Autodock vina: spec (#5333)

* Autodock vina: spec

* Adding comment to patch. The implemnetation of boost is version dependent on older boost replacing depecrated function of boost.

* Adding in boost version dependency

var/spack/repos/builtin/packages/autodock-vina/main.patch

@@ -0,0 +1,29 @@
+--- autodock_vina_1_1_2/src/main/main.cpp	2011-05-11 15:35:00.000000000 -0500
++++ autodock_vina_1_1_2/src/main/main.cpp	2017-09-11 10:06:44.939452217 -0500
+@@ -47,7 +47,7 @@
+ using boost::filesystem::path;
+ 
+ path make_path(const std::string& str) {
+-	return path(str, boost::filesystem::native);
++	return path(str);
+ }
+ 
+ void doing(int verbosity, const std::string& str, tee& log) {
+@@ -661,7 +661,7 @@
+ 					cpu, seed, verbosity, max_modes_sz, energy_range, log);
+ 	}
+ 	catch(file_error& e) {
+-		std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++		std::cerr << "\n\nError: could not open \"" << e.name.filename() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
+ 		return 1;
+ 	}
+ 	catch(boost::filesystem::filesystem_error& e) {
+@@ -673,7 +673,7 @@
+ 		return 1;
+ 	}
+ 	catch(parse_error& e) {
+-		std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++		std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.filename() << "\": " << e.reason << '\n';
+ 		return 1;
+ 	}
+ 	catch(std::bad_alloc&) {

var/spack/repos/builtin/packages/autodock-vina/package.py

@@ -0,0 +1,72 @@
+##############################################################################
+# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+from shutil import copyfile
+from shutil import copymode
+import sys
+
+
+class AutodockVina(MakefilePackage):
+    """AutoDock Vina is an open-source program for doing molecular docking"""
+
+    homepage = "http://vina.scripps.edu/"
+    url = "http://vina.scripps.edu/download/autodock_vina_1_1_2.tgz"
+
+    version('1_1_2', 'b467b71ee77dd155b65b1c5364e4220f')
+
+    depends_on('boost@1.65.0')
+
+    # Replacing depecrated function call of boost with current function call
+    patch('main.patch')
+    patch('split.patch')
+
+    @property
+    def build_directory(self):
+        if sys.platform == "darwin":
+            return join_path('build', 'mac', 'release')
+        else:
+            return join_path('build', 'linux', 'release')
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            makefile = FileFilter('Makefile')
+            makefile.filter('BOOST_INCLUDE = .*', 'BOOST_INCLUDE = %s' %
+                            self.spec['boost'].prefix.include)
+            makefile.filter('C_PLATFORM=.*', 'C_PLATFORM=-pthread')
+            makefile.filter('GPP=.*', 'GPP=%s' % spack_cc)
+            mcp = FileFilter('../../makefile_common')
+            mcp.filter('LIBS = ', 'LIBS = -l stdc++ -lm ')
+
+    def build(self, spec, prefix):
+        with working_dir(self.build_directory):
+            make()
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            mkdirp(prefix.bin)
+            copyfile("vina", join_path(prefix.bin, "vina"))
+            copymode("vina", join_path(prefix.bin, "vina"))
+            copyfile("vina_split", join_path(prefix.bin, "vina_split"))
+            copymode("vina_split", join_path(prefix.bin, "vina_split"))

var/spack/repos/builtin/packages/autodock-vina/split.patch

@@ -0,0 +1,29 @@
+--- autodock_vina_1_1_2/src/split/split.cpp	2011-05-11 15:35:00.000000000 -0500
++++ autodock_vina_1_1_2/src/split/split.cpp	2017-09-11 10:06:44.933452243 -0500
+@@ -38,7 +38,7 @@
+ using boost::filesystem::path;
+ 
+ path make_path(const std::string& str) {
+-	return path(str, boost::filesystem::native);
++	return path(str);
+ }
+ 
+ std::string default_prefix(const std::string& input_name, const std::string& add) {
+@@ -208,7 +208,7 @@
+ 		write_multimodel_pdbqt(tmp, ligand_prefix, flex_prefix);
+ 	}
+ 	catch(file_error& e) {
+-		std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++		std::cerr << "\n\nError: could not open \"" << e.name.filename() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
+ 		return 1;
+ 	}
+ 	catch(boost::filesystem::filesystem_error& e) {
+@@ -220,7 +220,7 @@
+ 		return 1;
+ 	}
+ 	catch(parse_error& e) {
+-		std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++		std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.filename() << "\": " << e.reason << '\n';
+ 		return 1;
+ 	}
+ 	catch(std::bad_alloc&) {