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- add eigen3 patch from fedora
[packages/avogadro.git] / avogadro_eigen3.patch
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JR		 1diff -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})
23diff -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
52diff -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")
79diff -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 }
116diff -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
151diff -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})
173diff -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
194diff -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();
206diff -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
218diff -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
229diff -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
240diff -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 {
251diff -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
290diff -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
308diff -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
319diff -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())
344diff -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();
381diff -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, ' ')
402diff -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
480diff -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 }
504diff -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;
516diff -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;
528diff -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
666diff -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 ##########
746diff -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
826diff -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));
839diff -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
873diff -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
885diff -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}
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