1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
|
{ stdenv
, lib
, fetchFromGitHub
, makeDesktopItem
, python3
, python3Packages
, netcdf
, glew
, glm
, libpng
, libxml2
, freetype
, msgpack
, qt5
}:
let
pname = "pymol";
description = "A Python-enhanced molecular graphics tool";
desktopItem = makeDesktopItem {
name = pname;
exec = pname;
desktopName = "PyMol Molecular Graphics System";
genericName = "Molecular Modeler";
comment = description;
icon = pname;
mimeTypes = [
"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
python3Packages.buildPythonApplication rec {
inherit pname;
version = "2.5.0";
src = fetchFromGitHub {
owner = "schrodinger";
repo = "pymol-open-source";
rev = "v${version}";
sha256 = "sha256-JdsgcVF1w1xFPZxVcyS+GcWg4a1Bd4SvxFOuSdlz9SM=";
};
nativeBuildInputs = [ qt5.wrapQtAppsHook ];
buildInputs = [ python3Packages.numpy python3Packages.pyqt5 glew glm libpng libxml2 freetype msgpack netcdf ];
env.NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";
hardeningDisable = [ "format" ];
installPhase = ''
python setup.py install --home="$out"
runHook postInstall
'';
postInstall = with python3Packages; ''
wrapProgram $out/bin/pymol \
--prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]}
mkdir -p "$out/share/icons/"
ln -s ../../lib/python/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg"
cp -r "${desktopItem}/share/applications/" "$out/share/"
'';
preFixup = ''
wrapQtApp "$out/bin/pymol"
'';
meta = with lib; {
inherit description;
mainProgram = "pymol";
homepage = "https://www.pymol.org/";
license = licenses.mit;
maintainers = with maintainers; [ samlich ];
};
}
|