From 62b5e11d0840129ffbaa56311e351d83e6a9100d Mon Sep 17 00:00:00 2001 From: mef Date: Thu, 20 Nov 2014 09:05:56 +0000 Subject: (upstream) update 2.3.0 to 2.3.2 (ChangeLog) 2012-08-20 Paolo Tosco * src/formats/mol2format.cpp: added a check for N.4 nitrogens (fixes PR#3557898) 2012-06-09 Paolo Tosco * src/kekulize.cpp: reverted the r4862 patch to kekulize.cpp; the incorrect aromaticity perception of oxonium salts concerned only the MOL2 format, so the fix was applied to mol2format.cpp instead * src/formats/mol2format.cpp: added a check to improve downstream aromaticity perception on charged molecules containing oxygen 2012-06-07 Paolo Tosco * include/openbabel/atom.h: added protos for CountFreeSulfurs() and IsThiocarboxylSulfur() functions which are equivalent to CountFreeOxygens() and IsCarboxylOxygen() and address (di)thiocarboxyl groups * src/atom.cpp: added the CountFreeSulfurs() and IsThiocarboxylSulfur() functions * src/forcefields/forcefieldmmff94.cpp: added some additional checks to make MMFF94 atom type assignment more robust * src/formats/mol2format.cpp: added some checks to improve downstream aromaticity perception on charged molecules containing nitrogen, oxygen and sulfur * src/kekulize.cpp: added a check to fix incorrect perception of aromatic oxonium and thionium cations (NEWS) Open Babel 2.3.1 (2011-10-14) This release represents a major bug-fix release and is a stable upgrade, strongly recommended for all users of Open Babel. Many bugs and enhancements have been added since the 2.3.0 release. Citation: Please consider citing this work if you publish work which used Open Babel: Noel M. O'Boyle , Michael Banck , Craig A. James , Chris Morley , Tim Vandermeersch and Geoffrey R. Hutchison. "Open Babel: An open chemical toolbox." Journal of Cheminformatics 2011, 3:33. http://dx.doi.org/10.1186/1758-2946-3-33 --- biology/openbabel/Makefile | 5 ++-- biology/openbabel/PLIST | 29 ++++++++++++++++------ biology/openbabel/distinfo | 13 +++++----- biology/openbabel/patches/patch-doc_CMakeLists.txt | 8 +++--- .../patches/patch-include_openbabel_shared__ptr.h | 19 ++++++++------ 5 files changed, 46 insertions(+), 28 deletions(-) (limited to 'biology') diff --git a/biology/openbabel/Makefile b/biology/openbabel/Makefile index 9d902bbc9a6..76f72f0b88a 100644 --- a/biology/openbabel/Makefile +++ b/biology/openbabel/Makefile @@ -1,8 +1,7 @@ -# $NetBSD: Makefile,v 1.22 2014/05/05 00:47:39 ryoon Exp $ +# $NetBSD: Makefile,v 1.23 2014/11/20 09:05:56 mef Exp $ # -DISTNAME= openbabel-2.3.0 -PKGREVISION= 17 +DISTNAME= openbabel-2.3.2 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=openbabel/} diff --git a/biology/openbabel/PLIST b/biology/openbabel/PLIST index 176ea911214..00c7342b70e 100644 --- a/biology/openbabel/PLIST +++ b/biology/openbabel/PLIST @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.1.1.1 2011/10/05 22:15:49 ryoon Exp $ +@comment $NetBSD: PLIST,v 1.2 2014/11/20 09:05:56 mef Exp $ ${PLIST.wx-gui}bin/OBGUI bin/babel bin/obabel @@ -79,6 +79,7 @@ include/openbabel-2.0/openbabel/rotamer.h include/openbabel-2.0/openbabel/rotor.h include/openbabel-2.0/openbabel/shared_ptr.h include/openbabel-2.0/openbabel/spectrophore.h +include/openbabel-2.0/openbabel/stereo/bindings.h include/openbabel-2.0/openbabel/stereo/cistrans.h include/openbabel-2.0/openbabel/stereo/squareplanar.h include/openbabel-2.0/openbabel/stereo/stereo.h @@ -89,21 +90,28 @@ include/openbabel-2.0/openbabel/text.h include/openbabel-2.0/openbabel/tokenst.h include/openbabel-2.0/openbabel/typer.h include/openbabel-2.0/openbabel/xml.h +lib/cmake/openbabel2/OpenBabel2Config.cmake +lib/cmake/openbabel2/OpenBabel2ConfigVersion.cmake +lib/cmake/openbabel2/OpenBabel2_EXPORTS-relwithdebinfo.cmake +lib/cmake/openbabel2/OpenBabel2_EXPORTS.cmake lib/libinchi.so lib/libinchi.so.0 -lib/libinchi.so.0.3.1 +lib/libinchi.so.0.4.1 lib/libopenbabel.so lib/libopenbabel.so.4 -lib/libopenbabel.so.4.0.0 +lib/libopenbabel.so.4.0.2 lib/openbabel/${PKGVERSION}/APIInterface.so lib/openbabel/${PKGVERSION}/CSRformat.so lib/openbabel/${PKGVERSION}/MCDLformat.so lib/openbabel/${PKGVERSION}/MNAformat.so lib/openbabel/${PKGVERSION}/PQSformat.so +lib/openbabel/${PKGVERSION}/abinitformat.so +lib/openbabel/${PKGVERSION}/acesformat.so lib/openbabel/${PKGVERSION}/acrformat.so lib/openbabel/${PKGVERSION}/adfformat.so lib/openbabel/${PKGVERSION}/alchemyformat.so lib/openbabel/${PKGVERSION}/amberformat.so +lib/openbabel/${PKGVERSION}/asciiformat.so lib/openbabel/${PKGVERSION}/balstformat.so lib/openbabel/${PKGVERSION}/bgfformat.so lib/openbabel/${PKGVERSION}/boxformat.so @@ -123,6 +131,7 @@ lib/openbabel/${PKGVERSION}/cmlformat.so lib/openbabel/${PKGVERSION}/cmlreactformat.so lib/openbabel/${PKGVERSION}/copyformat.so lib/openbabel/${PKGVERSION}/crkformat.so +lib/openbabel/${PKGVERSION}/crystal09format.so lib/openbabel/${PKGVERSION}/cssrformat.so lib/openbabel/${PKGVERSION}/dlpolyformat.so lib/openbabel/${PKGVERSION}/dmolformat.so @@ -133,6 +142,7 @@ lib/openbabel/${PKGVERSION}/featformat.so lib/openbabel/${PKGVERSION}/fhformat.so lib/openbabel/${PKGVERSION}/fhiaimsformat.so lib/openbabel/${PKGVERSION}/fingerprintformat.so +lib/openbabel/${PKGVERSION}/fpsformat.so lib/openbabel/${PKGVERSION}/freefracformat.so lib/openbabel/${PKGVERSION}/gamessformat.so lib/openbabel/${PKGVERSION}/gamessukformat.so @@ -140,11 +150,13 @@ lib/openbabel/${PKGVERSION}/gausscubeformat.so lib/openbabel/${PKGVERSION}/gaussformat.so lib/openbabel/${PKGVERSION}/gausszmatformat.so lib/openbabel/${PKGVERSION}/ghemicalformat.so +lib/openbabel/${PKGVERSION}/groformat.so lib/openbabel/${PKGVERSION}/gromos96format.so lib/openbabel/${PKGVERSION}/gulpformat.so lib/openbabel/${PKGVERSION}/hinformat.so lib/openbabel/${PKGVERSION}/inchiformat.so lib/openbabel/${PKGVERSION}/jaguarformat.so +lib/openbabel/${PKGVERSION}/lmpdatformat.so lib/openbabel/${PKGVERSION}/mdlformat.so lib/openbabel/${PKGVERSION}/mmcifformat.so lib/openbabel/${PKGVERSION}/mmodformat.so @@ -170,6 +182,7 @@ lib/openbabel/${PKGVERSION}/plugin_fingerprints.so lib/openbabel/${PKGVERSION}/plugin_forcefields.so lib/openbabel/${PKGVERSION}/plugin_ops.so lib/openbabel/${PKGVERSION}/pngformat.so +lib/openbabel/${PKGVERSION}/posformat.so lib/openbabel/${PKGVERSION}/povrayformat.so lib/openbabel/${PKGVERSION}/pqrformat.so lib/openbabel/${PKGVERSION}/pubchem.so @@ -191,32 +204,33 @@ lib/openbabel/${PKGVERSION}/vaspformat.so lib/openbabel/${PKGVERSION}/viewmolformat.so lib/openbabel/${PKGVERSION}/xedformat.so lib/openbabel/${PKGVERSION}/xmlformat.so +lib/openbabel/${PKGVERSION}/xsfformat.so lib/openbabel/${PKGVERSION}/xyzformat.so lib/openbabel/${PKGVERSION}/yasaraformat.so lib/openbabel/${PKGVERSION}/zindoformat.so -lib/openbabel/OpenBabel2Config.cmake -lib/openbabel/OpenBabel2ConfigVersion.cmake -lib/openbabel/OpenBabel2_EXPORTS-relwithdebinfo.cmake -lib/openbabel/OpenBabel2_EXPORTS.cmake lib/pkgconfig/openbabel-2.0.pc man/man1/babel.1 +man/man1/obabel.1 man/man1/obchiral.1 man/man1/obconformer.1 man/man1/obenergy.1 man/man1/obfit.1 man/man1/obgen.1 man/man1/obgrep.1 +man/man1/obgui.1 man/man1/obminimize.1 man/man1/obprobe.1 man/man1/obprop.1 man/man1/obrotamer.1 man/man1/obrotate.1 +man/man1/obspectrophore.1 man/man1/roundtrip.1 share/openbabel/${PKGVERSION}/MACCS.txt share/openbabel/${PKGVERSION}/SMARTS_InteLigand.txt share/openbabel/${PKGVERSION}/UFF.prm share/openbabel/${PKGVERSION}/aromatic.txt share/openbabel/${PKGVERSION}/atomtyp.txt +share/openbabel/${PKGVERSION}/babel_povray3.inc share/openbabel/${PKGVERSION}/bondtyp.txt share/openbabel/${PKGVERSION}/element.txt share/openbabel/${PKGVERSION}/fragments.txt @@ -251,6 +265,7 @@ share/openbabel/${PKGVERSION}/qeq.txt share/openbabel/${PKGVERSION}/resdata.txt share/openbabel/${PKGVERSION}/ringtyp.txt share/openbabel/${PKGVERSION}/space-groups.txt +share/openbabel/${PKGVERSION}/splash.png share/openbabel/${PKGVERSION}/superatom.txt share/openbabel/${PKGVERSION}/svgformat.script share/openbabel/${PKGVERSION}/torlib.txt diff --git a/biology/openbabel/distinfo b/biology/openbabel/distinfo index c7c752f3e69..89eaf37460a 100644 --- a/biology/openbabel/distinfo +++ b/biology/openbabel/distinfo @@ -1,9 +1,8 @@ -$NetBSD: distinfo,v 1.4 2013/10/09 11:39:28 obache Exp $ +$NetBSD: distinfo,v 1.5 2014/11/20 09:05:56 mef Exp $ -SHA1 (openbabel-2.3.0.tar.gz) = 408a4bddb7f052fd89c57ea51b4204b721856b16 -RMD160 (openbabel-2.3.0.tar.gz) = 96dafa3c2aca544f79e08b5617ab0da845c28a16 -Size (openbabel-2.3.0.tar.gz) = 14321281 bytes -SHA1 (patch-doc_CMakeLists.txt) = 9fa0e651d35a0e3ea88603b8a428938b83f103cd +SHA1 (openbabel-2.3.2.tar.gz) = b8831a308617d1c78a790479523e43524f07d50d +RMD160 (openbabel-2.3.2.tar.gz) = dc9aa026a81b987b08c60709a624a192418ee7fb +Size (openbabel-2.3.2.tar.gz) = 20509105 bytes +SHA1 (patch-doc_CMakeLists.txt) = ce39c53c4edfec2f557e785f750e09a62a209d05 SHA1 (patch-include_openbabel_obmolecformat.h) = e12a42b67106899d5285651f27e4830e0cc42fe2 -SHA1 (patch-include_openbabel_shared__ptr.h) = 6678f49249eacacb61ddc14a4d9e6af1c479c67b -SHA1 (patch-src_ops_unique.cpp) = 4ae8b0bbd3c3880bb971e59bcd90219762ca895c +SHA1 (patch-include_openbabel_shared__ptr.h) = 92a16f7bcdd10cf44cf6c9302d80670563074c2c diff --git a/biology/openbabel/patches/patch-doc_CMakeLists.txt b/biology/openbabel/patches/patch-doc_CMakeLists.txt index ecbf38197a2..39dae5d5c36 100644 --- a/biology/openbabel/patches/patch-doc_CMakeLists.txt +++ b/biology/openbabel/patches/patch-doc_CMakeLists.txt @@ -1,13 +1,13 @@ -$NetBSD: patch-doc_CMakeLists.txt,v 1.3 2013/10/09 11:39:28 obache Exp $ +$NetBSD: patch-doc_CMakeLists.txt,v 1.4 2014/11/20 09:05:56 mef Exp $ Fix man path. ---- doc/CMakeLists.txt.orig 2010-07-12 13:05:06.000000000 +0000 -+++ doc/CMakeLists.txt +--- doc/CMakeLists.txt.orig 2012-10-04 04:08:55.000000000 +0900 ++++ doc/CMakeLists.txt 2014-11-20 17:53:33.000000000 +0900 @@ -1,5 +1,5 @@ file(GLOB man_1 *.1) -install(FILES ${man_1} DESTINATION share/man/man1) +install(FILES ${man_1} DESTINATION ${CMAKE_INSTALL_MANDIR}/man1) + install(FILES splash.png DESTINATION share/openbabel/${BABEL_VERSION}) OPTION(BUILD_DOCS "Build Open Babel documentation" OFF) - IF(BUILD_DOCS) diff --git a/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h b/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h index 459f34bda07..6d9ed3145a8 100644 --- a/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h +++ b/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h @@ -1,8 +1,8 @@ -$NetBSD: patch-include_openbabel_shared__ptr.h,v 1.1 2013/05/06 14:22:43 joerg Exp $ +$NetBSD: patch-include_openbabel_shared__ptr.h,v 1.2 2014/11/20 09:05:56 mef Exp $ ---- include/openbabel/shared_ptr.h.orig 2013-05-05 20:23:37.000000000 +0000 -+++ include/openbabel/shared_ptr.h -@@ -21,10 +21,14 @@ GNU General Public License for more deta +--- include/openbabel/shared_ptr.h.orig 2011-10-13 05:24:02.000000000 +0900 ++++ include/openbabel/shared_ptr.h 2014-11-20 17:51:30.000000000 +0900 +@@ -21,10 +21,19 @@ GNU General Public License for more deta #define shared_ptr boost::shared_ptr #else #include @@ -11,10 +11,15 @@ $NetBSD: patch-include_openbabel_shared__ptr.h,v 1.1 2013/05/06 14:22:43 joerg E + #if defined(_LIBCPP_VERSION) || __cplusplus >= 201103L + using std::shared_ptr; + #else -+ #if __GNUC__ == 4 //&& __GNUC_MINOR__ < 3 removed at the suggestion of Konstantin Tokarev -+ #include ++ #if defined(_LIBCPP_VERSION) || __cplusplus >= 201103L ++ using std::shared_ptr; ++ #else ++ #if __GNUC__ == 4 //&& __GNUC_MINOR__ < 3 removed at the suggestion of Konstantin Tokarev ++ #include ++ #endif ++ using std::tr1::shared_ptr; ++ + #endif -+ using std::tr1::shared_ptr; #endif - using std::tr1::shared_ptr; #endif -- cgit v1.2.3