3 files changed, 158 insertions, 0 deletions
diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix
new file mode 100644
index 000000000000..c85e1143d103
--- /dev/null
+++ b/pkgs/applications/science/chemistry/jmol/default.nix
@@ -0,0 +1,44 @@
+{ stdenv
+, fetchurl
+, unzip
+, jre
+}:
+
+stdenv.mkDerivation rec {
+  version = "${baseVersion}.${patchVersion}";
+  baseVersion = "14.29";
+  patchVersion = "12";
+  pname = "jmol";
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
+    sha256 = "1ndq9am75janshrnk26334z1nmyh3k4bp20napvf2zv0lfp8k3bv";
+  };
+
+  buildInputs = [
+    jre
+  ];
+
+  installPhase = ''
+    mkdir -p "$out/share/jmol"
+    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"
+  '';
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+     description = "A Java 3D viewer for chemical structures";
+     homepage = https://sourceforge.net/projects/jmol;
+     license = licenses.lgpl2;
+     platforms = platforms.all;
+     maintainers = with maintainers; [ timokau ];
+  };
+}
+
diff --git a/pkgs/applications/science/math/palp/default.nix b/pkgs/applications/science/math/palp/default.nix
new file mode 100644
index 000000000000..3484c369db3b
--- /dev/null
+++ b/pkgs/applications/science/math/palp/default.nix
@@ -0,0 +1,67 @@
+{ stdenv
+, fetchurl
+, dimensions ? 6 # works for <= dimensions dimensions, but is only optimized for that exact value
+, doSymlink ? true # symlink the executables to the default location (without dimension postfix)
+}:
+
+stdenv.mkDerivation rec {
+  version = "2.1";
+  dim = toString dimensions;
+  name = "palp-${dim}d-${version}";
+
+  src = fetchurl {
+    url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-${version}.tar.gz";
+    sha256 = "1s7s2lc5f0ig1yy7ygsh3sddm3sbq4mxwybqsj8lp9wjdxs7qfrs";
+  };
+
+  hardeningDisable = [ "format" ];
+
+  preBuild = ''
+      echo Building PALP optimized for ${dim} dimensions
+      sed -i "s/^#define[^a-zA-Z]*POLY_Dmax.*/#define POLY_Dmax ${dim}/" Global.h
+  '';
+
+  installPhase = ''
+    mkdir -p "$out/bin"
+    for file in poly class cws nef mori; do
+        cp -p $file.x "$out/bin/$file-${dim}d.x"
+    done
+  '' + stdenv.lib.optionalString doSymlink ''
+    cd "$out/bin"
+    for file in poly class cws nef mori; do
+        ln -sf $file-6d.x $file.x
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A Package for Analyzing Lattice Polytopes";
+    longDescription = ''
+      A Package for Analyzing Lattice Polytopes (PALP) is a set of C
+      programs for calculations with lattice polytopes and applications to
+      toric geometry.
+
+      It contains routines for vertex and facet enumeration, computation of
+      incidences and symmetries, as well as completion of the set of lattice
+      points in the convex hull of a given set of points. In addition, there
+      are procedures specialised to reflexive polytopes such as the
+      enumeration of reflexive subpolytopes, and applications to toric
+      geometry and string theory, like the computation of Hodge data and
+      fibration structures for toric Calabi-Yau varieties.  The package is
+      well tested and optimised in speed as it was used for time consuming
+      tasks such as the classification of reflexive polyhedra in 4
+      dimensions and the creation and manipulation of very large lists of
+      5-dimensional polyhedra.
+
+      While originally intended for low-dimensional applications, the
+      algorithms work in any dimension and our key routine for vertex and
+      facet enumeration compares well with existing packages.
+    '';
+    homepage = http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html;
+    # Just a link on the website pointing to gpl -- now gplv3. When the last
+    # version was released that pointed to gplv2 however, so thats probably
+    # the right license.
+    license = licenses.gpl2;
+    maintainers = with maintainers; [ timokau ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/applications/science/math/pynac/default.nix b/pkgs/applications/science/math/pynac/default.nix
new file mode 100644
index 000000000000..fd566abd9a9a
--- /dev/null
+++ b/pkgs/applications/science/math/pynac/default.nix
@@ -0,0 +1,47 @@
+{ stdenv
+, fetchFromGitHub
+, autoreconfHook
+, pkgconfig
+, flint
+, gmp
+, python2
+, singular
+}:
+
+stdenv.mkDerivation rec {
+  version = "0.7.19";
+  name = "pynac-${version}";
+
+  src = fetchFromGitHub {
+    owner = "pynac";
+    repo = "pynac";
+    rev = "pynac-${version}";
+    sha256 = "132bibvapm245c5xy29j3xmjs0pawvw7lv05374m8vv1m39127d3";
+  };
+
+  buildInputs = [
+    flint
+    gmp
+    singular
+    singular
+    python2
+  ];
+
+  nativeBuildInputs = [
+    autoreconfHook
+    pkgconfig
+  ];
+
+  meta = with stdenv.lib; {
+    description = "Python is Not a CAS -- modified version of Ginac";
+    longDescription = ''
+      Pynac -- "Python is Not a CAS" is a modified version of Ginac that
+      replaces the depency of GiNaC on CLN by a dependency instead of Python.
+      It is a lite version of GiNaC as well, not implementing all the features
+      of the full GiNaC, and it is *only* meant to be used as a Python library.
+    '';
+    homepage    = http://pynac.org;
+    maintainers = with maintainers; [ timokau ];
+    platforms   = platforms.linux;
+  };
+}