mirror of
https://github.com/NixOS/nixpkgs.git
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Merge pull request #107268 from rmcgibbo/rdkit
This commit is contained in:
commit
70d71ec338
29
pkgs/development/libraries/coordgenlibs/default.nix
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29
pkgs/development/libraries/coordgenlibs/default.nix
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@ -0,0 +1,29 @@
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{ fetchFromGitHub
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, lib
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, stdenv
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, boost
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, zlib
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, cmake
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, maeparser
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}:
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stdenv.mkDerivation rec {
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pname = "coordgenlibs";
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version = "1.4.2";
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src = fetchFromGitHub {
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owner = "schrodinger";
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repo = pname;
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rev = "v${version}";
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sha256 = "18s3y9v6x246hapxy0cy4srnll4qqzqfx003j551l5f27b2ng8fn";
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};
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nativeBuildInputs = [ cmake ];
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buildInputs = [ boost zlib maeparser ];
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meta = with lib; {
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description = "Schrodinger-developed 2D Coordinate Generation";
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maintainers = [ maintainers.rmcgibbo ];
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license = licenses.bsd3;
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};
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}
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@ -1,4 +1,11 @@
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{ pkgs, fetchurl, lib, stdenv, unzip }:
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{ pkgs
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, fetchurl
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, lib
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, stdenv
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, unzip
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, fixDarwinDylibNames
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}:
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stdenv.mkDerivation {
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pname = "inchi";
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version = "1.05";
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@ -7,15 +14,23 @@ stdenv.mkDerivation {
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sha1 = "e3872a46d58cb321a98f4fd4b93a989fb6920b9c";
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};
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nativeBuildInputs = [ pkgs.unzip ];
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nativeBuildInputs = [ unzip ] ++ lib.optional stdenv.isDarwin fixDarwinDylibNames;
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outputs = [ "out" "doc" ];
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enableParallelBuilding = true;
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preBuild = ''
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preConfigure = ''
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cd ./INCHI_API/libinchi/gcc
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'' + lib.optionalString stdenv.isDarwin ''
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substituteInPlace makefile \
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--replace ",--version-script=libinchi.map" "" \
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--replace "LINUX_Z_RELRO = ,-z,relro" "" \
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--replace "-soname" "-install_name" \
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--replace "gcc" $CC
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'';
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installPhase = ''
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runHook preInstall
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cd ../../..
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mkdir -p $out/lib
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mkdir -p $out/include/inchi
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@ -29,6 +44,10 @@ stdenv.mkDerivation {
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runHook postInstall
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'';
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preFixup = lib.optionalString stdenv.isDarwin ''
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fixDarwinDylibNames $(find "$out" -name "*.so.*")
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'';
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postInstall =
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let
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src-doc = fetchurl {
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@ -45,7 +64,6 @@ stdenv.mkDerivation {
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homepage = "https://www.inchi-trust.org/";
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description = "IUPAC International Chemical Identifier library";
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license = licenses.lgpl2Plus;
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platforms = platforms.all;
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maintainers = with maintainers; [ rmcgibbo ];
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};
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}
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28
pkgs/development/libraries/maeparser/default.nix
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28
pkgs/development/libraries/maeparser/default.nix
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@ -0,0 +1,28 @@
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{ fetchFromGitHub
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, lib
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, stdenv
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, boost
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, zlib
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, cmake
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}:
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stdenv.mkDerivation rec {
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pname = "maeparser";
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version = "1.2.4";
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src = fetchFromGitHub {
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owner = "schrodinger";
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repo = "maeparser";
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rev = "v${version}";
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sha256 = "1qzp8d58ksy88y4fx1b0x65wycslm7zxzbb8ns28gkjh12xpzhwz";
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};
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nativeBuildInputs = [ cmake ];
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buildInputs = [ boost zlib ];
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meta = with lib; {
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description = "maestro file parser";
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maintainers = [ maintainers.rmcgibbo ];
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license = licenses.mit;
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};
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}
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157
pkgs/development/python-modules/rdkit/default.nix
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157
pkgs/development/python-modules/rdkit/default.nix
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@ -0,0 +1,157 @@
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{ lib
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, buildPythonPackage
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, fetchFromGitHub
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, fetchzip
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, cmake
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, boost
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, catch
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, inchi
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, cairo
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, eigen
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, python
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, rapidjson
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, maeparser
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, coordgenlibs
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, numpy
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, pandas
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, pillow
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, git
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}:
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let
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external = {
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avalon = fetchzip {
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url = "http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar";
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sha256 = "0nhxfxckb5a5qs0g148f55yarhncqjgjzcvdskkv9rxi2nrs7160";
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stripRoot = false;
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};
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yaehmop = fetchFromGitHub {
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owner = "greglandrum";
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repo = "yaehmop";
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rev = "1b13b52e2738a77715b1bad876e3b4e93f2b5269";
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sha256 = "1jp7wz8win4mgwxkaz2gnrgsaaqgln04n2lwgfr96isdv1klf62d";
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};
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freesasa = fetchFromGitHub
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{
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owner = "mittinatten";
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repo = "freesasa";
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rev = "2.0.3";
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sha256 = "0x686zm9fpyg5647fdgxnxgbwav99nc6ymh4bmkr2063yyda4kzc";
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};
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};
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in
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buildPythonPackage rec {
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version = "2020.09.3";
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pname = "rdkit";
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src =
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let
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versionTag = lib.replaceStrings [ "." ] [ "_" ] version;
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in
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fetchFromGitHub {
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owner = pname;
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repo = pname;
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rev = "Release_${versionTag}";
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sha256 = "1k1wvzcd1yfx4nhz3iq2aaadzdk5w6sfcb4imhvm7pkbzij0nicx";
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};
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unpackPhase = ''
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mkdir -p source/External/AvalonTools/avalon source/External/YAeHMOP/yaehmop source/External/FreeSASA/freesasa
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cp -r ${src}/* source
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cp -r ${external.avalon}/SourceDistribution/* source/External/AvalonTools/avalon
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cp -r ${external.yaehmop}/* source/External/YAeHMOP/yaehmop
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cp -r ${external.freesasa}/* source/External/FreeSASA/freesasa
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find source -type d -exec chmod 755 {} +
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cp source/External/FreeSASA/freesasa2.c source/External/FreeSASA/freesasa/src
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ln -s ${rapidjson} source/External/rapidjson-1.1.0
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'';
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sourceRoot = "source";
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nativeBuildInputs = [
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cmake
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git # required by freesasa
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];
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buildInputs = [
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boost
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catch
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inchi
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eigen
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cairo
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rapidjson
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];
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propagatedBuildInputs = [
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numpy
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pandas
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pillow
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];
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hardeningDisable = [ "format" ]; # required by yaehmop
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# doCheck = false;
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dontUseSetuptoolsBuild = true;
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dontUsePipInstall = true;
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dontUseSetuptoolsCheck = true;
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preConfigure = ''
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# Don't want this contacting the git remote during the build
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substituteInPlace External/YAeHMOP/CMakeLists.txt --replace \
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'GIT_TAG master' 'DOWNLOAD_COMMAND true'
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# Since we can't expand with bash in cmakeFlags
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cmakeFlags="$cmakeFlags -DPYTHON_NUMPY_INCLUDE_PATH=$(${python}/bin/python -c 'import numpy; print(numpy.get_include())')"
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cmakeFlags="$cmakeFlags -DFREESASA_DIR=$PWD/External/FreeSASA/freesasa"
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cmakeFlags="$cmakeFlags -DFREESASA_SRC_DIR=$PWD/External/FreeSASA/freesasa"
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cmakeFlags="$cmakeFlags -DAVALONTOOLS_DIR=$PWD/External/AvalonTools/avalon"
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'';
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cmakeFlags = [
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"-DCATCH_DIR=${catch}/include/catch"
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"-DINCHI_LIBRARY=${inchi}/lib/libinchi.so"
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"-DINCHI_LIBRARIES=${inchi}/lib/libinchi.so"
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"-DINCHI_INCLUDE_DIR=${inchi}/include/inchi"
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"-DEIGEN3_INCLUDE_DIR=${eigen}/include/eigen3"
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"-DRDK_INSTALL_INTREE=OFF"
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"-DRDK_INSTALL_STATIC_LIBS=OFF"
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"-DRDK_BUILD_INCHI_SUPPORT=ON"
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"-DRDK_BUILD_AVALON_SUPPORT=ON"
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"-DRDK_BUILD_FREESASA_SUPPORT=ON"
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"-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
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"-DRDK_BUILD_MAEPARSER_SUPPORT=ON"
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"-DMAEPARSER_DIR=${maeparser}"
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"-DRDK_BUILD_COORDGEN_SUPPORT=ON"
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"-DCOORDGEN_DIR=${coordgenlibs}"
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"-DRDK_USE_URF=OFF"
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"-DRDK_USE_FLEXBISON=OFF"
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"-DRDK_BUILD_CAIRO_SUPPORT=ON"
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"-DRDK_BUILD_THREADSAFE_SSS=ON"
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"-DRDK_TEST_MULTITHREADED=ON"
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"-DRDK_BUILD_CPP_TESTS=ON"
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"-DRDK_TEST_MULTITHREADED=ON"
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"-DPYTHON_EXECUTABLE=${python}/bin/python"
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"-DBOOST_ROOT=${boost}"
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"-DBoost_NO_SYSTEM_PATHS=ON"
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"-DBoost_NO_BOOST_CMAKE=TRUE"
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];
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checkPhase = ''
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export QT_QPA_PLATFORM='offscreen'
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export RDBASE=$(realpath ..)
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export PYTHONPATH="$out/lib/${python.libPrefix}/site-packages:$PYTHONPATH"
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(cd $RDBASE/rdkit/Chem && python $RDBASE/rdkit/TestRunner.py test_list.py)
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'';
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pythonImportsCheck = [
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"rdkit"
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"rdkit.Chem"
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"rdkit.Chem.AllChem"
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];
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meta = with lib; {
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description = "Open source toolkit for cheminformatics";
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maintainers = [ maintainers.rmcgibbo ];
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license = licenses.bsd3;
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homepage = "https://www.rdkit.org";
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};
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}
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@ -218,6 +218,8 @@ in
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containerpilot = callPackage ../applications/networking/cluster/containerpilot { };
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coordgenlibs = callPackage ../development/libraries/coordgenlibs { };
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cp437 = callPackage ../tools/misc/cp437 { };
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cpu-x = callPackage ../applications/misc/cpu-x { };
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@ -6061,6 +6063,8 @@ in
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madlang = haskell.lib.justStaticExecutables haskellPackages.madlang;
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maeparser = callPackage ../development/libraries/maeparser { };
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mailcheck = callPackage ../applications/networking/mailreaders/mailcheck { };
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maildrop = callPackage ../tools/networking/maildrop { };
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@ -6657,6 +6657,8 @@ in {
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rdflib-jsonld = callPackage ../development/python-modules/rdflib-jsonld { };
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rdkit = callPackage ../development/python-modules/rdkit { };
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re-assert = callPackage ../development/python-modules/re-assert { };
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readchar = callPackage ../development/python-modules/readchar { };
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