mirror of https://github.com/CGAL/cgal
remove dependance on CGAL_PDB: merge from the branche created for that purpose
I do not remove the directory CGAL_PDB as I am allowed to use svn remove.
This commit is contained in:
Sébastien Loriot
parent
93f042b6d7
commit
d72337785c
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@ -1423,6 +1423,7 @@ Installation/cmake/modules/FindBoost.cmake -text
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Installation/cmake/modules/FindCGAL.cmake -text
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Installation/cmake/modules/FindCGAL_CORE.cmake -text
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Installation/cmake/modules/FindCORE.cmake -text
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Installation/cmake/modules/FindESBTL.cmake -text
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Installation/cmake/modules/FindF2C.cmake -text
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Installation/cmake/modules/FindGMP.cmake -text
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Installation/cmake/modules/FindGMPXX.cmake -text
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@ -1441,6 +1442,7 @@ Installation/cmake/modules/FindRS.cmake -text
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Installation/cmake/modules/FindTAUCS.cmake -text
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Installation/cmake/modules/Qt3Macros-patched.cmake -text
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Installation/cmake/modules/UseCGAL.cmake -text
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Installation/cmake/modules/UseESBTL.cmake -text
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Installation/cmake/modules/test_MPFI.cpp -text
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Installation/config/support/print_BOOST_version.cpp -text
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Installation/config/support/print_GMP_version.cpp -text
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@ -1459,7 +1461,6 @@ Installation/test/Installation/CMakeLists.txt -text
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Installation/test/Installation/link_to_CGAL.cpp -text
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Installation/test/Installation/link_to_CGAL_Core.cpp -text
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Installation/test/Installation/link_to_CGAL_ImageIO.cpp -text
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Installation/test/Installation/link_to_CGAL_PDB.cpp -text
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Installation/test/Installation/link_to_CGAL_Qt3.cpp -text
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Installation/test/Installation/link_to_CGAL_Qt4.cpp -text
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Interpolation/demo/Interpolation/CMakeLists.txt -text
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@ -23,6 +23,9 @@ x.y 2D Mesh Generation
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- The execution of the 2D mesh generator is now deterministic (same at
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each run).
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x CGAL_PDB is no longer provided with CGAL. An alternative solution for people
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interested in reading PDB files is to use ESBTL (http://esbtl.sourceforge.net/).
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----------------------------- Release 3.6.1 --------------------------------
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CGAL 3.6.1 is a bug-fixes release. The following has been changed
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since CGAL-3.6:
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@ -97,7 +97,7 @@ message( STATUS "System: ${CMAKE_SYSTEM_NAME}" )
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# The base name of all CGAL libraries (including "CGAL" itself. That
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# variables can be used by foreach() loops that deal with library variables.
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set(ALL_CGAL_LIBRARIES CGAL CGAL_Core CGAL_ImageIO CGAL_PDB CGAL_Qt3 CGAL_Qt4 CACHE INTERNAL "Name of all CGAL libraries.")
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set(ALL_CGAL_LIBRARIES CGAL CGAL_Core CGAL_ImageIO CGAL_Qt3 CGAL_Qt4 CACHE INTERNAL "Name of all CGAL libraries.")
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#--------------------------------------------------------------------------------------------------
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#
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@ -213,11 +213,6 @@ cache_set(CGAL_Qt4_3RD_PARTY_INCLUDE_DIRS "" )
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cache_set(CGAL_Qt4_3RD_PARTY_LIBRARIES "" )
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cache_set(CGAL_Qt4_3RD_PARTY_LIBRARIES_DIRS "" )
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cache_set(CGAL_PDB_3RD_PARTY_DEFINITIONS "" )
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cache_set(CGAL_PDB_3RD_PARTY_INCLUDE_DIRS "" )
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cache_set(CGAL_PDB_3RD_PARTY_LIBRARIES "" )
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cache_set(CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS "" )
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include(CGAL_SetupDependencies)
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#--------------------------------------------------------------------------------------------------
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@ -366,7 +361,6 @@ add_subdirectory(src)
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cache_get(CGAL_LIBRARY)
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cache_get(CGAL_Core_LIBRARY)
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cache_get(CGAL_ImageIO_LIBRARY)
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cache_get(CGAL_PDB_LIBRARY)
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cache_get(CGAL_Qt3_LIBRARY)
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cache_get(CGAL_Qt4_LIBRARY)
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@ -395,11 +389,6 @@ cache_get(CGAL_Qt4_3RD_PARTY_INCLUDE_DIRS )
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cache_get(CGAL_Qt4_3RD_PARTY_LIBRARIES )
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cache_get(CGAL_Qt4_3RD_PARTY_LIBRARIES_DIRS)
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cache_get(CGAL_PDB_3RD_PARTY_DEFINITIONS )
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cache_get(CGAL_PDB_3RD_PARTY_INCLUDE_DIRS )
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cache_get(CGAL_PDB_3RD_PARTY_LIBRARIES )
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cache_get(CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS)
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hide_variable(EXECUTABLE_OUTPUT_PATH)
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hide_variable(LIBRARY_OUTPUT_PATH)
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@ -7,8 +7,8 @@ from GeometryFactory (www.geometryfactory.com) for all or parts of CGAL.
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The source code of the CGAL library can be found in the directories
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"src/CGAL", "src/CGALQt", "src/CGALQt4" and "include/CGAL" (with the
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exception of "include/CGAL/CORE", "include/CGAL/OpenNL" and
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"include/CGAL/PDB"). It is specified in each file of the CGAL library which
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exception of "include/CGAL/CORE", "include/CGAL/OpenNL").
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It is specified in each file of the CGAL library which
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license applies to it. This is either the GNU Lesser General Public License
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(as published by the Free Software Foundation; version 2.1 of the License)
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or the Q Public License (version 1.0), *depending on each file*. The texts
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@ -22,8 +22,6 @@ licenses:
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licensed under the QPL (see LICENSE.QPL).
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- ImageIO, in the directory "src/CGALimageIO", is licensed under the LGPL
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(see LICENSE.LGPL).
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- PDB, in the directory "include/CGAL/PDB" and "src/CGALPDB" is licensed
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under the LGPL (see LICENSE.LGPL).
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- OpenNL, in the directory "include/CGAL/OpenNL", is licensed under the LGPL
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(see LICENSE.LGPL).
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@ -35,14 +35,12 @@ set(CGAL_LIBRARIES_DIR "@CGAL_LIBRARIES_DIR@" )
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set(WITH_CGAL "ON")
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set(WITH_CGAL_Core "@WITH_CGAL_Core@")
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set(WITH_CGAL_ImageIO "@WITH_CGAL_ImageIO@")
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set(WITH_CGAL_PDB "@WITH_CGAL_PDB@" )
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set(WITH_CGAL_Qt3 "@WITH_CGAL_Qt3@" )
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set(WITH_CGAL_Qt4 "@WITH_CGAL_Qt4@" )
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set(CGAL_LIBRARY "@CGAL_LIBRARY@")
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set(CGAL_Core_LIBRARY "@CGAL_Core_LIBRARY@")
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set(CGAL_ImageIO_LIBRARY "@CGAL_ImageIO_LIBRARY@")
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set(CGAL_PDB_LIBRARY "@CGAL_PDB_LIBRARY@" )
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set(CGAL_Qt3_LIBRARY "@CGAL_Qt3_LIBRARY@" )
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set(CGAL_Qt4_LIBRARY "@CGAL_Qt4_LIBRARY@" )
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@ -62,11 +60,6 @@ set(CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIRS "@CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIR
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set(CGAL_ImageIO_3RD_PARTY_LIBRARIES "@CGAL_ImageIO_3RD_PARTY_LIBRARIES@" )
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set(CGAL_ImageIO_USE_ZLIB "@CGAL_ImageIO_USE_ZLIB@" )
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set(CGAL_PDB_3RD_PARTY_INCLUDE_DIRS "@CGAL_PDB_3RD_PARTY_INCLUDE_DIRS@" )
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set(CGAL_PDB_3RD_PARTY_DEFINITIONS "@CGAL_PDB_3RD_PARTY_DEFINITIONS@" )
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set(CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS "@CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS@" )
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set(CGAL_PDB_3RD_PARTY_LIBRARIES "@CGAL_PDB_3RD_PARTY_LIBRARIES@" )
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set(CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS "@CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS@" )
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set(CGAL_Qt3_3RD_PARTY_DEFINITIONS "@CGAL_Qt3_3RD_PARTY_DEFINITIONS@" )
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set(CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS "@CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS@" )
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@ -37,14 +37,12 @@ set(CGAL_LIBRARIES_DIR "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@" )
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set(WITH_CGAL "ON")
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set(WITH_CGAL_Core "@WITH_CGAL_Core@")
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set(WITH_CGAL_ImageIO "@WITH_CGAL_ImageIO@")
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set(WITH_CGAL_PDB "@WITH_CGAL_PDB@" )
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set(WITH_CGAL_Qt3 "@WITH_CGAL_Qt3@" )
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set(WITH_CGAL_Qt4 "@WITH_CGAL_Qt4@" )
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set(CGAL_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_LIBRARY_NAME@")
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set(CGAL_Core_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_Core_LIBRARY_NAME@")
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set(CGAL_ImageIO_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_ImageIO_LIBRARY_NAME@")
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set(CGAL_PDB_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_PDB_LIBRARY_NAME@" )
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set(CGAL_Qt3_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_Qt3_LIBRARY_NAME@" )
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set(CGAL_Qt4_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_Qt4_LIBRARY_NAME@" )
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@ -64,11 +62,6 @@ set(CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIRS "@CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIR
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set(CGAL_ImageIO_3RD_PARTY_LIBRARIES "@CGAL_ImageIO_3RD_PARTY_LIBRARIES@" )
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set(CGAL_ImageIO_USE_ZLIB "@CGAL_ImageIO_USE_ZLIB@" )
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set(CGAL_PDB_3RD_PARTY_INCLUDE_DIRS "@CGAL_PDB_3RD_PARTY_INCLUDE_DIRS@" )
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set(CGAL_PDB_3RD_PARTY_DEFINITIONS "@CGAL_PDB_3RD_PARTY_DEFINITIONS@" )
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set(CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS "@CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS@" )
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set(CGAL_PDB_3RD_PARTY_LIBRARIES "@CGAL_PDB_3RD_PARTY_LIBRARIES@" )
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set(CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS "@CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS@" )
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set(CGAL_Qt3_3RD_PARTY_DEFINITIONS "@CGAL_Qt3_3RD_PARTY_DEFINITIONS@" )
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set(CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS "@CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS@" )
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@ -35,14 +35,12 @@ set(CGAL_LIBRARIES_DIR "$(CGAL_INSTALL_PREFIX)/@CGAL_INSTALL_LIB_DIR@" )
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set(WITH_CGAL "ON")
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set(WITH_CGAL_Core "@WITH_CGAL_Core@")
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set(WITH_CGAL_ImageIO "@WITH_CGAL_ImageIO@")
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set(WITH_CGAL_PDB "@WITH_CGAL_PDB@" )
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set(WITH_CGAL_Qt3 "@WITH_CGAL_Qt3@" )
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set(WITH_CGAL_Qt4 "@WITH_CGAL_Qt4@" )
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set(CGAL_LIBRARY "@CGAL_LIBRARY@")
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set(CGAL_Core_LIBRARY "@CGAL_Core_LIBRARY@")
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set(CGAL_ImageIO_LIBRARY "@CGAL_ImageIO_LIBRARY@")
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set(CGAL_PDB_LIBRARY "@CGAL_PDB_LIBRARY@" )
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set(CGAL_Qt3_LIBRARY "@CGAL_Qt3_LIBRARY@" )
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set(CGAL_Qt4_LIBRARY "@CGAL_Qt4_LIBRARY@" )
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@ -62,11 +60,6 @@ set(CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIRS "@CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIR
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set(CGAL_ImageIO_3RD_PARTY_LIBRARIES "@CGAL_ImageIO_3RD_PARTY_LIBRARIES@" )
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set(CGAL_ImageIO_USE_ZLIB "@CGAL_ImageIO_USE_ZLIB@" )
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set(CGAL_PDB_3RD_PARTY_INCLUDE_DIRS "@CGAL_PDB_3RD_PARTY_INCLUDE_DIRS@" )
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set(CGAL_PDB_3RD_PARTY_DEFINITIONS "@CGAL_PDB_3RD_PARTY_DEFINITIONS@" )
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set(CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS "@CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS@" )
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set(CGAL_PDB_3RD_PARTY_LIBRARIES "@CGAL_PDB_3RD_PARTY_LIBRARIES@" )
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set(CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS "@CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS@" )
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set(CGAL_Qt3_3RD_PARTY_DEFINITIONS "@CGAL_Qt3_3RD_PARTY_DEFINITIONS@" )
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set(CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS "@CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS@" )
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@ -0,0 +1,28 @@
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#This modules tries to find ESBTL
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# Once done this will define
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#
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# ESBTL_FOUND - system has ESBTL
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# ESBTL_INCLUDE_DIR - ESBTL include directory
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#
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# Is it already configured?
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if (ESBTL_INCLUDE_DIR)
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set(ESBTL_FOUND TRUE)
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else()
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find_path(ESBTL_INCLUDE_DIR
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NAMES ESBTL/default.h
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PATHS /usr/include
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/usr/local/include
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)
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if(ESBTL_INCLUDE_DIR)
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set(ESBTL_FOUND TRUE)
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endif()
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endif()
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if(ESBTL_FOUND)
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message(STATUS "Found ESBTL: ${ESBTL_INCLUDE_DIR}")
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set(ESBTL_USE_FILE "UseESBTL")
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endif()
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@ -0,0 +1,4 @@
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# This module setups the compiler for using ESBTL library.
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# It assumes that find_package(ESBTL) was already called.
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include_directories( ${ESBTL_INCLUDE_DIR} )
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@ -373,7 +373,6 @@ are switched \texttt{ON}.
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\texttt{CGAL\_Qt3} & \texttt{WITH\_CGAL\_Qt3} & \ccc{CGAL::Qt_widget} used by Qt3-based demos & Qt3 and OpenGL\\\hline
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\texttt{CGAL\_Qt4} & \texttt{WITH\_CGAL\_Qt4} & \ccc{QGraphicsView} support for Qt4-based demos & Qt4 and OpenGL\\\hline
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\texttt{CGAL\_ImageIO} & \texttt{WITH\_CGAL\_ImageIO} & Utilities to read and write image files & OpenGL, ZLib, VTK (optional)\\\hline
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\texttt{CGAL\_PDB} & \texttt{WITH\_CGAL\_PDB} & \ccc{CGAL::PDB} used to manipulate \texttt{PDB} files & {\em none}\\\hline
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\end{tabular}
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\end{center}
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@ -682,7 +681,6 @@ The following boolean variables indicate which \cgal\ components to configure an
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\texttt{WITH\_CGAL\_Qt3} & ON\\\hline
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\texttt{WITH\_CGAL\_Qt4} & ON\\\hline
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\texttt{WITH\_CGAL\_ImageIO} & ON\\\hline
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\texttt{WITH\_CGAL\_PDB} & ON\\\hline
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\end{tabular}
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}
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@ -1130,7 +1128,6 @@ cmake -DWITH_examples=false
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-- Configuring CGALimageIO. Set WITH_CGALimageIO to FALSE to unselect it.
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-- Could NOT find ZLIB
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-- CGAL-ImageIO needs ZLib and OpenGL, cannot be configured.
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-- Configuring CGALPDB. Set WITH_CGALPDB to FALSE to unselect it.
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-- Configuring CGALQt. Set WITH_CGALQt to FALSE to unselect it.
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-- CGAL-Qt3 needs Qt3, cannot be configured.
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-- Configuring CGALQt4. Set WITH_CGALQt4 to FALSE to unselect it.
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@ -1,30 +0,0 @@
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// Copyright (c) 2007 GeometryFactory (France). All rights reserved.
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//
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// This file is part of CGAL (www.cgal.org); you can redistribute it and/or
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// modify it under the terms of the GNU Lesser General Public License as
|
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// published by the Free Software Foundation; version 2.1 of the License.
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// See the file LICENSE.LGPL distributed with CGAL.
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//
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// Licensees holding a valid commercial license may use this file in
|
||||
// accordance with the commercial license agreement provided with the software.
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//
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// This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
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// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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//
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// $URL$
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// $Id$
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//
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//
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// Author(s) : Fernando Cacciola (fernando.cacciola@geometryfactry.com)
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#ifndef CGAL_AUTO_LINK_PDB_H
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#define CGAL_AUTO_LINK_PDB_H
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#ifndef CGAL_NO_AUTOLINK_PDB
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#define CGAL_LIB_NAME CGAL_PDB
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#include <CGAL/auto_link/auto_link.h>
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#endif // CGAL_NO_AUTOLINK_PDB
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#endif // CGAL_AUTO_LINK_PDB_H
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@ -18,6 +18,5 @@ else(NOT CGAL_NO_CORE)
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endif(NOT CGAL_NO_CORE)
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configure_component( CGALimageIO ImageIO )
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configure_component( CGALPDB PDB )
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configure_component( CGALQt Qt3 )
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configure_component( CGALQt4 Qt4 )
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@ -51,10 +51,6 @@ if ( CGAL_FOUND )
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create_link_to_program(CGAL_ImageIO)
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endif()
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if ( WITH_CGAL_PDB )
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create_link_to_program(CGAL_PDB)
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endif()
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if ( WITH_CGAL_Qt3 )
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create_link_to_program(CGAL_Qt3)
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endif()
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|
|
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@ -1,12 +0,0 @@
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// Use something defined not in headers but in the CGAL library to test that is was indeed properly built and linked to,
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#include <CGAL/PDB/PDB.h>
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int main()
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{
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std::ifstream in("");
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volatile CGAL::PDB::PDB pdb(in,false);
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return 0;
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}
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@ -155,8 +155,8 @@ Copyright (from upstream file LICENSE)
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|||
|
||||
The source code of the CGAL library can be found in the directories
|
||||
"src/CGAL", "src/CGALQt", "src/CGALQt4" and "include/CGAL" (with the
|
||||
exception of "include/CGAL/CORE", "include/CGAL/OpenNL" and
|
||||
"include/CGAL/PDB"). It is specified in each file of the CGAL library which
|
||||
exception of "include/CGAL/CORE", "include/CGAL/OpenNL").
|
||||
It is specified in each file of the CGAL library which
|
||||
license applies to it. This is either the GNU Lesser General Public License
|
||||
(as published by the Free Software Foundation; version 2.1 of the License)
|
||||
or the Q Public License (version 1.0), *depending on each file*. The texts
|
||||
|
|
@ -170,8 +170,6 @@ Copyright (from upstream file LICENSE)
|
|||
licensed under the QPL (see LICENSE.QPL).
|
||||
- ImageIO, in the directory "src/CGALimageIO", is licensed under the LGPL
|
||||
(see LICENSE.LGPL).
|
||||
- PDB, in the directory "include/CGAL/PDB" and "src/CGALPDB" is licensed
|
||||
under the LGPL (see LICENSE.LGPL).
|
||||
- OpenNL, in the directory "include/CGAL/OpenNL", is licensed under the LGPL
|
||||
(see LICENSE.LGPL).
|
||||
|
||||
|
|
@ -310,34 +308,6 @@ src/CGALimageIO.
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|||
|
||||
|
||||
|
||||
PDB
|
||||
===
|
||||
|
||||
The following copyright statement applies to the PDB library in
|
||||
include/CGAL/PDB and src/CGALPDB.
|
||||
|
||||
Copyright 2004
|
||||
Stanford University
|
||||
|
||||
This file is part of the DSR PDB Library.
|
||||
|
||||
The DSR PDB Library is free software; you can redistribute it and/or modify
|
||||
it under the terms of the GNU Lesser General Public License as published by
|
||||
the Free Software Foundation; either version 2.1 of the License, or (at your
|
||||
option) any later version.
|
||||
|
||||
The DSR PDB Library 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 Lesser General Public
|
||||
License for more details.
|
||||
|
||||
You should have received a copy of the GNU Lesser General Public License
|
||||
along with the DSR PDB Library; see the file /usr/share/common-licenses/LGPL-2.1.
|
||||
If not, write to the Free Software Foundation, Inc., 51 Franklin Street,
|
||||
Fifth Floor, Boston, MA 02110-1301, USA.
|
||||
|
||||
|
||||
|
||||
OpenNL
|
||||
======
|
||||
|
||||
|
|
|
|||
|
|
@ -1,6 +1,5 @@
|
|||
libCGAL 5 libcgal5
|
||||
libCGAL_Core 5 libcgal5
|
||||
libCGAL_ImageIO 5 libcgal5
|
||||
libCGAL_PDB 5 libcgal5
|
||||
libCGAL_Qt3 5 libcgal5
|
||||
libCGAL_Qt4 5 libcgal5
|
||||
|
|
|
|||
|
|
@ -155,8 +155,8 @@ Copyright (from upstream file LICENSE)
|
|||
|
||||
The source code of the CGAL library can be found in the directories
|
||||
"src/CGAL", "src/CGALQt", "src/CGALQt4" and "include/CGAL" (with the
|
||||
exception of "include/CGAL/CORE", "include/CGAL/OpenNL" and
|
||||
"include/CGAL/PDB"). It is specified in each file of the CGAL library which
|
||||
exception of "include/CGAL/CORE", "include/CGAL/OpenNL").
|
||||
It is specified in each file of the CGAL library which
|
||||
license applies to it. This is either the GNU Lesser General Public License
|
||||
(as published by the Free Software Foundation; version 2.1 of the License)
|
||||
or the Q Public License (version 1.0), *depending on each file*. The texts
|
||||
|
|
@ -170,8 +170,6 @@ Copyright (from upstream file LICENSE)
|
|||
licensed under the QPL (see LICENSE.QPL).
|
||||
- ImageIO, in the directory "src/CGALimageIO", is licensed under the LGPL
|
||||
(see LICENSE.LGPL).
|
||||
- PDB, in the directory "include/CGAL/PDB" and "src/CGALPDB" is licensed
|
||||
under the LGPL (see LICENSE.LGPL).
|
||||
- OpenNL, in the directory "include/CGAL/OpenNL", is licensed under the LGPL
|
||||
(see LICENSE.LGPL).
|
||||
|
||||
|
|
@ -310,34 +308,6 @@ src/CGALimageIO.
|
|||
|
||||
|
||||
|
||||
PDB
|
||||
===
|
||||
|
||||
The following copyright statement applies to the PDB library in
|
||||
include/CGAL/PDB and src/CGALPDB.
|
||||
|
||||
Copyright 2004
|
||||
Stanford University
|
||||
|
||||
This file is part of the DSR PDB Library.
|
||||
|
||||
The DSR PDB Library is free software; you can redistribute it and/or modify
|
||||
it under the terms of the GNU Lesser General Public License as published by
|
||||
the Free Software Foundation; either version 2.1 of the License, or (at your
|
||||
option) any later version.
|
||||
|
||||
The DSR PDB Library 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 Lesser General Public
|
||||
License for more details.
|
||||
|
||||
You should have received a copy of the GNU Lesser General Public License
|
||||
along with the DSR PDB Library; see the file /usr/share/common-licenses/LGPL-2.1.
|
||||
If not, write to the Free Software Foundation, Inc., 51 Franklin Street,
|
||||
Fifth Floor, Boston, MA 02110-1301, USA.
|
||||
|
||||
|
||||
|
||||
OpenNL
|
||||
======
|
||||
|
||||
|
|
|
|||
|
|
@ -1,6 +1,5 @@
|
|||
libCGAL 5 libcgal5
|
||||
libCGAL_Core 5 libcgal5
|
||||
libCGAL_ImageIO 5 libcgal5
|
||||
libCGAL_PDB 5 libcgal5
|
||||
libCGAL_Qt3 5 libcgal5
|
||||
libCGAL_Qt4 5 libcgal5
|
||||
|
|
|
|||
|
|
@ -155,8 +155,8 @@ Copyright (from upstream file LICENSE)
|
|||
|
||||
The source code of the CGAL library can be found in the directories
|
||||
"src/CGAL", "src/CGALQt", "src/CGALQt4" and "include/CGAL" (with the
|
||||
exception of "include/CGAL/CORE", "include/CGAL/OpenNL" and
|
||||
"include/CGAL/PDB"). It is specified in each file of the CGAL library which
|
||||
exception of "include/CGAL/CORE", "include/CGAL/OpenNL").
|
||||
It is specified in each file of the CGAL library which
|
||||
license applies to it. This is either the GNU Lesser General Public License
|
||||
(as published by the Free Software Foundation; version 2.1 of the License)
|
||||
or the Q Public License (version 1.0), *depending on each file*. The texts
|
||||
|
|
@ -170,8 +170,6 @@ Copyright (from upstream file LICENSE)
|
|||
licensed under the QPL (see LICENSE.QPL).
|
||||
- ImageIO, in the directory "src/CGALimageIO", is licensed under the LGPL
|
||||
(see LICENSE.LGPL).
|
||||
- PDB, in the directory "include/CGAL/PDB" and "src/CGALPDB" is licensed
|
||||
under the LGPL (see LICENSE.LGPL).
|
||||
- OpenNL, in the directory "include/CGAL/OpenNL", is licensed under the LGPL
|
||||
(see LICENSE.LGPL).
|
||||
|
||||
|
|
@ -310,34 +308,6 @@ src/CGALimageIO.
|
|||
|
||||
|
||||
|
||||
PDB
|
||||
===
|
||||
|
||||
The following copyright statement applies to the PDB library in
|
||||
include/CGAL/PDB and src/CGALPDB.
|
||||
|
||||
Copyright 2004
|
||||
Stanford University
|
||||
|
||||
This file is part of the DSR PDB Library.
|
||||
|
||||
The DSR PDB Library is free software; you can redistribute it and/or modify
|
||||
it under the terms of the GNU Lesser General Public License as published by
|
||||
the Free Software Foundation; either version 2.1 of the License, or (at your
|
||||
option) any later version.
|
||||
|
||||
The DSR PDB Library 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 Lesser General Public
|
||||
License for more details.
|
||||
|
||||
You should have received a copy of the GNU Lesser General Public License
|
||||
along with the DSR PDB Library; see the file /usr/share/common-licenses/LGPL-2.1.
|
||||
If not, write to the Free Software Foundation, Inc., 51 Franklin Street,
|
||||
Fifth Floor, Boston, MA 02110-1301, USA.
|
||||
|
||||
|
||||
|
||||
OpenNL
|
||||
======
|
||||
|
||||
|
|
|
|||
|
|
@ -1,6 +1,5 @@
|
|||
libCGAL 5 libcgal5
|
||||
libCGAL_Core 5 libcgal5
|
||||
libCGAL_ImageIO 5 libcgal5
|
||||
libCGAL_PDB 5 libcgal5
|
||||
libCGAL_Qt3 5 libcgal5
|
||||
libCGAL_Qt4 5 libcgal5
|
||||
|
|
|
|||
|
|
@ -525,7 +525,7 @@ cmake '${CMAKE_GENERATOR}' -DRUNNING_CGAL_AUTO_TEST=TRUE \\
|
|||
-DCGAL_REFERENCE_CACHE_DIR="\$CGAL_REFERENCE_CACHE_DIR" \\
|
||||
VERBOSE=1 \\
|
||||
../../..;
|
||||
${MAKE_CMD} VERBOSE=ON -k -fMakefile CGAL CGAL_Core CGAL_PDB CGAL_ImageIO CGAL_Qt3 CGAL_Qt4 ;
|
||||
${MAKE_CMD} VERBOSE=ON -k -fMakefile CGAL CGAL_Core CGAL_ImageIO CGAL_Qt3 CGAL_Qt4 ;
|
||||
cd ..;
|
||||
EOF
|
||||
chmod ugo+x "${CGAL_BINARY_DIR}/localbuildscript"
|
||||
|
|
|
|||
|
|
@ -55,11 +55,11 @@ if [ ! -f INSTALL ]; then
|
|||
fi
|
||||
|
||||
grep -r -L "^\(//\| \*\|#\) See the file LICENSE\.\(LG\|Q\)PL distributed with CGAL\." * | \
|
||||
grep -v "^$DIR/\|^include/CGAL/CORE/\|^include/CGAL/OpenNL/\|^include/CGAL/PDB/\|^src/CGALCore/\|^src/CGALimageIO/\|^src/CGALPDB/\|^config/support/\|test/\|^Packages/\|^developer_scripts\|^doc_tex/\|^winutils/" | sort >$PREFIX1 || true
|
||||
grep -v "^$DIR/\|^include/CGAL/CORE/\|^include/CGAL/OpenNL/\|^src/CGALCore/\|^src/CGALimageIO/\|^config/support/\|test/\|^Packages/\|^developer_scripts\|^doc_tex/\|^winutils/" | sort >$PREFIX1 || true
|
||||
|
||||
echo Note that files in the following directories are ignored:
|
||||
echo include/CGAL/CORE, include/CGAL/OpenNL, include/CGAL/PDB,
|
||||
echo src/CGALCore, src/CGALimageIO, src/CGALPDB, config/support,
|
||||
echo include/CGAL/CORE, include/CGAL/OpenNL,
|
||||
echo src/CGALCore, src/CGALimageIO, config/support,
|
||||
echo test, Packages, developer_scripts, doc_tex, winutils
|
||||
|
||||
echo
|
||||
|
|
|
|||
|
|
@ -626,7 +626,7 @@ usage()
|
|||
echo "Usage: `basename $0` [-s source] [-c cgal-component1:cgal-component2:...] [-b boost-component1:boost-component2:...] [-p /path/to/package1:/path/to/package2:...] [-d /path/to/directory1:/path/to/directory2:...] [-o options_file='`pwd`/cgal_cmake_options:$HOME/.cgal_cmake_options_rc'] [-v] [-h]" >&2
|
||||
echo >&2
|
||||
echo " -s source If this parameter is given the script will create one single executable for 'source' with all source files; otherwise it creates one executable for each main'ed source." >&2
|
||||
echo " cgal_componentX - must be a valid cgal component, examples are 'Core','imageIO','PDB','Qt3','Qt4' ('benchmark')." >&2
|
||||
echo " cgal_componentX - must be a valid cgal component, examples are 'Core','imageIO','Qt3','Qt4' ('benchmark')." >&2
|
||||
echo " boost_componentX - must be a valid boost component, like 'filesystem', 'program_options'." >&2
|
||||
echo " options_file - file with PACKAGE, DIRECTORY, CGAL_COMPONENT, and BOOST_COMPONENT directives" >&2
|
||||
echo " -v the version" >&2
|
||||
|
|
|
|||
|
|
@ -11,26 +11,33 @@ if ( COMMAND cmake_policy )
|
|||
cmake_policy( SET CMP0003 NEW )
|
||||
endif()
|
||||
|
||||
find_package(CGAL QUIET COMPONENTS PDB )
|
||||
find_package(CGAL)
|
||||
find_package(ESBTL)
|
||||
|
||||
|
||||
|
||||
if (CGAL_FOUND)
|
||||
include( ${CGAL_USE_FILE} )
|
||||
|
||||
if(CGAL_PDB_FOUND)
|
||||
|
||||
include( CGAL_CreateSingleSourceCGALProgram )
|
||||
|
||||
include_directories (BEFORE include)
|
||||
|
||||
create_single_source_cgal_program( "NGHK_skin_surface_simple.cpp" )
|
||||
create_single_source_cgal_program( "NGHK_skin_surface_subdiv.cpp" )
|
||||
create_single_source_cgal_program( "skin_surface_pdb_reader.cpp" )
|
||||
create_single_source_cgal_program( "skin_surface_simple.cpp" )
|
||||
create_single_source_cgal_program( "skin_surface_subdiv.cpp" )
|
||||
create_single_source_cgal_program( "skin_surface_subdiv_with_normals.cpp" )
|
||||
create_single_source_cgal_program( "union_of_balls_simple.cpp" )
|
||||
create_single_source_cgal_program( "union_of_balls_subdiv.cpp" )
|
||||
if(ESBTL_FOUND)
|
||||
include( ${ESBTL_USE_FILE} )
|
||||
create_single_source_cgal_program( "skin_surface_pdb_reader.cpp" )
|
||||
else(ESBTL_FOUND)
|
||||
message(STATUS "NOTICE: skin_surface_pdb_reader.cpp requires ESBTL library, and will not be compiled.")
|
||||
endif(ESBTL_FOUND)
|
||||
|
||||
else(CGAL_PDB_FOUND)
|
||||
else(CGAL_FOUND)
|
||||
|
||||
message(STATUS "NOTICE: This directory requires CGAL PDB library, and will not be compiled.")
|
||||
message(STATUS "NOTICE: This directory requires CGAL library, and will not be compiled.")
|
||||
|
||||
endif(CGAL_PDB_FOUND)
|
||||
endif(CGAL_FOUND)
|
||||
|
|
|
|||
|
|
@ -1,44 +1,38 @@
|
|||
// AUTHOR: Daniel Russel drussel@graphics.stanford.edu
|
||||
|
||||
// See http://graphics.stanford.edu/~drussel/pdb for documentation.
|
||||
//
|
||||
// Feel free to contact me (Daniel, drussel@graphics.stanford.edu)
|
||||
// if you have any suggestions or patches. Thanks.
|
||||
|
||||
#ifndef EXTRACT_BALLS_FROM_PDB_H
|
||||
#define EXTRACT_BALLS_FROM_PDB_H
|
||||
|
||||
#include <CGAL/PDB/PDB.h>
|
||||
#include <CGAL/PDB/range.h>
|
||||
#include <fstream>
|
||||
#include <ESBTL/atom_classifier.h>
|
||||
#include <ESBTL/weighted_atom_iterator.h>
|
||||
|
||||
template <class Range, class OIt>
|
||||
void copy(Range r, OIt out) {
|
||||
std::copy(r.begin(), r.end(), out);
|
||||
}
|
||||
|
||||
template <class Traits, class OutputIterator>
|
||||
template <class K,class System, class OutputIterator>
|
||||
void extract_balls_from_pdb(const char *filename,
|
||||
Traits const &t,
|
||||
std::vector<System>& systems,
|
||||
OutputIterator weighted_points)
|
||||
{
|
||||
std::ifstream in(filename);
|
||||
|
||||
if (!in) {
|
||||
std::cerr << "Error opening input file " << filename << std::endl;
|
||||
typedef ESBTL::Generic_classifier<ESBTL::Radius_of_atom<double,typename System::Atom> > T_Atom_classifier;
|
||||
typedef ESBTL::Accept_none_occupancy_policy<ESBTL::PDB::Line_format<> > Accept_none_occupancy_policy;
|
||||
typedef ESBTL::Weighted_atom_iterator<typename System::Model,
|
||||
CGAL::Weighted_point<typename K::Point_3,double>,
|
||||
ESBTL::Weight_of_atoms<T_Atom_classifier> > Weighted_atom_iterator;
|
||||
|
||||
ESBTL::PDB_line_selector sel;
|
||||
|
||||
ESBTL::All_atom_system_builder<System> builder(systems,sel.max_nb_systems());
|
||||
T_Atom_classifier atom_classifier;
|
||||
|
||||
ESBTL::read_a_pdb_file(filename,sel,builder,Accept_none_occupancy_policy());
|
||||
|
||||
if ( systems.empty() || systems[0].has_no_model() ){
|
||||
std::cerr << "No atoms found" << std::endl;
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
using namespace CGAL::PDB;
|
||||
|
||||
PDB pdb(in);
|
||||
Model m=pdb.models().begin()->model();
|
||||
Chain c=m.chains().begin()->chain();
|
||||
// get all weighted_points
|
||||
|
||||
|
||||
::copy
|
||||
(make_weighted_point_range(make_atom_range(m.atoms()), t),
|
||||
const typename System::Model& model=* systems[0].models_begin();
|
||||
std::copy(Weighted_atom_iterator(model.atoms_begin(),&atom_classifier),
|
||||
Weighted_atom_iterator(model.atoms_end(),&atom_classifier),
|
||||
weighted_points);
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,11 @@
|
|||
#include <CGAL/Skin_surface_polyhedral_items_3.h>
|
||||
#include <list>
|
||||
|
||||
typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
|
||||
#include <ESBTL/CGAL/EPIC_kernel_with_atom.h>
|
||||
#include <ESBTL/default.h>
|
||||
|
||||
typedef ESBTL::CGAL::EPIC_kernel_with_atom K;
|
||||
typedef ESBTL::CGAL::Default_system System;
|
||||
typedef CGAL::Skin_surface_traits_3<K> Traits;
|
||||
typedef CGAL::Skin_surface_3<Traits> Skin_surface_3;
|
||||
typedef Skin_surface_3::FT FT;
|
||||
|
|
@ -13,11 +17,10 @@ typedef Skin_surface_3::Weighted_point Weighted_point;
|
|||
typedef Weighted_point::Point Bare_point;
|
||||
typedef CGAL::Polyhedron_3<K> Polyhedron;
|
||||
|
||||
#include <extract_balls_from_pdb.h>
|
||||
|
||||
#include <list>
|
||||
#include <fstream>
|
||||
#include "skin_surface_writer.h"
|
||||
#include "include/extract_balls_from_pdb.h"
|
||||
|
||||
|
||||
int main(int argc, char *argv[]) {
|
||||
|
|
@ -28,11 +31,18 @@ int main(int argc, char *argv[]) {
|
|||
filename = "data/1t7i.pdb";
|
||||
}
|
||||
|
||||
|
||||
std::list<Weighted_point> l;
|
||||
double shrinkfactor = 0.5;
|
||||
//Container for molecular system
|
||||
std::vector<System> systems;
|
||||
|
||||
|
||||
|
||||
// Retrieve input balls:
|
||||
extract_balls_from_pdb(filename, Traits(), std::back_inserter(l));
|
||||
extract_balls_from_pdb<K>(filename,systems,std::back_inserter(l));
|
||||
|
||||
|
||||
|
||||
// Construct skin surface:
|
||||
Skin_surface_3 skin_surface(l.begin(), l.end(), shrinkfactor);
|
||||
|
|
|
|||
|
|
@ -262,7 +262,6 @@ parse_flags_and_third_party_choices
|
|||
parse_lib_building_results "libCGALCore" "CGAL_Core"
|
||||
parse_lib_building_results "libCGAL" "CGAL"
|
||||
parse_lib_building_results "libCGALimageIO" "CGAL_ImageIO"
|
||||
parse_lib_building_results "libCGALPDB" "CGAL_PDB"
|
||||
parse_lib_building_results "libCGALQt" "CGAL_Qt3"
|
||||
parse_lib_building_results "libCGALQt4" "CGAL_Qt4"
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue