From 5243106e796d8c90154fe7946d7cc2da3c18fa8c Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@uni-jena.de>
Date: Fri, 2 Aug 2024 11:34:49 +0200
Subject: [PATCH 1/3] openbabel: fix python 3.12 compatibility

---
 .../libraries/openbabel/default.nix           | 33 ++++++++++++++-----
 1 file changed, 24 insertions(+), 9 deletions(-)

diff --git a/pkgs/development/libraries/openbabel/default.nix b/pkgs/development/libraries/openbabel/default.nix
index 0030b1cfa171..259fc8ce6903 100644
--- a/pkgs/development/libraries/openbabel/default.nix
+++ b/pkgs/development/libraries/openbabel/default.nix
@@ -1,4 +1,18 @@
-{ stdenv, lib, fetchFromGitHub, cmake, perl, zlib, libxml2, eigen, python, cairo, pcre, pkg-config, swig, rapidjson }:
+{ stdenv
+, lib
+, fetchFromGitHub
+, cmake
+, perl
+, zlib
+, libxml2
+, eigen
+, python
+, cairo
+, pcre
+, pkg-config
+, swig
+, rapidjson
+}:
 
 stdenv.mkDerivation rec {
   pname = "openbabel";
@@ -19,18 +33,19 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ cmake pkg-config ];
 
-  pythonMajorMinor = "${python.sourceVersion.major}.${python.sourceVersion.minor}";
-
-  cmakeFlags = [
-    "-DRUN_SWIG=ON"
-    "-DPYTHON_BINDINGS=ON"
-  ];
+  preConfigure = ''
+    cmakeFlagsArray+=(
+      "-DRUN_SWIG=ON"
+      "-DPYTHON_BINDINGS=ON"
+      "-DPYTHON_INSTDIR=$out/${python.sitePackages}"
+    )
+  '';
 
   # Setuptools only accepts PEP 440 version strings. The "unstable" identifier
   # can not be used. Instead we pretend to be the 3.2 beta release.
   postFixup = ''
-    cat <<EOF > $out/lib/python$pythonMajorMinor/site-packages/setup.py
-    from distutils.core import setup
+    cat << EOF > $out/${python.sitePackages}/setup.py
+    from setuptools import setup
 
     setup(
         name = 'pyopenbabel',

From 628efa585002d487be18b4ce8d44c197520638f1 Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@uni-jena.de>
Date: Fri, 2 Aug 2024 11:33:44 +0200
Subject: [PATCH 2/3] python3Packages.openbabel-bindings: move openbabel C++
 libs to buildInputs

---
 .../development/python-modules/openbabel-bindings/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/openbabel-bindings/default.nix b/pkgs/development/python-modules/openbabel-bindings/default.nix
index b0e935061743..4ab6b77465c1 100644
--- a/pkgs/development/python-modules/openbabel-bindings/default.nix
+++ b/pkgs/development/python-modules/openbabel-bindings/default.nix
@@ -8,9 +8,9 @@
 buildPythonPackage rec {
   inherit (openbabel) pname version;
 
-  src = "${openbabel}/lib/python${python.sourceVersion.major}.${python.sourceVersion.minor}/site-packages";
+  src = "${openbabel}/${python.sitePackages}";
 
-  nativeBuildInputs = [ openbabel ];
+  buildInputs = [ openbabel ];
 
   # these env variables are used by the bindings to find libraries
   # they need to be included explicitly in your nix-shell for

From 3525519558670643f8d3c90fc71084f52a83f4cf Mon Sep 17 00:00:00 2001
From: Phillip Seeber <phillip.seeber@uni-jena.de>
Date: Fri, 2 Aug 2024 11:34:05 +0200
Subject: [PATCH 3/3] =?UTF-8?q?openbabel:=20enable=20maestro=20and=20Schr?=
 =?UTF-8?q?=C3=B6dinger=20file=20support?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pkgs/development/libraries/openbabel/default.nix | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pkgs/development/libraries/openbabel/default.nix b/pkgs/development/libraries/openbabel/default.nix
index 259fc8ce6903..c08053d6786b 100644
--- a/pkgs/development/libraries/openbabel/default.nix
+++ b/pkgs/development/libraries/openbabel/default.nix
@@ -12,6 +12,9 @@
 , pkg-config
 , swig
 , rapidjson
+, boost
+, maeparser
+, coordgenlibs
 }:
 
 stdenv.mkDerivation rec {
@@ -29,7 +32,7 @@ stdenv.mkDerivation rec {
     sed '1i#include <ctime>' -i include/openbabel/obutil.h # gcc12
   '';
 
-  buildInputs = [ perl zlib libxml2 eigen python cairo pcre swig rapidjson ];
+  buildInputs = [ perl zlib libxml2 eigen python cairo pcre swig rapidjson boost maeparser coordgenlibs ];
 
   nativeBuildInputs = [ cmake pkg-config ];