--- /dev/null
+diff -rupN avogadro-1.2.0/avogadro/src/CMakeLists.txt avogadro-1.2.0-new/avogadro/src/CMakeLists.txt
+--- avogadro-1.2.0/avogadro/src/CMakeLists.txt 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/avogadro/src/CMakeLists.txt 2018-01-03 14:47:08.649568522 +0100
+@@ -22,15 +22,9 @@ include_directories(
+ ${CMAKE_CURRENT_BINARY_DIR}
+ )
+
+-if(EIGEN3_FOUND)
+- include_directories(
+- ${EIGEN3_INCLUDE_DIR}
+- )
+-elseif(EIGEN2_FOUND)
+- include_directories(
+- ${EIGEN2_INCLUDE_DIR}
+- )
+-endif(EIGEN3_FOUND)
++include_directories(
++ ${EIGEN3_INCLUDE_DIR}
++)
+
+ if(GLEW_FOUND)
+ include_directories(${GLEW_INCLUDE_DIR})
+diff -rupN avogadro-1.2.0/avogadro/src/mainwindow.cpp avogadro-1.2.0-new/avogadro/src/mainwindow.cpp
+--- avogadro-1.2.0/avogadro/src/mainwindow.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/avogadro/src/mainwindow.cpp 2018-01-03 14:45:25.170574246 +0100
+@@ -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());
+
+diff -rupN avogadro-1.2.0/CMakeLists.txt avogadro-1.2.0-new/CMakeLists.txt
+--- avogadro-1.2.0/CMakeLists.txt 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/CMakeLists.txt 2018-01-03 14:48:31.478563940 +0100
+@@ -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
+
+ find_package(ZLIB REQUIRED)
+ find_package(OpenBabel2 REQUIRED) # find and setup OpenBabel
+@@ -473,7 +466,6 @@ install(FILES
+
+ # Install the find modules we require to be present
+ install(FILES
+- "${CMAKE_MODULE_PATH}/FindEigen2.cmake"
+ "${CMAKE_MODULE_PATH}/FindEigen3.cmake"
+ "${CMAKE_MODULE_PATH}/FindGLEW.cmake"
+ DESTINATION "${Avogadro_PLUGIN_INSTALL_DIR}/cmake")
+diff -rupN avogadro-1.2.0/libavogadro/src/camera.cpp avogadro-1.2.0-new/libavogadro/src/camera.cpp
+--- avogadro-1.2.0/libavogadro/src/camera.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/camera.cpp 2018-01-03 14:45:25.171574246 +0100
+@@ -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;
+ }
+diff -rupN avogadro-1.2.0/libavogadro/src/camera.h avogadro-1.2.0-new/libavogadro/src/camera.h
+--- avogadro-1.2.0/libavogadro/src/camera.h 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/camera.h 2018-01-03 14:45:25.171574246 +0100
+@@ -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();
+ }
+ };
+
+diff -rupN avogadro-1.2.0/libavogadro/src/CMakeLists.txt avogadro-1.2.0-new/libavogadro/src/CMakeLists.txt
+--- avogadro-1.2.0/libavogadro/src/CMakeLists.txt 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/CMakeLists.txt 2018-01-03 14:48:09.786565140 +0100
+@@ -14,15 +14,9 @@ include_directories(
+ ${OPENBABEL2_INCLUDE_DIR}
+ )
+
+-if(EIGEN3_FOUND)
+- include_directories(
+- ${EIGEN3_INCLUDE_DIR}
+- )
+-elseif(EIGEN2_FOUND)
+- include_directories(
+- ${EIGEN2_INCLUDE_DIR}
+- )
+-endif(EIGEN3_FOUND)
++include_directories(
++ ${EIGEN3_INCLUDE_DIR}
++)
+
+ # I think this is necessary now in order to tell the linker where openbabel is
+ link_directories(${OPENBABEL2_LIBRARY_DIRS})
+diff -rupN avogadro-1.2.0/libavogadro/src/engines/wireengine.cpp avogadro-1.2.0-new/libavogadro/src/engines/wireengine.cpp
+--- avogadro-1.2.0/libavogadro/src/engines/wireengine.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/engines/wireengine.cpp 2018-01-03 14:45:25.171574246 +0100
+@@ -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
+diff -rupN avogadro-1.2.0/libavogadro/src/extensions/crystallography/crystallographyextension.cpp avogadro-1.2.0-new/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
+--- avogadro-1.2.0/libavogadro/src/extensions/crystallography/crystallographyextension.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/extensions/crystallography/crystallographyextension.cpp 2018-01-03 14:45:25.172574245 +0100
+@@ -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();
+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
+--- avogadro-1.2.0/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp 2018-01-03 14:45:25.173574245 +0100
+@@ -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
+diff -rupN avogadro-1.2.0/libavogadro/src/extensions/orca/orcaanalysedialog.cpp avogadro-1.2.0-new/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
+--- avogadro-1.2.0/libavogadro/src/extensions/orca/orcaanalysedialog.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/extensions/orca/orcaanalysedialog.cpp 2018-01-03 14:45:25.173574245 +0100
+@@ -41,7 +41,6 @@
+ #include <openbabel/mol.h>
+
+ #include <Eigen/Geometry>
+-#include <Eigen/LeastSquares>
+
+ #include <vector>
+
+diff -rupN avogadro-1.2.0/libavogadro/src/extensions/orca/orcainputdialog.cpp avogadro-1.2.0-new/libavogadro/src/extensions/orca/orcainputdialog.cpp
+--- avogadro-1.2.0/libavogadro/src/extensions/orca/orcainputdialog.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/extensions/orca/orcainputdialog.cpp 2018-01-03 14:45:25.174574245 +0100
+@@ -33,7 +33,6 @@
+ #include <openbabel/mol.h>
+
+ #include <Eigen/Geometry>
+-#include <Eigen/LeastSquares>
+
+ #include <vector>
+
+diff -rupN avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp avogadro-1.2.0-new/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
+--- avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp 2018-01-03 14:45:25.174574245 +0100
+@@ -28,6 +28,7 @@
+
+ #include <cmath>
+ #include <Eigen/QR>
++#include <Eigen/Eigenvalues>
+
+ namespace Avogadro {
+ namespace QTAIMMathUtilities {
+diff -rupN avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp avogadro-1.2.0-new/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
+--- avogadro-1.2.0/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp 2018-01-03 14:45:25.186574245 +0100
+@@ -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<const Matrix<qreal,Dynamic,1> >(wfn.xNuclearCoordinates(),m_nnuc);
++ m_nucycoord=Map<const Matrix<qreal,Dynamic,1> >(wfn.yNuclearCoordinates(),m_nnuc);
++ m_nuczcoord=Map<const Matrix<qreal,Dynamic,1> >(wfn.zNuclearCoordinates(),m_nnuc);
++ m_nucz=Map<const Matrix<qint64,Dynamic,1> >(wfn.nuclearCharges(),m_nnuc);
++ m_X0=Map<const Matrix<qreal,Dynamic,1> >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1);
++ m_Y0=Map<const Matrix<qreal,Dynamic,1> >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1);
++ m_Z0=Map<const Matrix<qreal,Dynamic,1> >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1);
++ m_xamom=Map<const Matrix<qint64,Dynamic,1> >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1);
++ m_yamom=Map<const Matrix<qint64,Dynamic,1> >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1);
++ m_zamom=Map<const Matrix<qint64,Dynamic,1> >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1);
++ m_alpha=Map<const Matrix<qreal,Dynamic,1> >(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<const Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1);
++ m_orbe=Map<const Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalEigenvalues(),m_nmo,1);
++ m_coef=Map<const Matrix<qreal,Dynamic,Dynamic,RowMajor> >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim);
+ m_totalEnergy=wfn.totalEnergy();
+ m_virialRatio=wfn.virialRatio();
+
+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
+--- avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt 2018-01-03 14:47:58.215565780 +0100
+@@ -1,13 +1,6 @@
+ find_package(Qt4 4.6 REQUIRED)
+-find_package(Eigen3)
+-if(NOT EIGEN3_FOUND)
+- message(STATUS "Cannot find Eigen3, trying Eigen2")
+- find_package(Eigen2 REQUIRED)
+-else()
+- set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
+-endif()
+
+-include_directories(${QT_INCLUDE_DIR} ${EIGEN2_INCLUDE_DIR})
++include_directories(${QT_INCLUDE_DIR} ${EIGEN3_INCLUDE_DIR})
+
+ # Headers for our public API
+ set(openqube_HDRS
+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
+--- avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp 2018-01-03 14:45:25.176574245 +0100
+@@ -19,6 +19,7 @@
+ using Eigen::Vector3d;
+ using std::vector;
+
++#include <iostream>
+ #include <fstream>
+
+ namespace OpenQube
+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
+--- avogadro-1.2.0/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp 2018-01-03 14:45:25.187574245 +0100
+@@ -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();
++
++ MatrixXd m = p * s.eigenvalues().array().inverse().sqrt().matrix().asDiagonal() * p.inverse();
++
+ m_normalized = m * m_eigenVectors;
+
+ if (!(m_overlap*m*m).isIdentity())
+diff -rupN avogadro-1.2.0/libavogadro/src/glpainter_p.cpp avogadro-1.2.0-new/libavogadro/src/glpainter_p.cpp
+--- avogadro-1.2.0/libavogadro/src/glpainter_p.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/glpainter_p.cpp 2018-01-03 14:45:25.177574245 +0100
+@@ -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();
+diff -rupN avogadro-1.2.0/libavogadro/src/glwidget.cpp avogadro-1.2.0-new/libavogadro/src/glwidget.cpp
+--- avogadro-1.2.0/libavogadro/src/glwidget.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/glwidget.cpp 2018-01-03 14:45:25.178574245 +0100
+@@ -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, ' ')
+diff -rupN avogadro-1.2.0/libavogadro/src/leastsquares.h avogadro-1.2.0-new/libavogadro/src/leastsquares.h
+--- avogadro-1.2.0/libavogadro/src/leastsquares.h 1970-01-01 01:00:00.000000000 +0100
++++ avogadro-1.2.0-new/libavogadro/src/leastsquares.h 2018-01-03 14:45:25.187574245 +0100
+@@ -0,0 +1,74 @@
++/**********************************************************************
++ LeastSquares - Least squares functions removed from Eigen2 codebase
++
++ Copyright (C) 2006-2009 Benoit Jacob <jacob.benoit.1@gmail.com>
++
++ This file is part of the Avogadro molecular editor project.
++ For more information, see <http://avogadro.cc/>
++
++ Avogadro is free software; you can redistribute it and/or modify
++ it under the terms of the GNU General Public License as published by
++ the Free Software Foundation; either version 2 of the License, or
++ (at your option) any later version.
++
++ Avogadro is distributed in the hope that it will be useful,
++ but WITHOUT ANY WARRANTY; without even the implied warranty of
++ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
++ GNU General Public License for more details.
++
++ You should have received a copy of the GNU General Public License
++ along with this program; if not, write to the Free Software
++ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
++ 02110-1301, USA.
++ **********************************************************************/
++
++#ifndef LEASTSQUARES_H
++#define LEASTSQUARES_H
++
++#include <Eigen/Eigenvalues>
++
++namespace Avogadro
++{
++
++template<typename VectorType, typename HyperplaneType>
++void fitHyperplane(int numPoints,
++ VectorType **points,
++ HyperplaneType *result,
++ typename Eigen::NumTraits<typename VectorType::Scalar>::Real* soundness = 0)
++{
++ typedef typename VectorType::Scalar Scalar;
++ typedef Eigen::Matrix<Scalar,VectorType::SizeAtCompileTime,VectorType::SizeAtCompileTime> CovMatrixType;
++ EIGEN_STATIC_ASSERT_VECTOR_ONLY(VectorType)
++ assert(numPoints >= 1);
++ int size = points[0]->size();
++ assert(size+1 == result->coeffs().size());
++
++ // compute the mean of the data
++ VectorType mean = VectorType::Zero(size);
++ for(int i = 0; i < numPoints; ++i)
++ mean += *(points[i]);
++ mean /= numPoints;
++
++ // compute the covariance matrix
++ 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();
++ }
++
++ // now we just have to pick the eigen vector with smallest eigen value
++ Eigen::SelfAdjointEigenSolver<CovMatrixType> eig(covMat);
++ result->normal() = eig.eigenvectors().col(0);
++ if (soundness)
++ *soundness = eig.eigenvalues().coeff(0)/eig.eigenvalues().coeff(1);
++
++ // let's compute the constant coefficient such that the
++ // plane pass trough the mean point:
++ result->offset() = - (result->normal().array() * mean.array()).sum();
++}
++
++} // end namespace Avogadro
++
++#endif
+diff -rupN avogadro-1.2.0/libavogadro/src/molecule.cpp avogadro-1.2.0-new/libavogadro/src/molecule.cpp
+--- avogadro-1.2.0/libavogadro/src/molecule.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/molecule.cpp 2018-01-03 14:45:25.188574245 +0100
+@@ -36,9 +36,9 @@
+ #include "primitivelist.h"
+ #include "residue.h"
+ #include "zmatrix.h"
++#include "leastsquares.h"
+
+ #include <Eigen/Geometry>
+-#include <Eigen/LeastSquares>
+
+ #include <vector>
+
+@@ -1908,7 +1908,8 @@ namespace Avogadro{
+ }
+ d->center /= static_cast<double>(nAtoms);
+ Eigen::Hyperplane<double, 3> planeCoeffs;
+- Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
++ fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
++
+ delete[] atomPositions;
+ d->normalVector = planeCoeffs.normal();
+ }
+diff -rupN avogadro-1.2.0/libavogadro/src/navigate.cpp avogadro-1.2.0-new/libavogadro/src/navigate.cpp
+--- avogadro-1.2.0/libavogadro/src/navigate.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/navigate.cpp 2018-01-03 14:45:25.179574245 +0100
+@@ -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;
+diff -rupN avogadro-1.2.0/libavogadro/src/python/camera.cpp avogadro-1.2.0-new/libavogadro/src/python/camera.cpp
+--- avogadro-1.2.0/libavogadro/src/python/camera.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/python/camera.cpp 2018-01-03 14:45:25.181574245 +0100
+@@ -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;
+diff -rupN avogadro-1.2.0/libavogadro/src/python/eigen.cpp avogadro-1.2.0-new/libavogadro/src/python/eigen.cpp
+--- avogadro-1.2.0/libavogadro/src/python/eigen.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/python/eigen.cpp 2018-01-03 14:45:25.182574245 +0100
+@@ -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();
+
+diff -rupN avogadro-1.2.0/libavogadro/src/tools/bondcentrictool.cpp avogadro-1.2.0-new/libavogadro/src/tools/bondcentrictool.cpp
+--- avogadro-1.2.0/libavogadro/src/tools/bondcentrictool.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/tools/bondcentrictool.cpp 2018-01-03 14:45:25.188574245 +0100
+@@ -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 ##########
+diff -rupN avogadro-1.2.0/libavogadro/src/tools/manipulatetool.cpp avogadro-1.2.0-new/libavogadro/src/tools/manipulatetool.cpp
+--- avogadro-1.2.0/libavogadro/src/tools/manipulatetool.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/tools/manipulatetool.cpp 2018-01-03 14:45:25.180574245 +0100
+@@ -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();
+ }
+
+diff -rupN avogadro-1.2.0/libavogadro/src/tools/navigatetool.cpp avogadro-1.2.0-new/libavogadro/src/tools/navigatetool.cpp
+--- avogadro-1.2.0/libavogadro/src/tools/navigatetool.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/tools/navigatetool.cpp 2018-01-03 14:45:25.180574245 +0100
+@@ -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));
+diff -rupN avogadro-1.2.0/libavogadro/src/tools/skeletontree.cpp avogadro-1.2.0-new/libavogadro/src/tools/skeletontree.cpp
+--- avogadro-1.2.0/libavogadro/src/tools/skeletontree.cpp 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/tools/skeletontree.cpp 2018-01-03 14:45:25.181574245 +0100
+@@ -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
+diff -rupN avogadro-1.2.0/libavogadro/src/tools/skeletontree.h avogadro-1.2.0-new/libavogadro/src/tools/skeletontree.h
+--- avogadro-1.2.0/libavogadro/src/tools/skeletontree.h 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/src/tools/skeletontree.h 2018-01-03 14:45:25.181574245 +0100
+@@ -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
+diff -rupN avogadro-1.2.0/libavogadro/tests/CMakeLists.txt avogadro-1.2.0-new/libavogadro/tests/CMakeLists.txt
+--- avogadro-1.2.0/libavogadro/tests/CMakeLists.txt 2016-06-08 16:19:45.000000000 +0200
++++ avogadro-1.2.0-new/libavogadro/tests/CMakeLists.txt 2018-01-03 14:46:31.890570555 +0100
+@@ -13,7 +13,7 @@ set_directory_properties(PROPERTIES INCL
+ include_directories(
+ ${CMAKE_SOURCE_DIR}
+ ${CMAKE_CURRENT_BINARY_DIR}
+- ${EIGEN2_INCLUDE_DIR}
++ ${EIGEN3_INCLUDE_DIR}
+ ${OPENBABEL2_INCLUDE_DIR}
+ ${BOOST_PYTHON_INCLUDES}
+ ${PYTHON_INCLUDE_PATH}
projects / packages / avogadro.git / commitdiff