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# Copyright 2013-2023 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 *
class ImprovedRdock(MakefilePackage):
"""Improved version of rDock.
rDock is a fast and versatile Open Source docking program
that can be used to dock small molecules against proteins and
nucleic acids.
The original version is found at the following URL:
https://sourceforge.net/projects/rdock/files/rDock_2013.1_src.tar.gz
"""
homepage = "https://github.com/clinfo/improved_rDock"
git = "https://github.com/clinfo/improved_rDock.git"
version("main", branch="main")
depends_on("popt")
depends_on("cppunit")
depends_on("openbabel @3.0.0: +python", type="run")
depends_on("py-numpy", type="run")
depends_on("mpi")
patch("rdock_ld.patch")
patch("rdock_python3.patch", when="^python@3:")
patch("rdock_newcxx.patch")
patch("rdock_useint.patch")
patch("rdock_erase.patch")
patch("rdock_loop.patch", when="target=aarch64:")
patch("rdock_const.patch", when="%fj")
patch("rdock_const2.patch", when="%fj")
def edit(self, spec, prefix):
# compiler path
tm = FileFilter(join_path("build", "tmakelib", "linux-g++-64", "tmake.conf"))
tm.filter("/usr/bin/gcc", spack_cc)
tm.filter("mpicxx", self.spec["mpi"].mpicxx)
# compiler option
if self.spec.target.family == "aarch64":
tm.filter("-m64", "")
if not self.spec.satisfies("%gcc"):
tm.filter("-pipe", "")
def build(self, spec, prefix):
with working_dir("build"):
make("linux-g++-64")
def install(self, spec, prefix):
for shfile in find("bin", "*"):
set_executable(shfile)
install_tree(".", prefix)
def setup_run_environment(self, env):
env.set("RBT_ROOT", self.prefix)
def test(self):
copy(join_path(self.prefix.example, "1sj0", "*"), ".")
opts = ["-r", "1sj0_rdock.prm", "-was"]
self.run_test("rbcavity", options=opts)
mpiexe = self.spec["mpi"].prefix.bin.mpirun
opts = [
self.prefix.bin.rbdock,
"-r",
"1sj0_rdock.prm",
"-p",
"dock.prm",
"-n",
"100",
"-i",
"1sj0_ligand.sd",
"-o",
"1sj0_docking_out",
"-s",
"1",
]
self.run_test(str(mpiexe), options=opts)
opts = [join_path(self.test_suite.current_test_data_dir, "test.sh")]
self.run_test("bash", options=opts)
pythonexe = self.spec["python"].command.path
opts = [self.spec.prefix.bin.sdrmsd, "1sj0_ligand.sd", "1sj0_docking_out_sorted.sd"]
expected = ["1\t0.55", "100\t7.91"]
self.run_test(pythonexe, options=opts, expected=expected)
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