.gitignore

@@ -8,4 +8,3 @@ openbabel-2.0.2.tar.gz
 /openbabel-3a63a9849f8d9719c5989c43875d51be50c53019.tar.gz
 /openbabel-2-4-0.tar.gz
 /openbabel-2-4-1.tar.gz
-/openbabel-openbabel-3-1-1.tar.gz

openbabel-3.1.1-bug2378.patch

@@ -1,44 +0,0 @@
-From 4ba2fec17b786afebadfae800a015704ad533843 Mon Sep 17 00:00:00 2001
-From: dkoes <dkoes@pitt.edu>
-Date: Mon, 7 Jun 2021 11:04:25 -0400
-Subject: [PATCH] Resolve ImportError with make test
-
-This change will build _openbabel.so in scripts/python/openbabel instead
-of the default build/lib.  This is necessary because openbabel.py tries
-to import _openbabel like this:
-
-if __package__ or "." in __name__:
-    from . import _openbabel
-else:
-    import _openbabel
-
-This results in a circular import error when running make test (the
-first branch of the if is triggered).  This code appears to be generated by
-SWIG with no obvious way to change it to catch the ImportError and call
-import _openbabel instead.  Note the PYTHONPATH is set to include
-build/lib, but it doesn't matter because SWIG is forcing the import to
-happen in scripts/python/openbabel.
-
-I'm not sure why this hasn't been a problem in the past, perhaps there's
-been a change in SWIG.  This is with SWIG 4.0.1 and cmake 3.18.6.
-
-I think the best solution is to move all the files that are being built
-in /scripts to the build directory rather than polluting the src tree
-with them, but this would require changing all the bindings and I'm not
-up for building and testing every binding.
----
- scripts/CMakeLists.txt | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
-index b715a546dd..56821641fe 100644
---- a/scripts/CMakeLists.txt
-+++ b/scripts/CMakeLists.txt
-@@ -106,6 +106,7 @@ if (DO_PYTHON_BINDINGS)
-         set_target_properties(bindings_python PROPERTIES
-             OUTPUT_NAME _openbabel
-             PREFIX ""
-+            LIBRARY_OUTPUT_DIRECTORY "${openbabel_SOURCE_DIR}/scripts/python/openbabel/"
-             SUFFIX .so )
-         execute_process(
-           COMMAND

openbabel-3.1.1-bug2493.patch

@@ -1,36 +0,0 @@
-From c0570bfeb2d7e0a6a6de1f257cf28e7f3cac8739 Mon Sep 17 00:00:00 2001
-From: Sam James <sam@gentoo.org>
-Date: Sun, 12 Jun 2022 11:23:59 +0100
-Subject: [PATCH] CMake: fix time check typo (fixes build failure w/ GCC 12)
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-Without this fixed check, we get a build failure with GCC 12:
-```
-/var/tmp/portage/sci-chemistry/openbabel-3.1.1_p20210225/work/openbabel-08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b/include/openbabel/obutil.h:65:14: error: ‘clock’ was not declared in this scope; did you mean ‘clock_t’?
-   65 |       start= clock();
-      |              ^~~~~
-      |              clock_t
-```
-
-Bug: https://bugs.gentoo.org/851510
----
- src/config.h.cmake | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/config.h.cmake b/src/config.h.cmake
-index 1c59c67699..26e5dde94f 100644
---- a/src/config.h.cmake
-+++ b/src/config.h.cmake
-@@ -182,8 +182,8 @@
- #define OB_MODULE_PATH "@OB_MODULE_PATH@"
- 
- #ifndef TIME_WITH_SYS_TIME
--  #ifdef HAVE_SYS_TIME
--    #ifdef HAVE_TIME
-+  #ifdef HAVE_SYS_TIME_H
-+    #ifdef HAVE_TIME_H
-       #define TIME_WITH_SYS_TIME 1
-     #else
-       #define TIME_WITH_SYS_TIME 0

openbabel-3.1.1-fix_bug2217.patch

@@ -1,39 +0,0 @@
-From 7de27f309db5f7ec026ef5c5235e5b33bf7d1a85 Mon Sep 17 00:00:00 2001
-From: John Bollinger <John.Bollinger@StJude.org>
-Date: Thu, 14 May 2020 08:46:40 -0500
-Subject: [PATCH] Fix test failure with Python 3
-
-When run with Python 3.6, test/testdistgeom.py fails with a SyntaxError
-about a malformed character escape.  This arises from a failure to escape
-literal backslash characters in single-quoted SMILES strings (several
-occurrences).  Python 2 accepts this and does the right things with it,
-but Python 3 rejects it.
-
-Fixes #2217
----
- test/testdistgeom.py | 10 +++++-----
- 1 file changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/test/testdistgeom.py b/test/testdistgeom.py
-index 0fa5adb576..fc3a7515b9 100644
---- a/test/testdistgeom.py
-+++ b/test/testdistgeom.py
-@@ -42,13 +42,13 @@ def testSMItoSMI(self):
-             'C1CC[C@H]2[C@@H](C1)CCCC2',  # cis-decalin
-             'C1CC[C@@H]2[C@@H](C1)CCCC2',  # trans-decalin
-             '[C@H]1(NC[C@H]2[C@H]1N2)OC',
--            'Clc1cccc(Cl)c1\C=N\NC(=O)c1cccs1',
--            'O=C1NC(=S)S\C1=C/c1ccco1',
-+            'Clc1cccc(Cl)c1\\C=N\\NC(=O)c1cccs1',
-+            'O=C1NC(=S)S\\C1=C/c1ccco1',
-             'S=C1NC(=O)/C(=C/c2ccco2)/S1',
--            'O=C1NC(=S)N\C1=C\c1ccncc1',
-+            'O=C1NC(=S)N\\C1=C\\c1ccncc1',
-             'S=C1NC(=O)C(=C)N1',
--            'CC(=O)N\N=C\c1ccncc1',
--            'N/N=c/1\sc2c(n1C)cccc2',
-+            'CC(=O)N\\N=C\\c1ccncc1',
-+            'N/N=c/1\\sc2c(n1C)cccc2',
-             'OCCN/C=C\\1/C(=NN(C1=O)c1ccccc1)C',
-             'Cc1ccc(o1)/C=C/C=O',
-             # disabled to make test run faster:

openbabel-3.1.1-fix_bug2223.patch

@@ -1,34 +0,0 @@
-From b75c392b75b3494d9dae15176f38facf7e61db17 Mon Sep 17 00:00:00 2001
-From: John Bollinger <John.Bollinger@StJude.org>
-Date: Fri, 15 May 2020 11:30:27 -0500
-Subject: [PATCH] Fix UB in UFF parameter parsing
-
-When evaluating atom coordination number, method
-OBForceFieldUFF::ParseParamFile() assumed that it may access a third character
-of the atom type string, but in fact that produces undefined behavior if the
-string is only one character long. A one-character atom type occurs in
-practice with the default parameter file (for deuterium).
-
-This change addresses the issue by verifying that the second character of
-each atom type string is not a C string terminator as a precondition for
-accessing the third. If the second is a string terminator then the same
-default behavior is provided as if the type were two characters long.
-
-Fixes #2223
----
- src/forcefields/forcefielduff.cpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/forcefields/forcefielduff.cpp b/src/forcefields/forcefielduff.cpp
-index 9bff879c9c..2e98e0e804 100644
---- a/src/forcefields/forcefielduff.cpp
-+++ b/src/forcefields/forcefielduff.cpp
-@@ -1647,7 +1647,7 @@ namespace OpenBabel {
-         parameter.b = 0; // used for tracking number of angles in 5-coordinate
-         parameter.c = 0;
- 
--        char coord = vs[1][2]; // 3rd character of atom type
-+        char coord = vs[1][1] ? vs[1][2] : '\0'; // 3rd character of atom type, if any
-         switch (coord) {
-         case '1': // linear
-           parameter._ipar.push_back(1);

openbabel-disable-tests-s390x.patch

@@ -1,21 +1,21 @@
-diff -up a/test/CMakeLists.txt.s390x b/test/CMakeLists.txt
+diff -up openbabel-openbabel-2-4-1/test/CMakeLists.txt.s390x openbabel-openbabel-2-4-1/test/CMakeLists.txt
---- a/test/CMakeLists.txt.s390x	2016-10-10 17:56:17.000000000 +0200
+--- openbabel-openbabel-2-4-1/test/CMakeLists.txt.s390x	2016-10-10 17:56:17.000000000 +0200
-+++ b/test/CMakeLists.txt	2019-01-27 19:32:21.568052461 +0100
++++ openbabel-openbabel-2-4-1/test/CMakeLists.txt	2019-01-27 19:32:21.568052461 +0100
-@@ -74,7 +74,7 @@
+@@ -62,7 +62,7 @@ set(origtests
      )
  set (atom_parts 1 2 3 4)
- set (ffmmff94_parts 1 2 3 4 5 6)
+ set (ffmmff94_parts 1 2)
 -set (math_parts 1 2 3 4)
 +set (math_parts 1 2 3)
- set (pdbreadfile_parts 1 2 3 4)
  
  if(BUILD_SHARED)
-@@ -250,8 +250,6 @@
+   if(LIBXML2_FOUND)
+@@ -238,7 +238,7 @@ endif(NOT MINGW AND NOT CYGWIN)
+ if (PYTHON_BINDINGS)
    include(UsePythonTest)
    set(pybindtests
-       bindings
+-      bindings _pybel example)
--      _pybel
++      bindings example)
--      example 
+   foreach(pybindtest ${pybindtests})
-       obconv_writers
+     SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES
-       cdjsonformat
+         PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}"
-       pcjsonformat

openbabel-disable-tests.patch

@@ -1,16 +1,16 @@
-diff -up a/test/CMakeLists.txt.tests b/test/CMakeLists.txt
+diff -up openbabel-openbabel-2-4-0/test/CMakeLists.txt.tests openbabel-openbabel-2-4-0/test/CMakeLists.txt
---- a/test/CMakeLists.txt.tests	2016-09-21 21:55:37.000000000 +0200
+--- openbabel-openbabel-2-4-0/test/CMakeLists.txt.tests	2016-09-21 21:55:37.000000000 +0200
-+++ b/test/CMakeLists.txt	2016-10-10 13:48:52.726803964 +0200
++++ openbabel-openbabel-2-4-0/test/CMakeLists.txt	2016-10-10 13:48:52.726803964 +0200
-@@ -39,7 +39,7 @@
+@@ -34,7 +34,7 @@ set (implicitH_parts 1)
- set (isomorphism_parts 1 2 3 4 5 6 7 8 9)
+ set (lssr_parts 1 2 3 4 5)
+ set (isomorphism_parts 1 2 3 4 5 6 7 8)
  set (multicml_parts 1)
- set (periodic_parts 1 2 3 4)
+-set (regressions_parts 1 221 222 223 224)
--set (regressions_parts 1 221 222 223 224 225 226 227 228 240 241 242 1794 2111)
 +set (regressions_parts 222 223 224)
  set (rotor_parts 1 2 3 4)
  set (shuffle_parts 1 2 3 4 5)
  set (smiles_parts 1 2 3)
-@@ -188,7 +188,7 @@
+@@ -177,7 +177,7 @@ if(WITH_INCHI)
      set_target_properties(test_inchiwrite PROPERTIES LINK_SEARCH_END_STATIC TRUE)
    endif()
    # files in test/inchi -- both .sdf and .txt
@@ -19,11 +19,11 @@ diff -up a/test/CMakeLists.txt.tests b/test/CMakeLists.txt
    set(inchidata ${CMAKE_SOURCE_DIR}/test/inchi)
    foreach(test ${inchitests})
      add_test(inchi${test}_Test
-@@ -226,7 +226,7 @@
+@@ -215,7 +215,7 @@ if(NOT MINGW AND NOT CYGWIN)
    include(UsePythonTest)
    if(PYTHON_EXECUTABLE)
      set(pytests
--        babel sym smartssym fastsearch distgeom unique kekule pdbformat RInChI)
+-        babel sym smartssym fastsearch unique kekule pdbformat)
 +        babel smartssym fastsearch unique kekule pdbformat)
      foreach(pytest ${pytests})
      SET_SOURCE_FILES_PROPERTIES(test${pytest}.py PROPERTIES

openbabel-fix-libdir-in-pkgconfig.patch

@@ -1,12 +1,11 @@
-diff -up a/openbabel-3.pc.cmake.p b/openbabel-3.pc.cmake
+diff -up openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake.p openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake
---- a/openbabel-3.pc.cmake.p
+--- openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake.p	2016-10-10 17:56:17.000000000 +0200
-+++ b/openbabel-3.pc.cmake
++++ openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake	2019-01-27 10:47:00.905546971 +0100
 @@ -1,6 +1,6 @@
  prefix=@CMAKE_INSTALL_PREFIX@
  exec_prefix=${prefix}
 -libdir=${exec_prefix}/@LIB_INSTALL_DIR@
 +libdir=${exec_prefix}/lib@LIB_SUFFIX@
  includedir=${prefix}/include
- pkgincludedir=${includedir}/openbabel@BABEL_MAJ_VER@
+ pkgincludedir=${includedir}/openbabel-2.0
- 
  

openbabel-inchi-license-lgpl-2.1.txt

@@ -1,502 +0,0 @@
-                  GNU LESSER GENERAL PUBLIC LICENSE
-                       Version 2.1, February 1999
-
- Copyright (C) 1991, 1999 Free Software Foundation, Inc.
- 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-[This is the first released version of the Lesser GPL.  It also counts
- as the successor of the GNU Library Public License, version 2, hence
- the version number 2.1.]
-
-                            Preamble
-
-  The licenses for most software are designed to take away your
-freedom to share and change it.  By contrast, the GNU General Public
-Licenses are intended to guarantee your freedom to share and change
-free software--to make sure the software is free for all its users.
-
-  This license, the Lesser General Public License, applies to some
-specially designated software packages--typically libraries--of the
-Free Software Foundation and other authors who decide to use it.  You
-can use it too, but we suggest you first think carefully about whether
-this license or the ordinary General Public License is the better
-strategy to use in any particular case, based on the explanations below.
-
-  When we speak of free software, we are referring to freedom of use,
-not price.  Our General Public Licenses are designed to make sure that
-you have the freedom to distribute copies of free software (and charge
-for this service if you wish); that you receive source code or can get
-it if you want it; that you can change the software and use pieces of
-it in new free programs; and that you are informed that you can do
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-
-  To protect your rights, we need to make restrictions that forbid
-distributors to deny you these rights or to ask you to surrender these
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-
-  <signature of Ty Coon>, 1 April 1990
-  Ty Coon, President of Vice
-
-That's all there is to it!

openbabel-narrowing-conversion.patch

@@ -0,0 +1,33 @@
+diff -up openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp.nc openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp
+--- openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp.nc	2016-02-16 23:47:25.000000000 +0100
++++ openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp	2016-02-18 19:01:40.509752461 +0100
+@@ -218,7 +218,7 @@ bool PNGFormat::ReadMolecule(OBBase* pOb
+     _count=0;
+     _hasInputPngFile=true;
+   }
+-  const char pngheader[] = {-119,80,78,71,13,10,26,10,0};
++  const signed char pngheader[] = {-119,80,78,71,13,10,26,10,0};
+   char readbytes[9];
+   ifs.read(readbytes, 8);
+ 
+diff -up openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp.nc openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp
+--- openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp.nc	2016-02-16 23:47:25.000000000 +0100
++++ openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp	2016-02-18 23:22:23.786793588 +0100
+@@ -472,7 +472,7 @@ bool YOBFormat::WriteMolecule(OBBase* pO
+ 
+   //  bool hetatom;
+   char buffer[32],/*resname[4],*/atomname[5];
+-  char double1[8]={0,0,0,0,0,0,-16,0x3f};
++  const signed char double1[8]={0,0,0,0,0,0,-16,0x3f};
+   //   char *str;
+   int i,j,/*m,q,*/pos;
+   int /*resno,chainNum,link,linktype,*/atoms,element,links/*,chain*/;
+@@ -500,7 +500,7 @@ bool YOBFormat::WriteMolecule(OBBase* pO
+   mem_set(buffer,0,8);
+   for (i=0;i<4;i++)
+   { for (j=0;j<4;j++)
+-    { if (i==j) ofs.write(double1,8);
++    { if (i==j) ofs.write(reinterpret_cast<const char*>(double1),8);
+       else ofs.write(buffer,8); } }
+   storeint32le(buffer,MOB_INFOEND);
+   storeint32le(&buffer[4],MOB_INFOENDSIZE);

openbabel-plugindir.patch

@@ -1,30 +1,12 @@
-diff -up a/CMakeLists.txt.plugindir b/CMakeLists.txt
+diff -up openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt.plugindir openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt
---- a/CMakeLists.txt.plugindir	2015-02-07 21:42:44.431479900 +0100
+--- openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt.plugindir	2015-02-07 21:42:44.431479900 +0100
-+++ b/CMakeLists.txt	2015-02-07 21:43:29.000429326 +0100
++++ openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt	2015-02-07 21:43:29.000429326 +0100
-@@ -24,7 +24,7 @@
+@@ -266,7 +266,7 @@ if(NOT MSVC)
- # had too many 1.100.1 releases. :-)
+     }
- set(BABEL_MAJ_VER   3)
+    " SCANDIR_NEEDS_CONST)
- 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(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}"
- set(BABEL_LIBRARY openbabel)
++  set(OB_MODULE_PATH "${OB_PLUGIN_INSTALL_DIR}"
-@@ -750,7 +750,7 @@
+       CACHE PATH "Set to system install for bindings only build")
-   "${openbabel_BINARY_DIR}/OpenBabel3ConfigVersion.cmake" @ONLY)
+   add_definitions(-DOB_MODULE_PATH="\\"${OB_MODULE_PATH}\\"")
  
- # Now to configure the installed config file.
--set(OB_CONFIG_DIR "${LIB_INSTALL_DIR}/cmake/openbabel3")
-+set(OB_CONFIG_DIR "lib${LIB_SUFFIX}/cmake/openbabel3")
- set(OpenBabel3_INCLUDE_DIRS "\${OpenBabel3_INSTALL_PREFIX}/${OB_INCLUDE_DIRS}")
- set(OpenBabel3_LIBRARIES "$<TARGET_FILE:openbabel>")
- 
---- a/OpenBabel3Config.cmake.orig.in	2020-05-08 17:38:02.000000000 +0200
-+++ b/OpenBabel3Config.cmake.in	2022-09-29 21:36:17.995630395 +0200
-@@ -1,5 +1,5 @@
- # The OpenBabel3 config file. To get the targets include the exports file.
--get_filename_component(OpenBabel3_INSTALL_PREFIX "${OpenBabel3_DIR}@REL_REF@"
-+get_filename_component(OpenBabel3_INSTALL_PREFIX "/usr"
-   ABSOLUTE)
- 
- set(OpenBabel3_VERSION_MAJOR   "@BABEL_MAJ_VER@")

openbabel-python-dl.patch

@@ -0,0 +1,15 @@
+diff -up openbabel-openbabel-2-4-1/scripts/CMakeLists.txt.py3 openbabel-openbabel-2-4-1/scripts/CMakeLists.txt
+--- openbabel-openbabel-2-4-1/scripts/CMakeLists.txt.py3	2019-03-04 11:12:54.369464503 +0100
++++ openbabel-openbabel-2-4-1/scripts/CMakeLists.txt	2019-03-04 11:59:39.323264995 +0100
+@@ -84,7 +84,10 @@ if (DO_PYTHON_BINDINGS)
+               COMMAND ${CMAKE_COMMAND} -E echo "  try:" >> ob.py
+               COMMAND ${CMAKE_COMMAND} -E echo "    import dl" >> ob.py
+               COMMAND ${CMAKE_COMMAND} -E echo "  except ImportError:" >> ob.py
+-              COMMAND ${CMAKE_COMMAND} -E echo "    import DLFCN as dl" >> ob.py
++              COMMAND ${CMAKE_COMMAND} -E echo "    try:" >> ob.py
++              COMMAND ${CMAKE_COMMAND} -E echo "      import DLFCN as dl" >> ob.py
++              COMMAND ${CMAKE_COMMAND} -E echo "    except ImportError:" >> ob.py
++              COMMAND ${CMAKE_COMMAND} -E echo "      import ctypes as dl" >> ob.py
+               COMMAND ${CMAKE_COMMAND} -E echo "  sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >> ob.py
+               COMMAND cat ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py >> ob.py
+               COMMAND ${CMAKE_COMMAND} -E copy ob.py ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py

openbabel-taberror.patch

@@ -0,0 +1,32 @@
+diff -up openbabel-openbabel-2-4-1/test/testpdbformat.py.taberror openbabel-openbabel-2-4-1/test/testpdbformat.py
+--- openbabel-openbabel-2-4-1/test/testpdbformat.py.taberror	2016-10-10 17:56:17.000000000 +0200
++++ openbabel-openbabel-2-4-1/test/testpdbformat.py	2019-03-04 11:09:24.786801658 +0100
+@@ -24,12 +24,12 @@ class TestPDBFormat(BaseTest):
+ 
+     def testInsertionCodes(self):
+         """
+-	Testing a PDB entry with insertion codes to distinguish residues
+-	upon conversion to FASTA.
++        Testing a PDB entry with insertion codes to distinguish residues
++        upon conversion to FASTA.
+         """
+         self.canFindExecutable("babel")
+ 
+-	self.entryPDBwithInsertioncodes="""ATOM    406  N   VAL L  29      58.041  17.797  48.254  1.00  0.00           N  
++        self.entryPDBwithInsertioncodes="""ATOM    406  N   VAL L  29      58.041  17.797  48.254  1.00  0.00           N  
+ ATOM    407  CA  VAL L  29      57.124  18.088  47.170  1.00  0.00           C  
+ ATOM    408  C   VAL L  29      55.739  17.571  47.538  1.00  0.00           C  
+ ATOM    409  O   VAL L  29      55.535  16.362  47.550  1.00  0.00           O  
+@@ -100,9 +100,9 @@ ATOM    473  HE1 TYR L  32      48.512
+ ATOM    474  HE2 TYR L  32      48.145  19.172  44.648  1.00  0.00           H  
+ ATOM    475  HH  TYR L  32      46.462  17.658  44.280  1.00  0.00           H  
+ """
+-	output, error = run_exec(self.entryPDBwithInsertioncodes,
+-				     "babel -ipdb -ofasta")
+-	self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
++        output, error = run_exec(self.entryPDBwithInsertioncodes,
++                                     "babel -ipdb -ofasta")
++        self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
+ 
+ if __name__ == "__main__":
+     testsuite = []

openbabel.spec

@@ -1,80 +1,54 @@
+%global commit 3a63a9849f8d9719c5989c43875d51be50c53019
+%global shortcommit %(c=%{commit}; echo ${c:0:7})
+
 %{!?perl_vendorarch:%global perl_vendorarch %(eval "`perl -V:installvendorarch`"; echo $installvendorarch)}
 
 # we don't want to provide private Perl or Python extension libs
 %global __provides_exclude_from ^(%{perl_vendorarch}/auto|%{python3_sitearch})/.*\\.so$
 
-# Avoid LTO flags in these architectures:
-# eigen3/Eigen/src/Core/arch/AltiVec/MatrixProduct.h:1199:26:
-# error: inlining failed in call to 'always_inline' 'Eigen::internal::bload<Eigen::internal::blas_data_mapper<double, long, 0, 0, 1>, double __vector(2), long, 2l, 0, 
-%if 0%{?rhel}
-%ifarch %{power64}
-%define _lto_cflags %{nil}
-%endif
-%endif
-
 Name: openbabel
-Version: 3.1.1
+Version: 2.4.1
-Release: 18%{?dist}
+Release: 28%{?dist}
 Summary: Chemistry software file format converter
-License: GPL-2.0-only
+License: GPLv2
 URL: https://openbabel.org/
-Source0: https://github.com/openbabel/openbabel/archive/openbabel-openbabel-%(echo %{version} | tr '.' '-').tar.gz
+Source0: https://github.com/openbabel/openbabel/archive/openbabel-%(echo %{version} | tr '.' '-').tar.gz
 Source1: obgui.desktop
-Source2: openbabel-inchi-license-lgpl-2.1.txt
-
 # fix perl modules install path
-Patch0: %{name}-perl.patch
+Patch1: %{name}-perl.patch
-
+# fix plugin directory location (#680292, patch by lg)
-# fix openbabel version + cmake config files
+Patch4: openbabel-plugindir.patch
-Patch1: %{name}-plugindir.patch
-
 # fix SWIG_init even when not using swig (#772149)
-Patch2: %{name}-noswig-rubymethod.patch
+Patch6: openbabel-noswig-rubymethod.patch
-
 # On F-17, directory for C ruby files changed to use vendorarch directory
-Patch3: %{name}-ruby19-vendorarch.patch
+Patch7: openbabel-ruby19-vendorarch.patch
-
 # temporarily disable some tests on:
 # - ppc64 and s390(x) to unblock other builds (#1108103)
 # - ARM (#1094491)
 # - aarch64 (#1094513)
 # Upstream bugs: https://sourceforge.net/p/openbabel/bugs/927/ https://sourceforge.net/p/openbabel/bugs/945/
-Patch4: %{name}-disable-tests.patch
+Patch8: openbabel-disable-tests.patch
-
+Patch9: openbabel-narrowing-conversion.patch
 # Fix path to libdir in .pc file
 # https://bugzilla.redhat.com/show_bug.cgi?id=1669664
-Patch5: %{name}-fix-libdir-in-pkgconfig.patch
+Patch10: openbabel-fix-libdir-in-pkgconfig.patch
-
 # Math 4 test is failing on s390x only
-Patch6: %{name}-disable-tests-s390x.patch
+Patch11: openbabel-disable-tests-s390x.patch
-
+# Fix inconsistent whitespace
-Patch7: %{name}-3.1.1-fix_bug2223.patch
+Patch12: openbabel-taberror.patch
-Patch8: %{name}-3.1.1-fix_bug2217.patch
+# Fix import of dl module in python3.7
-Patch9: %{name}-3.1.1-bug2378.patch
+# https://github.com/openbabel/openbabel/pull/372
-Patch10: %{name}-3.1.1-bug2493.patch
+Patch13: openbabel-python-dl.patch
-
+BuildRequires: cmake
-BuildRequires: make
-%if 0%{?el7}
-BuildRequires: boost169-devel
-%else
-BuildRequires: boost-devel
-%endif
-BuildRequires: swig
-BuildRequires: cmake3
 BuildRequires: dos2unix
 BuildRequires: desktop-file-utils
 BuildRequires: eigen3-devel
 BuildRequires: gcc-c++
-%if 0%{?fedora}
 BuildRequires: inchi-devel >= 1.0.3
-BuildRequires: wxGTK-devel
-%else
-BuildRequires: wxGTK3-devel
-%endif
 BuildRequires: libxml2-devel
+BuildRequires: swig
+BuildRequires: wxGTK3-devel
 BuildRequires: ImageMagick
-BuildRequires: rapidjson-devel
-Requires:      %{name}-libs%{?_isa} = %{version}-%{release}
 
 %description
 Open Babel is a free, open-source version of the Babel chemistry file
@@ -92,6 +66,7 @@ software.
 %package devel
 Summary: Development tools for programs which will use the Open Babel library
 Requires: %{name}-libs%{?_isa} = %{version}-%{release}
+Requires: pkgconfig
 
 %description devel
 The %{name}-devel package includes the header files and libraries
@@ -106,7 +81,6 @@ This package contains additional documentation for Open Babel.
 
 %package gui
 Summary: Chemistry software file format converter - GUI version
-Requires: %{name}-libs%{?_isa} = %{version}-%{release}
 
 %description gui
 Open Babel is a free, open-source version of the Babel chemistry file
@@ -119,10 +93,6 @@ This package contains the graphical interface.
 
 %package libs
 Summary: Chemistry software file format converter - libraries
-%if 0%{?rhel}
-License: GPL-2.0-only AND LGPL-2.1-or-later
-Provides: bundled(libinchi) = 1.0.4
-%endif
 
 %description libs
 Open Babel is a free, open-source version of the Babel chemistry file
@@ -136,6 +106,7 @@ file-translation code.
 
 %package -n perl-%{name}
 Summary: Perl wrapper for the Open Babel library
+Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
 Requires: %{name}-libs%{?_isa} = %{version}-%{release}
 BuildRequires: perl-devel
 BuildRequires: perl-generators
@@ -147,9 +118,8 @@ Perl wrapper for the Open Babel library.
 Summary: Python wrapper for the Open Babel library
 Requires: %{name}-libs%{?_isa} = %{version}-%{release}
 BuildRequires: python3-devel
-BuildRequires: python3-setuptools
 %{?python_provide:%python_provide python3-%{name}}
-Obsoletes: python2-%{name} < 0:%{version}-%{release}
+Obsoletes: python2-%{name} < 2.4.1-21
 
 %description -n python3-%{name}
 Python3 wrapper for the Open Babel library.
@@ -165,28 +135,20 @@ Ruby wrapper for the Open Babel library.
 
 %prep
 %setup -q -n %{name}-%{name}-%(echo %{version} | tr '.' '-')
-%patch0 -p1 -b .perl_path
+%patch1 -p1 -b .perl_path
-%patch1 -p1 -b .plugindir
+%patch4 -p1 -b .plugindir
-%patch2 -p1 -b .noswig_ruby
+%patch6 -p1 -b .noswig_ruby
-%patch3 -p1 -b .ruby_vendor
+%patch7 -p1 -b .ruby_vendor
-%ifarch aarch64 %{arm} %{power64} s390x
+%ifarch aarch64 %{arm} %{power64} s390 s390x
-%patch4 -p1 -b .tests
+%patch8 -p1 -b .tests
 %endif
-%patch5 -p1 -b .s390x
 %ifarch s390x
-%patch6 -p1 -b .backup
+%patch11 -p1 -b .s390x
 %endif
-%patch7 -p1 -b .backup
+%patch9 -p1 -b .nc
-%patch8 -p1 -b .backup
+%patch10 -p1
-%patch9 -p1 -b .backup
+%patch12 -p1 -b .taberr
-%patch10 -p1 -b .backup
+%patch13 -p1 -b .py3dl
-
-%if 0%{?fedora}
-rm -rf src/formats/libinchi
-%else
-cp -p %{SOURCE2} ./inchi-license-lgpl-2.1.txt
-%endif
-
 # convert to Unix line endings
 dos2unix -k \
   data/chemdrawcdx.h \
@@ -207,94 +169,41 @@ done
 popd
 
 %build
-mkdir -p %{_target_platform}
+%cmake \
-%if 0%{?fedora} || 0%{?eln}
-# RHBZ #1996330
-%ifarch %{power64}
-export CXXFLAGS="%{optflags} -DEIGEN_ALTIVEC_DISABLE_MMA"
-%endif
-%endif
-%cmake3 -B %{_target_platform} \
- -Wno-dev \
  -DCMAKE_SKIP_RPATH:BOOL=ON \
  -DBUILD_GUI:BOOL=ON \
  -DPYTHON_BINDINGS:BOOL=ON \
  -DPYTHON_EXECUTABLE=%{__python3} \
  -DPERL_BINDINGS:BOOL=ON \
  -DRUBY_BINDINGS:BOOL=ON \
- -DWITH_MAEPARSER:BOOL=OFF \
- -DWITH_COORDGEN:BOOL=OFF \
- -DOB_PLUGIN_INSTALL_DIR:PATH=%{_lib}/openbabel3 \
-%if 0%{?rhel}
- -DOPENBABEL_USE_SYSTEM_INCHI=false \
-%else
  -DOPENBABEL_USE_SYSTEM_INCHI=true \
-%endif
  -DENABLE_VERSIONED_FORMATS=false \
  -DRUN_SWIG=true \
  -DENABLE_TESTS:BOOL=ON \
  -DOPTIMIZE_NATIVE=OFF \
- -DGLIBC_24_COMPATIBLE:BOOL=OFF \
+ .
-%if 0%{?el7}
+make VERBOSE=1 %{?_smp_mflags}
- -DBoost_FILESYSTEM_LIBRARY_RELEASE:FILEPATH=%{_libdir}/boost169/libboost_filesystem.so \
- -DBoost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=%{_libdir}/boost169/libboost_serialization.so \
- -DBoost_SYSTEM_LIBRARY_RELEASE:FILEPATH=%{_libdir}/boost169/libboost_system.so \
- -DBoost_INCLUDE_DIR:PATH=%{_includedir}/boost169 \
- -DBoost_LIBRARY_DIR_RELEASE:PATH=%{_libdir}/boost169
-%endif
-
-%make_build -C %{_target_platform}
 
 %install
-%make_install -C %{_target_platform}
+make VERBOSE=1 DESTDIR=%{buildroot} install
 
-rm -f %{buildroot}%{_libdir}/cmake/openbabel2/*.cmake
+rm %{buildroot}%{_libdir}/cmake/openbabel2/*.cmake
 
 desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE1}
 install -Dpm644 babel.png %{buildroot}%{_datadir}/pixmaps/babel.png
 
-# Create profile files
-mkdir -p %{buildroot}%{_sysconfdir}/profile.d
-cat > %{buildroot}%{_sysconfdir}/profile.d/openbabel3.sh <<EOF
-BABEL_LIBDIR=%{_libdir}/%{name}3
-export BABEL_LIBDIR
-BABEL_DATADIR=%{_datadir}/%{name}
-export BABEL_DATADIR
-EOF
-cat > %{buildroot}%{_sysconfdir}/profile.d/openbabel3.csh <<EOF
-setenv BABEL_LIBDIR %{_libdir}/%{name}3
-setenv BABEL_DATADIR %{_datadir}/%{name}
-EOF
-
 %if 1
 %check
-%define _vpath_builddir %{_target_platform}
+# rm the built ruby bindings for testsuite to succeed (bug #1191173)
-pushd %{_vpath_builddir}
+rm %{_lib}/openbabel.so
-
+export CTEST_OUTPUT_ON_FAILURE=1 PYTHONPATH=%{buildroot}%{python3_sitearch}
-# rm the built ruby bindings for testsuite to succeed (Red Hat bugzilla ticket #1191173)
+%make_build test
-rm -f %{_lib}/openbabel.so
-
-export CTEST_OUTPUT_ON_FAILURE=1
-export PYTHONPATH=%{buildroot}%{python3_sitearch}
-%if 0%{?el7}
-ctest3 -j1 --force-new-ctest-process -E 'test_cifspacegroup_1|test_cifspacegroup_2'
-%else
-# See https://github.com/openbabel/openbabel/issues/2138
-%ifarch aarch64 %{arm} %{power64} s390x
-ctest3 -j1 --force-new-ctest-process -E 'pybindtest_bindings|pybindtest_obconv_writers'
-%else
-ctest3 -j1 --force-new-ctest-process
-%endif
-%endif
 %endif
 
-%if 0%{?el7}
 %ldconfig_scriptlets libs
-%endif
 
 %files
-%config(noreplace) %{_sysconfdir}/profile.d/openbabel3.sh
+%{_bindir}/babel
-%config(noreplace) %{_sysconfdir}/profile.d/openbabel3.csh
 %{_bindir}/ob*
 %{_bindir}/roundtrip
 %{_mandir}/man1/*.1*
@@ -302,15 +211,9 @@ ctest3 -j1 --force-new-ctest-process
 %exclude %{_mandir}/man1/obgui.1*
 
 %files devel
-%{_includedir}/%{name}3/
+%{_includedir}/%{name}-2.0
 %{_libdir}/libopenbabel.so
-%{_libdir}/libopenbabel.so.7
+%{_libdir}/pkgconfig/*.pc
-%{_libdir}/pkgconfig/openbabel-3.pc
-%{_libdir}/cmake/openbabel3/
-%if 0%{?rhel}
-%{_libdir}/libinchi.so
-%{_includedir}/inchi/
-%endif
 
 %files doc
 %doc doc/*.html doc/README* doc/dioxin.*
@@ -322,16 +225,9 @@ ctest3 -j1 --force-new-ctest-process
 %{_mandir}/man1/obgui.1*
 
 %files libs
-%license COPYING
-%doc THANKS AUTHORS authors.txt README.md
 %{_datadir}/%{name}/
-%{_libdir}/%{name}3/
+%{_libdir}/%{name}/
-%{_libdir}/libopenbabel.so.7.0.0
+%{_libdir}/libopenbabel.so.*
-%if 0%{?rhel}
-%license inchi-license-lgpl-2.1.txt
-%{_libdir}/libinchi.so.0.4.1
-%{_libdir}/libinchi.so.0
-%endif
 
 %files -n perl-%{name}
 %{perl_vendorarch}/Chemistry/OpenBabel.pm
@@ -339,100 +235,15 @@ ctest3 -j1 --force-new-ctest-process
 %{perl_vendorarch}/*/Chemistry/OpenBabel/OpenBabel.so
 
 %files -n python3-%{name}
-%{python3_sitearch}/openbabel/
+%{python3_sitearch}/_openbabel.so
+%{python3_sitearch}/openbabel.py
+%{python3_sitearch}/pybel.py
+%{python3_sitearch}/__pycache__/*
 
 %files -n ruby-%{name}
 %{ruby_vendorarchdir}/openbabel.so
 
 %changelog
-* Wed Feb 08 2023 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-18
-- Fix config files (rhbz#2168290)
-
-* Thu Jan 19 2023 Fedora Release Engineering <releng@fedoraproject.org> - 3.1.1-17
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
-
-* Wed Jan 04 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 3.1.1-16
-- Rebuild for https://fedoraproject.org/wiki/Changes/Ruby_3.2
-
-* Thu Sep 29 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-15
-- Fix openbabel version in CMakeLists.txt
-- Fix rhbz#2130870
-
-* Tue Sep 27 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-14
-- Fix EPEL builds
-
-* Tue Sep 27 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-13
-- New rebuild
-
-* Sun Aug 07 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-12
-- Add profile file openbabel3.sh (rhbz#2112710)
-
-* Thu Aug 04 2022 Scott Talbert <swt@techie.net> - 3.1.1-11
-- Rebuild with wxWidgets 3.2
-
-* Fri Jul 22 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.1.1-10
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
-
-* Fri Jul 08 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-9
-- Patched for rhbz#2105259
-
-* Mon Jun 13 2022 Python Maint <python-maint@redhat.com> - 3.1.1-8
-- Rebuilt for Python 3.11
-
-* Mon May 30 2022 Jitka Plesnikova <jplesnik@redhat.com> - 3.1.1-7
-- Perl 5.36 rebuild
-
-* Thu Jan 27 2022 Vít Ondruch <vondruch@redhat.com> - 3.1.1-6
-- Rebuilt for https://fedoraproject.org/wiki/Changes/Ruby_3.1
-
-* Thu Jan 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.1.1-5
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
-
-* Sun Dec 12 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-4
-- Use bundled inchi on EPEL
-
-* Sat Nov 06 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-3
-- Fix CMake config file
-
-* Wed Sep 22 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-2
-- Fix patches order
-
-- Release 3.1.1
-
-* Thu Sep 02 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-1
-* Wed Sep 01 2021 Antonio Trande <sagitter@fedoraproject.org> - 2.4.1-39
-- Install license file and some release documentation
-
-* Mon Aug 30 2021 Antonio Trande <sagitter@fedoraproject.org> - 2.4.1-38
-- Use CMake3 in EPEL7
-
-* Thu Jul 22 2021 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-37
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
-
-* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 2.4.1-36
-- Rebuilt for Python 3.10
-
-* Fri May 21 2021 Jitka Plesnikova <jplesnik@redhat.com> - 2.4.1-35
-- Perl 5.34 rebuild
-
-* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-34
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
-
-* Wed Jan 06 2021 Mamoru TASAKA <mtasaka@fedoraproject.org> - 2.4.1-33
-- F-34: rebuild against ruby 3.0
-
-* Thu Jul 30 2020 Rex Dieter <rdieter@fedoraproject.org> - 2.4.1-32
-- adjust for new %%cmake macros (#1859850)
-
-* Tue Jul 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-31
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
-
-* Mon Jun 22 2020 Jitka Plesnikova <jplesnik@redhat.com> - 2.4.1-30
-- Perl 5.32 rebuild
-
-* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 2.4.1-29
-- Rebuilt for Python 3.9
-
 * Wed Jan 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-28
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
 

sources

@@ -1 +1 @@
-SHA512 (openbabel-openbabel-3-1-1.tar.gz) = d46807e8f4e2f0f691e69943e5c5eda9c271271cfca6f66b6df136bbf384502fd3b65a4adf134a4e9e1f2452e1316c9515aa92292b73205b9eb4d7e4d7a85f18
+c0e0aefeef0f9f2bb2c78109d65c30a5  openbabel-2-4-1.tar.gz