diff --git a/misc/openbabel/Makefile b/misc/openbabel/Makefile index 932e4d4fe65..83411b21b34 100644 --- a/misc/openbabel/Makefile +++ b/misc/openbabel/Makefile @@ -1,15 +1,17 @@ COMMENT= chemistry file translation program -V= 3.1.1 -REVISION= 7 -DISTNAME= openbabel-${V} +V= 3.2.0 +DIST_TUPLE= github openbabel openbabel openbabel-${V:S/./-/g} . \ + github schrodinger maeparser v1.3.3 maeparser \ + github schrodinger coordgenlibs d20e735d96480385b2e257522288004038a08cc9 coordgen +PKGNAME= openbabel-${V} CATEGORIES= misc -SHARED_LIBS += coordgen 0.0 \ - inchi 0.0 \ - maeparser 0.0 \ - openbabel 6.1 +SHARED_LIBS= coordgen 1.0 \ + inchi 1.0 \ + maeparser 1.0 \ + openbabel 7.0 HOMEPAGE= https://openbabel.org @@ -18,11 +20,8 @@ MAINTAINER= Bjorn Ketelaars # GPLv2 PERMIT_PACKAGE= Yes -WANTLIB+= ${COMPILER_LIBCXX} boost_iostreams-mt boost_regex-mt -WANTLIB+= c cairo m xml2 z boost_random-mt - -SITES= https://github.com/openbabel/openbabel/releases/download/openbabel-${V:S/./-/g}/ -EXTRACT_SUFX= -source.tar.bz2 +WANTLIB= ${COMPILER_LIBCXX} boost_iostreams-mt boost_regex-mt \ + c cairo m xml2 z boost_random-mt COMPILER= base-clang ports-gcc @@ -40,13 +39,8 @@ BUILD_DEPENDS= math/eigen3 \ CONFIGURE_ARGS= -DBUILD_GUI=OFF -MODCMAKE_POLICY_VERSION_OVERRIDE = Yes - SEPARATE_BUILD= No SUBST_VARS= V - -MODCMAKE_POLICY_VERSION_OVERRIDE = Yes - .include diff --git a/misc/openbabel/distinfo b/misc/openbabel/distinfo index 50d4216b590..6000b65dc55 100644 --- a/misc/openbabel/distinfo +++ b/misc/openbabel/distinfo @@ -1,2 +1,6 @@ -SHA256 (openbabel-3.1.1-source.tar.bz2) = puyDgdWeoypLJByLH715mstSvpSrZM29clBvtOInDmg= -SIZE (openbabel-3.1.1-source.tar.bz2) = 27743669 +SHA256 (openbabel-openbabel-openbabel-3-2-0.tar.gz) = mq358Bs9D/FdSfzSjX12uSMhjXC/EPmepMxGZgf0x+I= +SHA256 (schrodinger-coordgenlibs-d20e735d96480385b2e257522288004038a08cc9.tar.gz) = 6LT1srPdnSz3xr1uV+2ry1Nv8F1/i4lFYOSBd7AYKMk= +SHA256 (schrodinger-maeparser-v1.3.3.tar.gz) = eOdXGneepJUudS7O9Xxi+yZGOUfinvf0sxsRmI2Iygc= +SIZE (openbabel-openbabel-openbabel-3-2-0.tar.gz) = 37815471 +SIZE (schrodinger-coordgenlibs-d20e735d96480385b2e257522288004038a08cc9.tar.gz) = 167157 +SIZE (schrodinger-maeparser-v1.3.3.tar.gz) = 39896 diff --git a/misc/openbabel/patches/patch-CMakeLists_txt b/misc/openbabel/patches/patch-CMakeLists_txt index f9e415be26d..7ddf727d6a4 100644 --- a/misc/openbabel/patches/patch-CMakeLists_txt +++ b/misc/openbabel/patches/patch-CMakeLists_txt @@ -1,25 +1,60 @@ -Revise for 3.1.1 release. Taken from -https://github.com/openbabel/openbabel/commit/650b1f829ac47cc84877a330366ec9485da3ec99 - Index: CMakeLists.txt --- CMakeLists.txt.orig +++ CMakeLists.txt -@@ -10,9 +10,6 @@ set (CMAKE_CXX_STANDARD 11) +@@ -505,14 +505,14 @@ if(WITH_MAEPARSER) - if(COMMAND cmake_policy) - cmake_policy(SET CMP0003 NEW) -- if(POLICY CMP0042) -- cmake_policy(SET CMP0042 OLD) -- endif() - endif() + set(MAEPARSER_VERSION "v1.3.3" CACHE STRING "Maeparser fallback version to download") + +- set(MAEPARSER_DIR "${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}") ++ set(MAEPARSER_DIR "${openbabel_SOURCE_DIR}/maeparser") + + option(MAEPARSER_BUILD_SHARED_LIBS "Build maeparser as a shared library" ${BUILD_SHARED}) + + # Do not build the test, as it will be put into the bin dir, where it won't be found by the test runner. + set(MAEPARSER_BUILD_TESTS OFF CACHE BOOL "Disable Maeparser tests") + +- if(EXISTS "${MAEPARSER_DIR}/maeparser/CMakeLists.txt") ++ if(EXISTS "${MAEPARSER_DIR}/CMakeLists.txt") + + message(STATUS "Building existing MaeParser '${MAEPARSER_VERSION}' source at ${MAEPARSER_DIR}.") + +@@ -535,9 +535,9 @@ if(WITH_MAEPARSER) + + endif() + +- add_subdirectory("${MAEPARSER_DIR}/maeparser") ++ add_subdirectory("${MAEPARSER_DIR}") + +- set(maeparser_INCLUDE_DIRS "${MAEPARSER_DIR}") ++ set(maeparser_INCLUDE_DIRS "${openbabel_SOURCE_DIR}") + set(maeparser_LIBRARIES maeparser) + + message(STATUS "Maestro formats will be supported. Using MaeParser '${MAEPARSER_VERSION}' at ${MAEPARSER_DIR}") +@@ -565,13 +565,13 @@ if(WITH_COORDGEN) + # v3.0.2-10-gd20e735 + set(COORDGEN_VERSION "d20e735d96480385b2e257522288004038a08cc9" CACHE STRING "Coordgen fallback version to download") + +- set(COORDGEN_DIR "${openbabel_SOURCE_DIR}/external/coordgen-${COORDGEN_VERSION}") ++ set(COORDGEN_DIR "${openbabel_SOURCE_DIR}/coordgen") + + # These won't work, since openbabel relocates them to the "bin" dir + set(COORDGEN_BUILD_TESTS OFF CACHE BOOL "Disable building Coordgen tests") + set(COORDGEN_BUILD_EXAMPLE OFF CACHE BOOL "Disable building Coordgen example") + +- if(EXISTS "${COORDGEN_DIR}/coordgen/CMakeLists.txt") ++ if(EXISTS "${COORDGEN_DIR}/CMakeLists.txt") + + message(STATUS "Building existing Coordgen '${COORDGEN_VERSION}' source at ${COORDGEN_DIR}.") + +@@ -594,9 +594,9 @@ if(WITH_COORDGEN) + + endif() + +- add_subdirectory("${COORDGEN_DIR}/coordgen") ++ add_subdirectory("${COORDGEN_DIR}") + +- set(coordgen_INCLUDE_DIRS "${COORDGEN_DIR}") ++ set(coordgen_INCLUDE_DIRS "${openbabel_SOURCE_DIR}") + set(coordgen_LIBRARIES coordgen) - include (CheckCXXCompilerFlag) -@@ -24,7 +21,7 @@ include (CheckCXXCompilerFlag) - # had too many 1.100.1 releases. :-) - set(BABEL_MAJ_VER 3) - set(BABEL_MIN_VER 1) --set(BABEL_PATCH_VER 0) -+set(BABEL_PATCH_VER 1) - # This should be phased out in preference for just using the target name - set(BABEL_LIBRARY openbabel) diff --git a/misc/openbabel/patches/patch-include_openbabel_inchiformat_h b/misc/openbabel/patches/patch-include_openbabel_inchiformat_h deleted file mode 100644 index f4ae29353f2..00000000000 --- a/misc/openbabel/patches/patch-include_openbabel_inchiformat_h +++ /dev/null @@ -1,14 +0,0 @@ -Remove std::binary_function, which is removed in C++17. Taken from -https://github.com/openbabel/openbabel/pull/2464 - -Index: include/openbabel/inchiformat.h ---- include/openbabel/inchiformat.h.orig -+++ include/openbabel/inchiformat.h -@@ -131,7 +131,6 @@ class InChIFormat : public OBMoleculeFormat (public) - // and "CH4" is less than "C2H6" - // and "CH4" is less than "ClH" (hydrogen chloride) - struct InchiLess -- : public std::binary_function - { - bool operator()(const std::string& s1, const std::string& s2) const - { diff --git a/misc/openbabel/patches/patch-include_openbabel_plugin_h b/misc/openbabel/patches/patch-include_openbabel_plugin_h deleted file mode 100644 index 78ce224a4a9..00000000000 --- a/misc/openbabel/patches/patch-include_openbabel_plugin_h +++ /dev/null @@ -1,15 +0,0 @@ -Remove std::binary_function, which is removed in C++17. Taken from -https://github.com/openbabel/openbabel/pull/2464 - -Index: include/openbabel/plugin.h ---- include/openbabel/plugin.h.orig -+++ include/openbabel/plugin.h -@@ -38,7 +38,7 @@ namespace OpenBabel - ///@{ - - /// @brief Case insensitive string comparison for PluginMapType key. --struct OBERROR CharPtrLess : public std::binary_function -+struct OBERROR CharPtrLess - { - bool operator()(const char* p1,const char* p2) const - { return strcasecmp(p1,p2)<0; } diff --git a/misc/openbabel/patches/patch-scripts_openbabel-R_i b/misc/openbabel/patches/patch-scripts_openbabel-R_i deleted file mode 100644 index c92c7402493..00000000000 --- a/misc/openbabel/patches/patch-scripts_openbabel-R_i +++ /dev/null @@ -1,20 +0,0 @@ -Remove std::binary_function, which is removed in C++17. Taken from -https://github.com/openbabel/openbabel/pull/2464 - -Index: scripts/openbabel-R.i ---- scripts/openbabel-R.i.orig -+++ scripts/openbabel-R.i -@@ -290,13 +290,6 @@ CAST_GENERICDATA_TO(VirtualBond) - - %include - %include -- --// To avoid warning in plugin.h about "Nothing known about std::binary_function" --namespace std { -- template -- class binary_function {}; --} --%template(dummy) std::binary_function ; - %include - - // To avoid warning in oberror.h about "Nothing known about std::stringbuf" diff --git a/misc/openbabel/patches/patch-scripts_openbabel-csharp_i b/misc/openbabel/patches/patch-scripts_openbabel-csharp_i deleted file mode 100644 index 35f54a3dba9..00000000000 --- a/misc/openbabel/patches/patch-scripts_openbabel-csharp_i +++ /dev/null @@ -1,20 +0,0 @@ -Remove std::binary_function, which is removed in C++17. Taken from -https://github.com/openbabel/openbabel/pull/2464 - -Index: scripts/openbabel-csharp.i ---- scripts/openbabel-csharp.i.orig -+++ scripts/openbabel-csharp.i -@@ -830,13 +830,6 @@ CAST_GENERICDATA_TO(VirtualBond); - - %include - %include -- --// To avoid warning in plugin.h about "Nothing known about std::binary_function" --namespace std { -- template -- class binary_function {}; --} --%template(dummy) std::binary_function ; - %include - - // To avoid warning in oberror.h about "Nothing known about std::stringbuf" diff --git a/misc/openbabel/patches/patch-scripts_openbabel-java_i b/misc/openbabel/patches/patch-scripts_openbabel-java_i deleted file mode 100644 index 4c88fdfb6a4..00000000000 --- a/misc/openbabel/patches/patch-scripts_openbabel-java_i +++ /dev/null @@ -1,20 +0,0 @@ -Remove std::binary_function, which is removed in C++17. Taken from -https://github.com/openbabel/openbabel/pull/2464 - -Index: scripts/openbabel-java.i ---- scripts/openbabel-java.i.orig -+++ scripts/openbabel-java.i -@@ -246,13 +246,6 @@ CAST_GENERICDATA_TO(VirtualBond) - - %include - %include -- --// To avoid warning in plugin.h about "Nothing known about std::binary_function" --namespace std { -- template -- class binary_function {}; --} --%template(dummy) std::binary_function ; - %include - - // To avoid warning in oberror.h about "Nothing known about std::stringbuf" diff --git a/misc/openbabel/patches/patch-scripts_openbabel-perl_i b/misc/openbabel/patches/patch-scripts_openbabel-perl_i deleted file mode 100644 index 5699a7c1a67..00000000000 --- a/misc/openbabel/patches/patch-scripts_openbabel-perl_i +++ /dev/null @@ -1,20 +0,0 @@ -Remove std::binary_function, which is removed in C++17. Taken from -https://github.com/openbabel/openbabel/pull/2464 - -Index: scripts/openbabel-perl.i ---- scripts/openbabel-perl.i.orig -+++ scripts/openbabel-perl.i -@@ -191,13 +191,6 @@ CAST_GENERICDATA_TO(VirtualBond) - - %import - %import -- --// To avoid warning in oberror.h about "Nothing known about std::binary_function" --namespace std { -- template -- class binary_function {}; --} --%template(Dummy) std::binary_function ; - %include - - // To avoid warning in oberror.h about "Nothing known about std::stringbuf" diff --git a/misc/openbabel/patches/patch-scripts_openbabel-php_i b/misc/openbabel/patches/patch-scripts_openbabel-php_i deleted file mode 100644 index 5ccdda13a26..00000000000 --- a/misc/openbabel/patches/patch-scripts_openbabel-php_i +++ /dev/null @@ -1,20 +0,0 @@ -Remove std::binary_function, which is removed in C++17. Taken from -https://github.com/openbabel/openbabel/pull/2464 - -Index: scripts/openbabel-php.i ---- scripts/openbabel-php.i.orig -+++ scripts/openbabel-php.i -@@ -223,13 +223,6 @@ CAST_GENERICDATA_TO(VirtualBond) - - %include - %include -- --// To avoid warning in plugin.h about "Nothing known about std::binary_function" --namespace std { -- template -- class binary_function {}; --} --%template(dummy) std::binary_function ; - %include - - // To avoid warning in oberror.h about "Nothing known about std::stringbuf" diff --git a/misc/openbabel/patches/patch-scripts_openbabel-python_i b/misc/openbabel/patches/patch-scripts_openbabel-python_i deleted file mode 100644 index f73b0009920..00000000000 --- a/misc/openbabel/patches/patch-scripts_openbabel-python_i +++ /dev/null @@ -1,20 +0,0 @@ -Remove std::binary_function, which is removed in C++17. Taken from -https://github.com/openbabel/openbabel/pull/2464 - -Index: scripts/openbabel-python.i ---- scripts/openbabel-python.i.orig -+++ scripts/openbabel-python.i -@@ -266,13 +266,6 @@ CAST_GENERICDATA_TO(SquarePlanarStereo) - - %include - %include -- --// To avoid warning in plugin.h about "Nothing known about std::binary_function" --namespace std { -- template -- class binary_function {}; --} --%template(dummy) std::binary_function ; - %include - - // To avoid warning in oberror.h about "Nothing known about std::stringbuf" diff --git a/misc/openbabel/patches/patch-scripts_openbabel-ruby_i b/misc/openbabel/patches/patch-scripts_openbabel-ruby_i deleted file mode 100644 index 1a994c05680..00000000000 --- a/misc/openbabel/patches/patch-scripts_openbabel-ruby_i +++ /dev/null @@ -1,20 +0,0 @@ -Remove std::binary_function, which is removed in C++17. Taken from -https://github.com/openbabel/openbabel/pull/2464 - -Index: scripts/openbabel-ruby.i ---- scripts/openbabel-ruby.i.orig -+++ scripts/openbabel-ruby.i -@@ -212,13 +212,6 @@ CAST_GENERICDATA_TO(SquarePlanarStereo) - - %import - %import -- --// To avoid warning in oberror.h about "Nothing known about std::binary_function" --namespace std { -- template -- class binary_function {}; --} --%template(Dummy) std::binary_function ; - %include - - // To avoid warning in oberror.h about "Nothing known about std::stringbuf" diff --git a/misc/openbabel/patches/patch-src_formats_libinchi_ichicano_c b/misc/openbabel/patches/patch-src_formats_libinchi_ichicano_c new file mode 100644 index 00000000000..6ddef8921aa --- /dev/null +++ b/misc/openbabel/patches/patch-src_formats_libinchi_ichicano_c @@ -0,0 +1,11 @@ +Index: src/formats/libinchi/ichicano.c +--- src/formats/libinchi/ichicano.c.orig ++++ src/formats/libinchi/ichicano.c +@@ -43,7 +43,6 @@ + #include + #include + #include +-#include + #include + + #include "mode.h" diff --git a/misc/openbabel/patches/patch-src_ops_sort_cpp b/misc/openbabel/patches/patch-src_ops_sort_cpp deleted file mode 100644 index 2de3f9e997b..00000000000 --- a/misc/openbabel/patches/patch-src_ops_sort_cpp +++ /dev/null @@ -1,15 +0,0 @@ -Remove std::binary_function, which is removed in C++17. Taken from -https://github.com/openbabel/openbabel/pull/2464 - -Index: src/ops/sort.cpp ---- src/ops/sort.cpp.orig -+++ src/ops/sort.cpp -@@ -29,7 +29,7 @@ namespace OpenBabel - { - - template --struct Order : public std::binary_function, std::pair, bool> -+struct Order - { - Order(OBDescriptor* pDesc, bool rev) : _pDesc(pDesc), _rev(rev){} - bool operator()(std::pair p1, std::pair p2) const diff --git a/misc/openbabel/pkg/PLIST b/misc/openbabel/pkg/PLIST index 4bf64c2796e..3545894bf39 100644 --- a/misc/openbabel/pkg/PLIST +++ b/misc/openbabel/pkg/PLIST @@ -99,6 +99,7 @@ include/openbabel3/openbabel/kekulize.h include/openbabel3/openbabel/kinetics.h include/openbabel3/openbabel/lineend.h include/openbabel3/openbabel/locale.h +include/openbabel3/openbabel/macrocycle.h include/openbabel3/openbabel/math/ include/openbabel3/openbabel/math/align.h include/openbabel3/openbabel/math/erf.h @@ -130,7 +131,6 @@ include/openbabel3/openbabel/residue.h include/openbabel3/openbabel/ring.h include/openbabel3/openbabel/rotamer.h include/openbabel3/openbabel/rotor.h -include/openbabel3/openbabel/shared_ptr.h include/openbabel3/openbabel/spectrophore.h include/openbabel3/openbabel/stereo/ include/openbabel3/openbabel/stereo/bindings.h @@ -145,8 +145,10 @@ include/openbabel3/openbabel/text.h include/openbabel3/openbabel/tokenst.h include/openbabel3/openbabel/typer.h include/openbabel3/openbabel/xml.h -lib/cmake/coordgen-config${MODCMAKE_BUILD_SUFFIX} -lib/cmake/coordgen-config.cmake +lib/cmake/coordgen/ +lib/cmake/coordgen/coordgen-config${MODCMAKE_BUILD_SUFFIX} +lib/cmake/coordgen/coordgen-config-version.cmake +lib/cmake/coordgen/coordgen-config.cmake lib/cmake/maeparser-config${MODCMAKE_BUILD_SUFFIX} lib/cmake/maeparser-config.cmake lib/cmake/openbabel3/ @@ -186,6 +188,7 @@ lib/openbabel/${V}/ @so lib/openbabel/${V}/chemdoodlejsonformat.so @so lib/openbabel/${V}/chemdrawcdx.so @so lib/openbabel/${V}/chemdrawct.so +@so lib/openbabel/${V}/chemicaljsonformat.so @so lib/openbabel/${V}/chemkinformat.so @so lib/openbabel/${V}/chemtoolformat.so @so lib/openbabel/${V}/cifformat.so @@ -222,6 +225,7 @@ lib/openbabel/${V}/ @so lib/openbabel/${V}/hinformat.so @so lib/openbabel/${V}/inchiformat.so @so lib/openbabel/${V}/jaguarformat.so +@so lib/openbabel/${V}/ketformat.so @so lib/openbabel/${V}/lmpdatformat.so @so lib/openbabel/${V}/lpmdformat.so @so lib/openbabel/${V}/maeformat.so