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alphafill 2.1.0 (new formula) (#1825)
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class Alphafill < Formula | ||
# cite Hekkelman_2023: "https://doi.org/10.1038/s41592-022-01685-y" | ||
desc "Transplant missing compounds to the AlphaFold models" | ||
homepage "https://github.com/PDB-REDO/alphafill" | ||
url "https://github.com/PDB-REDO/alphafill/archive/refs/tags/v2.1.0.tar.gz" | ||
sha256 "30b554a936fcf052c562020ac6dd516386863dfc710ac91be3a11b83bb4c69d1" | ||
license "BSD-2-Clause" | ||
head "https://github.com/PDB-REDO/alphafill.git", branch: "trunk" | ||
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depends_on "cmake" => :build | ||
depends_on "pkg-config" => :build | ||
depends_on "boost" | ||
depends_on "brewsci/bio/libcifpp" | ||
depends_on "brewsci/bio/libmcfp" | ||
depends_on "brewsci/bio/libzeep" | ||
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uses_from_macos "bzip2" | ||
uses_from_macos "zlib" | ||
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def install | ||
inreplace "CMakeLists.txt" do |s| | ||
s.gsub! "find_package(libmcfp 1.2.4 QUIET)", "find_package(libmcfp REQUIRED)" | ||
s.gsub! "find_package(libpqxx 7.8.0 QUIET)", | ||
"find_package(PkgConfig)\npkg_check_modules(libpqxx REQUIRED libpqxx>=7.8.0)" | ||
s.gsub! "libpqxx::pqxx", "${LIBPQXX_LIBRARIES}" | ||
end | ||
# WEB_APPLICATION and BUILD_DOCUMENTATION were OFF because they failed to build | ||
system "cmake", "-S", ".", "-B", "build", | ||
"-DBUILD_DOCUMENTATION=OFF", | ||
"-DBUILD_WEB_APPLICATION=OFF", | ||
"-DALPHAFILL_DATA_DIR=#{pkgshare}", | ||
*std_cmake_args | ||
system "cmake", "--build", "build" | ||
system "cmake", "--install", "build" | ||
prefix.install "test" | ||
end | ||
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test do | ||
(testpath/"alphafill.conf").write <<~EOS | ||
pdb-dir=#{prefix}/test/mini-pdb-redo/ | ||
pdb-fasta=#{testpath}/pdb-redo.fa | ||
ligands=#{share}/alphafill/af-ligands.cif | ||
EOS | ||
system "#{bin}/alphafill", "create-index" | ||
assert_match ">pdb-entity|2CBS|1|R13\nPNFSGNW", File.read("#{testpath}/pdb-redo.fa") | ||
system "#{bin}/alphafill", "process", "--config", "#{testpath}/alphafill.conf", | ||
"#{prefix}/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz", | ||
"#{testpath}/out.cif.gz" | ||
assert_predicate testpath/"out.cif.gz", :exist? | ||
assert_match "RETINOIC ACID", shell_output("gunzip -c #{testpath}/out.cif.gz") | ||
end | ||
end |