New addition for NMR assignment and structure calculation software

(Portage version: 2.2_rc65/cvs/Linux x86_64)

5 files changed, 191 insertions, 0 deletions

diff --git a/sci-chemistry/cyana/ChangeLog b/sci-chemistry/cyana/ChangeLog
new file mode 100644
index 000000000000..ef815124905b
--- /dev/null
+++ b/sci-chemistry/cyana/ChangeLog
@@ -0,0 +1,15 @@
+# ChangeLog for sci-chemistry/cyana
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cyana/ChangeLog,v 1.1 2010/03/07 10:07:09 jlec Exp $
+
+*cyana-2.1 (07 Mar 2010)
+
+  07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> +files/2.1-exec.patch,
+  +files/2.1-typo.patch, +cyana-2.1.ebuild, +metadata.xml:
+  CYANA ((c) by Peter Gu"ntert) is a program for automated structure
+  calculation of biological macromolecules on the basis of conformational
+  constraints from NMR. The combination of automated NOESY cross peak
+  assignment, structure calculation with a fast torsion angle dynamics
+  algorithm, and the ease-of-use of CYANA provide for unprecedented
+  efficiency in NMR protein structure determination.
+
diff --git a/sci-chemistry/cyana/cyana-2.1.ebuild b/sci-chemistry/cyana/cyana-2.1.ebuild
new file mode 100644
index 000000000000..2628b038ba06
--- /dev/null
+++ b/sci-chemistry/cyana/cyana-2.1.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cyana/cyana-2.1.ebuild,v 1.1 2010/03/07 10:07:09 jlec Exp $
+
+EAPI="3"
+
+inherit eutils fortran toolchain-funcs
+
+# we need libg2c for gfortran # 136988
+FORTRAN="ifc"
+
+DESCRIPTION="Combined assignment and dynamics algorithm for NMR applications"
+HOMEPAGE="http://www.las.jp/english/products/s08_cyana/index.html"
+SRC_URI="${P}.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="as-is"
+IUSE="examples"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+	elog "Please visit"
+	elog "http://www.las.jp/english/products/s08_cyana/licenses.html"
+	elog "and get a copy of ${A}."
+	elog "Place it in ${DISTDIR}."
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-typo.patch
+	epatch "${FILESDIR}"/${PV}-exec.patch
+
+	cat >> etc/config <<- EOF
+	VERSION=${PV}
+	SHELL=${EPREFIX}/bin/sh
+	FC=${FORTRANC}
+	FFLAGS=${FFLAGS}
+	FFLAGS2=${FFLAGS}
+	CC=$(tc-getCC)
+	FORK=g77fork.o
+	LDFLAGS=${LDFLAGS}
+	LIBS=-pthread -lpthread -liomp5
+	EOF
+
+	if [[ ${FORTRANC} == gfortran ]]; then
+		cat >> etc/config <<- EOF
+		DEFS=-Dgfortran
+		SYSTEM=gfortran
+		EOF
+	else
+		cat >> etc/config <<- EOF
+		DEFS=-Dintel
+		SYSTEM=intel
+		EOF
+	fi
+}
+
+src_compile() {
+	cd src
+	emake \
+		|| die
+}
+
+src_install() {
+	source etc/config
+	dobin cyana{job,table,filter,clean} || die
+	newbin src/${PN}/${PN}exe.${SYSTEM} ${PN} || die
+	insinto /usr/share/${PN}
+	doins -r lib macro help || die
+	use examples && doins -r demo
+
+	cat >> "${T}"/20cyana <<- EOF
+	CYANALIB="${EPREFIX}/usr/share/${PN}"
+	EOF
+
+	doenvd "${T}"/20cyana || die
+}
diff --git a/sci-chemistry/cyana/files/2.1-exec.patch b/sci-chemistry/cyana/files/2.1-exec.patch
new file mode 100644
index 000000000000..28cd88d3eee6
--- /dev/null
+++ b/sci-chemistry/cyana/files/2.1-exec.patch
@@ -0,0 +1,77 @@
+diff --git a/cyana b/cyana
+index 4f746cf..a7ff060 100755
+--- a/cyana
++++ b/cyana
+@@ -45,16 +45,13 @@ shift `expr $optind - 1`
+ 
+ if [ "$h" ]; then usage=1; fi
+ if [ "$usage" ]; then
+-  echo "Usage: $prog -hctx parameters ..."					         
++  echo "Usage: $prog -hS parameters ..."					         
+   echo  									         
+   echo "       -h	     help"						         
+   echo "       -c command    command to start program (must contain \$exefile)"          
+   echo "       -S            run in safe mode, i.e. within one directory"				         
+-  echo "       -t system     explicit system type"				         
+-  echo "       -x	     display name of executable without executing it"	         
+   exit 2
+ fi
+-if [ "$c" ]; then cmd="$c"; fi
+ sys=$t
+ mode=$x
+ safe=$S
+@@ -65,23 +62,6 @@ safe=$S
+ eval ${PROG}ARG='$*'
+ export ${PROG}ARG
+ 
+-
+-# ------ Set library name ------ 
+-
+-f=$0
+-if [ `echo $f | sed 's,^/.*,+,'` != "+" ]; then f=`which $0`; fi
+-odir=`pwd`
+-while [ "`ls -l $f | awk '{ print substr($1,1,1) }'`" = "l" ]; do
+-  l=`ls -l $f | awk '{ i = NF; print $i }'`
+-  cd `dirname $f`; cd `dirname $l`; l=`pwd`/`basename $l`
+-  f=$l
+-done
+-cd `dirname $f`
+-libdir=`pwd | sed 's,/src/'${prog}'$,,'`
+-cd $odir
+-eval ${PROG}LIB=$libdir
+-export ${PROG}LIB
+-
+ if [ "$safe" ]; then 
+   CYANAINIT=initsafe; export CYANAINIT
+ fi
+@@ -89,29 +69,4 @@ fi
+ 
+ # ------ Start the program ------
+ 
+-if [ -d $libdir/src/$prog ]; then
+-  exe=$libdir/src/$prog/$exe
+-else
+-  exe=$libdir/$exe
+-fi
+-if [ "$sys" = "" ]; then
+-  sys=`$libdir/etc/identify`
+-  files="$exe.$sys* $exe.gnu $exe.*"
+-else
+-  files=$exe.$sys
+-fi
+-for exefile in $files; do
+-  if [ -x $exefile ]; then
+-    if [ "$mode" ]; then
+-      echo $exefile; exit 0
+-    else
+-      if [ "`echo $cmd | grep -c '\$exefile'`" -gt 0 ]; then
+-        eval exec $cmd
+-      else
+-        eval exec $cmd $exefile
+-      fi
+-    fi
+-  fi
+-done
+-echo "No executable found in \"`dirname $exe`\"."
+-exit 1
++exec cyana
diff --git a/sci-chemistry/cyana/files/2.1-typo.patch b/sci-chemistry/cyana/files/2.1-typo.patch
new file mode 100644
index 000000000000..3f011a9b2c28
--- /dev/null
+++ b/sci-chemistry/cyana/files/2.1-typo.patch
@@ -0,0 +1,13 @@
+diff --git a/src/cyana/putpro.f b/src/cyana/putpro.f
+index d4080f9..4490225 100644
+--- a/src/cyana/putpro.f
++++ b/src/cyana/putpro.f
+@@ -66,7 +66,7 @@ c     ------------------------------------------------------ BMRB header
+      *    '   _Mol_residue_sequence',
+      *    ';'
+         do i=1,nr,20
+-          write (iunit,'(20A1))') (rcode(rnam(j)),j=i,min(nr,i+19))
++          write (iunit,'(20A1)') (rcode(rnam(j)),j=i,min(nr,i+19))
+         end do
+ 
+         write (iunit,'(A)')
diff --git a/sci-chemistry/cyana/metadata.xml b/sci-chemistry/cyana/metadata.xml
new file mode 100644
index 000000000000..c6856dc7f2cf
--- /dev/null
+++ b/sci-chemistry/cyana/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+  <email>jlec@gentoo.org</email>
+</maintainer>
+</pkgmetadata>