Add GNINA and related packages (#35439)

var/spack/repos/builtin/packages/coordgen/package.py

@@ -0,0 +1,32 @@
+# 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 Coordgen(CMakePackage):
+    """Schrödinger, Inc's 2D coordinate generation"""
+
+    homepage = "https://github.com/schrodinger/coordgenlibs"
+    url = "https://github.com/schrodinger/coordgenlibs/archive/refs/tags/v3.0.2.tar.gz"
+
+    maintainers("RMeli")
+
+    version("3.0.2", sha256="f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3")
+
+    variant("maeparser", default=True, description="Use MAE parser")
+    variant("example", default=False, description="Build sample executable")
+    variant("shared", default=True, description="Build as shared library")
+
+    depends_on("maeparser", when="+maeparser")
+    depends_on("boost", when="+maeparser")
+
+    def cmake_args(self):
+        args = [
+            self.define_from_variant("COORDGEN_BUILD_EXAMPLE", "example"),
+            self.define_from_variant("COORDGEN_USE_MAEPARSER", "maeparser"),
+            self.define_from_variant("COORDGEN_BUILD_SHARED_LIBS", "shared"),
+        ]
+        return args

var/spack/repos/builtin/packages/gnina/package.py

@@ -0,0 +1,69 @@
+# 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 Gnina(CMakePackage, CudaPackage):
+    """gnina (pronounced NEE-na) is a molecular docking program with integrated support
+    for scoring and optimizing ligands using convolutional neural networks."""
+
+    homepage = "https://github.com/gnina/gnina"
+    url = "https://github.com/gnina/gnina/archive/refs/tags/v1.0.3.tar.gz"
+    git = "https://github.com/gnina/gnina.git"
+
+    maintainers("RMeli")
+
+    version("1.0.3", sha256="4274429f38293d79c7d22ab08aca91109e327e9ce3f682cd329a8f9c6ef429da")
+
+    _boost = "boost" + "".join(
+        [
+            "+atomic",
+            "+chrono",
+            "+date_time",
+            "+exception",
+            "+filesystem",
+            "+graph",
+            "+iostreams",
+            "+locale",
+            "+log",
+            "+math",
+            "+python",
+            "+program_options",
+            "+random",
+            "+regex",
+            "+serialization",
+            "+signals",
+            "+system",
+            "+test",
+            "+thread",
+            "+timer",
+            "+wave",
+        ]
+    )
+
+    depends_on("zlib")
+    depends_on(_boost)
+    depends_on("glog")
+    depends_on("protobuf")
+    depends_on("hdf5+cxx+hl")
+    depends_on("openblas~fortran")
+
+    depends_on("libmolgrid")
+
+    depends_on("openbabel@3:~gui~cairo~maeparser~coordgen")
+    # depends_on("rdkit")
+
+    depends_on("python", type="build")
+    depends_on("py-numpy", type="build")
+    depends_on("py-pytest", type="build")
+
+    depends_on("cuda@11")
+
+    def cmake_args(self):
+        args = [
+            "-DBLAS=Open",  # Use OpenBLAS instead of Atlas' BLAS
+        ]
+        return args

var/spack/repos/builtin/packages/libmolgrid/package.py

@@ -0,0 +1,40 @@
+# 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)
+
+import os
+
+from spack.package import *
+
+
+class Libmolgrid(CMakePackage):
+    """libmolgrid is a library to generate tensors from molecular data, with properties
+    that make its output particularly suited to machine learning."""
+
+    homepage = "https://gnina.github.io/libmolgrid/"
+    url = "https://github.com/gnina/libmolgrid/archive/refs/tags/v0.5.2.tar.gz"
+
+    maintainers("RMeli")
+
+    version("0.5.3", sha256="a9f7a62cdeb516bc62a06b324cdd33b095a787df175c6166d74a8d30b6916abb")
+    version("0.5.2", sha256="e732d13a96c2f374d57a73999119bef700172d392c195c751214aa6ac6680c3a")
+
+    depends_on("zlib")
+    depends_on("boost +regex +test +program_options +system +filesystem +iostreams +python")
+    depends_on("openbabel@3:~gui~cairo")
+    depends_on("cuda@11")
+
+    depends_on("python")
+    depends_on("py-numpy")
+    depends_on("py-pytest")
+
+    def cmake_args(self):
+        ob_incl = os.path.join(self.spec["openbabel"].prefix.include, "openbabel3")
+        ob_libs = self.spec["openbabel"].libs.joined(";")
+
+        args = [
+            "-DOPENBABEL3_INCLUDE_DIR=" + ob_incl,
+            "-DOPENBABEL3_LIBRARIES=" + ob_libs,
+        ]
+        return args

var/spack/repos/builtin/packages/openbabel/package.py

@@ -4,7 +4,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack.package import *
-from spack.pkg.builtin.boost import Boost
 
 
 class Openbabel(CMakePackage):
@@ -28,6 +27,10 @@ class Openbabel(CMakePackage):
 
     variant("python", default=True, description="Build Python bindings")
     variant("gui", default=True, description="Build with GUI")
+    variant("cairo", default=True, description="Build with Cairo (PNG output support)")
+    variant("openmp", default=False, description="Build with OpenMP")
+    variant("maeparser", default=False, description="Built with MAE parser")
+    variant("coordgen", default=False, description="Build with Coordgen")
 
     extends("python", when="+python")
 
@@ -36,12 +39,9 @@ class Openbabel(CMakePackage):
     depends_on("pkgconfig", type="build")
     depends_on("swig@2.0:", type="build", when="+python")
 
-    # 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)
-    depends_on("cairo")  # required to support PNG depiction
-    depends_on("pango")  # custom cairo requires custom pango
+    depends_on("boost +filesystem +iostreams +test")
+    depends_on("cairo", when="+cairo")  # required to support PNG depiction
+    depends_on("pango", when="+cairo")  # custom cairo requires custom pango
     depends_on("eigen@3.0:")  # required if using the language bindings
     depends_on("libxml2")  # required to read/write CML files, XML formats
     depends_on("zlib")  # required to support reading gzipped files
@@ -49,6 +49,9 @@ class Openbabel(CMakePackage):
     depends_on("libsm")
     depends_on("uuid")
 
+    depends_on("maeparser", when="+maeparser")
+    depends_on("coordgen", when="+coordgen")
+
     # Needed for Python 3.6 support
     patch("python-3.6-rtld-global.patch", when="@:2.4.1+python")
 
@@ -71,8 +74,9 @@ def cmake_args(self):
             args.append("-DPYTHON_BINDINGS=OFF")
 
         args.append(self.define_from_variant("BUILD_GUI", "gui"))
-
-        args.append("-DWITH_MAEPARSER=OFF")  # maeparser is currently broken
+        args.append(self.define_from_variant("ENABLE_OPENMP", "openmp"))
+        args.append(self.define_from_variant("WITH_MAEPARSER", "maeparser"))
+        args.append(self.define_from_variant("WITH_COORDGEN", "coordgen"))
 
         return args
 

var/spack/repos/builtin/packages/rdkit/package.py

@@ -42,14 +42,19 @@ class Rdkit(CMakePackage):
     version("2020_09_1", sha256="ac105498be52ff77f7e9328c41d0e61a2318cac0789d6efc30f5f50dc78a992c")
     version("2020_03_6", sha256="a3663295a149aa0307ace6d1995094d0334180bc8f892fa325558a110154272b")
 
+    variant("freetype", default=True, description="Build freetype support")
+
     depends_on("python@3:")
     depends_on("boost@1.53.0: +python +serialization +iostreams +system")
 
     depends_on("py-numpy")
     depends_on("sqlite")
 
+    depends_on("freetype", when="@2020_09_1: +freetype")
+
     extends("python")
 
     def cmake_args(self):
         args = ["-DCMAKE_CXX_STANDARD=14", "-DRDK_INSTALL_INTREE=OFF"]
+        args.append(self.define_from_variant("RDK_BUILD_FREETYPE_SUPPORT", "freetype"))
         return args