[pkgsrc/trunk]: pkgsrc/biology/openbabel (upstream) update 2.3.0 to 2.3.2

To: pkgsrc-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/biology/openbabel (upstream) update 2.3.0 to 2.3.2
From: mef <mef%pkgsrc.org@localhost>
Date: Thu, 14 Oct 2021 16:46:21 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/62f465856b97
branches:  trunk
changeset: 641863:62f465856b97
user:      mef <mef%pkgsrc.org@localhost>
date:      Thu Nov 20 09:05:56 2014 +0000

description:
(upstream) update 2.3.0 to 2.3.2

(ChangeLog)
2012-08-20  Paolo Tosco <paolo.tosco%unito.it@localhost>
        * src/formats/mol2format.cpp: added a check for N.4 nitrogens
        (fixes PR#3557898)

2012-06-09  Paolo Tosco <paolo.tosco%unito.it@localhost>
        * 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 <paolo.tosco%unito.it@localhost>
        * 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

diffstat:

 biology/openbabel/Makefile                                      |   5 +-
 biology/openbabel/PLIST                                         |  29 +++++++--
 biology/openbabel/distinfo                                      |  13 ++--
 biology/openbabel/patches/patch-doc_CMakeLists.txt              |   8 +-
 biology/openbabel/patches/patch-include_openbabel_shared__ptr.h |  19 ++++--
 5 files changed, 46 insertions(+), 28 deletions(-)

diffs (221 lines):

diff -r 7553a2ea252a -r 62f465856b97 biology/openbabel/Makefile
--- a/biology/openbabel/Makefile        Thu Nov 20 08:39:09 2014 +0000
+++ b/biology/openbabel/Makefile        Thu Nov 20 09:05:56 2014 +0000
@@ -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 -r 7553a2ea252a -r 62f465856b97 biology/openbabel/PLIST
--- a/biology/openbabel/PLIST   Thu Nov 20 08:39:09 2014 +0000
+++ b/biology/openbabel/PLIST   Thu Nov 20 09:05:56 2014 +0000
@@ -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 $
 ${PLIST.wx-gui}bin/OBGUI
 bin/babel
 bin/obabel
@@ -79,6 +79,7 @@
 include/openbabel-2.0/openbabel/rotor.h
 include/openbabel-2.0/openbabel/shared_ptr.h
 include/openbabel-2.0/openbabel/spectrophore.h
+include/openbabel-2.0/openbabel/stereo/bindings.h
 include/openbabel-2.0/openbabel/stereo/cistrans.h
 include/openbabel-2.0/openbabel/stereo/squareplanar.h
 include/openbabel-2.0/openbabel/stereo/stereo.h
@@ -89,21 +90,28 @@
 include/openbabel-2.0/openbabel/tokenst.h
 include/openbabel-2.0/openbabel/typer.h
 include/openbabel-2.0/openbabel/xml.h
+lib/cmake/openbabel2/OpenBabel2Config.cmake
+lib/cmake/openbabel2/OpenBabel2ConfigVersion.cmake
+lib/cmake/openbabel2/OpenBabel2_EXPORTS-relwithdebinfo.cmake
+lib/cmake/openbabel2/OpenBabel2_EXPORTS.cmake
 lib/libinchi.so
 lib/libinchi.so.0
-lib/libinchi.so.0.3.1
+lib/libinchi.so.0.4.1
 lib/libopenbabel.so
 lib/libopenbabel.so.4
-lib/libopenbabel.so.4.0.0
+lib/libopenbabel.so.4.0.2
 lib/openbabel/${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/${PKGVERSION}/cmlreactformat.so
 lib/openbabel/${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}/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/${PKGVERSION}/gaussformat.so
 lib/openbabel/${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_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/${PKGVERSION}/viewmolformat.so
 lib/openbabel/${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/${PKGVERSION}/resdata.txt
 share/openbabel/${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/${PKGVERSION}/torlib.txt
diff -r 7553a2ea252a -r 62f465856b97 biology/openbabel/distinfo
--- a/biology/openbabel/distinfo        Thu Nov 20 08:39:09 2014 +0000
+++ b/biology/openbabel/distinfo        Thu Nov 20 09:05:56 2014 +0000
@@ -1,9 +1,8 @@
-$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 -r 7553a2ea252a -r 62f465856b97 biology/openbabel/patches/patch-doc_CMakeLists.txt
--- a/biology/openbabel/patches/patch-doc_CMakeLists.txt        Thu Nov 20 08:39:09 2014 +0000
+++ b/biology/openbabel/patches/patch-doc_CMakeLists.txt        Thu Nov 20 09:05:56 2014 +0000
@@ -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 -r 7553a2ea252a -r 62f465856b97 biology/openbabel/patches/patch-include_openbabel_shared__ptr.h
--- a/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h   Thu Nov 20 08:39:09 2014 +0000
+++ b/biology/openbabel/patches/patch-include_openbabel_shared__ptr.h   Thu Nov 20 09:05:56 2014 +0000
@@ -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 <memory>
@@ -11,10 +11,15 @@
 +  #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 <tr1/memory>
++   #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 <tr1/memory>
++     #endif
++     using std::tr1::shared_ptr;
++
 +    #endif
-+    using std::tr1::shared_ptr;
    #endif
 -  using std::tr1::shared_ptr;
  #endif
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