sci-chemistry/cns: Drop old

(Portage version: 2.2.0_alpha116/cvs/Linux x86_64)

6 files changed, 7 insertions, 889 deletions

diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
index daf8908ac717..11c0e231291d 100644
--- a/sci-chemistry/cns/ChangeLog
+++ b/sci-chemistry/cns/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/cns
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.50 2012/07/10 06:58:28 jdhore Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.51 2012/07/10 07:12:52 jlec Exp $
+
+  10 Jul 2012; Justin Lecher <jlec@gentoo.org> -cns-1.1.ebuild,
+  -cns-1.2.1-r6.ebuild, -files/1.2.1-aria.patch,
+  -files/1.1-time-length-10.patch,
+  -files/1.2-allow-unknown-architectures.patch:
+  Drop old
 
   10 Jul 2012; Jeff Horelick <jdhore@gentoo.org> cns-1.2.1-r7.ebuild:
   marked x86 per bug 419859
diff --git a/sci-chemistry/cns/cns-1.1.ebuild b/sci-chemistry/cns/cns-1.1.ebuild
deleted file mode 100644
index 20993d47664a..000000000000
--- a/sci-chemistry/cns/cns-1.1.ebuild
+++ /dev/null
@@ -1,144 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.1.ebuild,v 1.10 2011/06/21 16:05:16 jlec Exp $
-
-inherit eutils fortran-2 toolchain-funcs
-
-MY_PN="${PN}_solve"
-MY_P="${MY_PN}_${PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="
-	${MY_P}_basic_inputs.tar.gz
-	${MY_P}_data.tar.gz
-	test? ( ${MY_P}_test.tar.gz )"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="ppc x86"
-IUSE="test"
-
-RDEPEND="
-	virtual/fortran
-	app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	einfo "and place these files:"
-	einfo ${A}
-	einfo "in ${DISTDIR}."
-}
-
-get_fcomp() {
-	case $(tc-getFC) in
-		*gfortran* )
-			FCOMP="gfortran" ;;
-		ifort )
-			FCOMP="ifc" ;;
-		* )
-			FCOMP=$(tc-getFC) ;;
-	esac
-}
-src_unpack() {
-	get_fcomp
-	unpack ${A}
-
-	# The length of time must be at least 10, not 9
-	# http://gcc.gnu.org/ml/fortran/2006-02/msg00198.html
-	epatch "${FILESDIR}"/${PV}-time-length-10.patch
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		"${S}"/cns_solve_env
-}
-
-src_compile() {
-	local GLOBALS
-	if [[ $(tc-getFC) =~ g77 ]]; then
-		GLOBALS="-fno-globals"
-	fi
-
-	# make install really means build, since it's expected to be used in-place
-	emake \
-		CC="$(tc-getCC)" \
-		F77=$(tc-getFC) \
-		LD=$(tc-getFC) \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		F77OPT="${FFLAGS:- -O2} \$(CNS_MALIGN_I86)" \
-		F77STD="${GLOBALS}" \
-		LDFLAGS="${LDFLAGS}" \
-		g77install \
-		|| die "emake failed"
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	csh -c \
-		"setenv CNS_G77; source cns_solve_env; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	# Install to locations resembling FHS
-	sed -i \
-		-e "s:${S}:usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/data:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-		-e "s:\$CNS_LIB:\$CNS_DATA:g" \
-		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/bin/cns_info:g" \
-		"${S}"/cns_solve_env
-
-	# Get rid of setup stuff we don't need in the installed script
-	sed -i \
-		-e "83,$ d" \
-		-e "37,46 d" \
-		"${S}"/cns_solve_env
-
-	newbin "${S}"/*_g77/bin/cns_solve* cns_solve \
-		|| die "install cns_solve failed"
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	# Don't want to install this
-	rm -f "${S}"/*_g77/utils/Makefile
-
-	dobin "${S}"/*_g77/utils/* || die "install utils failed"
-
-	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib
-	doins "${S}"/bin/cns_info
-	doins "${S}"/cns_solve_env
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/*
-
-	# Conflits with app-text/dos2unix
-	rm -f "${D}"/usr/bin/dos2unix
-}
-
-pkg_postinst() {
-	ewarn "You must source ${ROOT}usr/share/cns/cns_solve_env"
-	ewarn "before running CNS. It's a C-shell script,"
-	ewarn "so you also must be using csh or tcsh."
-}
diff --git a/sci-chemistry/cns/cns-1.2.1-r6.ebuild b/sci-chemistry/cns/cns-1.2.1-r6.ebuild
deleted file mode 100644
index 6d0fc21497bd..000000000000
--- a/sci-chemistry/cns/cns-1.2.1-r6.ebuild
+++ /dev/null
@@ -1,243 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r6.ebuild,v 1.9 2012/02/04 15:01:15 tomka Exp $
-
-EAPI=3
-
-inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic
-
-MY_PN="${PN}_solve"
-MY_PV="$(delete_version_separator 2)"
-MY_P="${MY_PN}_${MY_PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="
-	${MY_P}_all-mp.tar.gz
-	aria? ( aria2.3.1.tar.gz )"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="aria openmp"
-
-RDEPEND="
-	virtual/fortran
-	app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-FORTRAN_NEED_OPENMP=1
-
-S="${WORKDIR}/${MY_P}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	use aria && elog "and http://aria.pasteur.fr/"
-	elog "and place these files:"
-	elog ${A}
-	elog "in ${DISTDIR}."
-}
-
-get_fcomp() {
-	case $(tc-getFC) in
-		*gfortran* )
-			FCOMP="gfortran" ;;
-		ifort )
-			FCOMP="ifc" ;;
-		* )
-			FCOMP=$(tc-getFC) ;;
-	esac
-}
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	get_fcomp
-}
-
-get_bitness() {
-	echo > "${T}"/test.c
-	$(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o
-	case $(file "${T}"/test.o) in
-		*64-bit*|*ppc64*|*x86_64*) export _bitness="64";;
-		*32-bit*|*ppc*|*i386*) export _bitness="32";;
-		*) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";;
-	esac
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-gentoo.patch \
-		"${FILESDIR}"/${PV}-parallel.patch
-
-	get_bitness
-
-	if use aria; then
-	pushd "${WORKDIR}"/aria* >& /dev/null
-		# Update the cns sources in aria for version 1.2.1
-		epatch "${FILESDIR}"/1.2.1-aria2.3.patch
-
-		# Update the code with aria specific things
-		cp -rf cns/src/* "${S}"/source/
-	popd >& /dev/null
-	fi
-
-	# the code uses Intel-compiler-specific directives
-	if [[ $(tc-getFC) =~ gfortran ]]; then
-		epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
-		use openmp && \
-			append-flags -fopenmp && append-ldflags -fopenmp
-		COMP="gfortran"
-		[[ ${_bitness} == 64 ]] && \
-			append-fflags -fdefault-integer-8
-	elif [[ $(tc-getFC) == if* ]]; then
-		epatch "${FILESDIR}"/${PV}-ifort.patch
-		use openmp && \
-			append-flags -openmp && append-ldflags -openmp
-		COMP="ifort"
-		[[ ${_bitness} == 64 ]] && append-fflags -i8
-	fi
-
-	[[ ${_bitness} == 64 ]] && \
-		append-cflags "-DINTEGER='long long int'"
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	cp "${FILESDIR}"/cns_solve_env_sh "${T}"/
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
-		"${T}"/cns_solve_env_sh
-
-	einfo "Fixing shebangs..."
-	find "${S}" -type f \
-		-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die
-}
-
-src_compile() {
-	local GLOBALS
-	local MALIGN
-	if [[ $(tc-getFC) =~ g77 ]]; then
-		GLOBALS="-fno-globals"
-		MALIGN='\$(CNS_MALIGN_I86)'
-	fi
-
-	# Set up the compiler to use
-	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
-	ln -s Makefile.header Makefile.header.${FCOMP} || die
-	popd 2>/dev/null
-
-	# make install really means build, since it's expected to be used in-place
-	# -j1 doesn't mean we do no respect MAKEOPTS!
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		F77=$(tc-getFC) \
-		LD=$(tc-getFC) \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		LDFLAGS="${LDFLAGS}" \
-		F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
-		F77STD="${GLOBALS}" \
-		OMPLIB="${OMPLIB}" \
-		compiler="${COMP}" \
-		install \
-		|| die "emake failed"
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	sh -c \
-		"export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	# Install to locations resembling FHS
-	sed -i \
-		-e "s:${S}:usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		-e "/^g77on/d" \
-		"${S}"/cns_solve_env
-	# I don't entirely understand why the sh version requires a leading /
-	# for CNS_SOLVE and CNS_ROOT, but it does
-	sed -i \
-		-e "s:${S}:/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		-e "/^g77on/d" \
-		-e "/^g77off/d" \
-		"${T}"/cns_solve_env_sh
-
-	# Get rid of setup stuff we don't need in the installed script
-	sed -i \
-		-e "83,$ d" \
-		-e "37,46 d" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "84,$ d" \
-		-e "39,50 d" \
-		"${T}"/cns_solve_env_sh
-
-	newbin "${S}"/*linux*/bin/cns_solve* cns_solve \
-		|| die "install cns_solve failed"
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	# Don't want to install this
-	rm -f "${S}"/*linux*/utils/Makefile
-
-	dobin "${S}"/*linux*/utils/* || die "install utils failed"
-
-	sed -i \
-		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
-		"${S}"/bin/cns_web || die
-
-	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib || die
-	doins "${S}"/bin/cns_info || die
-
-	insinto /etc/profile.d
-	newins "${S}"/cns_solve_env cns_solve_env.csh || die
-	newins "${T}"/cns_solve_env_sh cns_solve_env.sh || die
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/* || die
-	# Conflits with app-text/dos2unix
-	rm -f "${D}"/usr/bin/dos2unix
-}
-
-pkg_info() {
-	if use openmp; then
-		elog "Set OMP_NUM_THREADS to the number of threads you want."
-		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
-		elog "variable if using gcc (16384 should be good)."
-	fi
-}
-
-pkg_postinst() {
-	pkg_info
-}
diff --git a/sci-chemistry/cns/files/1.1-time-length-10.patch b/sci-chemistry/cns/files/1.1-time-length-10.patch
deleted file mode 100644
index 2b38bad6254b..000000000000
--- a/sci-chemistry/cns/files/1.1-time-length-10.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- cns_solve_1.1.orig/instlib/machine/unsupported/g77-unix/machine_f.f	2006-06-07 11:04:45.000000000 -0700
-+++ cns_solve_1.1/instlib/machine/unsupported/g77-unix/machine_f.f	2006-06-07 11:04:59.000000000 -0700
-@@ -65,7 +65,7 @@
-       CHARACTER*(*) A
-       INTEGER AMAX, ALEN
- C local
--      CHARACTER  DSTR*8, TSTR*9
-+      CHARACTER  DSTR*8, TSTR*10
- C begin
-       IF (AMAX.LT.8) THEN
-       WRITE(6,'(A)') ' %VTIME-ERR: string to small'
diff --git a/sci-chemistry/cns/files/1.2-allow-unknown-architectures.patch b/sci-chemistry/cns/files/1.2-allow-unknown-architectures.patch
deleted file mode 100644
index 327ffb2811b3..000000000000
--- a/sci-chemistry/cns/files/1.2-allow-unknown-architectures.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- cns_solve_1.2.orig/bin/install	2008-01-09 17:21:43.000000000 -0800
-+++ cns_solve_1.2/bin/install	2008-01-09 17:21:59.000000000 -0800
-@@ -78,12 +78,6 @@
-   exit 1
- endif
- #
--if ( $CNS_ARCH =~ unknown* ) then
--  echo "the architecture of the machine is unknown - CNS_ARCH=$CNS_ARCH"
--  echo 'aborting installation'
--  exit 1
--endif
--#
- set prod=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'`
- set cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'`
- set os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'`
diff --git a/sci-chemistry/cns/files/1.2.1-aria.patch b/sci-chemistry/cns/files/1.2.1-aria.patch
deleted file mode 100644
index 35c962b882c9..000000000000
--- a/sci-chemistry/cns/files/1.2.1-aria.patch
+++ /dev/null
@@ -1,475 +0,0 @@
-diff -arNu aria2.2/cns/src/cns.f aria2.2.new/cns/src/cns.f
---- aria2.2/cns/src/cns.f	2007-08-22 17:25:51.000000000 +0200
-+++ aria2.2.new/cns/src/cns.f	2009-06-14 15:28:39.907685273 +0200
-@@ -12,7 +12,7 @@
- C  +          J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,          +
- C  +          L.M.Rice, T.Simonson, G.L.Warren                     +
- C  +===============================================================+
--C  + Copyright 1997-2007 Yale University                           +
-+C  + Copyright 1997-2008 Yale University                           +
- C  +===============================================================+
- C  +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- C
-@@ -470,6 +470,7 @@
-       INTEGER      HNLEN, TMP, PTRSZ, STLEN
-       CHARACTER*(1) CNSPTMP
-       CHARACTER*(4) ST
-+!$    integer omp_get_max_threads
- C
- C write header
-       WRITE(6,'(10X,A)')
-@@ -511,7 +512,7 @@
-      &'             J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,',
-      &'             L.M.Rice, T.Simonson, G.L.Warren.'
-       WRITE(6,'(10X,A)')
--     &' Copyright (c) 1997-2007 Yale University'
-+     &' Copyright (c) 1997-2008 Yale University'
-       WRITE(6,'(10X,A)')
-      &'============================================================'
- C
-@@ -526,6 +527,9 @@
-       WRITE(6,'(10X,7A)')
-      & ' Running on machine: ',HOSTNM(1:HNLEN),
-      & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)'
-+!$    write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(),
-+!$   &  ' threads'
-+!$C (to change use setenv OMP_NUM_THREADS x)
- C
-       CALL GETNAM(USERNM,12,TMP)
-       WRITE(6,'(10X,2A)')
-diff -arNu aria2.2/cns/src/energy.f aria2.2.new/cns/src/energy.f
---- aria2.2/cns/src/energy.f	2006-12-18 16:26:49.000000000 +0100
-+++ aria2.2.new/cns/src/energy.f	2009-06-14 14:47:57.421262637 +0200
-@@ -23,7 +23,8 @@
-       INTEGER I, NDIM, N
-       DOUBLE PRECISION TOTAL
-       DOUBLE COMPLEX DCVAL
--      DOUBLE COMPLEX EDUMMY
-+CCC modifcation ATB 4/27/08
-+      DOUBLE PRECISION EDUMMY
- C parameters
-       DOUBLE PRECISION ZERO, ONE
-       PARAMETER (ZERO=0.0D0, ONE=1.0D0)
-diff -arNu aria2.2/cns/src/noe.f aria2.2.new/cns/src/noe.f
---- aria2.2/cns/src/noe.f	2007-08-22 17:25:51.000000000 +0200
-+++ aria2.2.new/cns/src/noe.f	2009-06-14 15:03:30.001587922 +0200
-@@ -36,8 +36,8 @@
-       INTEGER ISLCT(*), JSLCT(*)
- C local
-       INTEGER I, II, NISLCT, NJSLCT, ICL1, ICL2, NN, ITEMP, IEMODE
--      CHARACTER*4 CLASS, CLASS2, STEMP, SRESET
--      DOUBLE PRECISION SCALE, RTEMP, NOEDST, THRESH
-+      CHARACTER*4 CLASS, CLASS2, STEMP, SRESET, DENMODE
-+      DOUBLE PRECISION SCALE, RTEMP, NOEDST, THRESH, GAMMA, KAPPA
-       LOGICAL MATCH
- C parameter
-       DOUBLE PRECISION ZERO, ONE, SIX
-@@ -140,7 +140,7 @@
-      &     NPEAKI,HEAP(HPNPID),HEAP(HPNSPC),
-      &     HEAP(HPNPP1),HEAP(HPNPP2),HEAP(HPNHP1),HEAP(HPNHP2),
-      &     HEAP(HPNVOL),HEAP(HPCDIS),HEAP(HPCVOL),NATOM,ISLCT,NISLCT,
--     &     JSLCT,NJSLCT,X,Y,Z)
-+     &     JSLCT,NJSLCT,X,Y,Z,HEAP(HPDENINIT))
- C===================================================================
-       ELSE IF (WD(1:4).EQ.'?   ') THEN
-       WRITE(6,'(A,I6,A,I6,A,/,A,F8.3,A,I6)')
-@@ -167,7 +167,8 @@
- C
- C get the class name:
-       CALL NEXTA4('class-name=',CLASS)
--      CALL NEXTF('AVERaging=',RTEMP)
-+CCC modification ATB 4/27/08
-+      CALL NEXTF('AVEXponent=',RTEMP)
-       DO I=1,NOECCN
-       CALL EQSTWC(NOECNM(I),4,CLASS,4,1,1,MATCH)
-       IF (MATCH) THEN
-@@ -179,7 +180,8 @@
- C
- C get the class name:
-       CALL NEXTA4('class-name=',CLASS)
--      CALL NEXTF('AVERaging=',RTEMP)
-+CCC modification ATB 4/27/08
-+      CALL NEXTF('OREXponent=',RTEMP)
-       DO I=1,NOECCN
-       CALL EQSTWC(NOECNM(I),4,CLASS,4,1,1,MATCH)
-       IF (MATCH) THEN
-@@ -585,6 +587,38 @@
-       IF (NOEICV.GT.0) CALL NOEPRI(THRESH,1)
-       END IF
- C====================================================================
-+CCC modification ATB 5/02/08
-+      ELSE IF (WD(1:4).EQ.'OUTD') THEN
-+      CALL NOEOUT(0)
-+      IF (NOEICV.GT.0) CALL NOEOUT(1)
-+C====================================================================
-+CCC modification ATB 4/25/08
-+      ELSE IF (WD(1:3).EQ.'DEN') THEN
-+      CALL NEXTWD('DEN>')
-+      IF (WD(1:4).NE.'INIT'.AND.WD(1:4).NE.'UPDA') THEN
-+      WRITE(6,'(A)') ' %NOE-ERR: DEN expects INIT or UPDAte'
-+      ELSE
-+      DENMODE=WD(1:4)
-+      GAMMA=0.0D0
-+      KAPPA=0.0D0
-+      IF (DENMODE.EQ.'UPDA') THEN
-+      CALL NEXTWD('DEN>')
-+      IF (WD(1:4).NE.'GAMM') THEN
-+      WRITE(6,'(A)') ' %NOE-ERR: DEN UPDAte expects GAMMa parameter'
-+      ELSE
-+      CALL NEXTF('GAMMa=',GAMMA)
-+      CALL NEXTWD('DEN>')
-+      IF (WD(1:4).NE.'KAPP') THEN
-+      WRITE(6,'(A)') ' %NOE-ERR: DEN UPDAte expects KAPPa parameter'
-+      ELSE
-+      CALL NEXTF('KAPPa=',KAPPA)
-+      END IF
-+      END IF
-+      END IF 
-+      CALL NOEDEN(DENMODE,GAMMA,KAPPA,0)
-+      IF (NOEICV.GT.0) CALL NOEDEN(DENMODE,GAMMA,KAPPA,1)
-+      END IF
-+C====================================================================
-       ELSE IF (WD(1:4).EQ.'ANAL') THEN
-       CALL NEXTA4('ANALyse=',RANA)
- C====================================================================
-@@ -683,7 +717,7 @@
-      &           NOEXCL,NPEAKI,NOEPID,NOESPC,NOEPP1,NOEPP2,NOEHP1,
-      $           NOEHP2,NOEVOL,NOECDI,
-      &           NOECVO,NATOM,ISLCT,NISLCT,
--     &           JSLCT,NJSLCT,X,Y,Z)
-+     &           JSLCT,NJSLCT,X,Y,Z,NOEDENINIT)
- C
- C Subroutine parses an NOE ASSIgn statement and
- C puts the information into the NOE restraints list
-@@ -706,7 +740,7 @@
-       DOUBLE PRECISION NOEPP1(*),NOEPP2(*),NOEHP1(*),NOEHP2(*)
-       DOUBLE PRECISION NOEVOL(*), NOECDI(*),NOECVO(*)
-       INTEGER NATOM, ISLCT(*), NISLCT, JSLCT(*), NJSLCT
--      DOUBLE PRECISION X(*), Y(*), Z(*)
-+      DOUBLE PRECISION X(*), Y(*), Z(*), NOEDENINIT(*)
- C local
-       INTEGER I, II, JJ, J, TISLCT, TJSLCT, PEAKID
-       LOGICAL SUCCES,OK
-@@ -737,6 +771,10 @@
-       CALL NEXTF('lower-average-distance=',NOELOW(NOENUM))
-       CALL NEXTF('higher-average-distance=',NOEHIG(NOENUM))
- C
-+C initialize initial DEN distance
-+      NOEDENINIT(NOENUM)=ZERO
-+
-+C
- C initialize time-average and running average stuff
- C
- C set the time-averaged distance and
-@@ -1732,6 +1770,232 @@
-       RETURN
-       END
- C====================================================================
-+      SUBROUTINE NOEOUT(ITEST)
-+C
-+C print a list of current NOE restraints
-+C as assign statements
-+C Front-end for NOEPR3
-+      IMPLICIT NONE
-+C I/O
-+      INCLUDE 'cns.inc'
-+      INCLUDE 'heap.inc'
-+      INCLUDE 'noe.inc'
-+      INTEGER ITEST
-+C begin
-+      CALL NOEPR3(ITEST,
-+     &           HEAP(HPNORR),HEAP(HPNIPR),HEAP(HPNILS),HEAP(HPNJPR),
-+     &           HEAP(HPNJLS),HEAP(HPNCND),HEAP(HPNRAV),HEAP(HPNRRV),
-+     &           HEAP(HPNDIS),HEAP(HPNLOW),HEAP(HPNHIG),
-+     &           HEAP(HPNVIO),HEAP(HPNCV), HEAP(HPNPID))
-+
-+      RETURN
-+      END
-+C====================================================================
-+      SUBROUTINE NOEPR3(ITEST,
-+     &           NOEORR,NOEIPR,NOEILS,NOEJPR,
-+     &           NOEJLS,NOECND,NOERAV,NOERRV,
-+     &           NOEDIS,NOELOW,NOEHIG,
-+     &           NOEVIO,NOECV,NOEPID)
-+      IMPLICIT NONE
-+C I/O
-+      INCLUDE 'cns.inc'
-+      INCLUDE 'noe.inc'
-+      INCLUDE 'mtf.inc'
-+      INCLUDE 'pick.inc'
-+      INCLUDE 'comand.inc'
-+      INCLUDE 'numbers.inc'
-+      INTEGER ITEST
-+C
-+C global NOE arrays on HEAP
-+C restraint and atom pointers
-+      INTEGER NOEORR(*),NOEIPR(*),NOEILS(*),NOEJPR(*),NOEJLS(*)
-+C classes
-+      INTEGER NOECND(*)
-+C averages
-+      DOUBLE PRECISION NOERAV(*),NOERRV(*)
-+C target distance and errors
-+      DOUBLE PRECISION NOEDIS(*),NOELOW(*),NOEHIG(*)
-+C number of violations
-+      INTEGER NOEVIO(*)
-+C time average pointer, test set, restraint number
-+      INTEGER NOECV(*), NOEPID(*)
-+C
-+C local
-+      INTEGER N, K, I, J, CLASS, NORR
-+      INTEGER I1, I2
-+C begin
-+      IF (NOENUM.GT.0) THEN
-+C
-+C loop over all classes
-+      DO CLASS=1,NOECCN
-+      IF (NOEPOT(CLASS).EQ.NOESYM.OR.
-+     &    NOEPOT(CLASS).EQ.NOEHDI.OR.
-+     &    NOEPOT(CLASS).EQ.NOE3DP) THEN
-+      CALL WRNDIE(-5,'NOEPRI',
-+     & 'DENOut not possible with POTEntial set to SYMM, HIGH, or 3DPO')
-+      ELSE
-+C
-+C loop over all NOE's belonging to this class
-+      DO N=1,NOENUM
-+      IF ((ITEST.EQ.0.AND.NOECV(N).NE.NOEICV).OR.
-+     &    (ITEST.EQ.1.AND.NOECV(N).EQ.NOEICV)) THEN
-+      IF (NOECND(N).EQ.CLASS) THEN
-+C
-+C     WE ONLY TAKE THE FIRST FROM EACH SET
-+      NORR=NOEORR(N)+1
-+C
-+C     DO I=NOEIPR(NORR)+1,NOEIPR(NORR+1)
-+C
-+C     WE ONLY TAKE THE FIRST FROM EACH SET
-+      I=NOEIPR(NORR)+1
-+      K=NOEILS(I)
-+      I1=K
-+C
-+C     WE ONLY TAKE THE FIRST FROM EACH SET
-+      J=NOEJPR(NORR)+1
-+      K=NOEJLS(J)
-+      I2=K
-+C
-+      WRITE(PUNIT,'(A,I6,A,I6,A,F6.3,A,F6.3,A,F6.3)') 
-+     & 'ASSIGn (id ',
-+     & I1, ' ) (id ', I2, ' ) ', NOEDIS(N), 
-+     & ' ', NOELOW(N), ' ', NOEHIG(N)
-+C
-+      END IF
-+      END IF
-+      END DO
-+      END IF
-+      END DO
-+      END IF
-+      RETURN
-+      END
-+C====================================================================
-+      SUBROUTINE NOEDEN(DENMODE,GAMMA,KAPPA,ITEST)
-+C
-+C print a list of current NOE restraints
-+C Front-end for NOEPR2
-+      IMPLICIT NONE
-+C I/O
-+      INCLUDE 'cns.inc'
-+      INCLUDE 'heap.inc'
-+      INCLUDE 'noe.inc'
-+      CHARACTER*4 DENMODE
-+      DOUBLE PRECISION GAMMA, KAPPA
-+      INTEGER ITEST
-+C begin
-+      CALL NOEDEN2(DENMODE,GAMMA,KAPPA,ITEST,
-+     &           HEAP(HPNORR),HEAP(HPNIPR),HEAP(HPNILS),HEAP(HPNJPR),
-+     &           HEAP(HPNJLS),HEAP(HPNCND),HEAP(HPNRAV),HEAP(HPNRRV),
-+     &           HEAP(HPNDIS),HEAP(HPNLOW),HEAP(HPNHIG),
-+     &           HEAP(HPNVIO),HEAP(HPNCV), HEAP(HPNPID),
-+     &           HEAP(HPDENINIT))
-+
-+      RETURN
-+      END
-+C====================================================================
-+      SUBROUTINE NOEDEN2(DENMODE,GAMMA,KAPPA,ITEST,
-+     &           NOEORR,NOEIPR,NOEILS,NOEJPR,
-+     &           NOEJLS,NOECND,NOERAV,NOERRV,
-+     &           NOEDIS,NOELOW,NOEHIG,
-+     &           NOEVIO,NOECV,NOEPID,NOEDENINIT)
-+      IMPLICIT NONE
-+C I/O
-+      INCLUDE 'cns.inc'
-+      INCLUDE 'noe.inc'
-+      INCLUDE 'mtf.inc'
-+      INCLUDE 'pick.inc'
-+      INCLUDE 'comand.inc'
-+      INCLUDE 'numbers.inc'
-+      CHARACTER*4 DENMODE
-+      DOUBLE PRECISION GAMMA,KAPPA
-+      INTEGER ITEST
-+C
-+C global NOE arrays on HEAP
-+C restraint and atom pointers
-+      INTEGER NOEORR(*),NOEIPR(*),NOEILS(*),NOEJPR(*),NOEJLS(*)
-+C classes
-+      INTEGER NOECND(*)
-+C averages
-+      DOUBLE PRECISION NOERAV(*),NOERRV(*)
-+C target distance and errors
-+      DOUBLE PRECISION NOEDIS(*),NOELOW(*),NOEHIG(*)
-+C number of violations
-+      INTEGER NOEVIO(*)
-+C time average pointer, test set, restraint number
-+      INTEGER NOECV(*), NOEPID(*)
-+C initial den distance
-+      DOUBLE PRECISION NOEDENINIT(*)
-+C
-+C local
-+      DOUBLE PRECISION EN, NOERMS, NOERM2(NOECMX), THRESH
-+      DOUBLE COMPLEX DBCOMP
-+      DOUBLE PRECISION DBPREC
-+      INTEGER NOENU2(NOECMX)
-+      INTEGER NOEVIT
-+      INTEGER N, K, I, J, CLASS, NOENUML, NORR
-+      CHARACTER*6 SSAVE
-+      CHARACTER*11 SSPOT
-+      LOGICAL QHEAD
-+C begin
-+      THRESH=-0.1
-+      NOERMS=ZERO
-+      NOEVIT=0
-+      NOENUML=0
-+      IF (NOENUM.GT.0) THEN
-+C
-+C
-+C loop over all classes
-+      DO CLASS=1,NOECCN
-+      NOENU2(CLASS)=0
-+      NOERM2(CLASS)=ZERO
-+      NOEVIO(CLASS)=0
-+      IF (NOEPOT(CLASS).EQ.NOESYM.OR.
-+     &    NOEPOT(CLASS).EQ.NOEHDI.OR.
-+     &    NOEPOT(CLASS).EQ.NOE3DP) THEN
-+      CALL WRNDIE(-5,'NOEPRI',
-+     & 'DEN not possible with POTEntial set to SYMM, HIGH, or 3DPO')
-+      ELSE
-+C
-+C loop over all NOE's belonging to this class
-+      QHEAD=.TRUE.
-+      DO N=1,NOENUM
-+      IF ((ITEST.EQ.0.AND.NOECV(N).NE.NOEICV).OR.
-+     &    (ITEST.EQ.1.AND.NOECV(N).EQ.NOEICV)) THEN
-+      IF (NOECND(N).EQ.CLASS) THEN
-+      NOENUML=NOENUML+1
-+C
-+C get NOE energy, current distance (in PCDATA(PCGEOM), and other results
-+      CALL ENOE(EN,'ANAL',N)
-+      NOERMS=NOERMS+PCDATA(PCDEVI)**2
-+      NOERM2(CLASS)=NOERM2(CLASS)+PCDATA(PCDEVI)**2
-+      NOENU2(CLASS)=NOENU2(CLASS)+1
-+      IF (ABS(PCDATA(PCDEVI)).GT.THRESH) THEN
-+      NOEVIO(CLASS)=NOEVIO(CLASS)+1
-+      NOEVIT=NOEVIT+1
-+      END IF
-+C
-+      IF (DENMODE.EQ.'INIT') THEN
-+C
-+C initialization
-+      NOEDENINIT(N)=PCDATA(PCGEOM)
-+CCCCxxx      NOEDIS(N)=PCDATA(PCGEOM)
-+      ELSE
-+C
-+C update step
-+      NOEDIS(N)=NOEDIS(N)+KAPPA*(GAMMA*(PCDATA(PCGEOM)-NOEDIS(N))+ 
-+     &          (ONE-GAMMA)*(NOEDENINIT(N)-NOEDIS(N)) )       
-+      END IF
-+C
-+      END IF      
-+      END IF
-+      END DO
-+      END IF
-+      END DO
-+C
-+      END IF
-+      RETURN
-+      END
-+C====================================================================
-       SUBROUTINE ENOE(EN,ANALYS,NA)
- C
- C Routine computes force field for NOE restraints
-@@ -3357,6 +3621,7 @@
-       HPNRRV=0
-       HPNNSP=0
-       HPNDIS=0
-+      HPDENINIT=0
-       HPNLOW=0
-       HPNHIG=0
-       HPNWGH=0
-@@ -3373,7 +3638,6 @@
-       HPNVOL=0
-       HPCVOL=0
-       HPCDIS=0
--      HPNPRD=0
- C
- C
- C reset other variables
-@@ -3463,6 +3727,7 @@
-       IF (HPNRRV.NE.0) CALL FREHP(HPNRRV,IREAL8(NOEMAX))
-       IF (HPNNSP.NE.0) CALL FREHP(HPNNSP,INTEG4(NOEMAX))
-       IF (HPNDIS.NE.0) CALL FREHP(HPNDIS,IREAL8(NOEMAX))
-+      IF (HPDENINIT.NE.0) CALL FREHP(HPDENINIT,IREAL8(NOEMAX))
-       IF (HPNLOW.NE.0) CALL FREHP(HPNLOW,IREAL8(NOEMAX))
-       IF (HPNHIG.NE.0) CALL FREHP(HPNHIG,IREAL8(NOEMAX))
-       IF (HPNWGH.NE.0) CALL FREHP(HPNWGH,IREAL8(NOEMAX))
-@@ -3495,6 +3760,7 @@
-       HPNRRV=0
-       HPNNSP=0
-       HPNDIS=0
-+      HPDENINIT=0
-       HPNLOW=0
-       HPNHIG=0
-       HPNWGH=0
-@@ -3511,7 +3777,6 @@
-       HPNVOL=0
-       HPCVOL=0
-       HPCDIS=0
--      HPNPRD=0
- C
- C now allocate new space
-       IF (NOENEW.GT.0) THEN
-@@ -3536,6 +3801,7 @@
-       HPNRRV=ALLHP(IREAL8(NOENEW))
-       HPNNSP=ALLHP(INTEG4(NOENEW))
-       HPNDIS=ALLHP(IREAL8(NOENEW))
-+      HPDENINIT=ALLHP(IREAL8(NOENEW))
-       HPNCND=ALLHP(INTEG4(NOENEW))
-       HPNJLS=ALLHP(INTEG4(NOENEW))
-       HPNJPR=ALLHP(INTEG4(NOENEW))
-diff -arNu aria2.2/cns/src/noe.inc aria2.2.new/cns/src/noe.inc
---- aria2.2/cns/src/noe.inc	2007-08-22 17:25:51.000000000 +0200
-+++ aria2.2.new/cns/src/noe.inc	2009-06-14 15:24:50.995208687 +0200
-@@ -29,6 +29,9 @@
- C list for distances and +/- error estimates (heap pointers)
-       INTEGER HPNDIS, HPNLOW, HPNHIG
- C
-+C list for initial DEN distances
-+      INTEGER HPDENINIT
-+C
- C individual weights on restraints
-       INTEGER HPNWGH
- C
-@@ -119,7 +122,7 @@
-       INTEGER HPNVIO, HPNEXC, HPNNUM
- 
- C peak identifier
--      INTEGER NPEAKI, HPNPID, HPNPRD
-+      INTEGER NPEAKI, HPNPID
- C
- C
- C
-@@ -142,7 +145,7 @@
-      &              NMONO,  RAVEXP, NOECOR, NOEICV, 
-      &              HPNVIO, HPNEXC, HPNNUM,
-      &              NPEAKI, HPNPID, IDIMER, HPNPP1, HPNPP2, 
--     &              HPNHP1, HPNHP2, HPNVOL, HPCVOL, HPCDIS, HPNPRD
-+     &              HPNHP1, HPNHP2, HPNVOL, HPCVOL, HPCDIS, HPDENINIT
- C
- C     character string block
- C