This is the new version 0.7.5.4.

The changes to previous version include:

1) Map re-sampling: Map re-sampling slightly moves (sub-index) position of the internal map, which causes issue for translation map. This has been improved, but not completely removed.
2) Symmetry detection: All polyhedral symmetries are always sought, no longer stopping if larger polyhedral symmetry is found.
3) getopt_port only: Now the external getopt library is used exclusively instead of only on Windows. This is because older GCC version were mixing system and external getopt files, causing segfaults.
4) M_PI: Older GCC version have cmath.h header without M_PI definition (which is not necessarily part of the header, but Unix libraries typically have it there). This has now been remedied and M_PI definition is no longer required.

README.md

@@ -308,7 +308,7 @@ The ProSHADE tool was developed in a modular fashion and the usage slightly chan
 
 In order to detect symmetry in either a co-ordinate input file or in a map input file, the ProSHADE executable needs to be supplied with the option **-S** or **--symmetry** and it will also require a single input file to be supplied using the **-f** option. These two options are the only mandatory options, although there are many optional values that the user can supply to supersede the default values and therefore modify the operation fo the ProSHADE executable to fit their purpose.
 
-One particular option regarding the symmetry detection mode should be noted; the **--sym** (or **-u**) option, which allows the user to state which symmetry they believe to exist in the structure. The allowed values for this command line argument are "Cx", "Dx", "T", "O" and "I", where the *x* should be an integer number specifying the fold of the requested symmetry. When this option is used, it removes the default behaviour of returning the "best" detected symmetry and instead the symmetry requested by the user is returned, if it can be found in the structure.
+One particular option regarding the symmetry detection mode should be noted; the **--reqSym** (or **-u**) option, which allows the user to state which symmetry they believe to exist in the structure. The allowed values for this command line argument are "Cx", "Dx", "T", "O" and "I", where the *x* should be an integer number specifying the fold of the requested symmetry. When this option is used, it removes the default behaviour of returning the "best" detected symmetry and instead the symmetry requested by the user is returned, if it can be found in the structure.
 
 Another noteworthy option is the **--center** or **-c** option, which  tells ProSHADE **NOT** to center the internal map representation over the centre of density before running any processing of the map (default is centering and adding this option will turn centering off). This may be important as ProSHADE detects symmetries over the centre of the co-ordinates and therefore a non-centered map (map which does not have the centre of mass at the centre of box) will be found to have no symmetries even if these are present, just not over the co-ordinate/box centre.
 
@@ -319,8 +319,8 @@ To demonstrate how the tool can be run and the standard output for the symmetry
 ![T4 Portal Protein](https://github.com/michaltykac/proshade/blob/experimental/proshade/documentation/ProSHADE_3JA7.jpg)
 
 ```
- $: ./proshade -S -f ./emd_6324.map -r 8 --sym C12
- ProSHADE 0.7.5.3 (FEB 2021):
+ $: ./proshade -S -f ./emd_6324.map -r 8 --reqSym C12
+ ProSHADE 0.7.5.4 (MAR 2021):
  ============================
 
   ... Starting to read the structure: ./emd_6324.map
@@ -338,17 +338,17 @@ To demonstrate how the tool can be run and the standard output for the symmetry
 
  Detected C symmetry with fold 12 .
    Fold       X           Y          Z           Angle        Height
-    +12     +0.00000   -0.00000   +1.00000     +0.52360      +0.94620
+    +12     +0.00000   +0.00000   +1.00000     +0.52360      +0.93476
 
  However, since the selection of the recommended symmetry needs improvement, here is a list of all detected C symmetries:
    Fold       X           Y          Z           Angle        Height
-    +12     +0.00000   -0.00000   +1.00000     +0.52360      +0.94620
+    +12     +0.00000   +0.00000   +1.00000     +0.52360      +0.93476
 
  Also, for the same reason, here is a list of all detected D symmetries:
 
  ======================
  ProSHADE run complete.
- Time taken: 14 seconds.
+ Time taken: 15 seconds.
  ======================
 ```
 
@@ -364,7 +364,7 @@ To demonstrate how the tool can be run and the standard output for the symmetry
 
 ```
   $: ./proshade -D -f ./1BFO_A_dom_1.pdb -f ./1H8N_A_dom_1.pdb -f ./3IGU_A_dom_1.pdb -r 6
-  ProSHADE 0.7.5.3 (FEB 2021):
+  ProSHADE 0.7.5.4 (MAR 2021):
   ============================
 
    ... Starting to read the structure: ./1BFO_A_dom_1.pdb
@@ -391,9 +391,9 @@ To demonstrate how the tool can be run and the standard output for the symmetry
    ... Starting trace sigma distance computation.
    ... Starting rotation function distance computation.
   Distances between ./1BFO_A_dom_1.pdb and ./1H8N_A_dom_1.pdb
-  Energy levels distance    : 0.895306
-  Trace sigma distance      : 0.960468
-  Rotation function distance: 0.756167
+  Energy levels distance    : 0.859485
+  Trace sigma distance      : 0.950227
+  Rotation function distance: 0.741744
    ... Starting to read the structure: ./3IGU_A_dom_1.pdb
    ... Map inversion (mirror image) not requested.
    ... Map normalisation not requested.
@@ -408,13 +408,13 @@ To demonstrate how the tool can be run and the standard output for the symmetry
    ... Starting trace sigma distance computation.
    ... Starting rotation function distance computation.
   Distances between ./1BFO_A_dom_1.pdb and ./3IGU_A_dom_1.pdb
-  Energy levels distance    : 0.559041
-  Trace sigma distance      : 0.736592
-  Rotation function distance: 0.452545
+  Energy levels distance    : 0.572315
+  Trace sigma distance      : 0.74436
+  Rotation function distance: 0.461415
 
   ======================
   ProSHADE run complete.
-  Time taken: 4 seconds.
+  Time taken: 1 seconds.
   ======================
 ```
 
@@ -432,7 +432,7 @@ To demonstrate how the tool can be run and the standard output for the symmetry
 
 ```
 $ ./proshade -RMf ./emd_5762.map.gz
-ProSHADE 0.7.5.3 (FEB 2021):
+ProSHADE 0.7.5.4 (MAR 2021):
 ============================
 
  ... Starting to read the structure: ./emd_5762.map.gz
@@ -474,7 +474,7 @@ Time taken: 9 seconds.
 
 ```
  $ ./proshade -O -f ./1BFO_A_dom_1.pdb -f ./1H8N_A_dom_1.pdb -r 4 -kjc
- ProSHADE 0.7.5.3 (FEB 2021):
+ ProSHADE 0.7.5.4 (MAR 2021):
  ============================
 
   ... Starting to read the structure: ./1BFO_A_dom_1.pdb
@@ -519,15 +519,15 @@ Time taken: 9 seconds.
   ... Starting spherical harmonics decomposition.
   ... Starting translation function computation.
 
- The rotation centre to origin translation vector is:  -17.5     -21     -24
+ The rotation centre to origin translation vector is:  -16.6     -20     -23.8
  The rotation matrix about origin is                 : -0.872     -0.0785     +0.483
                                                      : -0.191     -0.854     -0.483
                                                      : +0.451     -0.514     +0.73
  The rotation centre to overlay translation vector is: +4     +4     -4
 
  ======================
  ProSHADE run complete.
- Time taken: 4 seconds.
+ Time taken: 5 seconds.
  ======================
 ```
 # Using the ProSHADE library

proshade/CMakeLists.txt

@@ -47,7 +47,7 @@ endif   ( ${PRODUCE_PYTHON_BINDINGS} MATCHES 1 )
 
 ##########################################################################################
 ################################### Set project name
-project ( proshade VERSION 0.7.5.3 LANGUAGES CXX C                                        )     
+project ( proshade VERSION 0.7.5.4 LANGUAGES CXX C                                        )     
 
 ##########################################################################################
 ################################### Force C++11
@@ -63,8 +63,6 @@ set     ( CMAKE_POSITION_INDEPENDENT_CODE ON
 file    ( GLOB SOURCES   "${CMAKE_SOURCE_DIR}/src/proshade/*.cpp"                         )
 file    ( GLOB EXEC_SRC  "${CMAKE_SOURCE_DIR}/src/bin/*.cpp"                              )
 
-list    ( APPEND SOURCES "${CMAKE_SOURCE_DIR}/extern/getopt_port/getopt.c"                )
-
 ##########################################################################################
 ################################### Define the command line options variables and defaults
 set     ( INSTALL_LOCALLY        ON      CACHE BOOL   "Should installation be done locally?"   )
@@ -220,6 +218,12 @@ else  ( CUSTOM_LAPACK_LIB_PATH )
     endif ( LAPACK_FOUND )
 endif  ( CUSTOM_LAPACK_LIB_PATH )
 
+
+##########################################################################################
+################################### Add getopt_port dependency
+set ( GETOPT_SOURCE  ${CMAKE_SOURCE_DIR}/extern/getopt_port/getopt_port.c   CACHE STRING "Getopt_port source" )
+set ( GETOPT_HEADER  ${CMAKE_SOURCE_DIR}/extern/getopt_port/getopt_port.h   CACHE STRING "Getopt_port header" )
+
 ##########################################################################################
 ################################### Add SOFT dependency
 

proshade/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = ProSHADE
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "0.7.5.3 (FEB 2021)"
+PROJECT_NUMBER         = "0.7.5.4 (MAR 2021)"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

proshade/cmake/bin/CMakeLists.txt

@@ -6,7 +6,7 @@
 
 ##########################################################################################
 ################################### Add the executable target
-add_executable          ( ${PROJECT_NAME} ${EXEC_SRC} ${OBJS}                             )
+add_executable          ( ${PROJECT_NAME} ${EXEC_SRC} ${GETOPT_SOURCE} ${OBJS}            )
 
 ##########################################################################################
 ### Add and link the dependencies

proshade/cmake/bin/bin.cmake

@@ -11,7 +11,7 @@ file                    ( GLOB EXEC_SRC "${CMAKE_SOURCE_DIR}/src/bin/*.cpp"
 
 ##########################################################################################
 ################################### Add the executable target
-add_executable          ( ${PROJECT_NAME} ${EXEC_SRC} ${SOURCES}                          )
+add_executable          ( ${PROJECT_NAME} ${EXEC_SRC} ${GETOPT_SOURCE} ${SOURCES}         )
 
 ##########################################################################################
 ################################### Link the executable

proshade/cmake/lib/CMakeLists.txt

@@ -6,7 +6,7 @@
 
 ##########################################################################################
 ################################### Add the library target
-add_library             ( ${PROJECT_NAME}_LIB SHARED ${OBJS}                              )
+add_library             ( ${PROJECT_NAME}_LIB SHARED ${OBJS} ${GETOPT_SOURCE}             )
 
 ##########################################################################################
 ### Add and link the dependencies

proshade/cmake/lib/lib.cmake

@@ -11,7 +11,7 @@ file                    ( GLOB EXEC_SRC "${CMAKE_SOURCE_DIR}/src/bin/*.cpp"
 
 ##########################################################################################
 ################################### Add the library target
-add_library             ( ${PROJECT_NAME}_LIB SHARED ${EXEC_SRC} ${SOURCES}               )
+add_library             ( ${PROJECT_NAME}_LIB SHARED ${EXEC_SRC} ${SOURCES} ${GETOPT_SOURCE} )
 
 ##########################################################################################
 ### Add and link the dependencies