Merge pull request #37855 from Mounium/chem3

jmol init, pymol -> 2.1.0 and tidied up all-packages.nix

pkgs/applications/science/chemistry/jmol/default.nix

@@ -1,9 +1,20 @@
 { stdenv
 , fetchurl
 , unzip
+, makeDesktopItem
 , jre
 }:
 
+let
+  desktopItem = makeDesktopItem {
+    name = "jmol";
+    exec = "jmol";
+    desktopName = "JMol";
+    genericName = "Molecular Modeler";
+    mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;";
+    categories = "Graphics;Education;Science;Chemistry;";
+  };
+in
 stdenv.mkDerivation rec {
   version = "${baseVersion}.${patchVersion}";
   baseVersion = "14.29";
@@ -16,19 +27,18 @@ stdenv.mkDerivation rec {
     sha256 = "1ndq9am75janshrnk26334z1nmyh3k4bp20napvf2zv0lfp8k3bv";
   };
 
-  buildInputs = [
+  patchPhase = ''
-    jre
+    sed -i -e "4s:.*:command=${jre}/bin/java:" -e "10s:.*:jarpath=$out/share/jmol/Jmol.jar:" -e "11,21d" jmol
-  ];
+  '';
 
   installPhase = ''
-    mkdir -p "$out/share/jmol"
+    mkdir -p "$out/share/jmol" "$out/bin"
-    mkdir -p "$out/bin"
 
     ${unzip}/bin/unzip jsmol.zip -d "$out/share/"
 
-    sed -i -e 's|command=java|command=${jre}/bin/java|' jmol.sh
     cp *.jar jmol.sh "$out/share/jmol"
-    ln -s $out/share/jmol/jmol.sh "$out/bin/jmol"
+    cp -r ${desktopItem}/share/applications $out/share
+    cp jmol $out/bin
   '';
 
   enableParallelBuilding = true;
@@ -38,7 +48,6 @@ stdenv.mkDerivation rec {
      homepage = https://sourceforge.net/projects/jmol;
      license = licenses.lgpl2;
      platforms = platforms.all;
-     maintainers = with maintainers; [ timokau ];
+     maintainers = with maintainers; [ timokau mounium ];
   };
 }
-

pkgs/applications/science/chemistry/pymol/default.nix

@@ -1,14 +1,14 @@
 { stdenv, fetchurl, makeDesktopItem
 , python3, python3Packages
-, glew, freeglut, libpng, libxml2, tk, freetype }:
+, glew, freeglut, libpng, libxml2, tk, freetype, libmsgpack }:
 
 
 with stdenv.lib;
 
 let
   pname = "pymol";
-  ver_maj = "1.8";
+  ver_maj = "2";
-  ver_min = "4";
+  ver_min = "1";
   version = "${ver_maj}.${ver_min}.0";
   description = "A Python-enhanced molecular graphics tool";
 
@@ -16,7 +16,7 @@ let
     name = "${pname}";
     exec = "${pname}";
     desktopName = "PyMol Molecular Graphics System";
-    genericName = "Molecular Modeller";
+    genericName = "Molecular Modeler";
     comment = description;
     mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;";
     categories = "Graphics;Education;Science;Chemistry;";
@@ -26,10 +26,10 @@ python3Packages.buildPythonApplication {
   name = "pymol-${version}";
   src = fetchurl {
     url = "mirror://sourceforge/project/pymol/pymol/${ver_maj}/pymol-v${version}.tar.bz2";
-    sha256 = "0yfj8g5yic9zz6f0bw2n8h6ifvgsn8qvhq84alixsi28wzppn55n";
+    sha256 = "1qpacd5w4r9a0nm5iqmkd92ym3ai00dp7v61cwd6jgakk6wfps3s";
   };
 
-  buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype ];
+  buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype libmsgpack ];
   NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";
 
   installPhase = ''

pkgs/top-level/all-packages.nix

@@ -2780,8 +2780,6 @@ with pkgs;
 
   gvolicon = callPackage ../tools/audio/gvolicon {};
 
-  gwyddion = callPackage ../applications/science/chemistry/gwyddion {};
-
   gzip = callPackage ../tools/compression/gzip { };
 
   gzrt = callPackage ../tools/compression/gzrt { };
@@ -3124,8 +3122,6 @@ with pkgs;
 
   jmespath = callPackage ../development/tools/jmespath { };
 
-  jmol = callPackage ../applications/science/chemistry/jmol { };
-
   jmtpfs = callPackage ../tools/filesystems/jmtpfs { };
 
   jnettop = callPackage ../tools/networking/jnettop { };
@@ -3754,8 +3750,6 @@ with pkgs;
 
   modsecurity_standalone = callPackage ../tools/security/modsecurity { };
 
-  molden = callPackage ../applications/science/chemistry/molden { };
-
   molly-guard = callPackage ../os-specific/linux/molly-guard { };
 
   moneyplex = callPackage ../applications/office/moneyplex { };
@@ -7167,8 +7161,6 @@ with pkgs;
 
   ocropus = callPackage ../applications/misc/ocropus { };
 
-  octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; };
-
   inherit (callPackages ../development/interpreters/perl {}) perl perl522 perl524 perl526;
 
   pachyderm = callPackage ../applications/networking/cluster/pachyderm { };
@@ -14859,10 +14851,6 @@ with pkgs;
 
   avidemux = libsForQt5.callPackage ../applications/video/avidemux { };
 
-  avogadro = callPackage ../applications/science/chemistry/avogadro {
-    eigen = eigen2;
-  };
-
   avrdudess = callPackage ../applications/misc/avrdudess { };
 
   avxsynth = callPackage ../applications/video/avxsynth {
@@ -17419,8 +17407,6 @@ with pkgs;
 
   puremapping = callPackage ../applications/audio/pd-plugins/puremapping { };
 
-  pymol = callPackage ../applications/science/chemistry/pymol { };
-
   pybitmessage = callPackage ../applications/networking/instant-messengers/pybitmessage { };
 
   pythonmagick = callPackage ../applications/graphics/PythonMagick { };
@@ -19751,6 +19737,22 @@ with pkgs;
 
   ### SCIENCE
 
+  ### SCIENCE/CHEMISTY
+
+  avogadro = callPackage ../applications/science/chemistry/avogadro {
+    eigen = eigen2;
+  };
+
+  gwyddion = callPackage ../applications/science/chemistry/gwyddion {};
+
+  jmol = callPackage ../applications/science/chemistry/jmol { };
+
+  molden = callPackage ../applications/science/chemistry/molden { };
+
+  octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; };
+
+  pymol = callPackage ../applications/science/chemistry/pymol { };
+
   ### SCIENCE/GEOMETRY
 
   drgeo = callPackage ../applications/science/geometry/drgeo {