class Dssp < Formula
  # cite Touw_2015: "https://doi.org/10.1093/nar/gku1028"
  # cite Kabsch_1983: "https://doi.org/10.1002/bip.360221211"
  desc "Assign secondary structure to proteins"
  homepage "https://github.com/PDB-REDO/dssp"
  url "https://github.com/PDB-REDO/dssp/archive/refs/tags/v4.4.0.tar.gz"
  sha256 "43494840d774e690dd4b7cfe0f4c1398426abf9499cc00770c882b1e7ec8cdd4"
  license "BSD-2-Clause"
  head "https://github.com/PDB-REDO/dssp.git", branch: "trunk"

  bottle do
    root_url "https://ghcr.io/v2/brewsci/bio"
    sha256 monterey:     "41258503b8ea048bc91779fc59f3a3bd1f3151de7ecdf1a0526c2e97a0984068"
    sha256 x86_64_linux: "87d38a0169af31362912fe3774d142cea5a5c84b5e42266d570b4dc628d03a71"
  end

  depends_on "cmake" => :build
  depends_on "eigen" => :build
  depends_on "boost"
  depends_on "icu4c"
  uses_from_macos "bzip2"
  uses_from_macos "zlib"

  resource "libcifpp" do
    url "https://github.com/PDB-REDO/libcifpp/archive/refs/tags/v5.1.0.1.tar.gz"
    sha256 "ae2cdf7851d1be4ef1fa5bdaf9abbc7d01df9d0935ae8baf9d6335577445d74b"
  end

  resource "libmcfp" do
    url "https://github.com/mhekkel/libmcfp/archive/refs/tags/v1.2.4.tar.gz"
    sha256 "97f7e6271d81fc6b562bd89e7e306315f63d3e3c65d68468217e40ad15ea5164"
  end

  resource "testdata" do
    url "https://github.com/PDB-REDO/dssp/raw/fa880e3d88f842703f680185fffc4de540284b25/test/1cbs.cif.gz"
    sha256 "c6a2e4716f843bd608c06cfa4b6a369a56a6021ae16e5f876237b8a73d0dcb5e"
  end

  def install
    resource("libcifpp").stage do
      # libcifpp should be installed in 'prefix' directory since the path of dic files are always required.
      system "cmake", "-S", ".", "-B", "build", *std_cmake_args(install_prefix: prefix/"libcifpp")
      system "cmake", "--build", "build"
      system "cmake", "--install", "build"
    end

    resource("libmcfp").stage do
      # libcifpp should be installed in 'prefix' directory since the path of dic files are always required.
      system "cmake", "-S", ".", "-B", "build", *std_cmake_args(install_prefix: prefix/"libmcfp")
      system "cmake", "--build", "build"
      system "cmake", "--install", "build"
    end

    system "cmake", "-S", ".", "-B", "build",
                    "-Dcifpp_DIR=#{prefix/"libcifpp/lib/cmake/cifpp"}",
                    "-Dlibmcfp_DIR=#{prefix/"libmcfp/lib/cmake/libmcfp"}",
                    "-DCMAKE_BUILD_TYPE=Release",
                    *std_cmake_args
    system "cmake", "--build", "build"
    system "cmake", "--install", "build"
  end

  test do
    resource("testdata").unpack testpath
    cp Dir[pkgshare/"*.dic"], testpath
    system bin/"mkdssp", "1cbs.cif", "test.dssp"
    assert_match "CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II", (testpath/"test.dssp").read
  end
end