogeneous()).head<3>();
 378
 379      glPushAttrib(GL_ALL_ATTRIB_BITS);
 380      glPushMatrix();
 381 diff -rupN avogadro-1.2.0/libavogadro/src/glwidget.cpp avogadro-1.2.0-new/libavogadro/src/glwidget.cpp
 382 --- avogadro-1.2.0/libavogadro/src/glwidget.cpp 2016-06-08 16:19:45.000000000 +0200
 383 +++ avogadro-1.2.0-new/libavogadro/src/glwidget.cpp     2018-01-03 14:45:25.178574245 +0100
 384 @@ -765,7 +765,7 @@ namespace Avogadro {
 385        GLfloat fogColor[4]= {static_cast<GLfloat>(d->background.redF()), static_cast<GLfloat>(d->background.greenF()),
 386                              static_cast<GLfloat>(d->background.blueF()), static_cast<GLfloat>(d->background.alphaF())};
 387        glFogfv(GL_FOG_COLOR, fogColor);
 388 -      Vector3d distance = camera()->modelview() * d->center;
 389 +      Vector3d distance = (camera()->modelview() * d->center.homogeneous()).head<3>();
 390        double distanceToCenter = distance.norm();
 391        glFogf(GL_FOG_DENSITY, 1.0);
 392        glHint(GL_FOG_HINT, GL_NICEST);
 393 @@ -1711,7 +1711,7 @@ namespace Avogadro {
 394
 395        if (d->renderModelViewDebug) {
 396          // Model view matrix:
 397 -        const Eigen::Transform3d &modelview = d->camera->modelview();
 398 +        const Eigen::Projective3d &modelview = d->camera->modelview();
 399          y += d->pd->painter()->drawText
 400              (x, y, tr("ModelView row 1: %L1 %L2 %L3 %L4")
 401               .arg(modelview(0, 0), 6, 'f', 2, ' ')
 402 diff -rupN avogadro-1.2.0/libavogadro/src/leastsquares.h avogadro-1.2.0-new/libavogadro/src/leastsquares.h
 403 --- avogadro-1.2.0/libavogadro/src/leastsquares.h       1970-01-01 01:00:00.000000000 +0100
 404 +++ avogadro-1.2.0-new/libavogadro/src/leastsquares.h   2018-01-03 14:45:25.187574245 +0100
 405 @@ -0,0 +1,74 @@
 406 +/**********************************************************************
 407 +  LeastSquares - Least squares functions removed from Eigen2 codebase
 408 +
 409 +  Copyright (C) 2006-2009 Benoit Jacob <jacob.benoit.1@gmail.com>
 410 +
 411 +  This file is part of the Avogadro molecular editor project.
 412 +  For more information, see <http://avogadro.cc/>
 413 +
 414 +  Avogadro is free software; you can redistribute it and/or modify
 415 +  it under the terms of the GNU General Public License as published by
 416 +  the Free Software Foundation; either version 2 of the License, or
 417 +  (at your option) any later version.
 418 +
 419 +  Avogadro is distributed in the hope that it will be useful,
 420 +  but WITHOUT ANY WARRANTY; without even the implied warranty of
 421 +  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 422 +  GNU General Public License for more details.
 423 +
 424 +  You should have received a copy of the GNU General Public License
 425 +  along with this program; if not, write to the Free Software
 426 +  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
 427 +  02110-1301, USA.
 428 + **********************************************************************/
 429 +
 430 +#ifndef LEASTSQUARES_H
 431 +#define LEASTSQUARES_H
 432 +
 433 +#include <Eigen/Eigenvalues>
 434 +
 435 +namespace Avogadro
 436 +{
 437 +
 438 +template<typename VectorType, typename HyperplaneType>
 439 +void fitHyperplane(int numPoints,
 440 +                   VectorType **points,
 441 +                   HyperplaneType *result,
 442 +                   typename Eigen::NumTraits<typename VectorType::Scalar>::Real* soundness = 0)
 443 +{
 444 +  typedef typename VectorType::Scalar Scalar;
 445 +  typedef Eigen::Matrix<Scalar,VectorType::SizeAtCompileTime,VectorType::SizeAtCompileTime> CovMatrixType;
 446 +  EIGEN_STATIC_ASSERT_VECTOR_ONLY(VectorType)
 447 +  assert(numPoints >= 1);
 448 +  int size = points[0]->size();
 449 +  assert(size+1 == result->coeffs().size());
 450 +
 451 +  // compute the mean of the data
 452 +  VectorType mean = VectorType::Zero(size);
 453 +  for(int i = 0; i < numPoints; ++i)
 454 +    mean += *(points[i]);
 455 +  mean /= numPoints;
 456 +
 457 +  // compute the covariance matrix
 458 +  CovMatrixType covMat = CovMatrixType::Zero(size, size);
 459 +  VectorType remean = VectorType::Zero(size);
 460 +  for(int i = 0; i < numPoints; ++i)
 461 +  {
 462 +    VectorType diff = (*(points[i]) - mean).conjugate();
 463 +    covMat += diff * diff.adjoint();
 464 +  }
 465 +
 466 +  // now we just have to pick the eigen vector with smallest eigen value
 467 +  Eigen::SelfAdjointEigenSolver<CovMatrixType> eig(covMat);
 468 +  result->normal() = eig.eigenvectors().col(0);
 469 +  if (soundness)
 470 +    *soundness = eig.eigenvalues().coeff(0)/eig.eigenvalues().coeff(1);
 471 +
 472 +  // let's compute the constant coefficient such that the
 473 +  // plane pass trough the mean point:
 474 +  result->offset() = - (result->normal().array() * mean.array()).sum();
 475 +}
 476 +
 477 +} // end namespace Avogadro
 478 +
 479 +#endif
 480 diff -rupN avogadro-1.2.0/libavogadro/src/molecule.cpp avogadro-1.2.0-new/libavogadro/src/molecule.cpp
 481 --- avogadro-1.2.0/libavogadro/src/molecule.cpp 2016-06-08 16:19:45.000000000 +0200
 482 +++ avogadro-1.2.0-new/libavogadro/src/molecule.cpp     2018-01-03 14:45:25.188574245 +0100
 483 @@ -36,9 +36,9 @@
 484  #include "primitivelist.h"
 485  #include "residue.h"
 486  #include "zmatrix.h"
 487 +#include "leastsquares.h"
 488
 489  #include <Eigen/Geometry>
 490 -#include <Eigen/LeastSquares>
 491
 492  #include <vector>
 493
 494 @@ -1908,7 +1908,8 @@ namespace Avogadro{
 495          }
 496          d->center /= static_cast<double>(nAtoms);
 497          Eigen::Hyperplane<double, 3> planeCoeffs;
 498 -        Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
 499 +        fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
 500 +
 501          delete[] atomPositions;
 502          d->normalVector = planeCoeffs.normal();
 503        }
 504 diff -rupN avogadro-1.2.0/libavogadro/src/navigate.cpp avogadro-1.2.0-new/libavogadro/src/navigate.cpp
 505 --- avogadro-1.2.0/libavogadro/src/navigate.cpp 2016-06-08 16:19:45.000000000 +0200
 506 +++ avogadro-1.2.0-new/libavogadro/src/navigate.cpp     2018-01-03 14:45:25.179574245 +0100
 507 @@ -40,7 +40,7 @@ namespace Avogadro {
 508    void Navigate::zoom(GLWidget *widget, const Eigen::Vector3d &goal,
 509                        double delta)
 510    {
 511 -    Vector3d transformedGoal = widget->camera()->modelview() * goal;
 512 +    Vector3d transformedGoal = (widget->camera()->modelview() * goal.homogeneous()).head<3>();
 513      double distanceToGoal = transformedGoal.norm();
 514
 515      double t = ZOOM_SPEED * delta;
 516 diff -rupN avogadro-1.2.0/libavogadro/src/python/camera.cpp avogadro-1.2.0-new/libavogadro/src/python/camera.cpp
 517 --- avogadro-1.2.0/libavogadro/src/python/camera.cpp    2016-06-08 16:19:45.000000000 +0200
 518 +++ avogadro-1.2.0-new/libavogadro/src/python/camera.cpp        2018-01-03 14:45:25.181574245 +0100
 519 @@ -10,7 +10,7 @@ using namespace Avogadro;
 520  void export_Camera()
 521  {
 522
 523 -  const Eigen::Transform3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
 524 +  const Eigen::Projective3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
 525    Eigen::Vector3d (Camera::*unProject_ptr1)(const Eigen::Vector3d&) const = &Camera::unProject;
 526    Eigen::Vector3d (Camera::*unProject_ptr2)(const QPoint&, const Eigen::Vector3d&) const = &Camera::unProject;
 527    Eigen::Vector3d (Camera::*unProject_ptr3)(const QPoint&) const = &Camera::unProject;
 528 diff -rupN avogadro-1.2.0/libavogadro/src/python/eigen.cpp avogadro-1.2.0-new/libavogadro/src/python/eigen.cpp
 529 --- avogadro-1.2.0/libavogadro/src/python/eigen.cpp     2016-06-08 16:19:45.000000000 +0200
 530 +++ avogadro-1.2.0-new/libavogadro/src/python/eigen.cpp 2018-01-03 14:45:25.182574245 +0100
 531 @@ -305,9 +305,9 @@ template <> struct ScalarTraits<double>
 532      struct innerclass
 533      {
 534        //
 535 -      //  Eigen::Transform3d --> python array (4x4)
 536 +      //  Eigen::Projective3d --> python array (4x4)
 537        //
 538 -      static PyObject* convert(Eigen::Transform3d const &trans)
 539 +      static PyObject* convert(Eigen::Projective3d const &trans)
 540        {
 541          npy_intp dims[2] = { 4, 4 };
 542          PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
 543 @@ -321,9 +321,9 @@ template <> struct ScalarTraits<double>
 544          return incref(result);
 545        }
 546        //
 547 -      //  Eigen::Transform3d* --> python array (4x4)
 548 +      //  Eigen::Projective3d* --> python array (4x4)
 549        //
 550 -      static PyObject* convert(Eigen::Transform3d *trans)
 551 +      static PyObject* convert(Eigen::Projective3d *trans)
 552        {
 553          npy_intp dims[2] = { 4, 4 };
 554          PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
 555 @@ -337,9 +337,9 @@ template <> struct ScalarTraits<double>
 556          return incref(result);
 557        }
 558        //
 559 -      //  const Eigen::Transform3d* --> python array (4x4)
 560 +      //  const Eigen::Projective3d* --> python array (4x4)
 561        //
 562 -      static PyObject* convert(const Eigen::Transform3d *trans)
 563 +      static PyObject* convert(const Eigen::Projective3d *trans)
 564        {
 565          npy_intp dims[2] = { 4, 4 };
 566          PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
 567 @@ -358,10 +358,10 @@ template <> struct ScalarTraits<double>
 568      Transform3d_to_python_array()
 569      {
 570        #ifndef WIN32
 571 -      to_python_converter<Eigen::Transform3d, innerclass>();
 572 +      to_python_converter<Eigen::Projective3d, innerclass>();
 573        #endif
 574 -      to_python_converter<Eigen::Transform3d*, innerclass>();
 575 -      to_python_converter<const Eigen::Transform3d*, innerclass>();
 576 +      to_python_converter<Eigen::Projective3d*, innerclass>();
 577 +      to_python_converter<const Eigen::Projective3d*, innerclass>();
 578      }
 579
 580    };
 581 @@ -373,17 +373,17 @@ template <> struct ScalarTraits<double>
 582        // Insert an rvalue from_python converter at the tail of the
 583        // chain. Used for implicit conversions
 584        //
 585 -      //  python array --> Eigen::Transform3d
 586 +      //  python array --> Eigen::Projective3d
 587        //
 588        // used for:
 589        //
 590 -      //  void function(Eigen::Transform3d vec)
 591 -      //  void function(Eigen::Transform3d & vec)
 592 -      //  void function(const Eigen::Transform3d & vec)
 593 +      //  void function(Eigen::Projective3d vec)
 594 +      //  void function(Eigen::Projective3d & vec)
 595 +      //  void function(const Eigen::Projective3d & vec)
 596        //
 597 -      converter::registry::push_back( &convertible, &construct, type_id<Eigen::Transform3d>() );
 598 +      converter::registry::push_back( &convertible, &construct, type_id<Eigen::Projective3d>() );
 599
 600 -      converter::registry::insert( &convert, type_id<Eigen::Transform3d>() );
 601 +      converter::registry::insert( &convert, type_id<Eigen::Projective3d>() );
 602      }
 603
 604      static void* convert(PyObject *obj_ptr)
 605 @@ -401,7 +401,7 @@ template <> struct ScalarTraits<double>
 606          throw_error_already_set(); // the 1D array does not have exactly 3 elements
 607
 608        double *values = reinterpret_cast<double*>(array->data);
 609 -      Eigen::Transform3d *c_obj = new Eigen::Transform3d();
 610 +      Eigen::Projective3d *c_obj = new Eigen::Projective3d();
 611        double *dataPtr = c_obj->data();
 612
 613        for (int i = 0; i < 16; ++i)
 614 @@ -432,7 +432,7 @@ template <> struct ScalarTraits<double>
 615        // I think this is a better way to get at the double array, where is this
 616        // deleted though? Does Boost::Python do it?
 617        double *values = reinterpret_cast<double*>(array->data);
 618 -      Eigen::Transform3d *storage = new Eigen::Transform3d();
 619 +      Eigen::Projective3d *storage = new Eigen::Projective3d();
 620        double *dataPtr = storage->data();
 621
 622        for (int i = 0; i < 16; ++i)
 623 @@ -467,21 +467,21 @@ class EigenUnitTestHelper
 624      void set_vector3d_ptr(Eigen::Vector3d* vec)                 { m_vector3d = *vec; }
 625      void set_const_vector3d_ptr(const Eigen::Vector3d* const vec) { m_vector3d = *vec; }
 626
 627 -    //Eigen::Transform3d             transform3d()              { return m_transform3d; }
 628 -    //Eigen::Transform3d&            transform3d_ref()          { return m_transform3d; }
 629 -    const Eigen::Transform3d&      const_transform3d_ref()    { return m_transform3d; }
 630 -    Eigen::Transform3d*            transform3d_ptr()          { return &m_transform3d; }
 631 -    const Eigen::Transform3d*      const_transform3d_ptr()    { return &m_transform3d; }
 632 -
 633 -    //void set_transform3d(Eigen::Transform3d vec)                      { m_transform3d = vec; }
 634 -    //void set_transform3d_ref(Eigen::Transform3d& vec)                 { m_transform3d = vec; }
 635 -    void set_const_transform3d_ref(const Eigen::Transform3d& vec)     { m_transform3d = vec; }
 636 -    void set_transform3d_ptr(Eigen::Transform3d* vec)                 { m_transform3d = *vec; }
 637 -    void set_const_transform3d_ptr(const Eigen::Transform3d* const vec) { m_transform3d = *vec; }
 638 +    //Eigen::Projective3d             transform3d()              { return m_transform3d; }
 639 +    //Eigen::Projective3d&            transform3d_ref()          { return m_transform3d; }
 640 +    const Eigen::Projective3d&      const_transform3d_ref()    { return m_transform3d; }
 641 +    Eigen::Projective3d*            transform3d_ptr()          { return &m_transform3d; }
 642 +    const Eigen::Projective3d*      const_transform3d_ptr()    { return &m_transform3d; }
 643 +
 644 +    //void set_transform3d(Eigen::Projective3d vec)                      { m_transform3d = vec; }
 645 +    //void set_transform3d_ref(Eigen::Projective3d& vec)                 { m_transform3d = vec; }
 646 +    void set_const_transform3d_ref(const Eigen::Projective3d& vec)     { m_transform3d = vec; }
 647 +    void set_transform3d_ptr(Eigen::Projective3d* vec)                 { m_transform3d = *vec; }
 648 +    void set_const_transform3d_ptr(const Eigen::Projective3d* const vec) { m_transform3d = *vec; }
 649
 650    private:
 651      Eigen::Vector3d m_vector3d;
 652 -    Eigen::Transform3d m_transform3d;
 653 +    Eigen::Projective3d m_transform3d;
 654
 655  };
 656  #endif
 657 @@ -529,7 +529,7 @@ void export_Eigen()
 658    Vector3x_to_python_array<Eigen::Vector3i>();
 659    Vector3x_from_python_array<Eigen::Vector3i>();
 660
 661 -  // Eigen::Transform3d
 662 +  // Eigen::Projective3d
 663    Transform3d_to_python_array();
 664    Transform3d_from_python_array();
 665
 666 diff -rupN avogadro-1.2.0/libavogadro/src/tools/bondcentrictool.cpp avogadro-1.2.0-new/libavogadro/src/tools/bondcentrictool.cpp
 667 --- avogadro-1.2.0/libavogadro/src/tools/bondcentrictool.cpp    2016-06-08 16:19:45.000000000 +0200
 668 +++ avogadro-1.2.0-new/libavogadro/src/tools/bondcentrictool.cpp        2018-01-03 14:45:25.188574245 +0100
 669 @@ -578,8 +578,13 @@ namespace Avogadro {
 670
 671            Vector3d clicked = *m_clickedAtom->pos();
 672
 673 -          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
 674 -                (widget->camera()->modelview() * center).z() ? -1 : 1));
 675 +          Eigen::Vector4d otherTransformedHomog = widget->camera()->modelview() * other.homogeneous();
 676 +          Vector3d otherTransformed = otherTransformedHomog.hnormalized();
 677 +          Eigen::Vector4d centerTransformedHomog = (widget->camera()->modelview() * center.homogeneous());
 678 +          Vector3d centerTransformed = centerTransformedHomog.hnormalized();
 679 +
 680 +          Vector3d axis = Vector3d(0, 0, (otherTransformed.z() >=
 681 +                                          centerTransformed.z() ? -1 : 1));
 682
 683            Vector3d centerProj = widget->camera()->project(center);
 684            centerProj -= Vector3d(0,0,centerProj.z());
 685 @@ -673,8 +678,13 @@ namespace Avogadro {
 686
 687            Vector3d clicked = *m_clickedAtom->pos();
 688
 689 -          Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
 690 -                (widget->camera()->modelview() * center).z() ? -1 : 1));
 691 +          Eigen::Vector4d otherTransformedHomog = (widget->camera()->modelview() * other.homogeneous());
 692 +          Vector3d otherTransformed = otherTransformedHomog.hnormalized();
 693 +          Eigen::Vector4d centerTransformedHomog = (widget->camera()->modelview() * center.homogeneous());
 694 +          Vector3d centerTransformed = centerTransformedHomog.hnormalized();
 695 +
 696 +          Vector3d axis = Vector3d(0, 0, (otherTransformed.z() >=
 697 +                                          centerTransformed.z() ? -1 : 1));
 698
 699            Vector3d centerProj = widget->camera()->project(center);
 700            centerProj -= Vector3d(0,0,centerProj.z());
 701 @@ -1362,10 +1372,10 @@ namespace Avogadro {
 702
 703      planeVec = length * (planeVec / planeVec.norm());
 704
 705 -    Vector3d topLeft = widget->camera()->modelview() * (left + planeVec);
 706 -    Vector3d topRight = widget->camera()->modelview() * (right + planeVec);
 707 -    Vector3d botRight = widget->camera()->modelview() * (right - planeVec);
 708 -    Vector3d botLeft = widget->camera()->modelview() * (left - planeVec);
 709 +    Vector3d topLeft = (widget->camera()->modelview() * (left + planeVec).homogeneous()).head<3>();
 710 +    Vector3d topRight = (widget->camera()->modelview() * (right + planeVec).homogeneous()).head<3>();
 711 +    Vector3d botRight = (widget->camera()->modelview() * (right - planeVec).homogeneous()).head<3>();
 712 +    Vector3d botLeft = (widget->camera()->modelview() * (left - planeVec).homogeneous()).head<3>();
 713
 714      float alpha = 0.4;
 715      double lineWidth = 1.5;
 716 @@ -1444,10 +1454,10 @@ namespace Avogadro {
 717        C = D + ((C-D).normalized() * minWidth);
 718      }
 719
 720 -    Vector3d topLeft = widget->camera()->modelview() * D;
 721 -    Vector3d topRight = widget->camera()->modelview() * C;
 722 -    Vector3d botRight = widget->camera()->modelview() * B;
 723 -    Vector3d botLeft = widget->camera()->modelview() * A;
 724 +    Vector3d topLeft = (widget->camera()->modelview() * D.homogeneous()).head<3>();
 725 +    Vector3d topRight = (widget->camera()->modelview() * C.homogeneous()).head<3>();
 726 +    Vector3d botRight = (widget->camera()->modelview() * B.homogeneous()).head<3>();
 727 +    Vector3d botLeft = (widget->camera()->modelview() * A.homogeneous()).head<3>();
 728
 729      float alpha = 0.4;
 730      double lineWidth = 1.5;
 731 @@ -1506,12 +1516,12 @@ namespace Avogadro {
 732        Vector3d positionVector)
 733    {
 734      //Rotate skeleton around a particular axis and center point
 735 -    Eigen::Transform3d rotation;
 736 +    Eigen::Projective3d rotation;
 737      rotation = Eigen::AngleAxisd(angle, rotationVector);
 738      rotation.pretranslate(centerVector);
 739      rotation.translate(-centerVector);
 740
 741 -    return rotation*positionVector;
 742 +    return (rotation*positionVector.homogeneous()).head<3>();
 743    }
 744
 745    // ##########  showAnglesChanged  ##########
 746 diff -rupN avogadro-1.2.0/libavogadro/src/tools/manipulatetool.cpp avogadro-1.2.0-new/libavogadro/src/tools/manipulatetool.cpp
 747 --- avogadro-1.2.0/libavogadro/src/tools/manipulatetool.cpp     2016-06-08 16:19:45.000000000 +0200
 748 +++ avogadro-1.2.0-new/libavogadro/src/tools/manipulatetool.cpp 2018-01-03 14:45:25.180574245 +0100
 749 @@ -40,7 +40,6 @@
 750  #include <QAbstractButton>
 751
 752  using Eigen::Vector3d;
 753 -using Eigen::Transform3d;
 754  using Eigen::AngleAxisd;
 755
 756  namespace Avogadro {
 757 @@ -138,7 +137,7 @@ namespace Avogadro {
 758      double yRotate = m_settingsWidget->yRotateSpinBox->value() * DEG_TO_RAD;
 759      double zRotate = m_settingsWidget->zRotateSpinBox->value() * DEG_TO_RAD;
 760
 761 -    Eigen::Transform3d rotation;
 762 +    Eigen::Projective3d rotation;
 763      rotation.matrix().setIdentity();
 764      rotation.translation() = center;
 765      rotation.rotate(AngleAxisd(xRotate, Vector3d::UnitX())
 766 @@ -152,12 +151,12 @@ namespace Avogadro {
 767          if (p->type() == Primitive::AtomType) {
 768            Atom *atom = static_cast<Atom*>(p);
 769            tempPos = translate + *(atom->pos());
 770 -          atom->setPos(rotation * tempPos);
 771 +          atom->setPos((rotation * tempPos.homogeneous()).head<3>());
 772          }
 773      } else {
 774        foreach(Atom *atom, widget->molecule()->atoms()) {
 775          tempPos = translate + *(atom->pos());
 776 -        atom->setPos(rotation * tempPos);
 777 +        atom->setPos((rotation * tempPos.homogeneous()).head<3>());
 778        }
 779      }
 780
 781 @@ -199,7 +198,7 @@ namespace Avogadro {
 782      widget->setCursor(Qt::SizeVerCursor);
 783
 784      // Move the selected atom(s) in to or out of the screen
 785 -    Vector3d transformedGoal = widget->camera()->modelview() * *goal;
 786 +    Vector3d transformedGoal = (widget->camera()->modelview() * goal->homogeneous()).head<3>();
 787      double distanceToGoal = transformedGoal.norm();
 788
 789      double t = ZOOM_SPEED * delta;
 790 @@ -255,7 +254,7 @@ namespace Avogadro {
 791
 792      // Rotate the selected atoms about the center
 793      // rotate only selected primitives
 794 -    Transform3d fragmentRotation;
 795 +    Eigen::Projective3d fragmentRotation;
 796      fragmentRotation.matrix().setIdentity();
 797      fragmentRotation.translation() = *center;
 798      fragmentRotation.rotate(
 799 @@ -266,7 +265,7 @@ namespace Avogadro {
 800
 801      foreach(Primitive *p, widget->selectedPrimitives())
 802        if (p->type() == Primitive::AtomType)
 803 -        static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
 804 +        static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
 805      widget->molecule()->update();
 806    }
 807
 808 @@ -274,7 +273,7 @@ namespace Avogadro {
 809                              double delta) const
 810    {
 811      // Tilt the selected atoms about the center
 812 -    Transform3d fragmentRotation;
 813 +    Eigen::Projective3d fragmentRotation;
 814      fragmentRotation.matrix().setIdentity();
 815      fragmentRotation.translation() = *center;
 816      fragmentRotation.rotate(AngleAxisd(delta * ROTATION_SPEED, widget->camera()->backTransformedZAxis()));
 817 @@ -282,7 +281,7 @@ namespace Avogadro {
 818
 819      foreach(Primitive *p, widget->selectedPrimitives())
 820        if (p->type() == Primitive::AtomType)
 821 -        static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
 822 +        static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
 823      widget->molecule()->update();
 824    }
 825
 826 diff -rupN avogadro-1.2.0/libavogadro/src/tools/navigatetool.cpp avogadro-1.2.0-new/libavogadro/src/tools/navigatetool.cpp
 827 --- avogadro-1.2.0/libavogadro/src/tools/navigatetool.cpp       2016-06-08 16:19:45.000000000 +0200
 828 +++ avogadro-1.2.0-new/libavogadro/src/tools/navigatetool.cpp   2018-01-03 14:45:25.180574245 +0100
 829 @@ -92,7 +92,8 @@ namespace Avogadro {
 830        double sumOfWeights = 0.;
 831        QList<Atom*> atoms = widget->molecule()->atoms();
 832        foreach (Atom *atom, atoms) {
 833 -        Vector3d transformedAtomPos = widget->camera()->modelview() * *atom->pos();
 834 +        Vector3d transformedAtomPos = (widget->camera()->modelview() *
 835 +                                       atom->pos()->homogeneous()).head<3>();
 836          double atomDistance = transformedAtomPos.norm();
 837          double dot = transformedAtomPos.z() / atomDistance;
 838          double weight = exp(-30. * (1. + dot));
 839 diff -rupN avogadro-1.2.0/libavogadro/src/tools/skeletontree.cpp avogadro-1.2.0-new/libavogadro/src/tools/skeletontree.cpp
 840 --- avogadro-1.2.0/libavogadro/src/tools/skeletontree.cpp       2016-06-08 16:19:45.000000000 +0200
 841 +++ avogadro-1.2.0-new/libavogadro/src/tools/skeletontree.cpp   2018-01-03 14:45:25.181574245 +0100
 842 @@ -29,6 +29,7 @@
 843  #include <avogadro/atom.h>
 844  #include <avogadro/bond.h>
 845  #include <avogadro/molecule.h>
 846 +#include <iostream>
 847
 848  using namespace Eigen;
 849  using namespace std;
 850 @@ -221,7 +222,7 @@ namespace Avogadro {
 851    {
 852      if (m_rootNode) {
 853        //Rotate skeleton around a particular axis and center point
 854 -      Eigen::Transform3d rotation;
 855 +      Eigen::Projective3d rotation;
 856        rotation = Eigen::AngleAxisd(angle, rotationAxis);
 857        rotation.pretranslate(centerVector);
 858        rotation.translate(-centerVector);
 859 @@ -248,11 +249,11 @@ namespace Avogadro {
 860    // ##########  recursiveRotate  ##########
 861
 862    void SkeletonTree::recursiveRotate(Node* n,
 863 -                                     const Eigen::Transform3d &rotationMatrix)
 864 +                                     const Eigen::Projective3d &rotationMatrix)
 865    {
 866      // Update the root node with the new position
 867      Atom* a = n->atom();
 868 -    a->setPos(rotationMatrix * (*a->pos()));
 869 +    a->setPos((rotationMatrix * (*a->pos()).homogeneous()).head<3>());
 870      a->update();
 871
 872      // Now update the children
 873 diff -rupN avogadro-1.2.0/libavogadro/src/tools/skeletontree.h avogadro-1.2.0-new/libavogadro/src/tools/skeletontree.h
 874 --- avogadro-1.2.0/libavogadro/src/tools/skeletontree.h 2016-06-08 16:19:45.000000000 +0200
 875 +++ avogadro-1.2.0-new/libavogadro/src/tools/skeletontree.h     2018-01-03 14:45:25.181574245 +0100
 876 @@ -230,7 +230,7 @@ namespace Avogadro {
 877         * @param centerVector Center location to rotate around.
 878         */
 879        void recursiveRotate(Node* n,
 880 -                           const Eigen::Transform3d &rotationMatrix);
 881 +                           const Eigen::Projective3d &rotationMatrix);
 882
 883    };
 884  } // End namespace Avogadro
 885 diff -rupN avogadro-1.2.0/libavogadro/tests/CMakeLists.txt avogadro-1.2.0-new/libavogadro/tests/CMakeLists.txt
 886 --- avogadro-1.2.0/libavogadro/tests/CMakeLists.txt     2016-06-08 16:19:45.000000000 +0200
 887 +++ avogadro-1.2.0-new/libavogadro/tests/CMakeLists.txt 2018-01-03 14:46:31.890570555 +0100
 888 @@ -13,7 +13,7 @@ set_directory_properties(PROPERTIES INCL
 889  include_directories(
 890    ${CMAKE_SOURCE_DIR}
 891    ${CMAKE_CURRENT_BINARY_DIR}
 892 -  ${EIGEN2_INCLUDE_DIR}
 893 +  ${EIGEN3_INCLUDE_DIR}
 894    ${OPENBABEL2_INCLUDE_DIR}
 895    ${BOOST_PYTHON_INCLUDES}
 896    ${PYTHON_INCLUDE_PATH}