reinit the tree, so we can have metadata

5 files changed, 187 insertions, 0 deletions

diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest
new file mode 100644
index 000000000000..ac9339e2d620
--- /dev/null
+++ b/sci-chemistry/procheck/Manifest
@@ -0,0 +1,9 @@
+AUX procheck-3.5.4-close.patch 1073 SHA256 8819ed952ac6361f19141dc589e2ce81310729c4308ec010dae187cc8308f340 SHA512 3d18df23858acc46a12f884d4904ca3f60e05e663746e768f5f08d0370b2e335cfde09c08566c4869adfa0f9c0d75ae527fe0ed2666f603818b11f91a3349307 WHIRLPOOL dc76f7d4cc062e8aa7a8bcee738c06a11b28670ee989aaf0290e5e57442f3627c9287361c073d9fb077ca8280c8c76217217142e53cc6f0a7fc345c355e067f3
+AUX procheck-3.5.4-ldflags.patch 1649 SHA256 d46c5f8fbb6d7f6f1fedc522f311ae4c5baa12b9ff47e6d3970312e1b2b34e57 SHA512 f7f2e06a77058f7e743a1c1367d40c2683a2aefbf2910a807d1b0a77d19024446f978ec34a8e5187338a7e98b6651592a37c024e8a2ea955d9bd736d47bfeb4f WHIRLPOOL 1b4c6b1563251d2b37edfcdaeb49c8c963559c1823a3cf724e78c6f8a2ba4e53fd79b0da4a40339a55a608f470c3db38c5869cc4c058cf5bc9cc21cf8ee77b52
+DIST procheck-3.5.4-README 6585 SHA256 202d5b4d9ffaebdad19c368e6e6fd8ab54744c511609b1c609ef46c21fa0ffa0 SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a WHIRLPOOL 53a618978a9285e8a8f09c7ebd3e34951a8c1056c0894c1f4e4c11f73ad3127829322c9c7597fc6dea98f1fa4c40552e6caf383eed15aaeef0594cf93887d196
+DIST procheck-3.5.4-manual.tar.gz 517840 SHA256 3c2faa505be05102ccbe23473abdddc1cd4dc87c6b5e74222b7ea5c27b18db5a SHA512 0fa9c7d50b7ca43c626d5261c524166938d3a92be1d02221721bc7ce7e91ac4919e7200b946ce563f9bb696d7dab9588c1d1b31a4d551cafa2f2bce4931a212c WHIRLPOOL 591afad0a534762d654779722b229e3dcb9cc1ed0f9216c443d4872dd7379257638e5cf3ee5844adf15b2ec55d5c5b15ab585ae52ae993678311985642aa8eaf
+DIST procheck-3.5.4.tar.gz 522013 SHA256 4923fe5a7b86d5369fd639d0c77cfb866e574f076ec8c52424d746e843a404f4 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc WHIRLPOOL 2732981bdbb5269567019a645b401009bd48d782ab20b4f68bd213a90f7248a9fa3f46ab3a026aa0515a677a99826040d4c3f5464816ed4390b5091a6a98b375
+EBUILD procheck-3.5.4-r3.ebuild 1687 SHA256 53450ba0e302dd1f7a4930235e114d3212851f8725969aabeaaa1323905aa688 SHA512 abc659dbe5947b16259e05128c5e0607fdbe3c251595b7c5589502c8d6465264bfec243820abec345980d66cfe0b3eaa8183a41aeb2e2a8a81a929b0128364e7 WHIRLPOOL 3ee37116675c8133ab0047a301364921bc78573f1bd0d4925ab49e19405e93f01677c0d0d632cf201f2505d658fbedc897c8fd1d9622d17a359fdae933ffe617
+MISC ChangeLog 2706 SHA256 59b2234decdf7f54d1f1eb4490cd94211d6a1ced3f7b535764178cfe7b6914f0 SHA512 f536b799232fd119c8531c4300b48761a41678cd85cb0270410d9a44aee0ac74c1955b40adb5bdbb8c259699fd327134c66bb13d27210e30aa2cf19ac62a72bd WHIRLPOOL 57331e6b198004b3c635f77983ae2c36f2fb2ba2fc83358b8f8571f643b41fb87465ebfc898b384fd543b8c69d594230b2a9f99cf735402ac80a754721dfc3a3
+MISC ChangeLog-2015 1737 SHA256 32c08c17c06bea867f3d413a81040737bd92aba7c5e0e0b738f739ce808d7ccc SHA512 b1a1c456069655bdebbc15db326ab7efcacef6d56a0cac67858676831529f41730fc2060e150623a571f9bcbde38d893231960a042f0e1aa4561a8e00048bae7 WHIRLPOOL 325a3d995cb55fefc26ff4dff076cd2f3bab9cfb0540521bd187c6c4e6af9cc35e03447fc6675da1dcd7f2478b0ab1e0e12f07b718d9fcae2b25ba3dc5b68bd1
+MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269
diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch
new file mode 100644
index 000000000000..16a0658e654d
--- /dev/null
+++ b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch
@@ -0,0 +1,35 @@
+diff --git a/pplot.f b/pplot.f
+index 7e06e68..c86b2b2 100644
+--- a/pplot.f
++++ b/pplot.f
+@@ -4720,6 +4720,7 @@ C---- Initialise variables
+           SCORE(IDIST) = 0.0
+  50   CONTINUE
+ 
++      REWIND(3)
+ C---- If the required residue is of a greater number than that required,
+ C     read through the file until come to it
+       IF (IRESID.GT.INRES) THEN
+diff --git a/ps.f b/ps.f
+index b652a7d..858b8e5 100644
+--- a/ps.f
++++ b/ps.f
+@@ -1705,12 +1705,14 @@ CVAX     -    CARRIAGECONTROL='LIST',
+ C---- If this is an existing file, then read through all its records until
+ C     get to the end of file
+       IF (.NOT.NEWFIL) THEN
++          CLOSE(14)
++          OPEN(14, file=fname, status='old', position='append', err=900)
+ 
+ C----     Loop through the file until reach the end
+- 100      CONTINUE
+-             READ(14,110,END=500) IREC
+- 110         FORMAT(A)
+-          GO TO 100
++C 100      CONTINUE
++C             READ(14,110,END=500) IREC
++C 110         FORMAT(A)
++C          GO TO 100
+ 
+ C---- If this is a new file, then write the header records to it
+       ELSE
\ No newline at end of file
diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch b/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch
new file mode 100644
index 000000000000..453aebe3211f
--- /dev/null
+++ b/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch
@@ -0,0 +1,49 @@
+diff --git a/Makefile b/Makefile
+index c5bb58f..0394b0a 100644
+--- a/Makefile
++++ b/Makefile
+@@ -35,31 +35,31 @@ distrib :
+ # Individual executables
+ # ----------------------
+ anglen : anglen.o
+-	$(F77) $(FOPTS) -o $@ anglen.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ anglen.o
+ clean : clean.o
+-	$(F77) $(FOPTS) -o $@ clean.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ clean.o
+ rmsdev : rmsdev.o
+-	$(F77) $(FOPTS) -o $@ rmsdev.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ rmsdev.o
+ secstr : secstr.o
+-	$(F77) $(FOPTS) -o $@ secstr.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ secstr.o
+ gfac2pdb : gfac2pdb.o ps.o
+-	$(F77) $(FOPTS) -o $@ gfac2pdb.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ gfac2pdb.o ps.o
+ pplot : pplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ pplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ pplot.o ps.o
+ bplot : bplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ bplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ bplot.o ps.o
+ tplot : tplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ tplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ tplot.o ps.o
+ mplot : mplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ mplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ mplot.o ps.o
+ vplot : vplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ vplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ vplot.o ps.o
+ viol2pdb : viol2pdb.o ps.o
+-	$(F77) $(FOPTS) -o $@ viol2pdb.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ viol2pdb.o ps.o
+ wirplot : wirplot.o ps.o
+-	$(F77) $(FOPTS) -o $@ wirplot.o ps.o
++	$(F77) $(FOPTS) $(LDFLAGS) -o $@ wirplot.o ps.o
+ nb : nb.c
+-	$(CC) $(COPTS) -o nb nb.c $(CLIBS)
++	$(CC) $(COPTS) $(LDFLAGS) -o nb nb.c $(CLIBS)
+ 
+ # Individual rules for FORTRAN files with .inc files
+ # --------------------------------------------------
diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml
new file mode 100644
index 000000000000..8937bad0b175
--- /dev/null
+++ b/sci-chemistry/procheck/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/procheck/procheck-3.5.4-r3.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild
new file mode 100644
index 000000000000..4b188e5a9824
--- /dev/null
+++ b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild
@@ -0,0 +1,86 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit fortran-2 multilib toolchain-funcs versionator
+
+DESCRIPTION="Checks the stereochemical quality of a protein structure"
+HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"
+SRC_URI="
+	${P}.tar.gz ${P}-README
+	doc? ( ${P}-manual.tar.gz )"
+
+LICENSE="procheck"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE="doc"
+
+RDEPEND="app-shells/tcsh"
+DEPEND="${RDEPEND}"
+
+RESTRICT="fetch"
+
+S="${WORKDIR}/${PN}"
+
+pkg_nofetch() {
+	elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
+	elog "And follow the instruction for downloading."
+	elog "Files should be stored in following way"
+	elog "${PN}.tar.gz  ->  ${DISTDIR}/${P}.tar.gz"
+	elog "README  ->  ${DISTDIR}/${P}-README"
+	use doc && elog "manual.tar.gz  ->  ${DISTDIR}/${P}-manual.tar.gz"
+}
+
+PATCHES=(
+		"${FILESDIR}"/${P}-ldflags.patch
+		"${FILESDIR}"/${P}-close.patch
+)
+
+src_compile() {
+	emake \
+		F77=$(tc-getFC) \
+		CC=$(tc-getCC) \
+		COPTS="${CFLAGS}" \
+		FOPTS="${FFLAGS} -std=legacy"
+}
+
+src_install() {
+	for i in *.scr; do
+		newbin ${i} ${i%.scr}
+	done
+
+	exeinto /usr/libexec/${PN}/
+	doexe \
+		anglen \
+		clean \
+		rmsdev \
+		secstr \
+		gfac2pdb \
+		pplot \
+		bplot \
+		tplot \
+		mplot \
+		vplot \
+		viol2pdb \
+		wirplot \
+		nb
+	dodoc "${DISTDIR}"/${P}-README
+
+	insinto /usr/libexec/${PN}/
+	doins *.dat *.prm
+	newins resdefs.dat resdefs.data
+
+	cat >> "${T}"/30${PN} <<- EOF
+	prodir="${EPREFIX}/usr/libexec/${PN}/"
+	EOF
+
+	doenvd "${T}"/30${PN}
+
+	if use doc; then
+		pushd "${WORKDIR}" > /dev/null
+			docinto html
+			dodoc -r manual
+		popd > /dev/null
+	fi
+}