ambertools: Add bugfix 28

4 files changed, 189 insertions, 1 deletions

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index 09fcfa633..6e9d91d38 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
+*ambertools-1.5-r4 (28 Aug 2012)
+
+  28 Aug 2012; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5-r4.ebuild,
+  +files/ambertools-1.5-bugfix_28.patch:
+  Add bugfix 28.
+
   03 Mar 2012; Reinis Danne <rei4dan@gmail.com> ambertools-1.5-r3.ebuild,
   +files/ambertools-1.5-overflow.patch:
   Add another buffer overflow patch.
diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
index 0d9cab2d5..55f45b80a 100644
--- a/sci-chemistry/ambertools/Manifest
+++ b/sci-chemistry/ambertools/Manifest
@@ -1 +1 @@
-DIST AmberTools-1.5.tar.bz2 121062582 RMD160 4a086b42c378f0904f7bf0b16adb042f1677be55 SHA1 92e47e7337fb4901a5a145d808c5ffd42c82d08d SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c
+DIST AmberTools-1.5.tar.bz2 121062582 SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c SHA512 3366bfe6d0ee1f9b5b99b1d6aad4111093919fe43ab5e9753c62ae815dca958bfc660a3af9db83de71690624869ee5e47af51a6c8412c6bdcb32aecbefb01677 WHIRLPOOL 192f027f5480807cd36693c6c7d8e3b809f4032ecb1a1bf97df888bd02974fbd2bc8da4ea0e9d52062dce10e969bb72cc2f1ba9c4d627f6097492175ab025120
diff --git a/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
new file mode 100644
index 000000000..d689579f9
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
@@ -0,0 +1,159 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $
+
+EAPI=4
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+	AmberTools-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="openmp X"
+
+RESTRICT="fetch"
+
+RDEPEND="
+	virtual/cblas
+	virtual/lapack
+	sci-libs/clapack
+	sci-libs/arpack
+	sci-libs/cifparse-obj
+	sci-chemistry/mopac7
+	sci-libs/netcdf
+	sci-libs/fftw:2.1
+	sci-chemistry/reduce
+	virtual/fortran"
+DEPEND="${RDEPEND}
+	dev-util/byacc
+	dev-libs/libf2c
+	sys-devel/ucpp"
+S="${WORKDIR}/amber11"
+
+pkg_nofetch() {
+	einfo "Go to ${HOMEPAGE} and get ${A}"
+	einfo "Place it in ${DISTDIR}"
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	if use openmp; then
+		tc-has-openmp || \
+			die "Please select an openmp capable compiler like gcc[openmp]"
+	fi
+	AMBERHOME="${S}"
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}/${P}-bugfix_1-21.patch" \
+		"${FILESDIR}/${P}-bugfix_22-27.patch" \
+		"${FILESDIR}/${P}-bugfix_28.patch" \
+		"${FILESDIR}/${P}-gentoo2.patch" \
+		"${FILESDIR}/${P}-overflow.patch"
+	cd "${S}"/AmberTools/src
+	rm -r \
+		arpack \
+		blas \
+		byacc \
+		lapack \
+		fftw-2.1.5 \
+		fftw-3.2.2 \
+		c9x-complex \
+		cifparse \
+		netcdf \
+		pnetcdf \
+		reduce \
+		ucpp-1.3 \
+		|| die
+}
+
+src_configure() {
+	cd "${S}"/AmberTools/src
+	sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+		-e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+		-e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+		-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
+		-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
+		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
+		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
+		-e "s:fc=g77:fc=$(tc-getFC):g" \
+		-e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \
+		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+		-i configure || die
+	sed -e "s:arsecond_:arscnd_:g" \
+		-i sff/time.c \
+		-i sff/sff.h \
+		-i sff/sff.c || die
+	sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \
+		-i nss/Makefile || die
+
+	local myconf
+
+	use X || myconf="${myconf} -noX11"
+
+	use openmp && myconf="${myconf} -openmp"
+
+	./configure \
+		${myconf} \
+		-nobintraj \
+		-nomdgx \
+		-nomtkpp \
+		-nopython \
+		-nosleap \
+		gnu
+}
+
+src_compile() {
+	cd "${S}"/AmberTools/src
+	emake || die
+}
+
+src_test() {
+	cd "${S}"/AmberTools/test
+	make test || die
+}
+
+src_install() {
+	rm -r bin/chemistry bin/MMPBSA_mods
+	rm bin/ante-MMPBSA.py bin/extractFrcmod.py
+
+	for x in bin/*
+		do dobin ${x} || die
+	done
+
+	dobin AmberTools/src/antechamber/mopac.sh
+	sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+		-i "${ED}/usr/bin/mopac.sh" || die
+
+	# Make symlinks untill binpath for amber will be fixed
+	dodir /usr/share/${PN}/bin
+	cd "${ED}/usr/bin"
+	for x in *
+		do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
+	done
+	cd "${S}"
+
+	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
+	dolib.a lib/*
+	insinto /usr/include/${PN}
+	doins include/*
+	insinto /usr/share/${PN}
+	doins -r dat
+	cd AmberTools
+	doins -r benchmarks
+	doins -r examples
+	doins -r test
+
+	cat >> "${T}"/99ambertools <<- EOF
+	AMBERHOME="${EPREFIX}/usr/share/ambertools"
+	EOF
+	doenvd "${T}"/99ambertools
+}
diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_28.patch b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_28.patch
new file mode 100644
index 000000000..f186f3387
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_28.patch
@@ -0,0 +1,23 @@
+diff -urN amber11.orig/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py
+--- amber11.orig/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py	2012-08-28 13:38:00.864249769 +0300
++++ amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py	2012-08-28 13:39:15.141238742 +0300
+@@ -2311,7 +2311,7 @@
+    def _tot_stdevs(self):
+       """ Returns the standard deviations of the total based on whether or not we were able to
+           calculate all frames or not. Use a sample stdev if we were, sum-of-squares if we weren't """
+-      if len(self.com_data) != len(self.rec_data) or len(self.com_data) != len(self.lig_data):
++      if len(self.com_data[0]) != len(self.rec_data[0]) or len(self.com_data[0]) != len(self.lig_data[0]):
+          return math.sqrt(abs(_stdev(self.com_data[0]) ** 2 + _stdev(self.rec_data[0]) ** 2 + _stdev(self.lig_data[0]) ** 2))
+ 
+       sum = sum2 = 0
+@@ -2319,8 +2319,8 @@
+          sum += self.com_data[0][i] - self.rec_data[0][i] - self.lig_data[0][i]
+          sum2 += (self.com_data[0][i] - self.rec_data[0][i] - self.lig_data[0][i]) ** 2
+ 
+-      avg = sum / len(self.com_data)
+-      return math.sqrt(abs(sum2 / len(self.com_data) - avg * avg))
++      avg = sum / len(self.com_data[0])
++      return math.sqrt(abs(sum2 / len(self.com_data[0]) - avg * avg))
+ 
+ #==============================
+