# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack.package import *
from spack.pkg.builtin.boost import Boost


class Dssp(AutotoolsPackage):
    """'mkdssp' utility. (dictionary of protein secondary structure)"""

    homepage = "https://github.com/cmbi/dssp"
    url = "https://github.com/cmbi/dssp/archive/3.1.4.tar.gz"

    license("GPL-3.0-or-later")

    version("3.1.4", sha256="496282b4b5defc55d111190ab9f1b615a9574a2f090e7cf5444521c747b272d4")
    version("2.3.0", sha256="4c95976d86dc64949cb0807fbd58c7bee5393df0001999405863dc90f05846c6")

    depends_on("autoconf", type="build")
    depends_on("automake", type="build")
    depends_on("libtool", type="build")
    depends_on("m4", type="build")
    depends_on("boost@1.48:")

    # TODO: replace this with an explicit list of components of Boost,
    # for instance depends_on('boost +filesystem')
    # See https://github.com/spack/spack/pull/22303 for reference
    depends_on(Boost.with_default_variants)

    # pdb data download.
    # 1ALK.pdb - PDB (protein data bank) : https://www.rcsb.org/
    resource(
        name="pdb_data",
        url="https://files.rcsb.org/download/1ALK.pdb",
        sha256="99f4cd7ab63b35d64eacc85dc1491af5a03a1a0a89f2c9aadfb705c591b4b6c9",
        expand=False,
        placement="pdb",
    )

    def configure_args(self):
        args = ["--with-boost=%s" % self.spec["boost"].prefix]
        return args

    @run_after("configure")
    def edit(self):
        makefile = FileFilter(join_path(self.stage.source_path, "Makefile"))
        makefile.filter(".*-Werror .*", "                    -Wno-error \\")

    @run_after("install")
    def cache_test_sources(self):
        """Save off the pdb sources for stand-alone testing."""
        self.cache_extra_test_sources("pdb")

    def test_mkdssp(self):
        """calculate structure for example"""
        pdb_path = self.test_suite.current_test_cache_dir.pdb
        mkdssp = which(self.prefix.bin.mkdssp)
        with working_dir(pdb_path):
            mkdssp("1ALK.pdb", "1alk.dssp")