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authorAlexey Shvetsov <alexxy@gentoo.org>2010-07-25 01:21:56 +0400
committerAlexey Shvetsov <alexxy@gentoo.org>2010-07-25 01:21:56 +0400
commit4e606693db31aaeb826fba74d6455307a6bc4374 (patch)
tree498ae86db563eaf8e8241769fc39105e000223ef
parent[dev-python/pysolar]: Initial import (diff)
downloadsci-4e606693db31aaeb826fba74d6455307a6bc4374.tar.gz
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[sci-chemistry/gromacs] ffamber now officialy shipped with gromacs =)
(Portage version: 2.2_rc67_p240/git/Linux x86_64, signed Manifest commit)
-rw-r--r--sci-chemistry/gromacs/ChangeLog3
-rw-r--r--sci-chemistry/gromacs/Manifest12
-rw-r--r--sci-chemistry/gromacs/gromacs-9999.ebuild52
3 files changed, 11 insertions, 56 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 8c014c748..7726449b3 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 24 Jul 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ ffamber officialy shipped with gromacs from now on
+
08 Jul 2010; Christoph Junghans <kleiner_otti@gmx.de>
gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
fix for bug #301854
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index c6938e41d..f6ba220bc 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -6,13 +6,13 @@ DIST ffamber_v4.0-doc.tar.gz 7915520 RMD160 aeadb18bd88bcd9e6fc45af22af15c51e32c
DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
DIST manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
EBUILD gromacs-4.0.9999.ebuild 9773 RMD160 5796e28f2e23c071bcf2458e557900aecc37eb4d SHA1 91dc1f13b1f24d2818103854787d66153afc27fb SHA256 fe65baaa974ef973dcaee4b6bc730649cf7916454ff45eb3e92adba51248989f
-EBUILD gromacs-9999.ebuild 9189 RMD160 3554047dee89ef9a03cbaac26cdc2da731486389 SHA1 d83030a2388a8a504575aeb2df7badd0bf987b83 SHA256 afd52b4714c54be3f4a1590571c7a75d8c2fb73a77699670e810d463e0dcedff
-MISC ChangeLog 4708 RMD160 05d5b601a1ce4a36ab6598dbb0b8bedfe1d45d09 SHA1 14d82482d57c391794b7b5972d960c0d967aa33a SHA256 a85e3d0e3153536d85a3a1a9754c12dfe55bb732b287cef7afdb3c61b07d00df
+EBUILD gromacs-9999.ebuild 7025 RMD160 ca8295764ddbe867afeefcbd5b557e534b7fef0d SHA1 ffe4e0e6697c8a42bd656448e26b1f72b651b7cb SHA256 39f699bfdb1010539877e1a393b00e601406db037929a01a6a5105b1cd248947
+MISC ChangeLog 4834 RMD160 f8297200737f6b7dd99104d683d671333e52bf4e SHA1 09c76f712a052115f22a38769ac745b775662bce SHA256 de84d0da3b17eae88b6d527ea05b59f686029ff36004528fc9dbfc0ef2923913
MISC metadata.xml 643 RMD160 e9ffc42d792f15f3d4438a0de225277ec4814041 SHA1 c83fd4a32d896b7a2586667bc684d46f9daf8693 SHA256 177885ec674e8630a9c9451a0e0a35fc83615b39b387a67002e27f1b0d6b19b2
-----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.15 (GNU/Linux)
+Version: GnuPG v2.0.16 (GNU/Linux)
-iEYEARECAAYFAkw2NtAACgkQy0OE/ans1/klmQCfeMGSD7x+yMLc0X5lmMKQI2i/
-vcwAn1R53FMFG9ODRYWI2fqwTlK7FZCF
-=JJCf
+iEYEARECAAYFAkxLWXQACgkQ5BmOA85PVLivEQCdFHUM9CyFvcg1lXzwopdytMu2
+k5QAnj+xTFWMtw63f5gjmIWaRl3QDUDm
+=gl5k
-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 3a4fc186a..1ac609d8c 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -15,13 +15,12 @@ inherit autotools bash-completion eutils fortran git multilib toolchain-funcs
DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"
SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )
- ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
+ doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
mpi +single-precision static static-libs test +threads +xml zsh-completion"
DEPEND="app-shells/tcsh
@@ -233,53 +232,6 @@ src_install() {
cd "${S}"
dodoc AUTHORS INSTALL README
use doc && dodoc "${DISTDIR}/manual-4.0.pdf"
- if use ffamber; then
- use doc && dodoc "${WORKDIR}/ffamber_v4.0/README/pdfs/*.pdf"
- # prepare vdwradii.dat
- cat >>"${ED}"/usr/share/gromacs/top/vdwradii.dat <<-EOF
- SOL MW 0
- SOL LP 0
- EOF
- # regenerate aminoacids.dat
- cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
- "${ED}"/usr/share/gromacs/top/aminoacids.dat \
- | awk '{print $1}' | sort -u | tail -n+4 | wc -l \
- >> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
- cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
- "${ED}"/usr/share/gromacs/top/aminoacids.dat \
- | awk '{print $1}' | sort -u | tail -n+4 \
- >> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
- mv -f "${ED}"/usr/share/gromacs/top/aminoacids.dat.new \
- "${ED}"/usr/share/gromacs/top/aminoacids.dat
- # copy ff files
- for x in ffamber94 ffamber96 ffamber99 ffamber99p ffamber99sb \
- ffamberGS ffamberGSs ffamber03 ; do
- einfo "Adding ${x} to gromacs"
- cp "${WORKDIR}"/ffamber_v4.0/${x}/* "${ED}"/usr/share/gromacs/top
- done
- # copy suplementary files
- cp "${WORKDIR}"/ffamber_v4.0/*.gro "${ED}"/usr/share/gromacs/top
- cp "${WORKDIR}"/ffamber_v4.0/*.itp "${ED}"/usr/share/gromacs/top
- # actualy add records to FF.dat
- cat >>"${ED}"/usr/share/gromacs/top/FF.dat.new <<-EOF
- ffamber94 AMBER94 Cornell protein/nucleic forcefield
- ffamber96 AMBER96 Kollman protein/nucleic forcefield
- ffamberGS AMBER-GS Garcia & Sanbonmatsu forcefield
- ffamberGSs AMBER-GSs Nymeyer & Garcia forcefield
- ffamber99 AMBER99 Wang protein/nucleic acid forcefield
- ffamber99p AMBER99p protein/nucleic forcefield
- ffamber99sb AMBER99sb Hornak protein/nucleic forcefield
- ffamber03 AMBER03 Duan protein/nucleic forcefield
- EOF
- cat "${ED}"/usr/share/gromacs/top/FF.dat \
- "${ED}"/usr/share/gromacs/top/FF.dat.new \
- | tail -n+2 > "${ED}"/usr/share/gromacs/top/FF.dat.new2
- cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 | wc -l > \
- "${ED}"/usr/share/gromacs/top/FF.dat
- cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 >> \
- "${ED}"/usr/share/gromacs/top/FF.dat
- rm -f "${ED}"/usr/share/gromacs/top/FF.dat.new*
- fi
}
pkg_postinst() {