diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index c85e1143d10..4c4278c30fa 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/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 = [ - jre - ]; + patchPhase = '' + 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/bin" + mkdir -p "$out/share/jmol" "$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 $out/bin ''; enableParallelBuilding = true; @@ -38,7 +48,6 @@ stdenv.mkDerivation rec { homepage = https://sourceforge.net/projects/jmol; license = licenses.lgpl2; platforms = platforms.all; - maintainers = with maintainers; [ timokau ]; + maintainers = with maintainers; [ timokau mounium ]; }; } - diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index 39c027706ee..e7dd04377be 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -1,14 +1,14 @@ { stdenv, fetchurl, makeDesktopItem , python3, python3Packages -, glew, freeglut, libpng, libxml2, tk, freetype }: +, glew, freeglut, libpng, libxml2, tk, freetype, libmsgpack }: with stdenv.lib; let pname = "pymol"; - ver_maj = "1.8"; - ver_min = "4"; + ver_maj = "2"; + ver_min = "1"; version = "${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 = '' diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index b3af7556633..0ab4ae69c50 100644 --- a/pkgs/top-level/all-packages.nix +++ b/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 {