Merge pull request #130359 from sheepforce/avogadro2

pkgs/applications/science/chemistry/avogadro2/default.nix

@@ -0,0 +1,37 @@
+{ lib, stdenv, fetchFromGitHub, cmake, eigen, avogadrolibs, molequeue, hdf5
+, openbabel, qttools, wrapQtAppsHook
+}:
+
+stdenv.mkDerivation rec {
+  pname = "avogadro2";
+  version = "1.94.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "avogadroapp";
+    rev = version;
+    sha256 = "6RaiX23YUMfTYAuSighcLGGlJtqeydNgi3PWGF77Jp8=";
+  };
+
+  nativeBuildInputs = [ cmake wrapQtAppsHook ];
+
+  buildInputs = [
+    avogadrolibs
+    molequeue
+    eigen
+    hdf5
+    qttools
+  ];
+
+  propagatedBuildInputs = [ openbabel ];
+
+  qtWrapperArgs = [ "--prefix PATH : ${openbabel}/bin" ];
+
+  meta = with lib; {
+    description = "Molecule editor and visualizer";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/avogadroapp";
+    platforms = platforms.mesaPlatforms;
+    license = licenses.bsd3;
+  };
+}

pkgs/development/libraries/science/chemistry/avogadrolibs/default.nix

@@ -0,0 +1,68 @@
+{ lib, stdenv, fetchFromGitHub, cmake, zlib, eigen, libGL, doxygen, spglib
+, mmtf-cpp, glew, python3, libarchive, libmsym, msgpack, qttools, wrapQtAppsHook
+}:
+
+let
+  pythonWP = python3.withPackages (p: with p; [ openbabel-bindings numpy ]);
+
+  # Pure data repositories
+  moleculesRepo = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "molecules";
+    rev = "1.0.0";
+    sha256 = "guY6osnpv7Oqt+HE1BpIqL10POp+x8GAci2kY0bLmqg=";
+  };
+  crystalsRepo = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = "crystals";
+    rev = "1.0.1";
+    sha256 = "sH/WuvLaYu6akOc3ssAKhnxD8KNoDxuafDSozHqJZC4=";
+  };
+
+in stdenv.mkDerivation rec {
+  pname = "avogadrolibs";
+  version = "1.94.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = pname;
+    rev = version;
+    sha256 = "6bChJhqrjOxeEWZBNToq3JExHPu7DUMsEHWBDe75zAo=";
+  };
+
+  postUnpack = ''
+    cp -r ${moleculesRepo} molecules
+    cp -r ${crystalsRepo} crystals
+  '';
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [
+    eigen
+    zlib
+    libGL
+    spglib
+    mmtf-cpp
+    glew
+    libarchive
+    libmsym
+    msgpack
+    qttools
+  ];
+
+  postFixup = ''
+    substituteInPlace $out/lib/cmake/${pname}/AvogadroLibsConfig.cmake \
+      --replace "''${AvogadroLibs_INSTALL_PREFIX}/$out" "''${AvogadroLibs_INSTALL_PREFIX}"
+  '';
+
+  meta = with lib; {
+    description = "Molecule editor and visualizer";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/avogadrolibs";
+    platforms = platforms.linux;
+    license = licenses.gpl2Only;
+  };
+}

pkgs/development/libraries/science/chemistry/libmsym/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, lib, fetchFromGitHub, cmake } :
+
+stdenv.mkDerivation rec {
+  pname = "libmsym";
+  version = "0.2.3";
+
+  src = fetchFromGitHub  {
+    owner = "mcodev31";
+    repo = pname;
+    rev = "v${version}";
+    sha256= "k+OEwrA/saupP/wX6Ii5My0vffiJ0X9xMCTrliMSMik=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  meta = with lib; {
+    description = " molecular point group symmetry lib";
+    homepage = "https://github.com/rcsb/mmtf-cpp";
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

pkgs/development/libraries/science/chemistry/mmtf-cpp/default.nix

@@ -0,0 +1,25 @@
+{ stdenv, lib, fetchFromGitHub, cmake, msgpack } :
+
+stdenv.mkDerivation rec {
+  pname = "mmtf-cpp";
+  version = "1.0.0";
+
+  src = fetchFromGitHub  {
+    owner = "rcsb";
+    repo = pname;
+    rev = "v${version}";
+    sha256= "17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ msgpack ];
+
+  meta = with lib; {
+    description = "A library of exchange-correlation functionals with arbitrary-order derivatives";
+    homepage = "https://github.com/rcsb/mmtf-cpp";
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

pkgs/development/libraries/science/chemistry/molequeue/default.nix

@@ -0,0 +1,33 @@
+{ lib, stdenv, fetchFromGitHub, cmake, qttools, wrapQtAppsHook }:
+
+stdenv.mkDerivation rec {
+  pname = "molequeue";
+  version = "0.9.0";
+
+  src = fetchFromGitHub {
+    owner = "OpenChemistry";
+    repo = pname;
+    rev = version;
+    sha256 = "+NoY8YVseFyBbxc3ttFWiQuHQyy1GN8zvV1jGFjmvLg=";
+  };
+
+  nativeBuildInputs = [
+    cmake
+    wrapQtAppsHook
+  ];
+
+  buildInputs = [ qttools ];
+
+  postFixup = ''
+    substituteInPlace $out/lib/cmake/molequeue/MoleQueueConfig.cmake \
+      --replace "''${MoleQueue_INSTALL_PREFIX}/$out" "''${MoleQueue_INSTALL_PREFIX}"
+  '';
+
+  meta = with lib; {
+    description = "Desktop integration of high performance computing resources";
+    maintainers = with maintainers; [ sheepforce ];
+    homepage = "https://github.com/OpenChemistry/molequeue";
+    platforms = platforms.linux;
+    license = licenses.bsd3;
+  };
+}

pkgs/top-level/all-packages.nix

@@ -6844,6 +6844,8 @@ in
 
   libmesode = callPackage ../development/libraries/libmesode {};
 
+  libmsym = callPackage ../development/libraries/science/chemistry/libmsym { };
+
   libnabo = callPackage ../development/libraries/libnabo { };
 
   libngspice = callPackage ../development/libraries/libngspice { };
@@ -14082,6 +14084,8 @@ in
 
   mkdocs = callPackage ../development/tools/documentation/mkdocs { };
 
+  mmtf-cpp = callPackage ../development/libraries/science/chemistry/mmtf-cpp { };
+
   mockgen = callPackage ../development/tools/mockgen { };
 
   modd = callPackage ../development/tools/modd { };
@@ -30101,6 +30105,12 @@ in
     eigen = eigen2;
   };
 
+  avogadrolibs = libsForQt5.callPackage ../development/libraries/science/chemistry/avogadrolibs { };
+
+  molequeue = libsForQt5.callPackage ../development/libraries/science/chemistry/molequeue { };
+
+  avogadro2 = libsForQt5.callPackage ../applications/science/chemistry/avogadro2 { };
+
   chemtool = callPackage ../applications/science/chemistry/chemtool { };
 
   cp2k = callPackage ../applications/science/chemistry/cp2k { };