diff --git a/.gitattributes b/.gitattributes index 867c760f25c..c07fc3236c8 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1423,6 +1423,7 @@ Installation/cmake/modules/FindBoost.cmake -text Installation/cmake/modules/FindCGAL.cmake -text Installation/cmake/modules/FindCGAL_CORE.cmake -text Installation/cmake/modules/FindCORE.cmake -text +Installation/cmake/modules/FindESBTL.cmake -text Installation/cmake/modules/FindF2C.cmake -text Installation/cmake/modules/FindGMP.cmake -text Installation/cmake/modules/FindGMPXX.cmake -text @@ -1441,6 +1442,7 @@ Installation/cmake/modules/FindRS.cmake -text Installation/cmake/modules/FindTAUCS.cmake -text Installation/cmake/modules/Qt3Macros-patched.cmake -text Installation/cmake/modules/UseCGAL.cmake -text +Installation/cmake/modules/UseESBTL.cmake -text Installation/cmake/modules/test_MPFI.cpp -text Installation/config/support/print_BOOST_version.cpp -text Installation/config/support/print_GMP_version.cpp -text @@ -1459,7 +1461,6 @@ Installation/test/Installation/CMakeLists.txt -text Installation/test/Installation/link_to_CGAL.cpp -text Installation/test/Installation/link_to_CGAL_Core.cpp -text Installation/test/Installation/link_to_CGAL_ImageIO.cpp -text -Installation/test/Installation/link_to_CGAL_PDB.cpp -text Installation/test/Installation/link_to_CGAL_Qt3.cpp -text Installation/test/Installation/link_to_CGAL_Qt4.cpp -text Interpolation/demo/Interpolation/CMakeLists.txt -text diff --git a/Installation/CHANGES b/Installation/CHANGES index f977ea0ee26..d5e5bf76e94 100644 --- a/Installation/CHANGES +++ b/Installation/CHANGES @@ -23,6 +23,9 @@ x.y 2D Mesh Generation - The execution of the 2D mesh generator is now deterministic (same at each run). +x CGAL_PDB is no longer provided with CGAL. An alternative solution for people + interested in reading PDB files is to use ESBTL (http://esbtl.sourceforge.net/). + ----------------------------- Release 3.6.1 -------------------------------- CGAL 3.6.1 is a bug-fixes release. The following has been changed since CGAL-3.6: diff --git a/Installation/CMakeLists.txt b/Installation/CMakeLists.txt index 2acb638c374..a4aba1771a0 100644 --- a/Installation/CMakeLists.txt +++ b/Installation/CMakeLists.txt @@ -97,7 +97,7 @@ message( STATUS "System: ${CMAKE_SYSTEM_NAME}" ) # The base name of all CGAL libraries (including "CGAL" itself. That # variables can be used by foreach() loops that deal with library variables. -set(ALL_CGAL_LIBRARIES CGAL CGAL_Core CGAL_ImageIO CGAL_PDB CGAL_Qt3 CGAL_Qt4 CACHE INTERNAL "Name of all CGAL libraries.") +set(ALL_CGAL_LIBRARIES CGAL CGAL_Core CGAL_ImageIO CGAL_Qt3 CGAL_Qt4 CACHE INTERNAL "Name of all CGAL libraries.") #-------------------------------------------------------------------------------------------------- # @@ -213,11 +213,6 @@ cache_set(CGAL_Qt4_3RD_PARTY_INCLUDE_DIRS "" ) cache_set(CGAL_Qt4_3RD_PARTY_LIBRARIES "" ) cache_set(CGAL_Qt4_3RD_PARTY_LIBRARIES_DIRS "" ) -cache_set(CGAL_PDB_3RD_PARTY_DEFINITIONS "" ) -cache_set(CGAL_PDB_3RD_PARTY_INCLUDE_DIRS "" ) -cache_set(CGAL_PDB_3RD_PARTY_LIBRARIES "" ) -cache_set(CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS "" ) - include(CGAL_SetupDependencies) #-------------------------------------------------------------------------------------------------- @@ -366,7 +361,6 @@ add_subdirectory(src) cache_get(CGAL_LIBRARY) cache_get(CGAL_Core_LIBRARY) cache_get(CGAL_ImageIO_LIBRARY) -cache_get(CGAL_PDB_LIBRARY) cache_get(CGAL_Qt3_LIBRARY) cache_get(CGAL_Qt4_LIBRARY) @@ -395,11 +389,6 @@ cache_get(CGAL_Qt4_3RD_PARTY_INCLUDE_DIRS ) cache_get(CGAL_Qt4_3RD_PARTY_LIBRARIES ) cache_get(CGAL_Qt4_3RD_PARTY_LIBRARIES_DIRS) -cache_get(CGAL_PDB_3RD_PARTY_DEFINITIONS ) -cache_get(CGAL_PDB_3RD_PARTY_INCLUDE_DIRS ) -cache_get(CGAL_PDB_3RD_PARTY_LIBRARIES ) -cache_get(CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS) - hide_variable(EXECUTABLE_OUTPUT_PATH) hide_variable(LIBRARY_OUTPUT_PATH) diff --git a/Installation/LICENSE b/Installation/LICENSE index 510ac185a95..5a33da7cfc9 100644 --- a/Installation/LICENSE +++ b/Installation/LICENSE @@ -7,8 +7,8 @@ from GeometryFactory (www.geometryfactory.com) for all or parts of CGAL. 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 @@ -22,8 +22,6 @@ licenses: 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). diff --git a/Installation/cmake/modules/CGALConfig_binary.cmake.in b/Installation/cmake/modules/CGALConfig_binary.cmake.in index f93be2faaa0..4a0a081593b 100644 --- a/Installation/cmake/modules/CGALConfig_binary.cmake.in +++ b/Installation/cmake/modules/CGALConfig_binary.cmake.in @@ -35,14 +35,12 @@ set(CGAL_LIBRARIES_DIR "@CGAL_LIBRARIES_DIR@" ) set(WITH_CGAL "ON") set(WITH_CGAL_Core "@WITH_CGAL_Core@") set(WITH_CGAL_ImageIO "@WITH_CGAL_ImageIO@") -set(WITH_CGAL_PDB "@WITH_CGAL_PDB@" ) set(WITH_CGAL_Qt3 "@WITH_CGAL_Qt3@" ) set(WITH_CGAL_Qt4 "@WITH_CGAL_Qt4@" ) set(CGAL_LIBRARY "@CGAL_LIBRARY@") set(CGAL_Core_LIBRARY "@CGAL_Core_LIBRARY@") set(CGAL_ImageIO_LIBRARY "@CGAL_ImageIO_LIBRARY@") -set(CGAL_PDB_LIBRARY "@CGAL_PDB_LIBRARY@" ) set(CGAL_Qt3_LIBRARY "@CGAL_Qt3_LIBRARY@" ) set(CGAL_Qt4_LIBRARY "@CGAL_Qt4_LIBRARY@" ) @@ -62,11 +60,6 @@ set(CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIRS "@CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIR set(CGAL_ImageIO_3RD_PARTY_LIBRARIES "@CGAL_ImageIO_3RD_PARTY_LIBRARIES@" ) set(CGAL_ImageIO_USE_ZLIB "@CGAL_ImageIO_USE_ZLIB@" ) -set(CGAL_PDB_3RD_PARTY_INCLUDE_DIRS "@CGAL_PDB_3RD_PARTY_INCLUDE_DIRS@" ) -set(CGAL_PDB_3RD_PARTY_DEFINITIONS "@CGAL_PDB_3RD_PARTY_DEFINITIONS@" ) -set(CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS "@CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS@" ) -set(CGAL_PDB_3RD_PARTY_LIBRARIES "@CGAL_PDB_3RD_PARTY_LIBRARIES@" ) - set(CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS "@CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS@" ) set(CGAL_Qt3_3RD_PARTY_DEFINITIONS "@CGAL_Qt3_3RD_PARTY_DEFINITIONS@" ) set(CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS "@CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS@" ) diff --git a/Installation/cmake/modules/CGALConfig_install.cmake.fhs.in b/Installation/cmake/modules/CGALConfig_install.cmake.fhs.in index e3ee5e43ec8..e90b9eef473 100644 --- a/Installation/cmake/modules/CGALConfig_install.cmake.fhs.in +++ b/Installation/cmake/modules/CGALConfig_install.cmake.fhs.in @@ -37,14 +37,12 @@ set(CGAL_LIBRARIES_DIR "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@" ) set(WITH_CGAL "ON") set(WITH_CGAL_Core "@WITH_CGAL_Core@") set(WITH_CGAL_ImageIO "@WITH_CGAL_ImageIO@") -set(WITH_CGAL_PDB "@WITH_CGAL_PDB@" ) set(WITH_CGAL_Qt3 "@WITH_CGAL_Qt3@" ) set(WITH_CGAL_Qt4 "@WITH_CGAL_Qt4@" ) set(CGAL_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_LIBRARY_NAME@") set(CGAL_Core_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_Core_LIBRARY_NAME@") set(CGAL_ImageIO_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_ImageIO_LIBRARY_NAME@") -set(CGAL_PDB_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_PDB_LIBRARY_NAME@" ) set(CGAL_Qt3_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_Qt3_LIBRARY_NAME@" ) set(CGAL_Qt4_LIBRARY "@CMAKE_INSTALL_PREFIX@/@CGAL_INSTALL_LIB_DIR@/@CGAL_Qt4_LIBRARY_NAME@" ) @@ -64,11 +62,6 @@ set(CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIRS "@CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIR set(CGAL_ImageIO_3RD_PARTY_LIBRARIES "@CGAL_ImageIO_3RD_PARTY_LIBRARIES@" ) set(CGAL_ImageIO_USE_ZLIB "@CGAL_ImageIO_USE_ZLIB@" ) -set(CGAL_PDB_3RD_PARTY_INCLUDE_DIRS "@CGAL_PDB_3RD_PARTY_INCLUDE_DIRS@" ) -set(CGAL_PDB_3RD_PARTY_DEFINITIONS "@CGAL_PDB_3RD_PARTY_DEFINITIONS@" ) -set(CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS "@CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS@" ) -set(CGAL_PDB_3RD_PARTY_LIBRARIES "@CGAL_PDB_3RD_PARTY_LIBRARIES@" ) - set(CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS "@CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS@" ) set(CGAL_Qt3_3RD_PARTY_DEFINITIONS "@CGAL_Qt3_3RD_PARTY_DEFINITIONS@" ) set(CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS "@CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS@" ) diff --git a/Installation/cmake/modules/CGALConfig_install.cmake.source.in b/Installation/cmake/modules/CGALConfig_install.cmake.source.in index 3afb0f9a150..dd9e37f2532 100644 --- a/Installation/cmake/modules/CGALConfig_install.cmake.source.in +++ b/Installation/cmake/modules/CGALConfig_install.cmake.source.in @@ -35,14 +35,12 @@ set(CGAL_LIBRARIES_DIR "$(CGAL_INSTALL_PREFIX)/@CGAL_INSTALL_LIB_DIR@" ) set(WITH_CGAL "ON") set(WITH_CGAL_Core "@WITH_CGAL_Core@") set(WITH_CGAL_ImageIO "@WITH_CGAL_ImageIO@") -set(WITH_CGAL_PDB "@WITH_CGAL_PDB@" ) set(WITH_CGAL_Qt3 "@WITH_CGAL_Qt3@" ) set(WITH_CGAL_Qt4 "@WITH_CGAL_Qt4@" ) set(CGAL_LIBRARY "@CGAL_LIBRARY@") set(CGAL_Core_LIBRARY "@CGAL_Core_LIBRARY@") set(CGAL_ImageIO_LIBRARY "@CGAL_ImageIO_LIBRARY@") -set(CGAL_PDB_LIBRARY "@CGAL_PDB_LIBRARY@" ) set(CGAL_Qt3_LIBRARY "@CGAL_Qt3_LIBRARY@" ) set(CGAL_Qt4_LIBRARY "@CGAL_Qt4_LIBRARY@" ) @@ -62,11 +60,6 @@ set(CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIRS "@CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIR set(CGAL_ImageIO_3RD_PARTY_LIBRARIES "@CGAL_ImageIO_3RD_PARTY_LIBRARIES@" ) set(CGAL_ImageIO_USE_ZLIB "@CGAL_ImageIO_USE_ZLIB@" ) -set(CGAL_PDB_3RD_PARTY_INCLUDE_DIRS "@CGAL_PDB_3RD_PARTY_INCLUDE_DIRS@" ) -set(CGAL_PDB_3RD_PARTY_DEFINITIONS "@CGAL_PDB_3RD_PARTY_DEFINITIONS@" ) -set(CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS "@CGAL_PDB_3RD_PARTY_LIBRARIES_DIRS@" ) -set(CGAL_PDB_3RD_PARTY_LIBRARIES "@CGAL_PDB_3RD_PARTY_LIBRARIES@" ) - set(CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS "@CGAL_Qt3_3RD_PARTY_INCLUDE_DIRS@" ) set(CGAL_Qt3_3RD_PARTY_DEFINITIONS "@CGAL_Qt3_3RD_PARTY_DEFINITIONS@" ) set(CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS "@CGAL_Qt3_3RD_PARTY_LIBRARIES_DIRS@" ) diff --git a/Installation/cmake/modules/FindESBTL.cmake b/Installation/cmake/modules/FindESBTL.cmake new file mode 100644 index 00000000000..d0623ed24e4 --- /dev/null +++ b/Installation/cmake/modules/FindESBTL.cmake @@ -0,0 +1,28 @@ +#This modules tries to find ESBTL +# Once done this will define +# +# ESBTL_FOUND - system has ESBTL +# ESBTL_INCLUDE_DIR - ESBTL include directory +# + +# Is it already configured? +if (ESBTL_INCLUDE_DIR) + set(ESBTL_FOUND TRUE) +else() + + find_path(ESBTL_INCLUDE_DIR + NAMES ESBTL/default.h + PATHS /usr/include + /usr/local/include + ) + + if(ESBTL_INCLUDE_DIR) + set(ESBTL_FOUND TRUE) + endif() +endif() + + +if(ESBTL_FOUND) + message(STATUS "Found ESBTL: ${ESBTL_INCLUDE_DIR}") + set(ESBTL_USE_FILE "UseESBTL") +endif() diff --git a/Installation/cmake/modules/UseESBTL.cmake b/Installation/cmake/modules/UseESBTL.cmake new file mode 100644 index 00000000000..d72567a5da9 --- /dev/null +++ b/Installation/cmake/modules/UseESBTL.cmake @@ -0,0 +1,4 @@ +# This module setups the compiler for using ESBTL library. +# It assumes that find_package(ESBTL) was already called. + +include_directories( ${ESBTL_INCLUDE_DIR} ) diff --git a/Installation/doc_tex/Installation/installation.tex b/Installation/doc_tex/Installation/installation.tex index 33071a61e54..8b28eae6640 100644 --- a/Installation/doc_tex/Installation/installation.tex +++ b/Installation/doc_tex/Installation/installation.tex @@ -373,7 +373,6 @@ are switched \texttt{ON}. \texttt{CGAL\_Qt3} & \texttt{WITH\_CGAL\_Qt3} & \ccc{CGAL::Qt_widget} used by Qt3-based demos & Qt3 and OpenGL\\\hline \texttt{CGAL\_Qt4} & \texttt{WITH\_CGAL\_Qt4} & \ccc{QGraphicsView} support for Qt4-based demos & Qt4 and OpenGL\\\hline \texttt{CGAL\_ImageIO} & \texttt{WITH\_CGAL\_ImageIO} & Utilities to read and write image files & OpenGL, ZLib, VTK (optional)\\\hline - \texttt{CGAL\_PDB} & \texttt{WITH\_CGAL\_PDB} & \ccc{CGAL::PDB} used to manipulate \texttt{PDB} files & {\em none}\\\hline \end{tabular} \end{center} @@ -682,7 +681,6 @@ The following boolean variables indicate which \cgal\ components to configure an \texttt{WITH\_CGAL\_Qt3} & ON\\\hline \texttt{WITH\_CGAL\_Qt4} & ON\\\hline \texttt{WITH\_CGAL\_ImageIO} & ON\\\hline - \texttt{WITH\_CGAL\_PDB} & ON\\\hline \end{tabular} } @@ -1130,7 +1128,6 @@ cmake -DWITH_examples=false -- Configuring CGALimageIO. Set WITH_CGALimageIO to FALSE to unselect it. -- Could NOT find ZLIB -- CGAL-ImageIO needs ZLib and OpenGL, cannot be configured. --- Configuring CGALPDB. Set WITH_CGALPDB to FALSE to unselect it. -- Configuring CGALQt. Set WITH_CGALQt to FALSE to unselect it. -- CGAL-Qt3 needs Qt3, cannot be configured. -- Configuring CGALQt4. Set WITH_CGALQt4 to FALSE to unselect it. diff --git a/Installation/include/CGAL/auto_link/PDB.h b/Installation/include/CGAL/auto_link/PDB.h deleted file mode 100644 index 730c29fc408..00000000000 --- a/Installation/include/CGAL/auto_link/PDB.h +++ /dev/null @@ -1,30 +0,0 @@ -// Copyright (c) 2007 GeometryFactory (France). All rights reserved. -// -// This file is part of CGAL (www.cgal.org); 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; version 2.1 of the License. -// See the file LICENSE.LGPL distributed with CGAL. -// -// Licensees holding a valid commercial license may use this file in -// accordance with the commercial license agreement provided with the software. -// -// This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE -// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. -// -// $URL$ -// $Id$ -// -// -// Author(s) : Fernando Cacciola (fernando.cacciola@geometryfactry.com) - -#ifndef CGAL_AUTO_LINK_PDB_H -#define CGAL_AUTO_LINK_PDB_H - -#ifndef CGAL_NO_AUTOLINK_PDB - -#define CGAL_LIB_NAME CGAL_PDB -#include - -#endif // CGAL_NO_AUTOLINK_PDB - -#endif // CGAL_AUTO_LINK_PDB_H diff --git a/Installation/src/CMakeLists.txt b/Installation/src/CMakeLists.txt index cc37f8a5359..db96d1a071b 100644 --- a/Installation/src/CMakeLists.txt +++ b/Installation/src/CMakeLists.txt @@ -18,6 +18,5 @@ else(NOT CGAL_NO_CORE) endif(NOT CGAL_NO_CORE) configure_component( CGALimageIO ImageIO ) -configure_component( CGALPDB PDB ) configure_component( CGALQt Qt3 ) configure_component( CGALQt4 Qt4 ) diff --git a/Installation/test/Installation/CMakeLists.txt b/Installation/test/Installation/CMakeLists.txt index be164cff661..742d4c1b82d 100644 --- a/Installation/test/Installation/CMakeLists.txt +++ b/Installation/test/Installation/CMakeLists.txt @@ -51,10 +51,6 @@ if ( CGAL_FOUND ) create_link_to_program(CGAL_ImageIO) endif() - if ( WITH_CGAL_PDB ) - create_link_to_program(CGAL_PDB) - endif() - if ( WITH_CGAL_Qt3 ) create_link_to_program(CGAL_Qt3) endif() diff --git a/Installation/test/Installation/link_to_CGAL_PDB.cpp b/Installation/test/Installation/link_to_CGAL_PDB.cpp deleted file mode 100644 index 5abba41f1bf..00000000000 --- a/Installation/test/Installation/link_to_CGAL_PDB.cpp +++ /dev/null @@ -1,12 +0,0 @@ -// Use something defined not in headers but in the CGAL library to test that is was indeed properly built and linked to, - -#include - -int main() -{ - std::ifstream in(""); - - volatile CGAL::PDB::PDB pdb(in,false); - - return 0; -} diff --git a/Maintenance/deb/lenny/debian/copyright b/Maintenance/deb/lenny/debian/copyright index b8ba9b383af..c966106e90f 100644 --- a/Maintenance/deb/lenny/debian/copyright +++ b/Maintenance/deb/lenny/debian/copyright @@ -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 ====== diff --git a/Maintenance/deb/lenny/debian/libcgal5.shlibs b/Maintenance/deb/lenny/debian/libcgal5.shlibs index 42b6f2913a9..a02291849ae 100644 --- a/Maintenance/deb/lenny/debian/libcgal5.shlibs +++ b/Maintenance/deb/lenny/debian/libcgal5.shlibs @@ -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 diff --git a/Maintenance/deb/sid/debian/copyright b/Maintenance/deb/sid/debian/copyright index b8ba9b383af..c966106e90f 100644 --- a/Maintenance/deb/sid/debian/copyright +++ b/Maintenance/deb/sid/debian/copyright @@ -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 ====== diff --git a/Maintenance/deb/sid/debian/libcgal5.shlibs b/Maintenance/deb/sid/debian/libcgal5.shlibs index 42b6f2913a9..a02291849ae 100644 --- a/Maintenance/deb/sid/debian/libcgal5.shlibs +++ b/Maintenance/deb/sid/debian/libcgal5.shlibs @@ -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 diff --git a/Maintenance/deb/squeeze/debian/copyright b/Maintenance/deb/squeeze/debian/copyright index b8ba9b383af..c966106e90f 100644 --- a/Maintenance/deb/squeeze/debian/copyright +++ b/Maintenance/deb/squeeze/debian/copyright @@ -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 ====== diff --git a/Maintenance/deb/squeeze/debian/libcgal5.shlibs b/Maintenance/deb/squeeze/debian/libcgal5.shlibs index 42b6f2913a9..a02291849ae 100644 --- a/Maintenance/deb/squeeze/debian/libcgal5.shlibs +++ b/Maintenance/deb/squeeze/debian/libcgal5.shlibs @@ -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 diff --git a/Scripts/developer_scripts/autotest_cgal b/Scripts/developer_scripts/autotest_cgal index ae10d3163d8..6154750426c 100755 --- a/Scripts/developer_scripts/autotest_cgal +++ b/Scripts/developer_scripts/autotest_cgal @@ -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" diff --git a/Scripts/developer_scripts/check_licenses b/Scripts/developer_scripts/check_licenses index 894e8c0b076..c06c4164117 100755 --- a/Scripts/developer_scripts/check_licenses +++ b/Scripts/developer_scripts/check_licenses @@ -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 diff --git a/Scripts/scripts/cgal_create_cmake_script_with_options b/Scripts/scripts/cgal_create_cmake_script_with_options index 3b823835d0b..6bbefedbf76 100755 --- a/Scripts/scripts/cgal_create_cmake_script_with_options +++ b/Scripts/scripts/cgal_create_cmake_script_with_options @@ -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 diff --git a/Skin_surface_3/examples/Skin_surface_3/CMakeLists.txt b/Skin_surface_3/examples/Skin_surface_3/CMakeLists.txt index 5100c612574..141310a70e8 100644 --- a/Skin_surface_3/examples/Skin_surface_3/CMakeLists.txt +++ b/Skin_surface_3/examples/Skin_surface_3/CMakeLists.txt @@ -11,26 +11,33 @@ if ( COMMAND cmake_policy ) cmake_policy( SET CMP0003 NEW ) endif() -find_package(CGAL QUIET COMPONENTS PDB ) -include( ${CGAL_USE_FILE} ) +find_package(CGAL) +find_package(ESBTL) -if(CGAL_PDB_FOUND) + +if (CGAL_FOUND) + include( ${CGAL_USE_FILE} ) 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" ) + 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) diff --git a/Skin_surface_3/examples/Skin_surface_3/include/extract_balls_from_pdb.h b/Skin_surface_3/examples/Skin_surface_3/include/extract_balls_from_pdb.h index ffde3a16e1c..e45a7a519b0 100644 --- a/Skin_surface_3/examples/Skin_surface_3/include/extract_balls_from_pdb.h +++ b/Skin_surface_3/examples/Skin_surface_3/include/extract_balls_from_pdb.h @@ -1,45 +1,39 @@ -// 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 -#include -#include +#include +#include -template -void copy(Range r, OIt out) { - std::copy(r.begin(), r.end(), out); -} -template -void extract_balls_from_pdb(const char *filename, - Traits const &t, - OutputIterator weighted_points) +template +void extract_balls_from_pdb(const char *filename, + std::vector& systems, + OutputIterator weighted_points) { - std::ifstream in(filename); - - if (!in) { - std::cerr << "Error opening input file " << filename << std::endl; - } - - 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), - weighted_points); + typedef ESBTL::Generic_classifier > T_Atom_classifier; + typedef ESBTL::Accept_none_occupancy_policy > Accept_none_occupancy_policy; + typedef ESBTL::Weighted_atom_iterator, + ESBTL::Weight_of_atoms > Weighted_atom_iterator; + + ESBTL::PDB_line_selector sel; + + ESBTL::All_atom_system_builder 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); + } + 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); + } - + #endif // EXTRACT_BALLS_FROM_PDB_H diff --git a/Skin_surface_3/examples/Skin_surface_3/skin_surface_pdb_reader.cpp b/Skin_surface_3/examples/Skin_surface_3/skin_surface_pdb_reader.cpp index b03ed4c1d6e..f37d27641b8 100644 --- a/Skin_surface_3/examples/Skin_surface_3/skin_surface_pdb_reader.cpp +++ b/Skin_surface_3/examples/Skin_surface_3/skin_surface_pdb_reader.cpp @@ -5,7 +5,11 @@ #include #include -typedef CGAL::Exact_predicates_inexact_constructions_kernel K; +#include +#include + +typedef ESBTL::CGAL::EPIC_kernel_with_atom K; +typedef ESBTL::CGAL::Default_system System; typedef CGAL::Skin_surface_traits_3 Traits; typedef CGAL::Skin_surface_3 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 Polyhedron; -#include - #include #include #include "skin_surface_writer.h" +#include "include/extract_balls_from_pdb.h" int main(int argc, char *argv[]) { @@ -27,12 +30,19 @@ int main(int argc, char *argv[]) { } else { filename = "data/1t7i.pdb"; } - + + std::list l; double shrinkfactor = 0.5; - + //Container for molecular system + std::vector systems; + + + // Retrieve input balls: - extract_balls_from_pdb(filename, Traits(), std::back_inserter(l)); + extract_balls_from_pdb(filename,systems,std::back_inserter(l)); + + // Construct skin surface: Skin_surface_3 skin_surface(l.begin(), l.end(), shrinkfactor); diff --git a/Testsuite/test/collect_cgal_testresults_from_cmake b/Testsuite/test/collect_cgal_testresults_from_cmake index abfd9b18d2a..ca3a328e2ac 100755 --- a/Testsuite/test/collect_cgal_testresults_from_cmake +++ b/Testsuite/test/collect_cgal_testresults_from_cmake @@ -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"