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ambertools: Add bugfix 28

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1 parent 2404051 commit 7f1c9ec1806f79a26cb7e62a41be34d3c5677b9e @Reinis Reinis committed Aug 28, 2012
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6 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.
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2 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
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159 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
+}
View
23 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))
+
+ #==============================
+

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