···

       
1
       
 
       
{ lib

     

       
2
       
 
       
, buildPythonPackage

     

       
3
       
 
       
, fetchFromGitHub

     

       
4
       
-
       
, fetchzip

     

       
5
       
 
       
, cmake

     

       
0
       
 
       

     

       
6
       
 
       
, boost

     

       
7
       
 
       
, catch2

     

       
8
       
 
       
, inchi

     
···

       
15
       
 
       
, numpy

     

       
16
       
 
       
, pandas

     

       
17
       
 
       
, pillow

     

       
18
       
-
       
, git

     

       
19
       
 
       
}:

     

       
20
       
 
       
let

     

       
21
       
 
       
  external = {

     

       
22
       
-
       
    avalon = fetchzip {

     

       
23
       
-
       
      url = "http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar";

     

       
24
       
-
       
      sha256 = "0nhxfxckb5a5qs0g148f55yarhncqjgjzcvdskkv9rxi2nrs7160";

     

       
25
       
-
       
      stripRoot = false;

     

       
0
       
 
       

     

       
26
       
 
       
    };

     

       
27
       
 
       
    yaehmop = fetchFromGitHub {

     

       
28
       
 
       
      owner = "greglandrum";

     

       
29
       
 
       
      repo = "yaehmop";

     

       
30
       
-
       
      rev = "cfb5aeebbdf5ae93c4f4eeb14c7a507dea54ae9e";

     

       
31
       
-
       
      sha256 = "sha256-QMnc5RyHlY3giw9QmrkGntiA+Srs7OhCIKs9GGo5DfQ=";

     

       
32
       
 
       
    };

     

       
33
       
 
       
    freesasa = fetchFromGitHub {

     

       
34
       
 
       
      owner = "mittinatten";

     

       
35
       
 
       
      repo = "freesasa";

     

       
36
       
-
       
      rev = "2.1.1";

     

       
37
       
-
       
      sha256 = "sha256-fUJvLDTVhpBWl9MavZwp0kAO5Df1QuHEKqe20CXNfcg=";

     

       
38
       
 
       
    };

     

       
39
       
 
       
  };

     

       
40
       
 
       
in

     

       
41
       
 
       
buildPythonPackage rec {

     

       
42
       
 
       
  pname = "rdkit";

     

       
43
       
-
       
  version = "2022.03.5";

     

       
44
       
 
       
  format = "other";

     

       
45
       
 
       


     

       
46
       
 
       
  src =

     
···

       
51
       
 
       
      owner = pname;

     

       
52
       
 
       
      repo = pname;

     

       
53
       
 
       
      rev = "Release_${versionTag}";

     

       
54
       
-
       
      sha256 = "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9";

     

       
55
       
 
       
    };

     

       
56
       
 
       


     

       
57
       
 
       
  unpackPhase = ''

     

       
58
       
-
       
    mkdir -p source/External/AvalonTools/avalon source/External/YAeHMOP/yaehmop source/External/FreeSASA/freesasa

     

       
59
       
-
       
    cp -r ${src}/* source

     

       
60
       
-
       
    cp -r ${external.avalon}/SourceDistribution/* source/External/AvalonTools/avalon

     

       
61
       
-
       
    cp -r ${external.yaehmop}/* source/External/YAeHMOP/yaehmop

     

       
62
       
-
       
    cp -r ${external.freesasa}/* source/External/FreeSASA/freesasa

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
63
       
 
       


     

       
64
       
-
       
    find source -type d -exec chmod 755 {} +

     

       
65
       
-
       
    cp source/External/FreeSASA/freesasa2.c source/External/FreeSASA/freesasa/src

     

       
66
       
-
       
    ln -s ${rapidjson} source/External/rapidjson-1.1.0

     

       
67
       
 
       
  '';

     

       
68
       
-
       


     

       
69
       
-
       
  sourceRoot = "source";

     

       
70
       
 
       


     

       
71
       
 
       
  nativeBuildInputs = [

     

       
72
       
 
       
    cmake

     

       
73
       
-
       
    git # required by freesasa

     

       
74
       
 
       
  ];

     

       
75
       
 
       


     

       
76
       
 
       
  buildInputs = [

     

       
77
       
 
       
    boost

     

       
78
       
-
       
    catch2

     

       
79
       
-
       
    inchi

     

       
80
       
-
       
    eigen

     

       
81
       
 
       
    cairo

     

       
82
       
-
       
    rapidjson

     

       
83
       
 
       
  ];

     

       
84
       
 
       


     

       
85
       
 
       
  propagatedBuildInputs = [

     
···

       
95
       
 
       
  dontUseSetuptoolsCheck = true;

     

       
96
       
 
       


     

       
97
       
 
       
  preConfigure = ''

     

       
98
       
-
       
    # Don't want this contacting the git remote during the build

     

       
99
       
-
       
    substituteInPlace External/YAeHMOP/CMakeLists.txt --replace \

     

       
100
       
-
       
      'GIT_TAG master' 'DOWNLOAD_COMMAND true'

     

       
101
       
-
       


     

       
102
       
 
       
    # Since we can't expand with bash in cmakeFlags

     

       
103
       
 
       
    cmakeFlags="$cmakeFlags -DPYTHON_NUMPY_INCLUDE_PATH=$(${python}/bin/python -c 'import numpy; print(numpy.get_include())')"

     

       
104
       
 
       
    cmakeFlags="$cmakeFlags -DFREESASA_DIR=$PWD/External/FreeSASA/freesasa"

     
···

       
114
       
 
       
    "-DEIGEN3_INCLUDE_DIR=${eigen}/include/eigen3"

     

       
115
       
 
       
    "-DRDK_INSTALL_INTREE=OFF"

     

       
116
       
 
       
    "-DRDK_INSTALL_STATIC_LIBS=OFF"

     

       
117
       
-
       
    "-DRDK_INSTALL_COMIC_FONTS=OFF"

     

       
118
       
 
       
    "-DRDK_BUILD_INCHI_SUPPORT=ON"

     

       
119
       
 
       
    "-DRDK_BUILD_AVALON_SUPPORT=ON"

     

       
120
       
 
       
    "-DRDK_BUILD_FREESASA_SUPPORT=ON"

     
···

       
145
       
 
       
  '';

     

       
146
       
 
       


     

       
147
       
 
       
  pythonImportsCheck = [

     

       
148
       
-
       
     "rdkit"

     

       
149
       
-
       
     "rdkit.Chem"

     

       
150
       
-
       
     "rdkit.Chem.AllChem"

     

       
151
       
 
       
  ];

     

       
152
       
 
       


     

       
153
       
 
       
  meta = with lib; {

     

···

       
1
       
 
       
{ lib

     

       
2
       
 
       
, buildPythonPackage

     

       
3
       
 
       
, fetchFromGitHub

     

       
0
       
 
       

     

       
4
       
 
       
, cmake

     

       
5
       
+
       
, comic-neue

     

       
6
       
 
       
, boost

     

       
7
       
 
       
, catch2

     

       
8
       
 
       
, inchi

     
···

       
15
       
 
       
, numpy

     

       
16
       
 
       
, pandas

     

       
17
       
 
       
, pillow

     

       
0
       
 
       

     

       
18
       
 
       
}:

     

       
19
       
 
       
let

     

       
20
       
 
       
  external = {

     

       
21
       
+
       
    avalon = fetchFromGitHub {

     

       
22
       
+
       
      owner = "rohdebe1";

     

       
23
       
+
       
      repo = "ava-formake";

     

       
24
       
+
       
      rev = "AvalonToolkit_2.0.2";

     

       
25
       
+
       
      hash = "sha256-YI39OknHiSyArNGqRKrSVzEJnFc1xJ0W3UcTZrTKeME=";

     

       
26
       
 
       
    };

     

       
27
       
 
       
    yaehmop = fetchFromGitHub {

     

       
28
       
 
       
      owner = "greglandrum";

     

       
29
       
 
       
      repo = "yaehmop";

     

       
30
       
+
       
      rev = "v2022.09.1";

     

       
31
       
+
       
      hash = "sha256-QMnc5RyHlY3giw9QmrkGntiA+Srs7OhCIKs9GGo5DfQ=";

     

       
32
       
 
       
    };

     

       
33
       
 
       
    freesasa = fetchFromGitHub {

     

       
34
       
 
       
      owner = "mittinatten";

     

       
35
       
 
       
      repo = "freesasa";

     

       
36
       
+
       
      rev = "2.0.3";

     

       
37
       
+
       
      hash = "sha256-7E+imvfDAJFnXQRWb5hNaSu+Xrf9NXeIKc9fl+o3yHQ=";

     

       
38
       
 
       
    };

     

       
39
       
 
       
  };

     

       
40
       
 
       
in

     

       
41
       
 
       
buildPythonPackage rec {

     

       
42
       
 
       
  pname = "rdkit";

     

       
43
       
+
       
  version = "2022.09.1";

     

       
44
       
 
       
  format = "other";

     

       
45
       
 
       


     

       
46
       
 
       
  src =

     
···

       
51
       
 
       
      owner = pname;

     

       
52
       
 
       
      repo = pname;

     

       
53
       
 
       
      rev = "Release_${versionTag}";

     

       
54
       
+
       
      hash = "sha256-AaawjCv3/ShByOKU0c37/hjuyfD7NhFC8UngDoG7C0s=";

     

       
55
       
 
       
    };

     

       
56
       
 
       


     

       
57
       
 
       
  unpackPhase = ''

     

       
58
       
+
       
    cp -r $src/* .

     

       
59
       
+
       
    find . -type d -exec chmod +w {} +

     

       
60
       
+
       


     

       
61
       
+
       
    mkdir External/AvalonTools/avalon

     

       
62
       
+
       
    ln -s ${external.avalon}/* External/AvalonTools/avalon

     

       
63
       
+
       


     

       
64
       
+
       
    mkdir External/YAeHMOP/yaehmop

     

       
65
       
+
       
    ln -s ${external.yaehmop}/* External/YAeHMOP/yaehmop

     

       
66
       
+
       


     

       
67
       
+
       
    mkdir -p External/FreeSASA/freesasa

     

       
68
       
+
       
    cp -r ${external.freesasa}/* External/FreeSASA/freesasa

     

       
69
       
+
       
    chmod +w External/FreeSASA/freesasa/src

     

       
70
       
+
       
    cp External/FreeSASA/freesasa2.c External/FreeSASA/freesasa/src

     

       
71
       
 
       


     

       
72
       
+
       
    ln -s ${rapidjson} External/rapidjson-1.1.0

     

       
73
       
+
       
    ln -s ${comic-neue}/share/fonts/truetype/ComicNeue-Regular.ttf Data/Fonts/

     

       
0
       
 
       

     

       
74
       
 
       
  '';

     

       
0
       
 
       

     

       
0
       
 
       

     

       
75
       
 
       


     

       
76
       
 
       
  nativeBuildInputs = [

     

       
77
       
 
       
    cmake

     

       
0
       
 
       

     

       
78
       
 
       
  ];

     

       
79
       
 
       


     

       
80
       
 
       
  buildInputs = [

     

       
81
       
 
       
    boost

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
82
       
 
       
    cairo

     

       
0
       
 
       

     

       
83
       
 
       
  ];

     

       
84
       
 
       


     

       
85
       
 
       
  propagatedBuildInputs = [

     
···

       
95
       
 
       
  dontUseSetuptoolsCheck = true;

     

       
96
       
 
       


     

       
97
       
 
       
  preConfigure = ''

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
0
       
 
       

     

       
98
       
 
       
    # Since we can't expand with bash in cmakeFlags

     

       
99
       
 
       
    cmakeFlags="$cmakeFlags -DPYTHON_NUMPY_INCLUDE_PATH=$(${python}/bin/python -c 'import numpy; print(numpy.get_include())')"

     

       
100
       
 
       
    cmakeFlags="$cmakeFlags -DFREESASA_DIR=$PWD/External/FreeSASA/freesasa"

     
···

       
110
       
 
       
    "-DEIGEN3_INCLUDE_DIR=${eigen}/include/eigen3"

     

       
111
       
 
       
    "-DRDK_INSTALL_INTREE=OFF"

     

       
112
       
 
       
    "-DRDK_INSTALL_STATIC_LIBS=OFF"

     

       
0
       
 
       

     

       
113
       
 
       
    "-DRDK_BUILD_INCHI_SUPPORT=ON"

     

       
114
       
 
       
    "-DRDK_BUILD_AVALON_SUPPORT=ON"

     

       
115
       
 
       
    "-DRDK_BUILD_FREESASA_SUPPORT=ON"

     
···

       
140
       
 
       
  '';

     

       
141
       
 
       


     

       
142
       
 
       
  pythonImportsCheck = [

     

       
143
       
+
       
    "rdkit"

     

       
144
       
+
       
    "rdkit.Chem"

     

       
145
       
+
       
    "rdkit.Chem.AllChem"

     

       
146
       
 
       
  ];

     

       
147
       
 
       


     

       
148
       
 
       
  meta = with lib; {