reinit the tree, so we can have metadata

5 files changed, 136 insertions, 0 deletions

diff --git a/sci-chemistry/prekin/Manifest b/sci-chemistry/prekin/Manifest
new file mode 100644
index 000000000000..93e42d87a87f
--- /dev/null
+++ b/sci-chemistry/prekin/Manifest
@@ -0,0 +1,7 @@
+AUX 6.51.081122-Makefile.patch 1456 SHA256 7f1b2d39007683b4ecb391ec5bd711ca32115f361dcfc0aa05b25fe52817bb4c SHA512 96b8cda8fc71b2e72c0e8e0a70560a7928456fe81aaa40810a8bcbe77835a7242e8e0d39fac3258e5848a4e4ac14bf9d7dfd4dff8385eb983f359a9f85af9838 WHIRLPOOL ab82e73a70d83b625e8e2e130327ab34a5eaabdce3ccf07a6bb5b62be9e6bb9067b653bfcb9fc1f90607b5d990053c1b4c92732a4dfc21e37dd2142168829f5b
+AUX 6.51.081122-overflow.patch 1156 SHA256 987a530c35f34b25783ce1b4ce0094614f06e97ae8ed652324b8b8ea7f897259 SHA512 fe0ff6e3432177653d29ef51ef3a767dc3872fc0a5350c786b3623b6b4d63866fbfbaf4369676feb545766cac5620b209bd87e92c0ecf2280bb39470e7dd5f7b WHIRLPOOL c868dd1fb4af3c855cd7c2f3e57719b857aab535e26de3c4a1bbc827fd52397e66d23c95670e69796537c34d39a6a964f241fff627f2b8b1186028dbfd04977c
+DIST prekin.6.51.081122.src.tgz 350756 SHA256 74a771cd8be000df13ac908f23a2e945e8bd3590884c6bc6ccff75804cc0fb7a SHA512 9a41f30a9de955c78ee5685807482b2b073705643cceb53bf57eaf7c0c4753dc88fa8dc19f09d4c8a07124c3c3c73716f29126860ae37ff4dd6fb6178b829d1f WHIRLPOOL 29e5b3a0f060bd46c8e00322a31365526be8e3eec0c4c95b630d3e5d6a22bd3e2538c649774a88c7a3c10841ae34f1b23163ab4b625237b46aabaadec35b0c79
+EBUILD prekin-6.51.081122-r1.ebuild 1082 SHA256 c5ea3cced7edb90b35d1c531602c44c5034b104d45e231280c78209d3c55b5ab SHA512 582752645be5f5b5c672b1f69cf3e42415dc0c7bfeefc8f5f7304457b59530cc3ca2eb936416113db203dbf12ec0651db8d96af1acaabd8125d3fa959461f41b WHIRLPOOL 662af50263e0bba42d9d405e0f439337b4a58962d4013402571fa1abcc58c6d99ff57ddec099304a4a253c0b690ece375da7e45d19fce80662d6a102ec3c0120
+MISC ChangeLog 2519 SHA256 0e38123839a278664cb938da296125d2605cee7b96ebec7121559d788e15b1f6 SHA512 9dc8e5b49371a5c48deeb8bcab04f45964942154fb837e148cc639ce757f1ca35f885fb6f0c339869316043e162d2647cfa1bb28d2a0a8a3f0cb9164e99068b8 WHIRLPOOL 8a438acbe16bbdb75578517577c0397cf68a02dbfe2350798cb1f8edbfbc3f16104ee26b9a14315731cbf0e34e94c5903349a2a95ddc74c8c773eaf9c78a4472
+MISC ChangeLog-2015 1159 SHA256 97f9e130cd473c501b2183c603d8c5b6a23f5eb4fa95093a8235b56afca2620a SHA512 b510a37b2fd93968dc832d2cf40ee9a9ea94b26ed4300c96c61726b82416dbf93e2097009e0b45bccd092f5e1573bbaad18e2e88c929f489dfc9786f818ae504 WHIRLPOOL 7e442bba4ab73b96c62c879de1f29000dd71b93f2d12eb9c86c33dfb6eb4ea30981fdc7945ebced76d9ba48ad6e0874006d20551a36e2045f2a35057915c7bb9
+MISC metadata.xml 261 SHA256 f53f2259ad8695c56f1457bcbd63ad8f51108ec471d728cd2fe6f523b36b09d8 SHA512 72682d17ec2b918131b551bd1ff41004965d3cf0c00d24222b34741d2eabf601cf36d4266be70ba7fb7bd0ab55d9dcb5b8e4ca41125bc31f176516797459c8c7 WHIRLPOOL 8ae9531cec25662e7d2a9df3c46039a66da22cb0becfc5cb2eacbb0ea5cfedf0491bd7110465ae37c4e8263b5a962f4973eed3dc569db0d524506943014444a2
diff --git a/sci-chemistry/prekin/files/6.51.081122-Makefile.patch b/sci-chemistry/prekin/files/6.51.081122-Makefile.patch
new file mode 100644
index 000000000000..5fd9d00d9b06
--- /dev/null
+++ b/sci-chemistry/prekin/files/6.51.081122-Makefile.patch
@@ -0,0 +1,41 @@
+diff --git a/Makefile.linux b/Makefile.linux
+index 65a021a..3daacd8 100755
+--- a/Makefile.linux
++++ b/Makefile.linux
+@@ -1,15 +1,15 @@
+ #
+-CFLAGS = -I/usr/X11R6/include  
++CFLAGS += -I/usr/X11R6/include  
+ 
+ ifeq ($(MAKECMDGOALS),debug)
+ CFLAGS = -g -I/usr/X11R6/include  
+ endif
+ 
+-LIBS = -L/usr/lib -L/usr/X11R6/lib -lXmu -lXm -lXt -lSM -lICE -lXext -lX11
++LIBS = -L/usr/GENTOOLIBDIR -L/usr/X11R6/lib -lXmu -lXm -lXt -lSM -lICE -lXext -lX11
+ 
+ ifeq ($(MAKECMDGOALS),nogui)
+-CFLAGS = -D NOGUI -I/usr/X11R6/include
+-LIBS = -L/usr/lib -L/usr/X11R6/lib -lXmu -lXt -lSM -lICE -lXext -lX11
++CFLAGS += -D NOGUI -I/usr/X11R6/include
++LIBS = -L/usr/GENTOOLIBDIR -L/usr/X11R6/lib -lXmu -lXt -lSM -lICE -lXext -lX11
+ endif
+ 
+ FIN =  -lm -pthread #for RH9.0, ok for RH7.3 & RH8.0
+@@ -26,13 +26,13 @@ OBJS = PKINANGL.o PKINCRTL.o PKINCSBS.o PKINCSUB.o PKINCOUT.o PKINMENU.o PKINROT
+ # Commands specific to clients created by this Makefile 
+ 
+ prekin: $(OBJS)
+-	cc -o prekin $(CFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN)
++	cc -o prekin $(CFLAGS) $(LDFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN)
+ 
+ debug: $(OBJS)
+-	cc -o prekin $(CFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN)
++	cc -o prekin $(CFLAGS) $(LDFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN)
+ 
+ nogui: $(OBJS)
+-	cc -o prekin $(CFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN)
++	cc -o prekin $(CFLAGS) $(LDFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN)
+ 
+ clean:
+ 	rm *.o
diff --git a/sci-chemistry/prekin/files/6.51.081122-overflow.patch b/sci-chemistry/prekin/files/6.51.081122-overflow.patch
new file mode 100644
index 000000000000..27bc01d61a52
--- /dev/null
+++ b/sci-chemistry/prekin/files/6.51.081122-overflow.patch
@@ -0,0 +1,28 @@
+diff --git a/PKIN.h b/PKIN.h
+index 6cb6670..c9c6b89 100755
+--- a/PKIN.h
++++ b/PKIN.h
+@@ -533,8 +533,8 @@ EXTERN float xnext,ynext,znext,onext,Bnext,Uvalnext;
+ EXTERN char  aspectstrnext[MAXaspects+3]; /*in parens: (XXXX)*/
+ 
+ /* possible overlap with earlier PREKIN variables */
+-EXTERN char word[256],texts[256],temps[256];
+-EXTERN char alertstr[256],alertstr2[256],alertstr3[256];
++EXTERN char word[256],texts[256],temps[512];
++EXTERN char alertstr[1024],alertstr2[256],alertstr3[256];
+ EXTERN char oldstr[256],olderstr[256],newstr[256],InfoStr[256],MolNameStr[16];
+ EXTERN char NameStr[256],OutfileStr[256],ScriptinStr[256],ShortNameStr[256];
+ EXTERN char DirStr[256],PDBfileStr[256],helpoutStr[256]; /*040425 helpout*/
+diff --git a/PKINCOUT.c b/PKINCOUT.c
+index af8eb24..a9f3a5f 100755
+--- a/PKINCOUT.c
++++ b/PKINCOUT.c
+@@ -17,7 +17,7 @@ static float VRMLx=0,VRMLy=0,VRMLz=0;
+ void   writeoutput()
+ {
+   char  cntl[5];  /* 4 actual characters */
+-  char  kol[20],extra[256],aname[13];
++  char  kol[20],extra[256],aname[32];
+   char  chain[32],atoms[32],cpks[32],hygen[32],hbond[32];
+   char  subname[32],allstr[32];
+   char  mastername[32]; /*051128*/
diff --git a/sci-chemistry/prekin/metadata.xml b/sci-chemistry/prekin/metadata.xml
new file mode 100644
index 000000000000..4ac68c154bb0
--- /dev/null
+++ b/sci-chemistry/prekin/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/prekin/prekin-6.51.081122-r1.ebuild b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild
new file mode 100644
index 000000000000..7f90ace13b9b
--- /dev/null
+++ b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="2"
+
+inherit toolchain-funcs eutils multilib
+
+MY_P=${PN}.${PV}
+
+DESCRIPTION="Prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/prekin.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${MY_P}.src.tgz"
+
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X"
+
+RDEPEND="x11-libs/libXext
+	x11-libs/libXmu
+	x11-libs/libX11
+	x11-libs/libXt
+	X? ( >=x11-libs/motif-2.3:0 )"
+DEPEND="${RDEPEND}"
+
+S=${WORKDIR}/${MY_P}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-Makefile.patch \
+		"${FILESDIR}"/${PV}-overflow.patch
+	sed  \
+		-e 's:cc:$(CC):g' \
+		-e "s:GENTOOLIBDIR:$(get_libdir):g" \
+		"${S}"/Makefile.linux > Makefile || die
+}
+
+src_compile() {
+	local mytarget
+
+	if use X; then
+		mytarget="${PN}"
+	else
+		mytarget="nogui"
+	fi
+
+	emake CC="$(tc-getCC)" ${mytarget} || die
+}
+
+src_install() {
+	dobin "${S}"/prekin || die
+}