reinit the tree, so we can have metadata

7 files changed, 135 insertions, 0 deletions

diff --git a/sci-chemistry/reduce/Manifest b/sci-chemistry/reduce/Manifest
new file mode 100644
index 000000000000..d1a6f3611091
--- /dev/null
+++ b/sci-chemistry/reduce/Manifest
@@ -0,0 +1,9 @@
+AUX 3.13.080428-CFLAGS.patch 706 SHA256 ce2b82b16421d58bf5de67703f5e9b718f73176891408867460c560ece42cf63 SHA512 849f0ccb7e452a93e4534b232e0ac89a08fcf1c5c34e74910f76e485f12b96ee0aee04728efd8d6a888538ba8a83d4e1604d1a02cdaeeb23aa0d21a80e7b2be9 WHIRLPOOL abfdcd1f5352c282be497a13dd4295fd3bb66267f88f8642fbda14e909d6c52c67d944ff3d0e4c4a27fe57995009290a7a9870ed589c66803890654addbad1a6
+AUX 3.13.080428-LDFLAGS.patch 230 SHA256 9cdcab6d020e8bed56b6938e77c78c66dda91789a29761548511f1ec3220c013 SHA512 f7b471998c1fa5bb5c4eba7fd3f0900469b3ce1d90399413a18b736e5d35d93875c2b1666afe307935c9e71c516a7bd2db7eee1fba9640d403a2401a4427a539 WHIRLPOOL 7d932a12731035f0a3349aaa053f059f83db71d004711c41c33869df7afaeef6fce643f38285ad3ff7215183907be7b42c331d0c8118d11b49d53e90dea11f94
+AUX 3.14.080821-CFLAGS.patch 736 SHA256 18c5e5e6a20f82b0bcfbc3875742fd3de6ac5ae34c4e2aa194aac5515323fc24 SHA512 f435a889845065374753841a0ba5de64e5be0d73935bd145d2e69980671cb3620441e99ec68bedbd876f45a0d61f406dc1a98f1ed7affaf4c923105d7540530a WHIRLPOOL 76b5aad71c1ccef0d0e73159da768f76fee1aea5d07899b82944ef89da3e8f6e44ce40d1f0121b105880279ae9c64af5132485041aaa776aab636ad2e7f5119c
+AUX reduce-3.16.111118-fix-c++14.patch 565 SHA256 785e4d0580150889303f868f630a61a137143f0ef653d00c81912af44774b60a SHA512 8b38d5cbcc76318bb1309185858000daf8cca15a466ce0d4174126c9a5caa50e79d8198d3e3ff3427aa4629d51d0e50773d96b7bce7d94e16cace4bb80f4eed0 WHIRLPOOL 9b9a7622a98b72f099840443d7af8a059af87c98d6c6f599259bcb9ef44369803b71443c3f09678340657a5b4396ef2a941066c5c2af80712c9da194fac19295
+DIST reduce.3.16.111118.src.zip 20342632 SHA256 a9f45dd31eb7022e056cdab1efbbed17fd8be7453396313904c95c839d41dbb3 SHA512 f7b4d8d91f1f57e9e96c91139fa919c570aebd07f3a440faf3df54bf5deb3a05ad998996a24b5fe9aff6280e00329c9914e338cbfe802c047c055f52ce8312a9 WHIRLPOOL 5d5e3c988e39986888eb23907e87ad180a2a441cf236c53406fc43f1cddd25e9e9051ae41d287f35bcf17f3882d720f9cee4c925cbae32139de5848c1fbcccdd
+EBUILD reduce-3.16.111118.ebuild 1149 SHA256 c55852f2a650f91389f1ceb9d044ddde7f18c76f524e51a4d82e882d5f1464be SHA512 18b7e9573b1364de97bc7ed54a7ff4480cc79a80dd2a6b1de551d22ef3bc7c0011ac99cc5d5c98f0a434ae99905d982e6f481e14a5a9cf0f43fa82cc0a522a55 WHIRLPOOL f61a7e7772e9695679c7979b6ae637956106742d7d99b9410cddd246c19980f19d0851cf71efb4749da4c3245c525fb4d504958f724e31d72bb172244ceb1ef0
+MISC ChangeLog 2963 SHA256 f13e554a6c19751903ae5d573d1cab3ff263b41a8b7af27f2b7fb2531724f104 SHA512 eac795843f4184ae0a41b593b88b8780a9a52be9786192c1f3d8ba17152e9b9902ff0fc63f65dd283d231216cb7942f8290cfe438b76dc3f743f9f1519664114 WHIRLPOOL ea364ef7d3e3d0aa6f2ded256a5eb4fb74db1e51d040e3a5b5c3019c78d7ca915acb90ff7776f7de32663640cfbae1504a80f1809f978b69a8cf4a4d23cea15f
+MISC ChangeLog-2015 3431 SHA256 4e4134fd5228f79a992f412589249f59d44d3ea6f5e66c62591c4ad53b10332c SHA512 6f4fea6138798282e846916b824a105151d703ec2209531d5ca1842b93a62a42f8d9eea1510f4d3a94020881f7831cf2161d19065d83970a9f6fd66287f45260 WHIRLPOOL b77b26ae8d476f222a3a9829d55949c326e03622c64565b4964c44865152dd0a679f0d4ed24a6a86b1521b2bbdfbb7349a08f156b2d758c335ad4fffc8861afe
+MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d
diff --git a/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch
new file mode 100644
index 000000000000..7daa5336f689
--- /dev/null
+++ b/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch
@@ -0,0 +1,22 @@
+diff --git a/reduce_src/Makefile b/reduce_src/Makefile
+index 598e367..067ace4 100644
+--- a/reduce_src/Makefile
++++ b/reduce_src/Makefile
+@@ -12,7 +12,7 @@ PROG_FLGS   = -DAROMATICS_ACCEPT_HBONDS \
+ #              -DDEBUGMOVABLENODE -DDEBUGDOTCOUNTS
+ #              -DMINPREDEFINED -DMAXPREDEFINED\
+ 
+-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC)\
++CXXFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC)\
+          -I$(PDBHOME) -I$(TOOLHOME) 
+ #         -Wall
+ 
+@@ -26,7 +26,7 @@ OBJLIST = GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o A
+ CXX		= g++
+ 
+ .cpp.o:
+-	$(CXX) -c $*.cpp $(CFLAGS)
++	$(CXX) -c $*.cpp $(CXXFLAGS)
+ 
+ OPT             = -O3
+ DEBUG           = $(CXXDEBUGFLAGS)
diff --git a/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch
new file mode 100644
index 000000000000..a615be088b24
--- /dev/null
+++ b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch
@@ -0,0 +1,11 @@
+--- a/reduce_src/Makefile
++++ b/reduce_src/Makefile
+@@ -34,7 +34,7 @@
+ all:    reduce
+ 
+ reduce: $(OBJLIST)
+-	$(CXX) -o $@ $(OBJLIST) $(LFLAGS)
++	$(CXX) $(LDFLAGS) -o $@ $(OBJLIST) $(LFLAGS)
+ 
+ clean:
+ 	@rm -rf *.o *.ckp ii_files
diff --git a/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch b/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch
new file mode 100644
index 000000000000..8294c8ca385d
--- /dev/null
+++ b/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch
@@ -0,0 +1,22 @@
+diff --git a/reduce_src/Makefile b/reduce_src/Makefile
+index 598e367..067ace4 100644
+--- a/reduce_src/Makefile
++++ b/reduce_src/Makefile
+@@ -12,7 +12,7 @@ PROG_FLGS   = -DAROMATICS_ACCEPT_HBONDS \
+ #              -DDEBUGMOVABLENODE -DDEBUGDOTCOUNTS
+ #              -DMINPREDEFINED -DMAXPREDEFINED\
+ 
+-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\
++CXXFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\
+          -I$(PDBHOME) -I$(TOOLHOME) 
+ #         -Wall
+ 
+@@ -26,7 +26,7 @@ OBJLIST = GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o A
+ CXX		= g++
+ 
+ .cpp.o:
+-	$(CXX) -c $*.cpp $(CFLAGS)
++	$(CXX) -c $*.cpp $(CXXFLAGS)
+ 
+ OPT             = -O3
+ DEBUG           = $(CXXDEBUGFLAGS)
diff --git a/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch b/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch
new file mode 100644
index 000000000000..5a45b7cef49c
--- /dev/null
+++ b/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch
@@ -0,0 +1,14 @@
+Fix building with C++14, which errors out due to an erroneous std::cerr.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=594202
+
+--- a/reduce_src/GraphToHoldScores.cpp
++++ b/reduce_src/GraphToHoldScores.cpp
+@@ -1150,7 +1150,7 @@
+ 		}
+ 	}
+ 	std::cerr << "CRITICAL ERROR IN whichVertex(" << vertex_index << ") called on edge [" <<
+-	std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
++		vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
+ 	assert(false);
+ 	exit(1);
+         return 0; // to avoid warnings
diff --git a/sci-chemistry/reduce/metadata.xml b/sci-chemistry/reduce/metadata.xml
new file mode 100644
index 000000000000..da36ecbfcd6a
--- /dev/null
+++ b/sci-chemistry/reduce/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/reduce/reduce-3.16.111118.ebuild b/sci-chemistry/reduce/reduce-3.16.111118.ebuild
new file mode 100644
index 000000000000..ef1349e6adef
--- /dev/null
+++ b/sci-chemistry/reduce/reduce-3.16.111118.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+MY_P="${PN}.${PV}.src"
+
+DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.zip"
+
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+
+S="${WORKDIR}/"
+PATCHES=(
+	"${FILESDIR}"/3.13.080428-LDFLAGS.patch
+	"${FILESDIR}"/3.14.080821-CFLAGS.patch
+	"${FILESDIR}"/${PN}-3.16.111118-fix-c++14.patch
+)
+
+src_compile() {
+	DICT_DIR="/usr/share/reduce"
+	DICT_FOLD="reduce_het_dict.txt"
+	DICT_FNEW="reduce_wwPDB_het_dict.txt"
+
+	emake clean
+	emake \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		OPT="${CXXFLAGS}" \
+		DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FNEW}" \
+		DICT_OLD="${EPREFIX}/${DICT_DIR}/${DICT_FOLD}"
+}
+
+src_install() {
+	dobin "${S}"/reduce_src/reduce
+	insinto ${DICT_DIR}
+	doins "${S}"/${DICT_FOLD} "${S}"/${DICT_FNEW}
+	dodoc README.usingReduce.txt
+}