From 0beb5c2c994f36ffd4fdd083a2586a0764de4815 Mon Sep 17 00:00:00 2001 From: =?utf8?q?Jan=20R=C4=99korajski?= Date: Sun, 21 Apr 2019 10:43:44 +0200 Subject: [PATCH] - add eigen3 patch from fedora - fix boost-python detection - rel 7 --- avogadro.spec | 9 +- avogadro_eigen3.patch | 896 ++++++++++++++++++++++++++++++++++++++++++ boost-python.patch | 22 ++ 3 files changed, 924 insertions(+), 3 deletions(-) create mode 100644 avogadro_eigen3.patch create mode 100644 boost-python.patch diff --git a/avogadro.spec b/avogadro.spec index db9fb50..1f89909 100644 --- a/avogadro.spec +++ b/avogadro.spec @@ -1,7 +1,7 @@ Summary: An advanced molecular editor for chemical purposes Name: avogadro Version: 1.2.0 -Release: 6 +Release: 7 License: GPL v2 Group: Applications/Editors Source0: http://downloads.sourceforge.net/avogadro/%{name}-%{version}.tar.gz @@ -11,6 +11,8 @@ Patch1: %{name}-cmake.patch Patch2: %{name}-moc-boost.patch Patch3: gcc6.patch Patch4: python-install.patch +Patch5: avogadro_eigen3.patch +Patch6: boost-python.patch URL: http://avogadro.openmolecules.net/ BuildRequires: QtNetwork-devel BuildRequires: QtOpenGL-devel @@ -19,7 +21,7 @@ BuildRequires: boost-python-devel BuildRequires: cmake >= 2.8.0 BuildRequires: desktop-file-utils BuildRequires: docbook-utils -BuildRequires: eigen >= 1:2.0.12 +BuildRequires: eigen3 BuildRequires: glew-devel >= 1.5.0 BuildRequires: openbabel-devel >= 2.2.2 BuildRequires: pkgconfig @@ -29,7 +31,6 @@ BuildRequires: qt4-build >= 4.8.2-5 BuildRequires: qt4-linguist BuildRequires: qt4-qmake >= 4.8.2-5 BuildRequires: sip -BuildConflicts: eigen3 Requires: %{name}-libs = %{version}-%{release} BuildRoot: %{tmpdir}/%{name}-%{version}-root-%(id -u -n) @@ -64,6 +65,8 @@ libraries. %patch2 -p1 %patch3 -p1 %patch4 -p1 +%patch5 -p1 +%patch6 -p1 %build install -d build diff --git a/avogadro_eigen3.patch b/avogadro_eigen3.patch new file mode 100644 index 0000000..e2b3693 --- /dev/null +++ b/avogadro_eigen3.patch @@ -0,0 +1,896 @@ +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 + + #include +-#include + #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::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 + + #include +-#include + + #include + +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 + + #include +-#include + + #include + +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 + #include ++#include + + 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 >(wfn.xNuclearCoordinates(),m_nnuc); +- m_nucycoord=Map >(wfn.yNuclearCoordinates(),m_nnuc); +- m_nuczcoord=Map >(wfn.zNuclearCoordinates(),m_nnuc); +- m_nucz=Map >(wfn.nuclearCharges(),m_nnuc); +- m_X0=Map >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1); +- m_Y0=Map >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1); +- m_Z0=Map >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1); +- m_xamom=Map >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1); +- m_yamom=Map >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1); +- m_zamom=Map >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1); +- m_alpha=Map >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1); ++ m_nucxcoord=Map >(wfn.xNuclearCoordinates(),m_nnuc); ++ m_nucycoord=Map >(wfn.yNuclearCoordinates(),m_nnuc); ++ m_nuczcoord=Map >(wfn.zNuclearCoordinates(),m_nnuc); ++ m_nucz=Map >(wfn.nuclearCharges(),m_nnuc); ++ m_X0=Map >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1); ++ m_Y0=Map >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1); ++ m_Z0=Map >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1); ++ m_xamom=Map >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1); ++ m_yamom=Map >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1); ++ m_zamom=Map >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1); ++ m_alpha=Map >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1); + // TODO Implement screening for unoccupied molecular orbitals. +- m_occno=Map >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1); +- m_orbe=Map >(wfn.molecularOrbitalEigenvalues(),m_nmo,1); +- m_coef=Map >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim); ++ m_occno=Map >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1); ++ m_orbe=Map >(wfn.molecularOrbitalEigenvalues(),m_nmo,1); ++ m_coef=Map >(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 + #include + + 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 + #include + #include ++#include + + #include + +@@ -250,7 +250,9 @@ bool SlaterSet::initialize() + + SelfAdjointEigenSolver 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(d->background.redF()), static_cast(d->background.greenF()), + static_cast(d->background.blueF()), static_cast(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 ++ ++ This file is part of the Avogadro molecular editor project. ++ For more information, see ++ ++ 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 ++ ++namespace Avogadro ++{ ++ ++template ++void fitHyperplane(int numPoints, ++ VectorType **points, ++ HyperplaneType *result, ++ typename Eigen::NumTraits::Real* soundness = 0) ++{ ++ typedef typename VectorType::Scalar Scalar; ++ typedef Eigen::Matrix 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 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 +-#include + + #include + +@@ -1908,7 +1908,8 @@ namespace Avogadro{ + } + d->center /= static_cast(nAtoms); + Eigen::Hyperplane 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 + 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 + 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 + 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 + Transform3d_to_python_array() + { + #ifndef WIN32 +- to_python_converter(); ++ to_python_converter(); + #endif +- to_python_converter(); +- to_python_converter(); ++ to_python_converter(); ++ to_python_converter(); + } + + }; +@@ -373,17 +373,17 @@ template <> struct ScalarTraits + // 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() ); ++ converter::registry::push_back( &convertible, &construct, type_id() ); + +- converter::registry::insert( &convert, type_id() ); ++ converter::registry::insert( &convert, type_id() ); + } + + static void* convert(PyObject *obj_ptr) +@@ -401,7 +401,7 @@ template <> struct ScalarTraits + throw_error_already_set(); // the 1D array does not have exactly 3 elements + + double *values = reinterpret_cast(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 + // 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(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(); + Vector3x_from_python_array(); + +- // 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 + + 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(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(p)->setPos(fragmentRotation * *static_cast(p)->pos()); ++ static_cast(p)->setPos((fragmentRotation * static_cast(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(p)->setPos(fragmentRotation * *static_cast(p)->pos()); ++ static_cast(p)->setPos((fragmentRotation * static_cast(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 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 + #include + #include ++#include + + 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} diff --git a/boost-python.patch b/boost-python.patch new file mode 100644 index 0000000..b743b76 --- /dev/null +++ b/boost-python.patch @@ -0,0 +1,22 @@ +--- avogadro-1.2.0/cmake/modules/PythonDeps.cmake~ 2016-06-08 16:19:45.000000000 +0200 ++++ avogadro-1.2.0/cmake/modules/PythonDeps.cmake 2019-04-21 10:19:54.127042217 +0200 +@@ -2,7 +2,7 @@ + # This CMake file defines + # ALL_PYTHON_FOUND, if false, do not try to use python. + +-if(Boost_PYTHON_FOUND AND PYTHONLIBS_FOUND AND NUMPY_FOUND) ++if(Boost_PYTHON27_FOUND AND PYTHONLIBS_FOUND AND NUMPY_FOUND) + # In cache already + set(ALL_PYTHON_FOUND TRUE) + +@@ -14,8 +14,8 @@ + # CMake's new FindBoost has an option to look for additional versions + set(Boost_ADDITIONAL_VERSIONS "1.45" "1.44" "1.43" "1.42" "1.41" "1.40" + "1.40.0" "1.39" "1.39.0" "1.38" "1.38.0" "1.37" "1.37.0") +- find_package(Boost COMPONENTS python) +- if (Boost_PYTHON_FOUND) ++ find_package(Boost COMPONENTS python27) ++ if (Boost_PYTHON27_FOUND) + message(STATUS "Boost Python found...") + else() + message(STATUS "Boost Python NOT found - Python support disabled.") -- 2.43.0