usalign: new package (#37646)

* usalign: adding new package
* usalign: updating shasum, adding note about distribution

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

@@ -0,0 +1,47 @@
+# 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 Usalign(Package):
+    """US-align (Universal Structural alignment) is a unified protocol
+    to compare 3D structures of different macromolecules (proteins,
+    RNAs and DNAs) in different forms (monomers, oligomers and
+    heterocomplexes) for both pairwise and multiple structure
+    alignments."""
+
+    homepage = "https://zhanggroup.org/US-align"
+    # this group prefers to distribute their software as single
+    # source files without any actual versioning.
+    # as such this recipe will likely need updating any time
+    # they update the source, with the old version being
+    # deprecated.
+    url = "https://zhanggroup.org/US-align/bin/module/USalign.cpp"
+
+    maintainers("snehring")
+
+    # date assumed from paper publication date
+    version(
+        "20220829",
+        sha256="9ee129017a68125c22ce89123ecbac9421add87ee077cd1994c6e8a39a8a8b21",
+        expand=False,
+    )
+
+    variant("fast-math", default=False)
+
+    phases = ["build", "install"]
+
+    def build(self, spec, prefix):
+        cxx = Executable(self.compiler.cxx)
+        args = ["-O3"]
+        if spec.satisfies("+fast-math"):
+            args.append("-ffast-math")
+        args.extend(["-lm", "-o", "USalign", "USalign.cpp"])
+        cxx(*args)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install("USalign", prefix.bin)