This is almost ready to become the new version 0.7.6.6 (JUL 2022) - t…

…he last thing missing is to make the final master changes (DOxygen documentation, make type Release, ...) and adding the Git tag for the new version.

The new version includes the ability to detect symmetry using multiple thresholds, returning a series of symmetry predictions based on these. Moreover, this version resolves the polyhedral symmetry detection primer axes problem, which become relevant after the previous version introduced the over-sampling.

Also, this version improves on the installation process by removing all the warnings caused by Gemmi includes on Windows machines and modyfing the Windows command line arguments to be comparible with the VS2022 default installation process.

Merge branch 'development'

proshade/CMakeLists.txt

@@ -47,7 +47,7 @@ endif   ( ${PRODUCE_PYTHON_BINDINGS} MATCHES 1 )
 
 ##########################################################################################
 ################################### Set project name
-project ( proshade VERSION 0.7.6.5 LANGUAGES CXX C                                        )     
+project ( proshade VERSION 0.7.6.6 LANGUAGES CXX C                                        )     
 
 ##########################################################################################
 ################################### Force C++11

proshade/error_list.txt

@@ -4,7 +4,7 @@
 ====================================
 ====================================
 
-== NEXT FREE MESSAGE NUMBER: 00075 ==
+== NEXT FREE MESSAGE NUMBER: 00076 ==
 
 ========
 GENERAL:
@@ -185,6 +185,8 @@ WS00071		Failed to find symmetry in Patterson map. Map rotation centre detection
 			vector with [Inf, Inf, Inf].
 WS00072		Failed to find eigenvalue with value 1 for this rotation matrix. Is this a rotation matrix?								This warning occurs when eigenvalue with value 1 is not found be LAPACK in the supplied rotation matrix. This should not happen, as all rotation matrices must have at least one eigenvalue with value 1, so this suggests the supplied matrix is not a rotation matrix.
 WS00073		Requested both symmetry centre detection and COM centering. COM centering turned off.									This warning means that symmetry centre detection was done (or at least symmetry centre position was supplied) and still centering on COM was requested - this makes no sense as the COM centering would over-write the previous centre of symmetry search and therefore the COM centering is turned off.
+WS00075		Will not search for fold >>X<< as the map sampling does not support its reliable detection. Increase 					The bandwidth determines the dimensions of rotation function. Thus, if we want to search for fold X, then the bandwidth is required to be at least X/2.
+			resolution/bandwidth if you suspect this fold could be present in the structure.
 
 ========
 OVERLAY:
@@ -209,3 +211,7 @@ WP00038		The rotation function distances are not available, yet already requeste
             getRotationFunctionDescrNumpy() function is called.  																	was already called. If this was not the case, please let me know!
 WP00043		Attempted to access shell index outside of the shell range.																This warning occurs when you call the getSphericalHarmonicsForShell() function with shell number argument larger than the largest available shell (or alternatively with negative number).
 
+
+========
+GENERAL:
+========

proshade/examples/libproshade/advancedAccess_distances.cpp

@@ -17,8 +17,8 @@
 
     \author    Michal Tykac
     \author    Garib N. Murshudov
-    \version   0.7.6.5
-    \date      JUN 2022
+    \version   0.7.6.6
+    \date      JUL 2022
 */
 
 //==================================================== ProSHADE
@@ -128,7 +128,7 @@ int main ( int argc, char **argv )
     //================================================ Expected output
 //  Energy levels distance       : 0.85561
 //  Trace sigma distance         : 0.97777
-//  Rotation function distance   : 0.59682
+//  Rotation function distance   : 0.599
 
     //================================================ Release the settings and runProshade objects
     delete structure1;

proshade/examples/libproshade/advancedAccess_overlay.cpp

@@ -18,8 +18,8 @@
 
     \author    Michal Tykac
     \author    Garib N. Murshudov
-    \version   0.7.6.5
-    \date      JUN 2022
+    \version   0.7.6.6
+    \date      JUL 2022
 */
 
 //==================================================== ProSHADE
@@ -126,10 +126,10 @@ int main ( int argc, char **argv )
     std::cout << "                                 :      " << rotMat[6] << " ; " << rotMat[7] << " ; " << rotMat[8] << std::endl;
 
     //================================================ Expected output
-//  Optimal rotation Euler angles are:      3.92784 ; 0.706802 ; 5.49658
-//  Optimal rotation matrix is       :      -0.880467 ; 0.120094 ; -0.458645
-//                                   :      0.119463 ; -0.879976 ; -0.459751
-//                                   :      -0.45881 ; -0.459587 ; 0.760443
+//  Optimal rotation Euler angles are:      3.9268 ; 0.71992 ; 5.49648
+//  Optimal rotation matrix is       :      -0.876066 ; 0.125383 ; -0.465604
+//                                   :      0.122759 ; -0.87579 ; -0.466821
+//                                   :      -0.466302 ; -0.466124 ; 0.751858
 
     //================================================ Delete the Patterson maps. They are no longer needed as we will now proceed with phased maps.
     delete staticStr;
@@ -185,8 +185,8 @@ int main ( int argc, char **argv )
     std::cout << "Rot. Centre to optimal overlay translation:  " << optimalTranslation.at(0) << " ; " << optimalTranslation.at(1) << " ; " << optimalTranslation.at(2) << std::endl;
 
     //================================================ Expected output
-//  Rot. Centre to origin translation:           13.0909 ; 19.3846 ; 19.3846
-//  Rot. Centre to optimal overlay translation:  12 ; 18 ; -6
+//  Rot. Centre to origin translation:           12.7059 ; 16.8421 ; 16.7619
+//  Rot. Centre to optimal overlay translation:  12 ; 20 ; -4
 
     //================================================ Write out the output files
     movingStr->writeOutOverlayFiles                   ( settings, optimalEulerRot.at(0), optimalEulerRot.at(1), optimalEulerRot.at(2), &rotationCentre, &optimalTranslation );

proshade/examples/libproshade/advancedAccess_reboxing.cpp

@@ -18,8 +18,8 @@
 
     \author    Michal Tykac
     \author    Garib N. Murshudov
-    \version   0.7.6.5
-    \date      JUN 2022
+    \version   0.7.6.6
+    \date      JUL 2022
 */
 
 //==================================================== ProSHADE