diff options
Diffstat (limited to 'sci-chemistry')
99 files changed, 3291 insertions, 0 deletions
diff --git a/sci-chemistry/abinit/Manifest b/sci-chemistry/abinit/Manifest new file mode 100644 index 0000000..e72b734 --- /dev/null +++ b/sci-chemistry/abinit/Manifest @@ -0,0 +1,15 @@ +MD5 cee88059956385392eed0c248cc14619 abinit-5.0.1.ebuild 3017 +RMD160 22e77df54bd7f4f9be06996cdfd2af9dc11dfb7b abinit-5.0.1.ebuild 3017 +SHA256 cdb0b1897b54d78d0c6d16d0aeeb0ce57a34d95950689c8f23e56cd30164d718 abinit-5.0.1.ebuild 3017 +MD5 ac5259d6354fc868b91677d6f5156aa6 files/change-default-directories.patch 1101 +RMD160 3f5ca414d2bae77cbe63ae153040429a4c645acc files/change-default-directories.patch 1101 +SHA256 0e0da3c28440c55c58f16f57051cc808146d20f7efe38ca928e746a729f5b14a files/change-default-directories.patch 1101 +MD5 956f4439794a55f7201ea7350623bf41 files/digest-abinit-5.0.1 244 +RMD160 6cc6e7749fe836a04a043a862e8e896bc36348ac files/digest-abinit-5.0.1 244 +SHA256 f507cdd0d35fbf41c1b97960774ad47957a417b16f927420592439cf18a06a3a files/digest-abinit-5.0.1 244 +MD5 99d257d7a03119e049db21cc1cc9f905 files/fix-blas-lapack-check.patch 1512 +RMD160 ab0a96f451c24150894942129acc9e01be8eade5 files/fix-blas-lapack-check.patch 1512 +SHA256 12e1e65fa85589dad61046cbb25aba25fd58bd13a80dd9b7bce68ecd702fee35 files/fix-blas-lapack-check.patch 1512 +MD5 90e52517d839635e4fdcdf052461e548 files/fix-test-tarball.patch 477 +RMD160 b09cffa5e2933f9cf29224e12ce53fa506535493 files/fix-test-tarball.patch 477 +SHA256 e140381f053193737c4c1e474f65c25024319b296678aa52b1df2ac1161540bd files/fix-test-tarball.patch 477 diff --git a/sci-chemistry/abinit/abinit-5.0.1.ebuild b/sci-chemistry/abinit/abinit-5.0.1.ebuild new file mode 100644 index 0000000..0246017 --- /dev/null +++ b/sci-chemistry/abinit/abinit-5.0.1.ebuild @@ -0,0 +1,113 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +inherit fortran toolchain-funcs + +DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory" +HOMEPAGE="http://www.abinit.org/" +SRC_URI="ftp://ftp.abinit.org/pub/abinitio/ABINIT_v${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86" +#IUSE="mpi netcdf test" +IUSE="mpi test" + +RDEPEND="virtual/blas + virtual/lapack" +# Doesn't build with 4.1-20060210 +# netcdf? ( sci-libs/netcdf )" +DEPEND="${RDEPEND}" + +# F90 code, g77 won't work +FORTRAN="gfortran ifc" + +pkg_setup() { + fortran_pkg_setup + + # Doesn't compile with gcc-4.0, only >=4.1-20060210 + local diemsg="Requires gcc-4.1.0-beta20060210 or newer" + if [[ "${FORTRANC}" = "gfortran" ]]; then + if [[ $(gcc-major-version) -eq 4 ]]; then + if [[ $(gcc-minor-version) -lt 1 ]]; then + die "${diemsg}" + elif [[ $(gcc-minor-version) -eq 1 ]] \ + && [[ $(gcc-minor-version) -eq 0 ]]; then + # If it's not a snap, we're good, and gcc-snapshot-version() + # will be empty + if [[ -n "$(gcc-snapshot-version)" ]] \ + && [[ $(gcc-snapshot-version) -lt 20060210 ]]; then + die "${diemsg}" + fi + fi + fi + fi +} + +src_unpack() { + unpack ${A} + cd ${S} + epatch ${FILESDIR}/change-default-directories.patch + epatch ${FILESDIR}/fix-blas-lapack-check.patch + epatch ${FILESDIR}/fix-test-tarball.patch + AT_M4DIR="config/m4" eautoreconf +} + +src_compile() { + econf \ + --with-install-type=debian \ + --disable-autodetect \ + --disable-config-file \ + --disable-mpi-search \ + --disable-library-search \ + --disable-netcdf \ + $(use_enable mpi) \ + --with-blas-prefix=/usr \ + --with-lapack-prefix=/usr \ + --with-c-optflags="${CFLAGS}" \ + --with-fortran-optflags="${FFLAGS}" \ + FC="${FORTRANC}" \ + CC="$(tc-getCC)" \ + || die "configure failed" +# $(use_enable netcdf) \ + + emake || die "make failed" +} + +src_test() { + einfo "The tests take quite a while, on the order of 2-3 hours" + einfo "on a dual Athlon 2000+." + cd ${S}/tests + emake tests_dev + + local REPORT + for REPORT in $(find . -name *fl*); do + einfo "Results for ${REPORT%%/*} tests" + cat ${REPORT} + done +} + +src_install() { + make DESTDIR="${D}" install || die "install failed" + + if use test; then + dodoc ${S}/tests/summary_tests.tar.gz + fi + + dodoc ${S}/KNOWN_PROBLEMS + prepalldocs +} + +pkg_postinst() { + ewarn "Upstream considers this version unready for production use." + ewarn "Major changes occurred in the build system since 4.x." + ewarn "If you intend to use it in production, be sure to run all tests" + ewarn "and read through the test results by emerging abinit" + ewarn "with FEATURES=test and USE=test. Also see the KNOWN_PROBLEMS document." + ewarn "The test results will be installed as summary_tests.tar.gz." +} + +gcc-snapshot-version() { + echo "$(gcc-fullversion | cut -f3 -d. | cut -f2 -d- | sed -e "s:[[:alpha:]]::g")" +} diff --git a/sci-chemistry/abinit/files/change-default-directories.patch b/sci-chemistry/abinit/files/change-default-directories.patch new file mode 100644 index 0000000..47c9152 --- /dev/null +++ b/sci-chemistry/abinit/files/change-default-directories.patch @@ -0,0 +1,24 @@ +diff -urN abinit-5.0.1.orig/config/m4/init.m4 abinit-5.0.1/config/m4/init.m4 +--- abinit-5.0.1.orig/config/m4/init.m4 2005-12-11 06:56:09.000000000 -0800 ++++ abinit-5.0.1/config/m4/init.m4 2006-02-10 23:31:47.000000000 -0800 +@@ -132,9 +132,9 @@ + + debian) + abinit_prefix="/usr" +- abinit_bindir="/usr/lib/abinit/${ABINIT_VERSION_BASE}/bin" ++ abinit_bindir="/usr/bin" + abinit_datdir="/usr/share/abinit" +- abinit_docdir="/usr/share/doc/abinit/${ABINIT_VERSION_BASE}" ++ abinit_docdir="/usr/share/doc/abinit-${ABINIT_VERSION_BASE}" + abinit_libdir="/usr/lib/abinit/${ABINIT_VERSION_BASE}/lib" + abinit_incdir="/usr/include/abinit/${ABINIT_VERSION_BASE}" + abinit_mandir="/usr/share/man" +@@ -212,7 +212,7 @@ + ABINIT_VERSION_MICRO=`echo "${ABINIT_VERSION}" | cut -d. -f3` + ABINIT_VERSION_BUILD=`date '+%Y%m%d'` + +- ABINIT_VERSION_BASE="${ABINIT_VERSION_MAJOR}.${ABINIT_VERSION_MINOR}" ++ ABINIT_VERSION_BASE="${ABINIT_VERSION_MAJOR}.${ABINIT_VERSION_MINOR}.${ABINIT_VERSION_MICRO}" + + dnl Make numbers available to source files + AC_DEFINE_UNQUOTED(ABINIT_VERSION,"${ABINIT_VERSION}", diff --git a/sci-chemistry/abinit/files/digest-abinit-5.0.1 b/sci-chemistry/abinit/files/digest-abinit-5.0.1 new file mode 100644 index 0000000..386d13b --- /dev/null +++ b/sci-chemistry/abinit/files/digest-abinit-5.0.1 @@ -0,0 +1,3 @@ +MD5 8dd67f91a089e1ab1646ddbb6160fc92 abinit-5.0.1.tar.gz 19509561 +RMD160 427412872d41490dfaa1777c94131a774d5f793c abinit-5.0.1.tar.gz 19509561 +SHA256 21ac8dc5b264cc3848bc26333920b4c11f80f3ca73517789dde84314f19ef9c2 abinit-5.0.1.tar.gz 19509561 diff --git a/sci-chemistry/abinit/files/fix-blas-lapack-check.patch b/sci-chemistry/abinit/files/fix-blas-lapack-check.patch new file mode 100644 index 0000000..92c20b9 --- /dev/null +++ b/sci-chemistry/abinit/files/fix-blas-lapack-check.patch @@ -0,0 +1,39 @@ +diff -urN abinit-5.0.1.orig/config/m4/extlibs.m4 abinit-5.0.1/config/m4/extlibs.m4 +--- abinit-5.0.1.orig/config/m4/extlibs.m4 2005-12-11 06:58:20.000000000 -0800 ++++ abinit-5.0.1/config/m4/extlibs.m4 2006-02-10 23:53:34.000000000 -0800 +@@ -52,7 +52,7 @@ + + dnl Look for library + blas_lib="${with_blas_prefix}/lib/libblas.a" +- blas_ldflags="-L${with_blas_prefix}/lib -lblas" ++ blas_ldflags="-L${with_blas_prefix}/lib -lblas -lpthread" + if test ! -s "${blas_lib}"; then + build_blas="yes" + fi +@@ -61,7 +61,7 @@ + + if test "${build_blas}" = "yes"; then + AC_MSG_NOTICE([the BLAS library will be built]) +- blas_ldflags="-L\$(top_builddir)/lib/blas -lblas" ++ blas_ldflags="-L\$(top_builddir)/lib/blas -lblas -lpthread" + blas_lib="\$(top_builddir)/lib/blas/libblas.a" + else + AC_MSG_NOTICE([the BLAS library will not be built]) +@@ -109,7 +109,7 @@ + + dnl Look for library + lapack_lib="${with_lapack_prefix}/lib/liblapack.a" +- lapack_ldflags="-L${with_lapack_prefix}/lib -llapack" ++ lapack_ldflags="-L${with_lapack_prefix}/lib -llapack -lpthread" + if test ! -s "${lapack_lib}"; then + build_lapack="yes" + fi +@@ -118,7 +118,7 @@ + + if test "${build_lapack}" = "yes"; then + AC_MSG_NOTICE([the LAPACK library will be built]) +- lapack_ldflags="-L\$(top_builddir)/lib/lapack -llapack" ++ lapack_ldflags="-L\$(top_builddir)/lib/lapack -llapack -lpthread" + lapack_lib="\$(top_builddir)/lib/lapack/liblapack.a" + else + AC_MSG_NOTICE([the LAPACK library will not be built]) diff --git a/sci-chemistry/abinit/files/fix-test-tarball.patch b/sci-chemistry/abinit/files/fix-test-tarball.patch new file mode 100644 index 0000000..585a3c8 --- /dev/null +++ b/sci-chemistry/abinit/files/fix-test-tarball.patch @@ -0,0 +1,11 @@ +--- abinit-5.0.1.orig/tests/Makefile.am 2006-02-12 14:41:17.000000000 -0800 ++++ abinit-5.0.1/tests/Makefile.am 2006-02-12 14:41:41.000000000 -0800 +@@ -1756,7 +1756,7 @@ + tar cvf summary_tests.tar \ + fast/,,test*/fl* fast/,,test*/*out* \ + v*/,,test*/fl* v*/,,test*/*out* \ +- paral/,,test*/fl* paral/,,test*/*out* \ ++ paral/,,test*/fl* paral/,,test*/*out* + gzip --best summary_tests.tar + + # ---------------------------------------------------------------------------- # diff --git a/sci-chemistry/caver/ChangeLog b/sci-chemistry/caver/ChangeLog new file mode 100644 index 0000000..1cd00b2 --- /dev/null +++ b/sci-chemistry/caver/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-chemistry/caver +# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/ChangeLog,v 1.1 2005/12/20 03:56:38 spyderous Exp $ + +*caver-0.99.1 (20 Dec 2005) + + 20 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; +metadata.xml, + +caver-0.99.1.ebuild: + New package providing rapid, accurate and fully automated calculation of + pathways leading from buried cavities to outside solvent in static and + dynamic protein structures. Also has a neat PyMol plugin. + diff --git a/sci-chemistry/caver/Manifest b/sci-chemistry/caver/Manifest new file mode 100644 index 0000000..56f61c7 --- /dev/null +++ b/sci-chemistry/caver/Manifest @@ -0,0 +1,18 @@ +MD5 8ce02fd5913949883e8686e441725d75 ChangeLog 546 +RMD160 f7ce1bbaa6f53a12834d4df1745701ef453d1644 ChangeLog 546 +SHA256 74496aeb2366a28bd2483be7884bdd4088a04997b7a1eb918661ca028142cb7d ChangeLog 546 +MD5 5ad3b6ca759c8086c47b7f7ff3ea6464 caver-0.99.1.ebuild 1387 +RMD160 ae780284703969589b6814da33d2612c17e31d2b caver-0.99.1.ebuild 1387 +SHA256 61244eb8aa3bc1930b5fbb1ce10fba022dd141518ae758f1e4389d5cb8b0815b caver-0.99.1.ebuild 1387 +MD5 264b9cd6a5c908903498103e8f88ad40 caver-0.99.2.ebuild 1424 +RMD160 eb04af646b375ffe9c37767c98c3ce716dd12753 caver-0.99.2.ebuild 1424 +SHA256 0b694b6880632a20c325db43700aedba21a65fa734a87bf74f387e2e791a43b6 caver-0.99.2.ebuild 1424 +MD5 946c4f9350e2386e497befe7afbe9cc2 files/digest-caver-0.99.1 130 +RMD160 9ca2102fa7a9b2c5257ff4044202c040d82ce628 files/digest-caver-0.99.1 130 +SHA256 fb5d883d649a3227ef05372d785aa49851202133670d2199ac6aecdf11ecae08 files/digest-caver-0.99.1 130 +MD5 8524c8b5718aaac466fa34658468955a files/digest-caver-0.99.2 524 +RMD160 1e54afa8530246f319c0b0a235d9cce35dc050c4 files/digest-caver-0.99.2 524 +SHA256 e7815fe179e318f1f736e8f6cf473f92fb8df0aae52222de71f0ce2fc82c88cf files/digest-caver-0.99.2 524 +MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248 +RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248 +SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248 diff --git a/sci-chemistry/caver/caver-0.99.1.ebuild b/sci-chemistry/caver/caver-0.99.1.ebuild new file mode 100644 index 0000000..5872bf7 --- /dev/null +++ b/sci-chemistry/caver/caver-0.99.1.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/caver-0.99.1.ebuild,v 1.1 2005/12/20 03:56:38 spyderous Exp $ + +inherit multilib python + +MY_PN="${PN}_unix" +MY_P="${MY_PN}_v${PV}" +DESCRIPTION="Rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures" +HOMEPAGE="http://viper.chemi.muni.cz/caver/" +SRC_URI="${MY_P}.tar.gz + pymol? ( pymolplug.tar.gz )" +LICENSE="CAVER" +SLOT="0" +KEYWORDS="~ppc ~x86" +IUSE="pymol" +RDEPEND="media-libs/qhull + pymol? ( sci-chemistry/pymol )" +DEPEND="${RDEPEND}" +RESTRICT="fetch" +S="${WORKDIR}/${MY_P}" + +pkg_nofetch() { + einfo "Download ${MY_P}.tar.gz" + if use pymol; then + einfo "and pymolplug.tar.gz" + fi + einfo "from ${HOMEPAGE}. This requires registration." + einfo "Place them in ${DISTDIR}." +} + +src_install() { + make DESTDIR="${D}" install + if use pymol; then + python_version + sed -i \ + -e "s:^\(CAVER_BINARY_LOCATION\).*:\1 = \"${ROOT}usr/bin/caver\":g" \ + ${WORKDIR}/pymolplug/caver.py + insinto /usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup + doins ${WORKDIR}/pymolplug/caver.py + fi +} + +pkg_postinst() { + if use pymol; then + python_mod_compile \ + /usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup/caver.py + fi +} diff --git a/sci-chemistry/caver/caver-0.99.2.ebuild b/sci-chemistry/caver/caver-0.99.2.ebuild new file mode 100644 index 0000000..c0639d9 --- /dev/null +++ b/sci-chemistry/caver/caver-0.99.2.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/caver-0.99.1.ebuild,v 1.1 2005/12/20 03:56:38 spyderous Exp $ + +inherit multilib python + +MY_PN="${PN}_unix" +MY_P="${MY_PN}_v${PV}" +PLUG_P="${MY_P/caver/caverPLUG}" +DESCRIPTION="Rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures" +HOMEPAGE="http://viper.chemi.muni.cz/caver/" +SRC_URI="${MY_P}.tar.gz + pymol? ( ${PLUG_P}.tar.gz )" +LICENSE="CAVER" +SLOT="0" +KEYWORDS="~ppc ~x86" +IUSE="pymol" +RDEPEND="media-libs/qhull + pymol? ( sci-chemistry/pymol )" +DEPEND="${RDEPEND}" +RESTRICT="fetch" +S="${WORKDIR}/${MY_P}" + +pkg_nofetch() { + einfo "Download ${MY_P}.tar.gz" + if use pymol; then + einfo "and ${PLUG_P}.tar.gz" + fi + einfo "from ${HOMEPAGE}. This requires registration." + einfo "Place tarballs in ${DISTDIR}." +} + +src_install() { + make DESTDIR="${D}" install + if use pymol; then + python_version + sed -i \ + -e "s:^\(CAVER_BINARY_LOCATION\).*:\1 = \"${ROOT}usr/bin/caver\":g" \ + ${WORKDIR}/${PLUG_P}/caver.py + insinto /usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup + doins ${WORKDIR}/${PLUG_P}/caver.py + fi +} + +pkg_postinst() { + if use pymol; then + python_mod_compile \ + /usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup/caver.py + fi +} diff --git a/sci-chemistry/caver/files/digest-caver-0.99.1 b/sci-chemistry/caver/files/digest-caver-0.99.1 new file mode 100644 index 0000000..80f3e37 --- /dev/null +++ b/sci-chemistry/caver/files/digest-caver-0.99.1 @@ -0,0 +1,2 @@ +MD5 7dfc10f67d345d81fa74f0c2c8bbca8d caver_unix_v0.99.1.tar.gz 898765 +MD5 522581ce929adb5d3bef0fa540382362 pymolplug.tar.gz 81137 diff --git a/sci-chemistry/caver/files/digest-caver-0.99.2 b/sci-chemistry/caver/files/digest-caver-0.99.2 new file mode 100644 index 0000000..d8d6005 --- /dev/null +++ b/sci-chemistry/caver/files/digest-caver-0.99.2 @@ -0,0 +1,6 @@ +MD5 e498466fa232d17fb483cc4568576d2b caverPLUG_unix_v0.99.2.tar.gz 81270 +RMD160 58a5b2b7a1efe41a86d507831f754419ae912b12 caverPLUG_unix_v0.99.2.tar.gz 81270 +SHA256 5b7ca30f26023e2ed9eda6a5430ca5db0ebef7b34f7f8d2391a49182ec0663b1 caverPLUG_unix_v0.99.2.tar.gz 81270 +MD5 b258994fab2957ab20eac77d7a74c276 caver_unix_v0.99.2.tar.gz 1152263 +RMD160 01b877bef15d0f0e1ccce8a3dbcda83826ba76c5 caver_unix_v0.99.2.tar.gz 1152263 +SHA256 9934b5e80f375159132c5327df1fa8bd19ce90682c04c4cd9b91e62476e0f98b caver_unix_v0.99.2.tar.gz 1152263 diff --git a/sci-chemistry/caver/metadata.xml b/sci-chemistry/caver/metadata.xml new file mode 100644 index 0000000..211b8bd --- /dev/null +++ b/sci-chemistry/caver/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<maintainer> +<email>spyderous@gentoo.org</email> +<name>Donnie Berkholz</name> +</maintainer> +</pkgmetadata> diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest new file mode 100644 index 0000000..67521db --- /dev/null +++ b/sci-chemistry/ccp4/Manifest @@ -0,0 +1,19 @@ +MD5 6297a21e1e45183fe8df70e18c8f2c2d ccp4-5.99.5.ebuild 12167 +MD5 b25f261958764a4ef684582b517d63c5 files/add-xdl-libdir.patch 1545 +MD5 5d4c15532a50ac2e00b68f9a57ce79f2 files/ccp4-5.99.5-install-libs-at-install-time.patch 890 +MD5 b7c4c90e38ef49651876128a209b4546 files/ccp4i-default-to-firefox.patch 717 +MD5 a9fd6533dc70e2c88e4623509e20c30b files/check-blas-lapack-pthread.patch 5335 +MD5 cee8a62b63386a13f4276cab7bf09260 files/clipper-find-mccp4-includes.patch 491 +MD5 fcf801c9c9f1cc7f35294ff95776ff5e files/create-mosflm-bindir.patch 438 +MD5 934ef33e2fc72b4c4ba6ec4fbc3d7122 files/digest-ccp4-5.99.5 129 +MD5 de25d6e610b32fbe607f62914e83a229 files/dont-build-pdb-extract.patch 914 +MD5 8638a4880d926711233e53382f35205a files/dont-build-rasmol.patch 725 +MD5 12cd3967d76e228401cfcd8d156e924d files/dont-chmod-python-binary.patch 606 +MD5 898701d32b28c3916d4374a6c58ef7b9 files/dont-make-dirs-in-configure.patch 2780 +MD5 5c89d8a6c5570d442a71a8c598a80f72 files/make-ipmosflm-dir.patch 375 +MD5 962cb5c0c55797f865254e4dc374183b files/make-mosflm-cbf-libdir.patch 415 +MD5 e38e0ef05c30c16148e8319e0bb0977d files/make-mosflm-index-libdir.patch 358 +MD5 703cb01ad626d4dbf4176a18ea5269a1 files/make-mosflm-libdir.patch 371 +MD5 88b9b19d31b2128746bb99fc27882357 files/make-phaser-bindir.patch 380 +MD5 e74f4860f9f1c929c3b4d4e06fba68e9 files/no-phaser-ld-assume-kernel.patch 581 +MD5 bcdb856dae7ea7b22d130474f6c17b7d files/pass-clipper-enablevals.patch 501 diff --git a/sci-chemistry/ccp4/ccp4-5.99.5.ebuild b/sci-chemistry/ccp4/ccp4-5.99.5.ebuild new file mode 100644 index 0000000..65fc05e --- /dev/null +++ b/sci-chemistry/ccp4/ccp4-5.99.5.ebuild @@ -0,0 +1,377 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +inherit fortran eutils gnuconfig + +FORTRAN="g77 ifc" + +DESCRIPTION="Protein X-ray crystallography toolkit" +HOMEPAGE="http://www.ccp4.ac.uk/" +SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${PV}/packed/${PN}-core.tar.gz" +# ftp://ftp.ccp4.ac.uk/ccp4/${PV}/packed/phaser-cctbx.tar.gz" +# ftp://ftp.ccp4.ac.uk/ccp4/${PV}/prerelease/${P}_gfortran.tar.gz" +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~ppc ~x86" +IUSE="X" +# app-office/sc overlaps sc binary and man page +# We can't rename ours since the automated ccp4i interface expects it there, +# as do many scripts. app-office/sc can't rename its because that's the name +# of the package. +RDEPEND="X? ( + || ( + ( + x11-libs/libX11 + x11-libs/libXt + x11-libs/libXaw + ) + virtual/x11 + ) + ) + >=dev-lang/tcl-8.3 + >=dev-lang/tk-8.3 + >=dev-tcltk/blt-2.4 + virtual/lapack + virtual/blas + =sci-libs/fftw-2* + sci-chemistry/pdb-extract + sci-chemistry/rasmol + sci-libs/mccp4 + app-shells/tcsh + !app-office/sc" +DEPEND="${RDEPEND} + X? ( + || ( + ( + x11-misc/imake + x11-proto/inputproto + x11-proto/xextproto + ) + virtual/x11 + ) + )" + +src_unpack() { + unpack ${A} + +# These two only needed when attempting to install outside build dir via +# --bindir and --libdir instead of straight copying after build + # it attempts to install some libraries during the build +# epatch ${FILESDIR}/${P}-install-libs-at-install-time.patch + # hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view + # without this patch when --libdir is set + # Rotgen still needs more patching to find it +# epatch ${FILESDIR}/add-xdl-libdir.patch + + # it tries to create libdir, bindir etc on live system in configure + epatch ${FILESDIR}/dont-make-dirs-in-configure.patch + + # We already have sci-chemistry/rasmol + epatch ${FILESDIR}/dont-build-rasmol.patch + + # We already have sci-chemistry/pdb-extract +# Use configure option instead +# epatch ${FILESDIR}/dont-build-pdb-extract.patch + + epatch ${FILESDIR}/create-mosflm-bindir.patch + epatch ${FILESDIR}/make-mosflm-libdir.patch + epatch ${FILESDIR}/make-mosflm-index-libdir.patch + epatch ${FILESDIR}/make-mosflm-cbf-libdir.patch + epatch ${FILESDIR}/make-ipmosflm-dir.patch + +# Don't use these when we aren't building phaser +# epatch ${FILESDIR}/make-phaser-bindir.patch +# epatch ${FILESDIR}/no-phaser-ld-assume-kernel.patch +# # scons config.py tries to chmod python on live system +# epatch ${FILESDIR}/dont-chmod-python-binary.patch + + # Don't use this when we aren't building clipper + # For some reason clipper check for $enableval even when --enable is passed + epatch ${FILESDIR}/pass-clipper-enablevals.patch + epatch ${FILESDIR}/clipper-find-mccp4-includes.patch + + # Default to firefox browser, not 'netscape' + epatch ${FILESDIR}/ccp4i-default-to-firefox.patch + + # Also use -lpthread when linking blas and lapack + # We may need more fixing to use libcblas for the C files + epatch ${FILESDIR}/check-blas-lapack-pthread.patch + + gnuconfig_update +} + +src_compile() { + # GENTOO_OSNAME can be one of: + # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd + # linux_compaq_compilers linux_intel_compilers generic Darwin + # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers + if [[ "${FORTRANC}" = "ifc" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + ${S}/include/ccp4.setup + + # We agree to the license by emerging this, set in LICENSE + sed -i \ + -e "s~^\(^agreed=\).*~\1yes~g" \ + ${S}/configure + + # Fix up variables -- need to reset CCP4_MASTER at install-time + sed -i \ + -e "s~^\(setenv CCP4_MASTER.*\)/xtal~\1${WORKDIR}~g" \ + -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \ + ${S}/include/ccp4.setup* + + # Set up variables for build + source ${S}/include/ccp4.setup + + export CC=$(tc-getCC) + export CXX=$(tc-getCXX) + export COPTIM=${CFLAGS} + export CXXOPTIM=${CXXFLAGS} + # Default to -O2 if FFLAGS is unset + export FC=${FORTRANC} + export FOPTIM=${FFLAGS:- -O2} + + # Can't use econf, configure rejects unknown options like --prefix + ./configure \ + $(use_enable X x) \ + --with-shared-libs \ + --with-fftw=/usr \ + --with-warnings \ + --disable-pdb_extract \ + --disable-cctbx \ + --disable-phaser \ + ${GENTOO_OSNAME} || die "econf failed" + emake -j1 || die "emake failed" +} + +src_install() { +# Only needed when using --bindir and --libdir + # Needed to avoid errors. Originally tried to make lib and bin + # in configure script, now patched out by dont-make-dirs-in-configure.patch +# dodir /usr/include /usr/$(get_libdir) /usr/bin + + make install || die "install failed" + + # Fix env + sed -i \ + -e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \ + -e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \ + -e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \ + -e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/$(get_libdir)/ccp4/include~g" \ + -e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/$(get_libdir)/ccp4/data~g" \ + -e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \ + -e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \ + ${S}/include/ccp4.setup* + + # Get rid of S instances + # Also the main clipper library is built as libclipper-core, not libclipper + sed -i \ + -e "s:${S}:${ROOT}usr:g" \ + -e "s:lclipper :lclipper-core:g" \ + ${S}/bin/clipper-config +# sed -i \ +# -e "s:${S}:${ROOT}usr:g" \ +# ${S}/$(get_libdir)/cctbx/cctbx_build/setpaths* + + # Bins + EXEDESTTREE="/usr/bin" doexe ${S}/bin/* + + # Libs + for file in ${S}/lib/*; do + if [[ -d ${file} ]]; then + continue + elif [[ -x ${file} ]]; then + dolib.so ${file} + else + INSDESTTREE="/usr/$(get_libdir)" doins ${file} + fi + done + + # Fix libdir in all *.la files + sed -i \ + -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \ + ${D}/usr/$(get_libdir)/*.la + + # Library symlinks + local LIBNAMES="libclipper-ccp4.so.0.0.0 + libclipper-cif.so.0.0.0 + libclipper-contrib.so.0.0.0 + libclipper-core.so.0.0.0 + libclipper-minimol.so.0.0.0 + libclipper-mmdbold.so.0.0.0 + libclipper-mmdb.so.0.0.0 + libclipper-mtz.so.1.0.0 + libclipper-phs.so.0.0.0 + libjwc_c.so.0.1.1 + libjwc_f.so.0.1.1 + libssm.so.0.0.0 + libxdl_viewextra.so.0.0.0 + libxdl_view.so.2.0.0" + + for LIBNAME in ${LIBNAMES}; do + library_dosym ${LIBNAME} + done + +# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so +# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0 +# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0 +# +# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so +# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0 +# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0 +# +# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so +# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0 +# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0 +# +# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so +# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0 +# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0 +# +# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so +# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0 +# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0 +# +# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so +# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0 +# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0 +# +# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so +# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0 +# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0 +# +# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so +# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1 +# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0 +# +# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so +# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0 +# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0 +# +# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so +# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0 +# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1 +# +# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so +# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0 +# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1 +# +# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so +# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0 +# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0 +# +# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so +# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0 +# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0 +# +# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so +# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2 +# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0 + + # Environment files, setup scripts, etc. + INSDESTTREE="/usr/$(get_libdir)/ccp4/include" doins ${S}/include/* + + # CCP4Interface - GUI + INSDESTTREE="/usr/$(get_libdir)/ccp4" doins -r ${S}/ccp4i + EXEDESTTREE="/usr/$(get_libdir)/ccp4/ccp4i/bin" doexe ${S}/ccp4i/bin/* + + # Data + INSDESTTREE="/usr/$(get_libdir)/ccp4" doins -r ${S}/lib/data + + # Include files + for i in ccp4 clipper mmdb ssm; do + INSDESTTREE="/usr/include" doins -r ${S}/include/${i} + done + + # Install docs and examples + + doman ${S}/man/cat1/* + + mv ${S}/manual/README ${S}/manual/README-manual + dodoc ${S}/manual/* + + dodoc ${S}/README ${S}/CHANGES + + dodoc ${S}/doc/* + rm ${D}/usr/share/doc/${PF}/GNUmakefile.gz + rm ${D}/usr/share/doc/${PF}/COPYING.gz + + dohtml -r ${S}/html/* + dodoc ${S}/examples/README + + for i in data rnase toxd; do + DOCDESTTREE="examples/${i}" dodoc ${S}/examples/${i}/* + done + + DOCDESTTREE="examples/tutorial" dohtml -r ${S}/examples/tutorial/html + DOCDESTTREE="examples/tutorial" dohtml examples/tutorial/tut.css + for i in data results; do + DOCDESTTREE="examples/tutorial/${i}" dodoc ${S}/examples/tutorial/${i}/* + done + + for i in non-runnable runnable; do + DOCDESTTREE="examples/unix/${i}" dodoc ${S}/examples/unix/${i} + done + + # Needed for ccp4i docs to work + dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/examples + + # Fix overlaps with other packages + rm ${D}/usr/share/man/man1/rasmol.1.gz +} + +pkg_postinst() { + einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" + einfo "in /usr/$(get_libdir)/ccp4/include/ccp4.setup* to modify this." + + ewarn "Set your .bashrc or other shell login file to source" + ewarn "one of the ccp4.setup* files in ${ROOT}usr/$(get_libdir)/ccp4/include." + ewarn "CCP4 will not work without this." +} + +# Links libname.so, libname.so.major and libname.so.major.minor +# to libname.so.major.minor.micro +library_dosym() { + local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS + + LIBNAME=${1} + LIBDIR=${2:-/usr/$(get_libdir)} + + # Tag / on the end of libdir if needed + if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then + LIBDIR="${LIBDIR}/" + fi + + if [[ "${LIBNAME}" != *.so.* ]]; then + msg="library_dosym() requires a shared, versioned library as an argument" + eerror "$msg" + die "$msg" + fi + + SUFFIX=${LIBNAME##*so.} + CORE_LIBNAME=${LIBNAME%.so.*} + CORE_LIBNAME="${CORE_LIBNAME}.so" + LIB_MAJOR=${SUFFIX%%.*} + LIB_MINOR=${SUFFIX#*.} + LIB_MINOR=${SUFFIX%%.*} + LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}" + for LIB_SUFFIX in .${LIB_MAJOR} .${LIB_MAJOR}.${LIB_MINOR} ""; do + einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}" + dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX} + done +} diff --git a/sci-chemistry/ccp4/files/add-xdl-libdir.patch b/sci-chemistry/ccp4/files/add-xdl-libdir.patch new file mode 100644 index 0000000..fbb5dad --- /dev/null +++ b/sci-chemistry/ccp4/files/add-xdl-libdir.patch @@ -0,0 +1,29 @@ +--- ccp4-5.99.5.orig/configure 2005-12-05 02:26:38.000000000 -0800 ++++ ccp4-5.99.5 /configure 2005-12-05 02:30:35.000000000 -0800 +@@ -1616,7 +1616,7 @@ + sftools_FLAGS='$XFFLAGS $FOPTIM' \ + lgglib_FLAGS='$XFFLAGS -O0' \ + arp_waters_FLAGS='$XFFLAGS $FOPTIM' "} +- XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -lxdl_view"} ++ XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -L${CCP4}/x-windows/xdl_view/src -lxdl_view"} + XWIN_LIB=${XWIN_LIB:-"-L/usr/X11R6/lib -lXt -lSM -lX11 -lICE"} + XTYPE=${XTYPE:-"LINUX"} + TIDY=${TIDY:-"rm -f sta*"} +@@ -1752,7 +1752,7 @@ + arp_waters_FLAGS='$XFFLAGS $FOPTIM -fforce-mem' \ + mlphare_FLAGS='$XFFLAGS $FOPTIM -fno-move-all-movables' \ + stereo_FLAGS='$XFFLAGS $FOPTIM -fno-move-all-movables' "} +- XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -lxdl_view"} ++ XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -L${CCP4}/x-windows/xdl_view/src -lxdl_view"} + XWIN_LIB=${XWIN_LIB:-"-L/usr/X11R6/lib -lXt -lSM -lX11 -lICE"} + XTYPE=${XTYPE:-"LINUX"} + CXX_LIBS=${CXX_LIBS:-"-lstdc++"} +@@ -1871,7 +1871,7 @@ + refmac5_FLAGS='$XFFLAGS $FOPTIM' \ + arp_waters_FLAGS='$XFFLAGS $FOPTIM'\ + distang_FLAGS='$XFFLAGS -O1' "} +- XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -lxdl_view"} ++ XDL_LIB=${XDL_LIB:-"-L${CCP4_LIB} -L${CCP4}/x-windows/xdl_view/src -lxdl_view"} + XWIN_LIB=${XWIN_LIB:-"-L/usr/X11R6/lib -lXt -lSM -lX11 -lICE"} + XTYPE=${XTYPE:-"LINUX"} + if test "$shared_lib" = yes; then diff --git a/sci-chemistry/ccp4/files/ccp4-5.99.5-install-libs-at-install-time.patch b/sci-chemistry/ccp4/files/ccp4-5.99.5-install-libs-at-install-time.patch new file mode 100644 index 0000000..9170124 --- /dev/null +++ b/sci-chemistry/ccp4/files/ccp4-5.99.5-install-libs-at-install-time.patch @@ -0,0 +1,40 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 01:30:59.000000000 -0800 ++++ ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 01:31:50.000000000 -0800 +@@ -42,8 +42,7 @@ + xdlview_dir = $(srcdir)/xdl_view/src + xdlview : + cd $(xdlview_dir) ; \ +- $(MAKE) $(MFLAGS) ; \ +- $(MAKE) install ++ $(MAKE) $(MFLAGS) + + # + # rotgen and libraries +@@ -56,15 +55,13 @@ + # + libjwc_c : + cd $(libjwc_c_dir) ; \ +- $(MAKE) $(MFLAGS) ; \ +- $(MAKE) install ++ $(MAKE) $(MFLAGS) + # + # libjwc_f + # + libjwc_f : + cd $(libjwc_f_dir) ; \ +- $(MAKE) $(MFLAGS) ; \ +- $(MAKE) install ++ $(MAKE) $(MFLAGS) + # + # rotgen + # +@@ -167,6 +164,9 @@ + $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install + $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) ++ cd $(xdlview_dir); $(MAKE) install ++ cd $(libjwc_c_dir); $(MAKE) install ++ cd $(libjwc_f_dir); $(MAKE) install + # + # clean + # diff --git a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch new file mode 100644 index 0000000..106db89 --- /dev/null +++ b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch @@ -0,0 +1,13 @@ +--- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist 2006-01-06 17:54:17.000000000 -0800 ++++ ccp4-5.99.5/ccp4i/etc/configure.def.dist 2006-01-06 17:54:47.000000000 -0800 +@@ -54,8 +54,8 @@ + MESSAGE _text "" + BLT_LIBRARY _text "" + MENU_LENGTH _positiveint 25 +-HYPERTEXT_VIEWER _text netscape +-START_NETSCAPE _text netscape ++HYPERTEXT_VIEWER _text firefox ++START_NETSCAPE _text firefox + O_MAPMAN _text mapman + MAPMAN_MAXSIZE _positiveint 4194304 + QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch new file mode 100644 index 0000000..02a2aa6 --- /dev/null +++ b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch @@ -0,0 +1,103 @@ +--- ccp4-5.99.5.orig/configure 2006-01-17 00:35:36.000000000 -0800 ++++ ccp4-5.99.5/configure 2006-01-17 10:44:39.000000000 -0800 +@@ -2410,12 +2410,12 @@ + end + EOF + #firslty test without -lblas +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread" + echo $test_compile + if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then + # Compilation was okay +- echo "... only -llapack needed" +- XLAPACK_LIB="-llapack" ++ echo "... only -llapack -lpthread needed" ++ XLAPACK_LIB="-llapack -lpthread" + # Set the next two variables so that configure + # doesn't try to build netlib libraries + LAPACKLIB="lapack" +@@ -2424,12 +2424,12 @@ + tryblas= + else + echo "more than just -llapack needed...." +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread" + echo $test_compile + if { (eval $test_compile ) 2>&1; } && test -s testlink ; then + # Compilation was okay +- echo "...-llapack and -lblas were needed" +- XLAPACK_LIB="-llapack -lblas" ++ echo "...-llapack, -lpthread and -lblas were needed" ++ XLAPACK_LIB="-llapack -lpthread -lblas" + # Set the next two variables so that configure + # doesn't try to build netlib libraries + LAPACKLIB="lapack blas" +@@ -2720,8 +2720,8 @@ + STOP + END + EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" + echo $test_compile + if { (eval $test_compile ) 2>&1; } && test -s testlink ; then + have_lapack=yes +@@ -2738,7 +2738,7 @@ + LAPACKDIR="$testdir" + echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" + # +- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" ++ XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread" + # + # Test to see if we need BLAS too + # Do this by trying to compile a test program +@@ -2750,8 +2750,8 @@ + if test -f testlsame ; then + rm -f testsame testlsame.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then + have_blas=yes +@@ -2830,8 +2830,8 @@ + STOP + END + EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlink ; then + have_blas=yes +@@ -3033,7 +3033,7 @@ + if test -f testlsame ; then + rm -f testsame testlsame.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then + echo "Found LSAME in lib$BLASLIB" +@@ -3046,7 +3046,7 @@ + if test -f testxerbla ; then + rm -f testxerbla testxerbla.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then + # Found lsame +@@ -3080,7 +3080,7 @@ + cd ../.. + # + lapackdir=lib/lapack +- XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB" ++ XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread" + # netlib lapack is in fortran, so we may need the fortran libraries when + # we are linking using the C or C++ compilers + case $system in diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch new file mode 100644 index 0000000..3bf5a06 --- /dev/null +++ b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5/lib/clipper/configure.orig 2006-01-07 16:54:13.000000000 -0800 ++++ ccp4-5.99.5/lib/clipper/configure 2006-01-07 16:54:31.000000000 -0800 +@@ -21751,7 +21751,7 @@ + + if test "x$mccp4_prefix" != x; then + # ie. mccp4=thing was given (thing is what we're checking for) +- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include" ++ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4" + ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4" + else + # treat as standard lib/include diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch new file mode 100644 index 0000000..34d6197 --- /dev/null +++ b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2006-01-06 12:31:02.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Makefile.in 2006-01-06 12:31:30.000000000 -0800 +@@ -158,6 +158,7 @@ + install_obj = ipdisp.exe hklview xdldataman xdlmapman \ + rotgen ipmosflm + install: all ++ mkdir -p $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) diff --git a/sci-chemistry/ccp4/files/digest-ccp4-5.99.5 b/sci-chemistry/ccp4/files/digest-ccp4-5.99.5 new file mode 100644 index 0000000..f00d379 --- /dev/null +++ b/sci-chemistry/ccp4/files/digest-ccp4-5.99.5 @@ -0,0 +1,2 @@ +MD5 1dc37afc2597bceaabd971ba20d86ac3 ccp4-core.tar.gz 59156210 +MD5 ac745815cdff2c4c719e9171f029b3ba phaser-cctbx.tar.gz 17821731 diff --git a/sci-chemistry/ccp4/files/dont-build-pdb-extract.patch b/sci-chemistry/ccp4/files/dont-build-pdb-extract.patch new file mode 100644 index 0000000..721b235 --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-build-pdb-extract.patch @@ -0,0 +1,21 @@ +--- ccp4-5.99.5.orig/src/Makefile.in 2006-01-05 22:52:56.000000000 -0800 ++++ ccp4-5.99.5/src/Makefile.in 2006-01-05 22:55:58.000000000 -0800 +@@ -57,7 +57,7 @@ + + PDB_EXTRACT_TARGETS = pdb_extract extract pdb_extract_sf + +-all : $(CTARGETS) $(CXXTARGETS) $(FTARGETS) $(OTHERS) $(PDB_EXTRACT_SUITE) ccp4mapwish phaser ++all : $(CTARGETS) $(CXXTARGETS) $(FTARGETS) $(OTHERS) ccp4mapwish phaser + + .PHONY : all install instsome clean realclean distclean + +@@ -67,9 +67,6 @@ + -for i in $(CTARGETS) $(CXXTARGETS) $(FTARGETS) $(OTHERS) $(JAVATARGETS); do \ + test -s $$i && $(INSTALL_PROGRAM) `pwd`/$$i $(bindir)/$$i || true ;\ + done +- for i in $(PDB_EXTRACT_TARGETS); do \ +- test -s harvest_app_/pdb_extract/bin/$$i && $(INSTALL_PROGRAM) harvest_app_/pdb_extract/bin/$$i $(bindir)/$$i || true ;\ +- done + if test -f ccp4mapwish_/Makefile; then \ + cd ccp4mapwish_; $(MAKE) -i $(MFLAGS) $@; \ + else true; fi diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch new file mode 100644 index 0000000..8da54fd --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-build-rasmol.patch @@ -0,0 +1,19 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 03:06:57.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Makefile.in 2005-12-05 03:07:23.000000000 -0800 +@@ -35,7 +35,7 @@ + # + # all + # +-all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm ++all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm + # + # xdl_view + # +@@ -161,7 +161,6 @@ + $(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir) + cd $(srcdir)/XCCPJIFFY ; $(MAKE) install +- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install + $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) + cd $(xdlview_dir); $(MAKE) install diff --git a/sci-chemistry/ccp4/files/dont-chmod-python-binary.patch b/sci-chemistry/ccp4/files/dont-chmod-python-binary.patch new file mode 100644 index 0000000..21f3053 --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-chmod-python-binary.patch @@ -0,0 +1,14 @@ +--- ccp4-5.99.5.orig/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py 2006-01-06 21:48:09.000000000 -0800 ++++ ccp4-5.99.5/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py 2006-01-06 21:46:24.000000000 -0800 +@@ -756,8 +756,9 @@ + else: + action = self.write_bin_sh_dispatcher + ext = "" +- try: os.chmod(source_file, 0755) +- except OSError: pass ++ if source_file != self.python_exe: ++ try: os.chmod(source_file, 0755) ++ except OSError: pass + target_file_ext = target_file + ext + remove_or_rename(target_file_ext) + try: action(source_file, target_file_ext) diff --git a/sci-chemistry/ccp4/files/dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/dont-make-dirs-in-configure.patch new file mode 100644 index 0000000..24504d9 --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-5.99.5.orig/configure 2005-12-05 02:03:51.000000000 -0800 ++++ ccp4-5.99.5/configure 2005-12-05 02:03:54.000000000 -0800 +@@ -604,45 +604,45 @@ + # echo "! Beware -- the $system installation isn't properly tested." ; } + syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' + +-if test -z "$onlylibs" ; then +- for i in CCP4_SCR BINSORT_SCR; do +- if ( eval test -d \$$i || eval mkdir \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the value of $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir; do +- if ( eval test -d \$$i || eval mkdir \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the argument of --$i." +- badvar=1 +- fi +- done +- +- for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do +- if test -d $i || mkdir $i; then : +- else +- eval echo "! No directory $i and can\'t create it." +- badvar=1 +- fi +- done +-else +- # Kludge to fool the "Makefile" target in the top-level CCP4 +- # Makefile into not trying to remake src/Makefile.in +- for i in $srcdir/src $srcdir/lib/src ; do +- if test -d $i || mkdir $i; then +- if ! test -f $i/Makefile.in ; then +- echo +- echo "onlylibs: making dummy file $i/Makefile.in" +- touch $i/Makefile.in +- fi +- fi +- done +-fi ++#if test -z "$onlylibs" ; then ++# for i in CCP4_SCR BINSORT_SCR; do ++# if ( eval test -d \$$i || eval mkdir \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the value of $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir; do ++# if ( eval test -d \$$i || eval mkdir \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the argument of --$i." ++# badvar=1 ++# fi ++# done ++# ++# for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do ++# if test -d $i || mkdir $i; then : ++# else ++# eval echo "! No directory $i and can\'t create it." ++# badvar=1 ++# fi ++# done ++#else ++# # Kludge to fool the "Makefile" target in the top-level CCP4 ++# # Makefile into not trying to remake src/Makefile.in ++# for i in $srcdir/src $srcdir/lib/src ; do ++# if test -d $i || mkdir $i; then ++# if ! test -f $i/Makefile.in ; then ++# echo ++# echo "onlylibs: making dummy file $i/Makefile.in" ++# touch $i/Makefile.in ++# fi ++# fi ++# done ++#fi + + ### sanity checks + diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch new file mode 100644 index 0000000..7813141 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:12.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:41.000000000 -0800 +@@ -37,6 +37,7 @@ + ${F77} ${FFLAGS} -o $@ $< + + ipmosflm: ${OBJS} ++ mkdir -p ${DPSBIN} + ${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \ + -o ${DPSBIN}/ipmosflm ${LDFLAGS} + diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch new file mode 100644 index 0000000..ae4b763 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:42:19.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:43:35.000000000 -0800 +@@ -132,7 +132,7 @@ + # + # CBF library + # +-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) ++$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB) + $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) + $(AR) cr $@ *.o + $(RANLIB) $@ diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch new file mode 100644 index 0000000..97607b6 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:09.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:30.000000000 -0800 +@@ -76,6 +76,7 @@ + + # local version of libdps_index.a + ${LIB}/dps_index.a: ${IOBJS} ${HOBJS} ++ mkdir -p ${LIB} + ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS} + + ${LIB}/libpeak.a: diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch new file mode 100644 index 0000000..eac1b9f --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:48:47.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:49:02.000000000 -0800 +@@ -42,6 +42,7 @@ + $(LOCALLIBS) $(LIBS) + + index: $(IOBJS) ++ mkdir -p $(LIBDIR) + ${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS) + chmod 644 $(LIBDIR)/libdps_index.a + diff --git a/sci-chemistry/ccp4/files/make-phaser-bindir.patch b/sci-chemistry/ccp4/files/make-phaser-bindir.patch new file mode 100644 index 0000000..cdf1460 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-phaser-bindir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/src/phaser/ccp4_build 2006-01-06 15:56:22.000000000 -0800 ++++ ccp4-5.99.5/src/phaser/ccp4_build 2006-01-06 15:55:49.000000000 -0800 +@@ -65,6 +65,7 @@ + ./install $phaseropts --static_libraries --component="phaser" --target="exe/phaser" + + # Install in CCP4 bindir ++mkdir -p $bindir + cp phaser-$PHASER_VERSION/build/$PHASER_MTYPE/exe/phaser $bindir + + echo " " diff --git a/sci-chemistry/ccp4/files/no-phaser-ld-assume-kernel.patch b/sci-chemistry/ccp4/files/no-phaser-ld-assume-kernel.patch new file mode 100644 index 0000000..8011c3f --- /dev/null +++ b/sci-chemistry/ccp4/files/no-phaser-ld-assume-kernel.patch @@ -0,0 +1,15 @@ +--- ccp4-5.99.5.orig/src/phaser/conf/configure-options 2006-01-06 11:27:28.000000000 -0800 ++++ ccp4-5.99.5/src/phaser/conf/configure-options 2006-01-06 11:26:29.000000000 -0800 +@@ -33,9 +33,9 @@ + set font_dirs = '' + set strip_command = 'strip' + set wxpython_env = '' +- if ( "$PHASER_MTYPE" == "intel-linux" ) then +- setenv LD_ASSUME_KERNEL 2.4.1 +- endif ++# if ( "$PHASER_MTYPE" == "intel-linux" ) then ++# setenv LD_ASSUME_KERNEL 2.4.1 ++# endif + else if ( "$PHASER_MTYPE" == "alpha-tru64" ) then + set python_configure = '--with-cxx=cxx' + set libpng_arch = 'dec' diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch new file mode 100644 index 0000000..3e1a8b0 --- /dev/null +++ b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5.orig/configure 2006-01-06 11:45:43.000000000 -0800 ++++ ccp4-5.99.5/configure 2006-01-06 11:46:53.000000000 -0800 +@@ -3210,7 +3210,7 @@ + #ccp4 setup + xopts="${xopts} --with-ccp4=${srcdir}" + #interface setup +- xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol" ++ xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr" + echo + echo "********* CLIPPER CONFIGURATION ***********" + echo diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest new file mode 100644 index 0000000..44f281a --- /dev/null +++ b/sci-chemistry/coot/Manifest @@ -0,0 +1,36 @@ +MD5 73492ab7c15201eb04ec25e684c40768 coot-0.0.33.ebuild 1738 +RMD160 c2ee74255ab0b5a01580fcb3c915ef2893abfc8f coot-0.0.33.ebuild 1738 +SHA256 3a90f07be537bb769bd0eb4e6c784beddd93affcaa3781d564dae70df025b2bc coot-0.0.33.ebuild 1738 +MD5 1cc73d156ed5718782f6055f1b011251 coot-0.1.ebuild 2036 +RMD160 442cd4151270ba62e907ce867a026b046631605f coot-0.1.ebuild 2036 +SHA256 13f4c22a845b16e770126c54c283f4f149c7b60469f9277458376c2733927361 coot-0.1.ebuild 2036 +MD5 848b7861d1b09fd6474ead9f9bdc1d08 files/0.1-fix-build.patch 6879 +RMD160 397f4c9636f3289e9798d9959333eac612b09162 files/0.1-fix-build.patch 6879 +SHA256 eddfe2e6c1cd8ca30353f3dbb25a6b14b3cd0a13b72e03aae90e0ad146b13dce files/0.1-fix-build.patch 6879 +MD5 6873d9a8bf2305521cdeadcfa45c5c98 files/add-mmdb-includedir.patch 551 +RMD160 e3ceb851e986a0938b1bf19203f849a17b106dda files/add-mmdb-includedir.patch 551 +SHA256 151e4e1166de7624c8b5ea2c6e84cbfa840285633ae61aedddb5ac3462b9d008 files/add-mmdb-includedir.patch 551 +MD5 e409414e5b1d9e1413f77c61ef69ece2 files/add-needed-includes-libs.patch 3132 +RMD160 b7aee685e04ed6a4de2de80b6c32fcbef1e62fa7 files/add-needed-includes-libs.patch 3132 +SHA256 42ed6b879cf56dbc702afe84f16e4c7da82ac19b3c17a94480dd20bcb8650b88 files/add-needed-includes-libs.patch 3132 +MD5 f3852c0023f7cc86e1f9589d6818cb89 files/coot-0.1_pre1-coot-fftw-single.patch 1819 +RMD160 e81813f144f5cbc41420720c04be8f9a45aee36a files/coot-0.1_pre1-coot-fftw-single.patch 1819 +SHA256 42bf86db30a9abff3eb9beb595a1dc7cd7e2e2a8f954fdb814683754e42ba653 files/coot-0.1_pre1-coot-fftw-single.patch 1819 +MD5 8fbf12b34d09d505c441d3d0a0264bd8 files/coot-0.1_pre1-scripts-in-bin.patch 490 +RMD160 a6cbbbd217e094eb0ea8f2d486f5a7af757c9e7a files/coot-0.1_pre1-scripts-in-bin.patch 490 +SHA256 d600efff3d02ca902f44b742c6129bcb2e162ff537ae1987fe2e14133ee890f9 files/coot-0.1_pre1-scripts-in-bin.patch 490 +MD5 79d5f3b8f68fe0c7ee1055efaf4933c7 files/digest-coot-0.0.33 214 +RMD160 ac8fe4f98830a804c994d480ae800e90a2e1e353 files/digest-coot-0.0.33 214 +SHA256 d1075a8573ed64b76aede5f4612be5878bf5343eefd1c560f6c10d14827c152c files/digest-coot-0.0.33 214 +MD5 f3c79d65a72ef891cda85959ffdb1f29 files/digest-coot-0.1 771 +RMD160 aafaa2ef744ec91459573ee5e71d601f85093f81 files/digest-coot-0.1 771 +SHA256 fd193c645ece8082b50b61224e4e08050ab2b2415b82c67cd777ea5f317df8da files/digest-coot-0.1 771 +MD5 626ca012306b9c9f81ece8fa6d0478c5 files/glutinit.patch 494 +RMD160 9dfadaa40bd6664a5ea593b7033d58418ff1ab36 files/glutinit.patch 494 +SHA256 00b99f0257fbba7a6164013fd2c45e2cb497bde447859fba183c917f58cd1bec files/glutinit.patch 494 +MD5 07e6d9582f242b8fe91b3b61179bf444 files/setupdir.patch 499 +RMD160 b1009b7207ed9fc4cecbd960a24e1f322a8210e2 files/setupdir.patch 499 +SHA256 872a7e8d1cfa03f4f56967c16f8db8453c2c7b96ed31c69b2b330130da6b8961 files/setupdir.patch 499 +MD5 90602c119834fb507bffef4028b20f3b files/use-fftw-single.patch 1417 +RMD160 f74e61ca89edb8ed268f42a4bd09f101da6d3cd5 files/use-fftw-single.patch 1417 +SHA256 9aa65d58fc08e0bbdae0af921bcbdfac974edd05c038c617eecf9df9bedd3e40 files/use-fftw-single.patch 1417 diff --git a/sci-chemistry/coot/coot-0.0.33.ebuild b/sci-chemistry/coot/coot-0.0.33.ebuild new file mode 100644 index 0000000..786c8e1 --- /dev/null +++ b/sci-chemistry/coot/coot-0.0.33.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +inherit eutils autotools + +DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" +HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/" +SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz + http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz + http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz" +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~ppc ~x86" +IUSE="" +RDEPEND=">=sci-libs/gsl-1.3 + =dev-libs/glib-1.2* + =x11-libs/gtkglarea-1.2* + virtual/glut + virtual/opengl + sci-chemistry/ccp4 + dev-lang/python + x11-libs/gtk-canvas + dev-lang/python + x11-libs/guile-gtk + dev-libs/goosh + dev-libs/guile-www" +DEPEND="${RDEPEND}" + +src_unpack() { + unpack ${A} + epatch ${FILESDIR}/add-needed-includes-libs.patch + epatch ${FILESDIR}/glutinit.patch + epatch ${FILESDIR}/setupdir.patch + epatch ${FILESDIR}/use-fftw-single.patch + cd ${S} + eautoconf + eautomake +} + +src_compile() { + # All the --with's are used to activate various parts. + # Yes, this is broken behavior. + econf \ + --includedir='${prefix}/include/coot' \ + --with-gtkcanvas-prefix=/usr \ + --with-clipper-prefix=/usr \ + --with-mmdb-prefix=/usr \ + --with-ssmlib-prefix=/usr \ + --with-guile=/usr \ + --with-python=/usr \ + || die "econf failed" + emake -j1 || die "emake failed" +} + +src_install() { + make DESTDIR=${D} install || die + ebegin "Copying reference structures to ${D}/usr/share/coot/" + cp -R ${WORKDIR}/reference-structures ${D}/usr/share/coot/ + eend + ebegin "Copying monomer library to ${D}/usr/share/coot/" + cp -R ${WORKDIR}/lib ${D}/usr/share/coot/ + eend +} diff --git a/sci-chemistry/coot/coot-0.1.ebuild b/sci-chemistry/coot/coot-0.1.ebuild new file mode 100644 index 0000000..25a8834 --- /dev/null +++ b/sci-chemistry/coot/coot-0.1.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +inherit eutils autotools + +DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" +HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/" +SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz + http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz + http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz" +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~ppc ~x86" +IUSE="" +RDEPEND=">=sci-libs/gsl-1.3 + =dev-libs/glib-1.2* + =x11-libs/gtkglarea-1.2* + virtual/glut + virtual/opengl + sci-chemistry/ccp4 + dev-lang/python + x11-libs/gtk-canvas + dev-lang/python + x11-libs/guile-gtk + dev-libs/goosh + dev-libs/guile-www" +DEPEND="${RDEPEND}" + +src_unpack() { + unpack ${A} + epatch ${FILESDIR}/${PV}-fix-build.patch + + # Link against single-precision fftw + sed -i \ + -e "s:lfttw:lsfttw:g" \ + -e "s:lrfttw:lsrfttw:g" \ + ${S}/macros/clipper.m4 + + # Don't install setup scripts, they're only needed for nonstandard prefixes + sed -i \ + -e "s:^\(setup.*\):#\1:g" \ + -e "s:.*\(bin_.*\):\1:g" \ + ${S}/setup/Makefile.am + + cd ${S} + AT_M4DIR="macros" eautoreconf +} + +src_compile() { + # All the --with's are used to activate various parts. + # Yes, this is broken behavior. + econf \ + --includedir='${prefix}/include/coot' \ + --with-gtkcanvas-prefix=/usr \ + --with-clipper-prefix=/usr \ + --with-mmdb-prefix=/usr \ + --with-ssmlib-prefix=/usr \ + --with-guile=/usr \ + --with-python=/usr \ + || die "econf failed" + + # Parallel build's broken + emake -j1 || die "emake failed" +} + +src_install() { + make DESTDIR=${D} install || die + + # Install misses this + insinto /usr/share/coot/python + doins ${S}/src/coot.py + + ebegin "Copying reference structures to ${D}/usr/share/coot/" + cp -R ${WORKDIR}/reference-structures ${D}/usr/share/coot/ + eend + ebegin "Copying monomer library to ${D}/usr/share/coot/" + cp -R ${WORKDIR}/lib ${D}/usr/share/coot/ + eend +} diff --git a/sci-chemistry/coot/files/0.1-fix-build.patch b/sci-chemistry/coot/files/0.1-fix-build.patch new file mode 100644 index 0000000..ddec03d --- /dev/null +++ b/sci-chemistry/coot/files/0.1-fix-build.patch @@ -0,0 +1,124 @@ +diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/coords/Cartesian.h coot-0.1/coords/Cartesian.h +--- coot-0.1.orig/coords/Cartesian.h 2005-05-09 15:56:01.000000000 -0700 ++++ coot-0.1/coords/Cartesian.h 2006-04-13 17:57:43.000000000 -0700 +@@ -155,6 +155,9 @@ + + short int is_an_in_triangle(surface_face_data face, const Cartesian &b, + const Cartesian &c); ++ double cos_angle_btwn_vecs(const Cartesian &a, const Cartesian &b); ++ float dot_product(const Cartesian &a, const Cartesian &b); ++ Cartesian cross_product(const Cartesian &a, const Cartesian &b); + + + class CartesianPairInfo { +diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/coot-utils/coot-map-heavy.hh coot-0.1/coot-utils/coot-map-heavy.hh +--- coot-0.1.orig/coot-utils/coot-map-heavy.hh 2005-11-05 16:43:03.000000000 -0800 ++++ coot-0.1/coot-utils/coot-map-heavy.hh 2006-04-13 17:20:24.000000000 -0700 +@@ -83,7 +83,7 @@ + // searching of the trns components of the rtops. We use the + // molecule size (min_molecule_radius_) to do that. + std::vector<std::pair<float, clipper::RTop_orth> > +- fffear_search::filter_by_distance_to_higher_peak(const std::vector<std::pair<float, clipper::RTop_orth> > &vr) const; ++ filter_by_distance_to_higher_peak(const std::vector<std::pair<float, clipper::RTop_orth> > &vr) const; + + public: + clipper::NXmap<float> nxmap; +@@ -97,7 +97,7 @@ + // transformations of the coords need to apply this + // translation of the molecule (to be centered round the + // origin) before applying the RTop of the (negative) peaks of the fffear map. +- clipper::RTop_orth coot::util::fffear_search::mid_point_transformation() const; ++ clipper::RTop_orth mid_point_transformation() const; + }; + + } +diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/coot-utils/peak-search.hh coot-0.1/coot-utils/peak-search.hh +--- coot-0.1.orig/coot-utils/peak-search.hh 2005-10-20 04:39:25.000000000 -0700 ++++ coot-0.1/coot-utils/peak-search.hh 2006-04-13 17:18:28.000000000 -0700 +@@ -40,7 +40,7 @@ + const clipper::Xmap<float> &xmap) const; + + const std::vector<int> +- coot::peak_search::find_protein_to_origin_translations(const std::vector<clipper::Coord_orth> &sampled_protein_coords, const clipper::Xmap<float> &xmap) const; ++ find_protein_to_origin_translations(const std::vector<clipper::Coord_orth> &sampled_protein_coords, const clipper::Xmap<float> &xmap) const; + + double + min_dist_to_protein(const clipper::Coord_orth &point, +diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/ligand/dunbrack.hh coot-0.1/ligand/dunbrack.hh +--- coot-0.1.orig/ligand/dunbrack.hh 2006-03-22 09:44:17.000000000 -0800 ++++ coot-0.1/ligand/dunbrack.hh 2006-04-13 18:12:51.000000000 -0700 +@@ -37,7 +37,7 @@ + double probability_score(double chi_angle, int ichi, const coot::simple_rotamer &rot); + + std::vector<coot::simple_rotamer> +- coot::dunbrack::get_all_rotamers(const std::string &res_type) const; ++ get_all_rotamers(const std::string &res_type) const; + std::pair<short int, double> probability_of_this_rotamer(const std::vector<double> &chi_angles, + const std::vector<coot::simple_rotamer> &rots) const; + std::vector<std::vector<int> > rotamer_atom_names_to_indices(const std::vector<std::vector<std::string> > &residue_rotamer_atoms, PCAtom *residue_atoms, int n_residue_atoms) const; +diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/ligand/helix-placement.hh coot-0.1/ligand/helix-placement.hh +--- coot-0.1.orig/ligand/helix-placement.hh 2005-10-07 11:56:00.000000000 -0700 ++++ coot-0.1/ligand/helix-placement.hh 2006-04-13 18:16:32.000000000 -0700 +@@ -68,12 +68,12 @@ + void build_on_N_end(minimol::fragment *m, float min_density_limit) const; + void build_on_C_end(minimol::fragment *m, float min_density_limit) const; + minimol::residue +- helix_placement::build_N_terminal_ALA(const clipper::Coord_orth &prev_n, ++ build_N_terminal_ALA(const clipper::Coord_orth &prev_n, + const clipper::Coord_orth &prev_ca, + const clipper::Coord_orth &prev_c, + int seqno) const; + minimol::residue +- helix_placement::build_C_terminal_ALA(const clipper::Coord_orth &prev_n, ++ build_C_terminal_ALA(const clipper::Coord_orth &prev_n, + const clipper::Coord_orth &prev_ca, + const clipper::Coord_orth &prev_c, + int seqno) const; +diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/ligand/residue_by_phi_psi.hh coot-0.1/ligand/residue_by_phi_psi.hh +--- coot-0.1.orig/ligand/residue_by_phi_psi.hh 2005-09-15 03:56:01.000000000 -0700 ++++ coot-0.1/ligand/residue_by_phi_psi.hh 2006-04-13 18:07:06.000000000 -0700 +@@ -58,7 +58,7 @@ + short int do_rigid_body_refinement); + + minimol::fragment +- coot::residue_by_phi_psi::make_2_res_joining_frag(const std::string &chain_id, ++ make_2_res_joining_frag(const std::string &chain_id, + const phi_psi_pair &pp1, + const phi_psi_pair &pp2, + int seqnum, +diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/src/graphics-info.h coot-0.1/src/graphics-info.h +--- coot-0.1.orig/src/graphics-info.h 2006-03-27 01:12:01.000000000 -0800 ++++ coot-0.1/src/graphics-info.h 2006-04-13 18:02:41.000000000 -0700 +@@ -657,7 +657,7 @@ + } + + // +- static short int graphics_info_t::use_graphics_interface_flag; ++ static short int use_graphics_interface_flag; + + // Display size + static int graphics_x_size; +diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/src/molecule-class-info.h coot-0.1/src/molecule-class-info.h +--- coot-0.1.orig/src/molecule-class-info.h 2006-03-30 23:25:04.000000000 -0800 ++++ coot-0.1/src/molecule-class-info.h 2006-04-13 18:02:09.000000000 -0700 +@@ -395,7 +395,7 @@ + + // change chain id internal function + std::pair<int, std::string> +- molecule_class_info_t::change_chain_id_with_residue_range(const std::string &from_chain_id, ++ change_chain_id_with_residue_range(const std::string &from_chain_id, + const std::string &to_chain_id, + int start_resno, + int end_resno); +diff -ur -x libtool -x coot_wrap_python.cc coot-0.1.orig/src/rama_plot.hh coot-0.1/src/rama_plot.hh +--- coot-0.1.orig/src/rama_plot.hh 2006-03-30 23:25:06.000000000 -0800 ++++ coot-0.1/src/rama_plot.hh 2006-04-13 18:02:24.000000000 -0700 +@@ -289,7 +289,7 @@ + // SelResidue is guaranteed to have 3 residues (there is no protection + // for that in this function). + std::pair<short int, coot::phi_psi_t> +- coot::rama_plot::get_phi_psi(PCResidue *SelResidue) const; ++ get_phi_psi(PCResidue *SelResidue) const; + + + void map_mouse_pos(double x, double y); diff --git a/sci-chemistry/coot/files/add-mmdb-includedir.patch b/sci-chemistry/coot/files/add-mmdb-includedir.patch new file mode 100644 index 0000000..cab1f64 --- /dev/null +++ b/sci-chemistry/coot/files/add-mmdb-includedir.patch @@ -0,0 +1,11 @@ +--- coot-0.0.33.orig/configure 2005-06-30 05:45:06.000000000 -0700 ++++ coot-0.0.33/configure 2006-01-07 20:03:08.000000000 -0800 +@@ -10417,7 +10417,7 @@ + # when MMDB and dependencies get installed - we infact, include both + # directories. + # +- ac_MMDB_CXXFLAGS="-I$mmdb_prefix/include -I$mmdb_prefix/src" ++ ac_MMDB_CXXFLAGS="-I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb -I$mmdb_prefix/src" + # + # Similarly for mmdb, the uninstalled library position is simply in + # $mmdb_prefix, but the installed is in the standard prefixed subdirectory. diff --git a/sci-chemistry/coot/files/add-needed-includes-libs.patch b/sci-chemistry/coot/files/add-needed-includes-libs.patch new file mode 100644 index 0000000..bbf8c59 --- /dev/null +++ b/sci-chemistry/coot/files/add-needed-includes-libs.patch @@ -0,0 +1,56 @@ +diff -urN -x Makefile -x autom4te.cache -x configure -x libtool -x make.log -x src -x setup coot-0.0.33.orig/aclocal.m4 coot-0.0.33/aclocal.m4 +--- coot-0.0.33.orig/aclocal.m4 2005-06-30 05:45:04.000000000 -0700 ++++ coot-0.0.33/aclocal.m4 2006-01-08 06:38:18.000000000 -0800 +@@ -5330,7 +5330,7 @@ + # --gtkcanvas-prefix=/some/thing + # + +- GTKCANVAS_CFLAGS="-DHAVE_GTK_CANVAS -I$gtkcanvas_prefix/include $IMLIB_CFLAGS" ++ GTKCANVAS_CFLAGS="-DHAVE_GTK_CANVAS -I$gtkcanvas_prefix/include -I$gtkcanvas_prefix/include/gnome-1.0 $IMLIB_CFLAGS" + # + # Similarly for gtkcanvas, the uninstalled library position is simply in + # $gtkcanvas_prefix, but the installed is in the standard prefixed subdirectory. +@@ -5731,7 +5731,7 @@ + # when MMDB and dependencies get installed - we infact, include both + # directories. + # +- ac_MMDB_CXXFLAGS="-I$mmdb_prefix/include -I$mmdb_prefix/src" ++ ac_MMDB_CXXFLAGS="-I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb -I$mmdb_prefix/src" + # + # Similarly for mmdb, the uninstalled library position is simply in + # $mmdb_prefix, but the installed is in the standard prefixed subdirectory. +@@ -5805,7 +5805,7 @@ + + if test x$with_ssmlib_prefix != x; then + +- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB -I$with_ssmlib_prefix/include" ++ MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB -I$with_ssmlib_prefix/include -I$with_ssmlib_prefix/include/ssm" + MMDBSSM_LIBS="-L$with_ssmlib_prefix/lib -lssm" + + else +@@ -5857,7 +5857,7 @@ + # should ideally be CLIPPER_CFLAGS="-I$clipper_prefix/include", and the like + # when clipper and dependencies get installed. + # +- CLIPPER_CXXFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include" ++ CLIPPER_CXXFLAGS="-I$clipper_prefix/include/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include" + # -I$clipper_prefix/cctbx + + # yes, libmmtz.a is in -L$clipper_prefix/umtz! +@@ -5868,14 +5868,14 @@ + # HACK! FIXME + # added lz, we should have proper autoconf check for this. + # +- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm" ++ CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm" + # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx + else + # the compiler looks in the "standard" places for clipper. In real life, + # it would be quite unlikely that clipper would be installed in /usr/include, + # /usr/lib etc. so this code will not usually find the right dependencies. + CLIPPER_CXXFLAGS="" +- CLIPPER_LDOPTS="-lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm" ++ CLIPPER_LDOPTS=" -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm" + fi + + AC_MSG_CHECKING([for Clipper]) diff --git a/sci-chemistry/coot/files/coot-0.1_pre1-coot-fftw-single.patch b/sci-chemistry/coot/files/coot-0.1_pre1-coot-fftw-single.patch new file mode 100644 index 0000000..f1b0d3e --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.1_pre1-coot-fftw-single.patch @@ -0,0 +1,22 @@ +diff -urN coot-0.1.0-pre-1.orig/aclocal.m4 coot-0.1.0-pre-1/aclocal.m4 +--- coot-0.1.0-pre-1.orig/aclocal.m4 2006-01-01 05:37:20.000000000 -0800 ++++ coot-0.1.0-pre-1/aclocal.m4 2006-01-08 10:01:37.000000000 -0800 +@@ -5826,15 +5826,15 @@ + # HACK! FIXME + # added lz, we should have proper autoconf check for this. + # +- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm" +- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lccp4c $MMDB_LIBS -lrfftw -lfftw -lz -lm" ++ CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lsrfftw -lsfftw -lz -lm" ++ CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lccp4c $MMDB_LIBS -lsrfftw -lsfftw -lz -lm" + # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx + else + # the compiler looks in the "standard" places for clipper. In real life, + # it would be quite unlikely that clipper would be installed in /usr/include, + # /usr/lib etc. so this code will not usually find the right dependencies. + CLIPPER_CXXFLAGS="" +- CLIPPER_LDOPTS="-lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm" ++ CLIPPER_LDOPTS="-lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lmccp4 $MMDB_LIBS -lsrfftw -lsfftw -lz -lm" + fi + + AC_MSG_CHECKING([for Clipper]) diff --git a/sci-chemistry/coot/files/coot-0.1_pre1-scripts-in-bin.patch b/sci-chemistry/coot/files/coot-0.1_pre1-scripts-in-bin.patch new file mode 100644 index 0000000..6d64437 --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.1_pre1-scripts-in-bin.patch @@ -0,0 +1,15 @@ +diff -urN coot-0.1.0-pre-1.orig/setup/Makefile.am coot-0.1.0-pre-1/setup/Makefile.am +--- coot-0.1.0-pre-1.orig/setup/Makefile.am 2005-12-30 11:48:18.000000000 -0800 ++++ coot-0.1.0-pre-1/setup/Makefile.am 2006-01-08 10:00:49.000000000 -0800 +@@ -1,8 +1,8 @@ + # Install in both bin and setup +-setupdir = $(prefix)/setup ++#setupdir = $(prefix)/setup + +-# bin_SCRIPTS = coot.csh coot.sh +-setup_SCRIPTS = coot.csh coot.sh ++bin_SCRIPTS = coot.csh coot.sh ++# setup_SCRIPTS = coot.csh coot.sh + + + diff --git a/sci-chemistry/coot/files/digest-coot-0.0.33 b/sci-chemistry/coot/files/digest-coot-0.0.33 new file mode 100644 index 0000000..94a28e8 --- /dev/null +++ b/sci-chemistry/coot/files/digest-coot-0.0.33 @@ -0,0 +1,3 @@ +MD5 22b87da19a1156f281844c84cd9b8375 coot-0.0.33.tar.gz 2227396 +MD5 c09bb6b5524901cb0fde14589546224e reference-structures.tar.gz 6945369 +MD5 88cdbabf47914740f2d13e6960eea3c6 refmac-lib-data-monomers.tar.gz 2163068 diff --git a/sci-chemistry/coot/files/digest-coot-0.1 b/sci-chemistry/coot/files/digest-coot-0.1 new file mode 100644 index 0000000..3ca87e2 --- /dev/null +++ b/sci-chemistry/coot/files/digest-coot-0.1 @@ -0,0 +1,9 @@ +MD5 f983b327ac7d80446efc38c375873a08 coot-0.1.tar.gz 2618089 +RMD160 f5499d539d1b26510675e72f6ba4d99f3a9d3a40 coot-0.1.tar.gz 2618089 +SHA256 7ccde5f0d719a71986d5329fdbb618f8285373a581a6c00d57d9bd0e0a3e5cf5 coot-0.1.tar.gz 2618089 +MD5 c09bb6b5524901cb0fde14589546224e reference-structures.tar.gz 6945369 +RMD160 0dd9b2057cf5d6b0d060d704231aa7c5518f0b3b reference-structures.tar.gz 6945369 +SHA256 ba0a21e1f7f9065c7dd691e784d6508edc9ffae8b31923e5def5f1cbb7108b06 reference-structures.tar.gz 6945369 +MD5 88cdbabf47914740f2d13e6960eea3c6 refmac-lib-data-monomers.tar.gz 2163068 +RMD160 1443977959247c28cf1e7ad6683d0e72228f4cce refmac-lib-data-monomers.tar.gz 2163068 +SHA256 e4c9f89fd3bc1d3ab74c8270ed187875524800e0b72fb8131e298baa2b555a58 refmac-lib-data-monomers.tar.gz 2163068 diff --git a/sci-chemistry/coot/files/glutinit.patch b/sci-chemistry/coot/files/glutinit.patch new file mode 100644 index 0000000..7c5a593 --- /dev/null +++ b/sci-chemistry/coot/files/glutinit.patch @@ -0,0 +1,20 @@ +diff -urN coot-0.0.33.orig/src/main.cc coot-0.0.33/src/main.cc +--- coot-0.0.33.orig/src/main.cc 2006-01-08 08:20:58.000000000 -0800 ++++ coot-0.0.33/src/main.cc 2006-01-08 08:31:44.000000000 -0800 +@@ -31,6 +31,7 @@ + + #include <gtk/gtk.h> + ++#include <GL/glut.h> // for glutInit + + #include "interface.h" + #ifndef HAVE_SUPPORT_H +@@ -121,6 +122,8 @@ + textdomain (PACKAGE); + #endif + ++ glutInit(&argc, argv); ++ + // command line + command_line_data cld = parse_command_line(argc, argv); + diff --git a/sci-chemistry/coot/files/setupdir.patch b/sci-chemistry/coot/files/setupdir.patch new file mode 100644 index 0000000..9b52d70 --- /dev/null +++ b/sci-chemistry/coot/files/setupdir.patch @@ -0,0 +1,15 @@ +diff -urN coot-0.0.33.orig/setup/Makefile.am coot-0.0.33/setup/Makefile.am +--- coot-0.0.33.orig/setup/Makefile.am 2006-01-08 08:20:58.000000000 -0800 ++++ coot-0.0.33/setup/Makefile.am 2006-01-08 08:25:34.000000000 -0800 +@@ -1,8 +1,8 @@ + # Install in both bin and setup +-setupdir = $(prefix)/setup ++#setupdir = $(prefix)/setup + +-# bin_SCRIPTS = coot.csh coot.sh +-setup_SCRIPTS = coot.csh coot.sh ++bin_SCRIPTS = coot.csh coot.sh ++# setup_SCRIPTS = coot.csh coot.sh + + EXTRA_DIST = coot.csh coot.sh + diff --git a/sci-chemistry/coot/files/use-fftw-single.patch b/sci-chemistry/coot/files/use-fftw-single.patch new file mode 100644 index 0000000..7623187 --- /dev/null +++ b/sci-chemistry/coot/files/use-fftw-single.patch @@ -0,0 +1,20 @@ +diff -urN coot-0.0.33.orig/aclocal.m4 coot-0.0.33/aclocal.m4 +--- coot-0.0.33.orig/aclocal.m4 2006-01-08 08:42:52.000000000 -0800 ++++ coot-0.0.33/aclocal.m4 2006-01-08 08:43:07.000000000 -0800 +@@ -5868,14 +5868,14 @@ + # HACK! FIXME + # added lz, we should have proper autoconf check for this. + # +- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm" ++ CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lsrfftw -lsfftw -lz -lm" + # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx + else + # the compiler looks in the "standard" places for clipper. In real life, + # it would be quite unlikely that clipper would be installed in /usr/include, + # /usr/lib etc. so this code will not usually find the right dependencies. + CLIPPER_CXXFLAGS="" +- CLIPPER_LDOPTS=" -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lrfftw -lfftw -lz -lm" ++ CLIPPER_LDOPTS=" -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper-core -lclipper-mtz -lmccp4 $MMDB_LIBS -lsrfftw -lsfftw -lz -lm" + fi + + AC_MSG_CHECKING([for Clipper]) diff --git a/sci-chemistry/espresso/Manifest b/sci-chemistry/espresso/Manifest new file mode 100644 index 0000000..7ebd355 --- /dev/null +++ b/sci-chemistry/espresso/Manifest @@ -0,0 +1,6 @@ +MD5 e9eff222fc8bc0a9417e209b974cea89 files/digest-gtk-gamess-1.04.1 253 +RMD160 26dac9544c8b0a3e9c5e4ce7136d7ad70c81fe1e files/digest-gtk-gamess-1.04.1 253 +SHA256 f4be243d027c7527ed0fdca0af8f8b3b188bb96ef32fda23aaad0d8d6f2c9ef8 files/digest-gtk-gamess-1.04.1 253 +MD5 a1daae598930e217f99793d7ddeda5af gtk-gamess-1.04.1.ebuild 672 +RMD160 ce67c36f994fa85f64f3cae5b651c1daf8fd8929 gtk-gamess-1.04.1.ebuild 672 +SHA256 8aa9a3a50ddc725acd162bab6192fbb5788d645f2dd14b72f2bb1fac309f618d gtk-gamess-1.04.1.ebuild 672 diff --git a/sci-chemistry/espresso/espresso-3.00.ebuild b/sci-chemistry/espresso/espresso-3.00.ebuild new file mode 100644 index 0000000..5fc64ee --- /dev/null +++ b/sci-chemistry/espresso/espresso-3.00.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +inherit fortran + +DESCRIPTION="opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization" +HOMEPAGE="http://www.pwscf.org/" +SRC_URI="http://www.pwscf.org/downloads/PWcodes/codes/${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86" +IUSE="mpi" + +RDEPEND="virtual/blas + virtual/lapack + dev-tcltk/itk" +DEPEND="${RDEPEND}" + +# Doesn't work with gfortran, last tested on 4.1_pre20060210 +FORTRAN="ifc" + +src_compile() { + # For some reason it uses the same fortran but not mpicc + econf \ + $(use_enable mpi parallel) \ + F90="${FORTRANC}" \ + CC="${CC}" \ + MPICC="${CC}" \ + || die "configure failed" + + emake || die "make failed" +} + +src_install() { + DESTTREE="/usr" dobin bin/* || die "install failed" + dodoc README +} diff --git a/sci-chemistry/espresso/files/digest-gtk-gamess-1.04.1 b/sci-chemistry/espresso/files/digest-gtk-gamess-1.04.1 new file mode 100644 index 0000000..410cbec --- /dev/null +++ b/sci-chemistry/espresso/files/digest-gtk-gamess-1.04.1 @@ -0,0 +1,3 @@ +MD5 b15544b8d4f20c0e39f9c4577b80f2a4 gtk-gamess-1.04.1.tar.gz 110334 +RMD160 da36f5b7270e0589dcc94982fc92f206aea0fbb4 gtk-gamess-1.04.1.tar.gz 110334 +SHA256 37304b864ec4cc00a7d70ec65e85e1a867a24e0787406676d4d801fe0ae867b9 gtk-gamess-1.04.1.tar.gz 110334 diff --git a/sci-chemistry/gabedit/Manifest b/sci-chemistry/gabedit/Manifest new file mode 100644 index 0000000..7ebd355 --- /dev/null +++ b/sci-chemistry/gabedit/Manifest @@ -0,0 +1,6 @@ +MD5 e9eff222fc8bc0a9417e209b974cea89 files/digest-gtk-gamess-1.04.1 253 +RMD160 26dac9544c8b0a3e9c5e4ce7136d7ad70c81fe1e files/digest-gtk-gamess-1.04.1 253 +SHA256 f4be243d027c7527ed0fdca0af8f8b3b188bb96ef32fda23aaad0d8d6f2c9ef8 files/digest-gtk-gamess-1.04.1 253 +MD5 a1daae598930e217f99793d7ddeda5af gtk-gamess-1.04.1.ebuild 672 +RMD160 ce67c36f994fa85f64f3cae5b651c1daf8fd8929 gtk-gamess-1.04.1.ebuild 672 +SHA256 8aa9a3a50ddc725acd162bab6192fbb5788d645f2dd14b72f2bb1fac309f618d gtk-gamess-1.04.1.ebuild 672 diff --git a/sci-chemistry/gabedit/files/digest-gtk-gamess-1.04.1 b/sci-chemistry/gabedit/files/digest-gtk-gamess-1.04.1 new file mode 100644 index 0000000..410cbec --- /dev/null +++ b/sci-chemistry/gabedit/files/digest-gtk-gamess-1.04.1 @@ -0,0 +1,3 @@ +MD5 b15544b8d4f20c0e39f9c4577b80f2a4 gtk-gamess-1.04.1.tar.gz 110334 +RMD160 da36f5b7270e0589dcc94982fc92f206aea0fbb4 gtk-gamess-1.04.1.tar.gz 110334 +SHA256 37304b864ec4cc00a7d70ec65e85e1a867a24e0787406676d4d801fe0ae867b9 gtk-gamess-1.04.1.tar.gz 110334 diff --git a/sci-chemistry/gabedit/gtk-gamess-1.04.1.ebuild b/sci-chemistry/gabedit/gtk-gamess-1.04.1.ebuild new file mode 100644 index 0000000..611ff42 --- /dev/null +++ b/sci-chemistry/gabedit/gtk-gamess-1.04.1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +DESCRIPTION="GTK+ frontend to GAMESS" +HOMEPAGE="http://www.uiowa.edu/~ghemical/gtk-gamess.shtml" +SRC_URI="mirror://sourceforge/gtk-gamess/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86" +IUSE="" + +RDEPEND="=gnome-base/libglade-0*" +DEPEND="${RDEPEND}" + +src_unpack() { + unpack ${A} + sed -i -e "s:/usr/local/gamess/rungms:/usr/bin/rungms:g" \ + ${S}/src/gg_config.cpp +} + +src_install() { + make DESTDIR="${D}" install || die "install failed" +} diff --git a/sci-chemistry/gtk-gamess/Manifest b/sci-chemistry/gtk-gamess/Manifest new file mode 100644 index 0000000..7ebd355 --- /dev/null +++ b/sci-chemistry/gtk-gamess/Manifest @@ -0,0 +1,6 @@ +MD5 e9eff222fc8bc0a9417e209b974cea89 files/digest-gtk-gamess-1.04.1 253 +RMD160 26dac9544c8b0a3e9c5e4ce7136d7ad70c81fe1e files/digest-gtk-gamess-1.04.1 253 +SHA256 f4be243d027c7527ed0fdca0af8f8b3b188bb96ef32fda23aaad0d8d6f2c9ef8 files/digest-gtk-gamess-1.04.1 253 +MD5 a1daae598930e217f99793d7ddeda5af gtk-gamess-1.04.1.ebuild 672 +RMD160 ce67c36f994fa85f64f3cae5b651c1daf8fd8929 gtk-gamess-1.04.1.ebuild 672 +SHA256 8aa9a3a50ddc725acd162bab6192fbb5788d645f2dd14b72f2bb1fac309f618d gtk-gamess-1.04.1.ebuild 672 diff --git a/sci-chemistry/gtk-gamess/files/digest-gtk-gamess-1.04.1 b/sci-chemistry/gtk-gamess/files/digest-gtk-gamess-1.04.1 new file mode 100644 index 0000000..410cbec --- /dev/null +++ b/sci-chemistry/gtk-gamess/files/digest-gtk-gamess-1.04.1 @@ -0,0 +1,3 @@ +MD5 b15544b8d4f20c0e39f9c4577b80f2a4 gtk-gamess-1.04.1.tar.gz 110334 +RMD160 da36f5b7270e0589dcc94982fc92f206aea0fbb4 gtk-gamess-1.04.1.tar.gz 110334 +SHA256 37304b864ec4cc00a7d70ec65e85e1a867a24e0787406676d4d801fe0ae867b9 gtk-gamess-1.04.1.tar.gz 110334 diff --git a/sci-chemistry/gtk-gamess/gtk-gamess-1.04.1.ebuild b/sci-chemistry/gtk-gamess/gtk-gamess-1.04.1.ebuild new file mode 100644 index 0000000..611ff42 --- /dev/null +++ b/sci-chemistry/gtk-gamess/gtk-gamess-1.04.1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +DESCRIPTION="GTK+ frontend to GAMESS" +HOMEPAGE="http://www.uiowa.edu/~ghemical/gtk-gamess.shtml" +SRC_URI="mirror://sourceforge/gtk-gamess/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86" +IUSE="" + +RDEPEND="=gnome-base/libglade-0*" +DEPEND="${RDEPEND}" + +src_unpack() { + unpack ${A} + sed -i -e "s:/usr/local/gamess/rungms:/usr/bin/rungms:g" \ + ${S}/src/gg_config.cpp +} + +src_install() { + make DESTDIR="${D}" install || die "install failed" +} diff --git a/sci-chemistry/king/Manifest b/sci-chemistry/king/Manifest new file mode 100644 index 0000000..634cdd7 --- /dev/null +++ b/sci-chemistry/king/Manifest @@ -0,0 +1,6 @@ +MD5 0ced5ad56d8c926ee1844540db04c881 files/digest-king-1.50.060207 259 +RMD160 d54139758f02dec90e337acc79644e80c6b3b3b4 files/digest-king-1.50.060207 259 +SHA256 ae9e09a316344c91fdd47a54059a84d51a64803133a4410f337b5f28b7293686 files/digest-king-1.50.060207 259 +MD5 c9c012d4f9ae9dd3128ab7a493942d1d king-1.50.060207.ebuild 1022 +RMD160 e062415da3b1dcce08b515b893516409fea25d4c king-1.50.060207.ebuild 1022 +SHA256 71e54d92199fe2b9c2221069593873e293e4876ec668aec0044ae21b6fd9a401 king-1.50.060207.ebuild 1022 diff --git a/sci-chemistry/king/files/digest-king-1.50.060207 b/sci-chemistry/king/files/digest-king-1.50.060207 new file mode 100644 index 0000000..9b9c854 --- /dev/null +++ b/sci-chemistry/king/files/digest-king-1.50.060207 @@ -0,0 +1,3 @@ +MD5 f8e7974198ab49eca972b2dc9ec6b20c king.1.50.060207.src.zip 13922914 +RMD160 74ff6b60d6ef4ed7bbbb1215fb7740e30c99ddee king.1.50.060207.src.zip 13922914 +SHA256 f6a798978a751b7431da244352ec09de0b1929cf806f9fb160b791fe12d2e0fc king.1.50.060207.src.zip 13922914 diff --git a/sci-chemistry/king/king-1.50.060207.ebuild b/sci-chemistry/king/king-1.50.060207.ebuild new file mode 100644 index 0000000..48b7e90 --- /dev/null +++ b/sci-chemistry/king/king-1.50.060207.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +MY_P="${PN}.${PV}" +DESCRIPTION="An interactive system for 3D graphics (primarily molecular)" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/king.php" +SRC_URI="http://kinemage.biochem.duke.edu/ftpsite/pub/software/${PN}/${MY_P}.src.zip" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86" +IUSE="" + +RDEPEND="virtual/jre" +DEPEND="${RDEPEND} + dev-java/ant-core + virtual/jdk" + +S="${WORKDIR}/${PN}" + +src_unpack() { + unpack ${A} + cd ${WORKDIR} + + for i in king chiropraxis driftwood; do + mv ${i}* $i + done +} + +src_compile() { + ant build || die "ant build failed" +} + +src_install() { + dojar king.jar || die "dojar failed" + dodoc doc/* || die "dodoc failed" + dohtml *.html || die "dohtml failed" + cat << EOF >> ${T}/king +#!/bin/sh +java -jar /usr/share/king/lib/king.jar +EOF + + DESTTREE="/usr" dobin ${T}/king +} diff --git a/sci-chemistry/maid/CVS/Entries b/sci-chemistry/maid/CVS/Entries new file mode 100644 index 0000000..865c984 --- /dev/null +++ b/sci-chemistry/maid/CVS/Entries @@ -0,0 +1,5 @@ +D/files//// +/metadata.xml/1.1/Thu Dec 15 20:31:24 2005// +/ChangeLog/1.3/Thu Dec 15 21:06:31 2005// +/maid-20011112.ebuild/1.3/Thu Dec 15 21:06:31 2005// +/Manifest/1.4/Thu Dec 15 21:06:37 2005// diff --git a/sci-chemistry/maid/CVS/Repository b/sci-chemistry/maid/CVS/Repository new file mode 100644 index 0000000..f75bd84 --- /dev/null +++ b/sci-chemistry/maid/CVS/Repository @@ -0,0 +1 @@ +gentoo-x86/sci-chemistry/maid diff --git a/sci-chemistry/maid/CVS/Root b/sci-chemistry/maid/CVS/Root new file mode 100644 index 0000000..c108e17 --- /dev/null +++ b/sci-chemistry/maid/CVS/Root @@ -0,0 +1 @@ +spyderous@cvs.gentoo.org:/var/cvsroot diff --git a/sci-chemistry/maid/ChangeLog b/sci-chemistry/maid/ChangeLog new file mode 100644 index 0000000..6bfd435 --- /dev/null +++ b/sci-chemistry/maid/ChangeLog @@ -0,0 +1,20 @@ +# ChangeLog for sci-chemistry/maid +# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maid/ChangeLog,v 1.3 2005/12/15 21:06:31 spyderous Exp $ + + 15 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; maid-20011112.ebuild: + Fix SRC_URI. + + 15 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; maid-20011112.ebuild: + Fix license. The author informed me by email that it's intended to be freely + distributed, modified and redistributed. + +*maid-20011112 (15 Dec 2005) + + 15 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; + +files/fix-compilation.patch, +files/fix-warnings.patch, +metadata.xml, + +maid-20011112.ebuild: + MAID does automatic fitting of protein X-ray crystallography electron + density maps. It can correctly build about 60% of alpha carbons on + medium-resolution maps and about 80% on high-resolution maps. + diff --git a/sci-chemistry/maid/Manifest b/sci-chemistry/maid/Manifest new file mode 100644 index 0000000..1489427 --- /dev/null +++ b/sci-chemistry/maid/Manifest @@ -0,0 +1,15 @@ +MD5 f2e1b0a0da29465b1b1f29bb3343e08b ChangeLog 895 +RMD160 9d3a38aa52e54035d13b4992dfead92b62f1d8f8 ChangeLog 895 +SHA256 f34fdd7d59c25194a4ab6153b2de22e2dc99a44806514aea73ea3b918d25c629 ChangeLog 895 +MD5 e427165dea82055785c9497e5ca3a85d files/digest-maid-20011112 518 +RMD160 02f506efa14ca843e5f0058e26515b315020e06c files/digest-maid-20011112 518 +SHA256 19a701e406c26fd88bc916e4ad7660c3955639f3fd6f5a59e282ae74604bc7f2 files/digest-maid-20011112 518 +MD5 bcc6fdf88e85ccb7f3a06ef3dd9011b7 files/fix-warnings.patch 17141 +RMD160 b10d94b75c684b3ac506c28dfdd70ec8fb000fc1 files/fix-warnings.patch 17141 +SHA256 338e595a56ea1592221f833ab368afa672b4571460a9d46667871ded7cf8e5c1 files/fix-warnings.patch 17141 +MD5 f65ff5531e9788cf6f87c30a61fa7994 maid-20011112.ebuild 1411 +RMD160 22fa1a82f1bd377ad09f453bfdbca337f3282598 maid-20011112.ebuild 1411 +SHA256 8dfe7c93bb6a5ec536e9c6be0091b8954db03e8c2a4690caf71aa70782fdac38 maid-20011112.ebuild 1411 +MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248 +RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248 +SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248 diff --git a/sci-chemistry/maid/files/CVS/Entries b/sci-chemistry/maid/files/CVS/Entries new file mode 100644 index 0000000..f049271 --- /dev/null +++ b/sci-chemistry/maid/files/CVS/Entries @@ -0,0 +1,4 @@ +/digest-maid-20011112/1.1/Thu Dec 15 20:31:19 2005// +/fix-compilation.patch/1.1/Thu Dec 15 20:31:19 2005// +/fix-warnings.patch/1.1/Thu Dec 15 20:31:19 2005// +D diff --git a/sci-chemistry/maid/files/CVS/Repository b/sci-chemistry/maid/files/CVS/Repository new file mode 100644 index 0000000..e2903d0 --- /dev/null +++ b/sci-chemistry/maid/files/CVS/Repository @@ -0,0 +1 @@ +gentoo-x86/sci-chemistry/maid/files diff --git a/sci-chemistry/maid/files/CVS/Root b/sci-chemistry/maid/files/CVS/Root new file mode 100644 index 0000000..c108e17 --- /dev/null +++ b/sci-chemistry/maid/files/CVS/Root @@ -0,0 +1 @@ +spyderous@cvs.gentoo.org:/var/cvsroot diff --git a/sci-chemistry/maid/files/digest-maid-20011112 b/sci-chemistry/maid/files/digest-maid-20011112 new file mode 100644 index 0000000..039bb50 --- /dev/null +++ b/sci-chemistry/maid/files/digest-maid-20011112 @@ -0,0 +1,6 @@ +MD5 aad12e496bed15581342d206282f03e6 maid-fix-compilation.patch.bz2 5044 +RMD160 fd196923baff07836bebd8cdd463b4f72a12cc87 maid-fix-compilation.patch.bz2 5044 +SHA256 17a2dda71af96d45f57c1cbf500bad1d1aca596cc4da4eee481b4bb62207d7be maid-fix-compilation.patch.bz2 5044 +MD5 23066037ad06f256d26e61a69d91c84a maid_unix_12nov01.tar.gz 480609 +RMD160 fcfcd63e2c68afb43ba576430aac23d5fbee419d maid_unix_12nov01.tar.gz 480609 +SHA256 4dcf2c2945a97efa7dcea8e89a2b3d65c8daf0f44705e11305c426854db5eaa0 maid_unix_12nov01.tar.gz 480609 diff --git a/sci-chemistry/maid/files/fix-warnings.patch b/sci-chemistry/maid/files/fix-warnings.patch new file mode 100644 index 0000000..b4f48d2 --- /dev/null +++ b/sci-chemistry/maid/files/fix-warnings.patch @@ -0,0 +1,419 @@ +diff -ur glmaid_dist.orig/assignseq.c++ glmaid_dist/assignseq.c++ +--- glmaid_dist.orig/assignseq.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/assignseq.c++ 2005-12-15 08:36:47.000000000 -0800 +@@ -2630,9 +2630,9 @@ + if(ibestden <= 1) // 0.8 or 1.0 + *maxngap = geo.maxngap; + else if(ibestden ==2) // 1.2 +- *maxngap = 1.5*geo.maxngap; ++ *maxngap = (int) (1.5*geo.maxngap); + else if (ibestden >2) // 1.4 or 1.6 +- *maxngap = 2.0 *geo.maxngap; ++ *maxngap = (int) (2.0 *geo.maxngap); + } + #endif + +diff -ur glmaid_dist.orig/bone.c++ glmaid_dist/bone.c++ +--- glmaid_dist.orig/bone.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/bone.c++ 2005-12-15 08:31:26.000000000 -0800 +@@ -815,7 +815,7 @@ + } + + +- bonemin = bone1.minden*maidfile.denscale; // lower limit used to make bone (round down) ++ bonemin = (int) (bone1.minden*maidfile.denscale); // lower limit used to make bone (round down) + fprintf(fpout,"bonemin = %d\n",bonemin); + defineiden(bone1,iden,den1,bonemin); // set point on boundary = REMOVE + bsort(den1,bone1,sortv,bonemin,sortnum,&maxsize); // sort density into bins; sort[i] is vector of 1 ..... max +diff -ur glmaid_dist.orig/checkfit.c++ glmaid_dist/checkfit.c++ +--- glmaid_dist.orig/checkfit.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/checkfit.c++ 2005-12-15 08:22:14.000000000 -0800 +@@ -2977,7 +2977,7 @@ + *maxden = -1000.0; + xtof(den1,pos,fd); /* convert from double word to float sccreen*/ + for(k=0;k<=2;k++) +- ir[k]=fd[k]+0.5; /*round to integer*/ ++ ir[k]=(int) (fd[k]+0.5); /*round to integer*/ + for(ii=ir[0]-2;ii<=ir[0]+2;ii++){ + if( (ii>=1)&& (ii<=den1.amax[0]-den1.amin[0]-1) ) + for(jj=ir[1]-2;jj<=ir[1]+2;jj++) +diff -ur glmaid_dist.orig/extend2.c++ glmaid_dist/extend2.c++ +--- glmaid_dist.orig/extend2.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/extend2.c++ 2005-12-15 08:24:45.000000000 -0800 +@@ -363,7 +363,7 @@ + nend[3]=geo.nend[1]+3; + #if 1 // Works well in most cases + mrot[0]= 2*nrot; +- mrot[1]= 1.5*nrot; ++ mrot[1]= (int) (1.5*nrot); + mrot[2]= nrot; + mrot[3]= nrot; + #endif +diff -ur glmaid_dist.orig/extendfit.c++ glmaid_dist/extendfit.c++ +--- glmaid_dist.orig/extendfit.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/extendfit.c++ 2005-12-15 08:26:43.000000000 -0800 +@@ -4024,7 +4024,7 @@ + ext.usenfits = 3;// I do not think this makes any difference since it reset in other routines -Number of unassigned connected that must be linked to assigne seq. value + geo.deldist = sqrt( dot(den1.delx,den1.delx) ); // length of den1.delx vector = 1.445 for shad , res = 2.5 + if(geo.deldist < 1.445) +- geo.gnmax = 7*(1.445/geo.deldist) +1; ++ geo.gnmax = (int) (7*(1.445/geo.deldist) +1); + else + geo.gnmax = 7; + geo.maxugap = 8; //Maximum gap allowed to connect unassigned fits +diff -ur glmaid_dist.orig/fit.c++ glmaid_dist/fit.c++ +--- glmaid_dist.orig/fit.c++ 2005-12-15 08:15:43.000000000 -0800 ++++ glmaid_dist/fit.c++ 2005-12-15 08:36:24.000000000 -0800 +@@ -65,7 +65,7 @@ + tordata.torconst=torconstorig; + tordata2.torconst=torconstorig; + tordata.rfor=rfororig; //-BE CAREFUL - MUST BE SURE rfororig defined/geo.maxside = origmaxside; +-geo.maxside = origmaxside; ++geo.maxside = (int) origmaxside; + if (&client_data) { + XtRemoveWorkProc (work_id); + } +diff -ur glmaid_dist.orig/initialize.c++ glmaid_dist/initialize.c++ +--- glmaid_dist.orig/initialize.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/initialize.c++ 2005-12-15 08:34:02.000000000 -0800 +@@ -300,7 +300,7 @@ + nless=nless+1; + dds= -MAXCHAR+1; + } +- den1.den[i][j][k]=dds; ++ den1.den[i][j][k]=(signed) dds; + } + } + } +Files glmaid_dist.orig/initialize.o and glmaid_dist/initialize.o differ +diff -ur glmaid_dist.orig/mapmenu.c++ glmaid_dist/mapmenu.c++ +--- glmaid_dist.orig/mapmenu.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/mapmenu.c++ 2005-12-15 08:35:53.000000000 -0800 +@@ -430,7 +430,7 @@ + { + int i; + for(i=0;i<3;i++) +- map.crange[i] = fcontradius[item_no]/map.delx[i]; ++ map.crange[i] = (int) (fcontradius[item_no]/map.delx[i]); + //printf("map radius = %d\n",map.crange[0]); + } + +diff -ur glmaid_dist.orig/math.c++ glmaid_dist/math.c++ +--- glmaid_dist.orig/math.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/math.c++ 2005-12-15 08:31:55.000000000 -0800 +@@ -51,9 +51,9 @@ + z=xx[2]/den1.cvz; + y=(xx[1]-z*den1.cvy)/den1.singam; + x=xx[0]-y*den1.cosgam-z*den1.cosbe; +- ijk[0]=x/den1.delx[0] - den1.amin[0]; +- ijk[1]=y/den1.delx[1] - den1.amin[1]; +- ijk[2]=z/den1.delx[2] - den1.amin[2]; ++ ijk[0]=(int) (x/den1.delx[0] - den1.amin[0]); ++ ijk[1]=(int) (y/den1.delx[1] - den1.amin[1]); ++ ijk[2]=(int) (z/den1.delx[2] - den1.amin[2]); + } + + void imcv(struct griddata& den1,int xi[3],float sx[3]) /*convert from integer xi,xj (grid point) +diff -ur glmaid_dist.orig/menu.c++ glmaid_dist/menu.c++ +--- glmaid_dist.orig/menu.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/menu.c++ 2005-12-15 08:35:15.000000000 -0800 +@@ -321,7 +321,7 @@ + { + int i; + sc.cubecol[0] += 0.01; +- i= sc.cubecol[0]; ++ i= (int) sc.cubecol[0]; + sc.cubecol[0]= sc.cubecol[0]-i;; + draw_screen(client_data); + return False; // Runs continually +@@ -987,14 +987,14 @@ + int i; + + for(i=0;i<=2;i++) // Use default contour radius +- den1.crange[i]=sc.contourradius/den1.delx[i]; ++ den1.crange[i]=(int) (sc.contourradius/den1.delx[i]); + den1.contonoff = -1; + den1.selectcontonoff = -1; + for(i=0;i<3;i++) + den1.color[i]=bluev[i]; + den1.conlevel = sc.conlevel*maidfile.denscale; // Set contourleve to default value + // Allocate arrays for contour routines +- den1.ntri = NTRI/(den1.delx[0]*den1.delx[1]*den1.delx[2]); // Scale ntri relative del = 1 ++ den1.ntri = (int) (NTRI/(den1.delx[0]*den1.delx[1]*den1.delx[2])); // Scale ntri relative del = 1 + printf("Allocating arrays for contour routines ntriangles = %d\n",den1.ntri); + imat2(den1.tri,den1.ntri,9); + printf(" Done\n"); +diff -ur glmaid_dist.orig/pdbtolev.c++ glmaid_dist/pdbtolev.c++ +--- glmaid_dist.orig/pdbtolev.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/pdbtolev.c++ 2005-12-15 08:27:19.000000000 -0800 +@@ -645,7 +645,7 @@ + { + int i,j,natot,bi; + float bsqr; +- natot=subst[snum].pos[0][0]; /*total # of atoms*/ ++ natot=(int) subst[snum].pos[0][0]; /*total # of atoms*/ + bsqr=tsqr(bondlength); + for(i=1;i<=natot;i++) + cmat[i][0]=0; /*initally no connections to i*/ +diff -ur glmaid_dist.orig/rankside.c++ glmaid_dist/rankside.c++ +--- glmaid_dist.orig/rankside.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/rankside.c++ 2005-12-15 08:33:32.000000000 -0800 +@@ -201,13 +201,13 @@ + #endif + tbad = fit.ibad[resn][a1] + fit.ibad[resn][a2] +fit.ibad[resn][a3]; + if(tbad==0) +- return 0+iadd; ++ return 0+(int) iadd; + if(tbad ==1) +- return 1+iadd; ++ return 1+(int) iadd; + if(tbad==2) +- return 2+iadd; ++ return 2+(int) iadd; + if(tbad==3) +- return 4+iadd; ++ return 4+(int) iadd; + else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) ) + return 3; + else +@@ -245,11 +245,11 @@ + iadd = iadd+1; + #endif + if(fit.ibad[resn][a1]==0 ) +- return 0+iadd; ++ return 0+(int) iadd; + else if( fit.ibad[resn][a2]==0 ) +- return 1+iadd; ++ return 1+(int) iadd; + else if( fit.ibad[resn][a3]==0 ) +- return 1+iadd; ++ return 1+(int) iadd; + else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) ) + return 3; + else +@@ -285,11 +285,11 @@ + iadd = iadd+1; + #endif + if(fit.ibad[resn][a1]==0 ) +- return 0+iadd; ++ return 0+(int) iadd; + else if( fit.ibad[resn][a2]==0 ) +- return 1+iadd; ++ return 1+(int) iadd; + else if( fit.ibad[resn][a3]==0 ) +- return 1+iadd; ++ return 1+(int) iadd; + else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) ) + return 3; + else +@@ -316,11 +316,11 @@ + if(valden> 1.1*ringden) //change2 + iadd = iadd+1; + if(fit.ibad[resn][a1]==0 ) +- return 0+iadd; ++ return 0+(int) iadd; + else if( fit.ibad[resn][a2]==0 ) +- return 1+iadd; ++ return 1+(int) iadd; + else if( fit.ibad[resn][a3]==0 ) +- return 1+iadd; ++ return 1+(int) iadd; + else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) ) + return 3; + else +Files glmaid_dist.orig/rankside.o and glmaid_dist/rankside.o differ +diff -ur glmaid_dist.orig/refine.c++ glmaid_dist/refine.c++ +--- glmaid_dist.orig/refine.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/refine.c++ 2005-12-15 08:26:15.000000000 -0800 +@@ -67,8 +67,8 @@ + */ + { + int ix,rnd; +- ix = floor(x); +- rnd = nn*(x-ix) + 0.5; ++ ix = (int) floor(x); ++ rnd = (int) (nn*(x-ix) + 0.5); + printf("nn = %d x = %5.3f rnd = %d Grid point %5.3f\n",nn,x,rnd,ix+(float)rnd/nn); + return rnd; + } +@@ -82,8 +82,8 @@ + int k; + + for(k=0;k<=2;k++){ +- ivec[k] = floor(fvec[k]); +- ival[k] = nn*(fvec[k]-ivec[k]) + 0.5; ++ ivec[k] = (int) floor(fvec[k]); ++ ival[k] = (int) (nn*(fvec[k]-ivec[k]) + 0.5); + } + } + +@@ -115,9 +115,9 @@ + } + for(k=0;k<=2;k++) + gzd.dvec[gzd.num][k] =ivec[k]; +- gzd.den[gzd.num] = scalechar* exp(-rad*rad/bfact) +0.5; // mult by 100 and round ++ gzd.den[gzd.num] = (int) (scalechar* exp(-rad*rad/bfact) +0.5); // mult by 100 and round + for(k=0;k<=2;k++) +- gzd.forv[gzd.num][k] = 4.0*rad*gzd.den[gzd.num]*diffv[k]/bfact; ++ gzd.forv[gzd.num][k] = (int) (4.0*rad*gzd.den[gzd.num]*diffv[k]/bfact); + } + + void assignforce(gzdhead) +@@ -421,7 +421,7 @@ + gzd[0].num = 0; + oneatomgrid(den1,geo,ivec0,cenpos,gzd[0],bfact,countfunc); + printf("totnum = %d\n",gzd[0].num); +- maxgzd = gzd[0].num = 1.5*gzd[0].num; // increase by 15% ++ maxgzd = gzd[0].num = (int) (1.5*gzd[0].num); // increase by 15% + allocategzd(gzd[0].num); + del = 1.0/NDIV; + for(i=0;i<=NDIV;i++){ +diff -ur glmaid_dist.orig/sphere.c++ glmaid_dist/sphere.c++ +--- glmaid_dist.orig/sphere.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/sphere.c++ 2005-12-15 08:36:06.000000000 -0800 +@@ -95,7 +95,7 @@ + fclose(fp); + } // spherefile opened + sc.isphere = maidfile.nsphere; // set active sphere to last read +- sc.drawspheres =1.0; ++ sc.drawspheres =1; + if (widget = XtNameToWidget (spheremenu,"button_0")) //DEFAULT: Turn off check box for label on/off button + XtVaSetValues (widget, XmNset,TRUE, NULL); + } +diff -ur glmaid_dist.orig/tordyn.c++ glmaid_dist/tordyn.c++ +--- glmaid_dist.orig/tordyn.c++ 2005-12-15 08:13:32.000000000 -0800 ++++ glmaid_dist/tordyn.c++ 2005-12-15 08:28:27.000000000 -0800 +@@ -337,8 +337,8 @@ + xtof(den1,apos,fd); + /* New version, interpolates all neighbors*/ + for(k=0;k<=2;k++){ +- ir[k]=fd[k]; /*round down*/ +- irh[k]=fd[k]+0.5; /*round to next 1/2*/ ++ ir[k]=(int) fd[k]; /*round down*/ ++ irh[k]=(int) (fd[k]+0.5); /*round to next 1/2*/ + if( (ir[k]<1)|| (irh[k]>den1.amax[k]-den1.amin[k]-1) ){ + // if(verbose>=1) + if(verbose>=2) // 30nov00 - do not print this line +@@ -683,7 +683,7 @@ + atomden = 0; + xtof(den1,pos,fd); /* convert from double word to float sccreen*/ + for(kc=0;kc<=2;kc++) +- ir[kc]=fd[kc]; /*round down to integer*/ ++ ir[kc]=(int) fd[kc]; /*round down to integer*/ + for(k=0;k<=2;k++){ // check if pos in density range + if( (ir[k]<2)|| (ir[k]>den1.amax[k]-den1.amin[k]-2) ){ + if(verbose>=2) +@@ -2898,7 +2898,7 @@ + //printf("oneside = %d geopos6(x) = geo.pos[geo.nend[0]+oneside][6][0] = %5.3f\n",geo.oneside,geo.pos[geo.nend[0]+geo.oneside][6][0]); + } + *returnden = bestden; // return best cterm density +- *returnbad = bestbad; ++ *returnbad = (int) bestbad; + }// quitcont <5 + quitrout:; + geo.fixend = origfixend; // set back to original value +diff -ur glmaid_dist.orig/trace.c++ glmaid_dist/trace.c++ +--- glmaid_dist.orig/trace.c++ 2005-12-15 08:09:55.000000000 -0800 ++++ glmaid_dist/trace.c++ 2005-12-15 08:31:07.000000000 -0800 +@@ -1079,7 +1079,7 @@ + + xtoi(den1,pos[resnum][atomnum],ig); + for(k=0;k<=2;k++) +- ig[k]=ig[k]+0.5; /*rounds to nearest grid point*/ ++ ig[k]=(int) (ig[k]+0.5); /*rounds to nearest grid point*/ + for(k=0;k<=2;k++){ // check if pos in density range + if( (ig[k]<2)|| (ig[k]>den1.amax[k]-den1.amin[k]-2) ) + return 0; +@@ -1099,7 +1099,7 @@ + + xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/ + for(k=0;k<=2;k++) +- ig[k]=ijk[k]+0.5; /*rounds to nearest grid point*/ ++ ig[k]=(int) (ijk[k]+0.5); /*rounds to nearest grid point*/ + for(k=0;k<=2;k++){ // check if pos in density range + if( (ig[k]<1)|| (ig[k]>den1.amax[k]-den1.amin[k]-1) ){ + if(verbose>=2) +@@ -1127,7 +1127,7 @@ + + xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/ + for(k=0;k<=2;k++) +- ig[k]=ijk[k]+0.5; /*rounds to nearest grid point*/ ++ ig[k]=(int) (ijk[k]+0.5); /*rounds to nearest grid point*/ + for(k=0;k<=2;k++){ // check if pos in density range + if( (ig[k]<1)|| (ig[k]>den1.amax[k]-den1.amin[k]-1) ){ + if(verbose>=2) +@@ -1204,7 +1204,7 @@ + + xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/ + for(k=0;k<=2;k++) +- ig[k]=ijk[k]+0.5; /*rounds to nearest grid point*/ ++ ig[k]=(int) (ijk[k]+0.5); /*rounds to nearest grid point*/ + for(k=0;k<=2;k++){ // check if pos in density range + if( ((ig[k]-geo.setrad)<0)|| ((ig[k]+geo.setrad)>den1.griddim[k]-1) ){ + if(verbose>=2) +@@ -2543,7 +2543,7 @@ + atomden = 0; + xtof(den1,pos,fd); /* convert from double word to float sccreen*/ + for(kc=0;kc<=2;kc++) +- ir[kc]=fd[kc]; /*round down to integer*/ ++ ir[kc]=(int) fd[kc]; /*round down to integer*/ + for(k=0;k<=2;k++){ // check if pos in density range + if( (ir[k]<1)|| (ir[k]>den1.amax[k]-den1.amin[k]-1) ){ + //if(verbose>=2) +@@ -2569,7 +2569,7 @@ + atomden = 0; + xtof(den1,pos[inum][itype],fd); /* convert from double word to float sccreen*/ + for(kc=0;kc<=2;kc++) +- ir[kc]=fd[kc]; /*round down to integer*/ ++ ir[kc]=(int) fd[kc]; /*round down to integer*/ + for(k=0;k<=2;k++){ // check if pos in density range + if( (ir[k]<1)|| (ir[k]>den1.amax[k]-den1.amin[k]-1) ){ + if(verbose>=2) +@@ -3438,7 +3438,7 @@ + dist =distv(pos[1][1],pos[n0+1][1]); // distance from Ca[geo.cafix] to Ca[1] + dist = dist/2.0; + thdel = rotdel/dist; // step size of theta rotation +- mth =1+ thtot/thdel; // max # of theta steps - round up ++ mth =1+ (int) (thtot/thdel); // max # of theta steps - round up + thdel = thtot/mth; // reset th del so that equal steps from 0 to thttot + maxden = -10000.0; + for(iaxis=0;iaxis<8;iaxis++){// rotate about origingalca1 caend axis +@@ -3455,7 +3455,7 @@ + } + else{ + delph = rotdel/(dist*sin(th));//the delta phi angle step +- mphi = phitot/delph +1; // round up ++ mphi = (int) (phitot/delph) +1; // round up + delph = phitot/mphi; // make phitot = mphi*delph + } + for(iph = 0;iph<=mphi;iph++){ // the phi step +@@ -3545,7 +3545,7 @@ + dist =distv(pos[1][1],pos[n0+1][1]); // distance from Ca[geo.cafix] to Ca[1] + dist = dist/2.0; + thdel = rotdel/dist; // step size of theta rotation +- mth =1+ thtot/thdel; // max # of theta steps - round up ++ mth =1+ (int) (thtot/thdel); // max # of theta steps - round up + thdel = thtot/mth; // reset th del so that equal steps from 0 to thttot + maxden = -10000.0; + for(iaxis=0;iaxis<8;iaxis++){// rotate about origingalca1 caend axis +@@ -3562,7 +3562,7 @@ + } + else{ + delph = rotdel/(dist*sin(th));//the delta phi angle step +- mphi = phitot/delph +1; // round up ++ mphi = (int) (phitot/delph) +1; // round up + delph = phitot/mphi; // make phitot = mphi*delph + } + for(iph = 0;iph<=mphi;iph++){ // the phi step +@@ -6905,8 +6905,8 @@ + for(i=0;i<=2;i++) + avegrid = avegrid+den1.delx[i]; + avegrid = avegrid/3.0; +- geo.nihel = 0.5 + geo.curdist[1]/(1.414*avegrid); // 0.5 so that rounds to nearest int +- geo.nisheet = geo.curdist[2]/(1.414*avegrid); ++ geo.nihel = (int) (0.5 + geo.curdist[1]/(1.414*avegrid)); // 0.5 so that rounds to nearest int ++ geo.nisheet = (int) (geo.curdist[2]/(1.414*avegrid)); + printf("\nGRID SIZE: %5.3f %5.3f %5.3f avegrid = %5.3f nihel = %d\n", + den1.delx[0],den1.delx[1],den1.delx[2],avegrid,geo.nihel); + +Files glmaid_dist.orig/trace.o and glmaid_dist/trace.o differ diff --git a/sci-chemistry/maid/maid-20011112.ebuild b/sci-chemistry/maid/maid-20011112.ebuild new file mode 100644 index 0000000..e6156bd --- /dev/null +++ b/sci-chemistry/maid/maid-20011112.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maid/maid-20011112.ebuild,v 1.3 2005/12/15 21:06:31 spyderous Exp $ + +inherit eutils toolchain-funcs + +MY_PN="${PN}_unix" +MY_PV="${PV:6:2}nov${PV:2:2}" +MY_P="${MY_PN}_${MY_PV}" +DESCRIPTION="Automates the fitting of protein X-ray crystallographic electron density maps" +HOMEPAGE="http://www.msi.umn.edu/~levitt/" +SRC_URI="http://www.msi.umn.edu/~levitt/${MY_P}.tar.gz + mirror://gentoo/maid-fix-compilation.patch.bz2" +LICENSE="as-is" +SLOT="0" +KEYWORDS="~x86" +IUSE="X" +DEPEND="X? ( virtual/motif + virtual/glu + virtual/opengl + || ( x11-libs/libXt virtual/x11 ) + )" +S="${WORKDIR}/glmaid_dist" + +src_unpack() { + if best_version virtual/opengl | grep mesa; then + if ! built_with_use media-libs/mesa motif; then + msg="Build media-libs/mesa with USE=motif" + eerror "${msg}" + die "${msg}" + fi + fi + + unpack ${A} + cd ${S} + + epatch ${DISTDIR}/maid-fix-compilation.patch.bz2 + epatch ${FILESDIR}/fix-warnings.patch + + if use X; then + ln -s makefile_graphics makefile + else + ln -s makefile_batch makefile + fi + + sed -i \ + -e "s:^Cgeneric = .*:Cgeneric = $(tc-getCXX):g" \ + -e "s:\(Copt.*\)-O:\1${CFLAGS}:g" \ + makefile +} + +src_compile() { + emake || die "emake failed" +} + +src_install() { + dodoc MANUAL* + if use X; then + dobin maid + else + dobin maidbatch + fi +} diff --git a/sci-chemistry/maid/metadata.xml b/sci-chemistry/maid/metadata.xml new file mode 100644 index 0000000..211b8bd --- /dev/null +++ b/sci-chemistry/maid/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<maintainer> +<email>spyderous@gentoo.org</email> +<name>Donnie Berkholz</name> +</maintainer> +</pkgmetadata> diff --git a/sci-chemistry/mpqc/ChangeLog b/sci-chemistry/mpqc/ChangeLog new file mode 100644 index 0000000..00b4646 --- /dev/null +++ b/sci-chemistry/mpqc/ChangeLog @@ -0,0 +1,80 @@ +# ChangeLog for sci-chemistry/mpqc +# Copyright 2002-2005 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mpqc/ChangeLog,v 1.8 2005/11/20 18:15:19 markusle Exp $ + + 20 Nov 2005; Markus Dittrich <markusle@gentoo.org> mpqc-2.3.0.ebuild: + Reworked install process to avoid sandbox violations. This fixes bug #113056. + +*mpqc-2.3.0 (20 Nov 2005) + + 20 Nov 2005; Markus Dittrich <markusle@gentoo.org> metadata.xml, + +mpqc-2.3.0.ebuild: + New version + + 11 Jun 2005; Markus Rothe <corsair@gentoo.org> mpqc-2.2.3.ebuild: + Added ~ppc64 and solved bug #62124: ppc64 needs --enable-shared + + 24 May 2005; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.2.2-r1.ebuild, + mpqc-2.2.3.ebuild: + (#54595) Inherit fortran eclass so we require a fortran compiler. + +*mpqc-2.2.3 (24 May 2005) + + 24 May 2005; Donnie Berkholz <spyderous@gentoo.org>; +mpqc-2.2.3.ebuild: + (#92179) Bump. Fix up indentation, use '-i' with sed instead of moving files + around, change .gz to .bz2 for distfiles. Add threads USE flag. + + 24 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +mpqc-2.2.2-r1.ebuild, +mpqc-2.2.2.ebuild: + Moved from app-sci/mpqc to sci-chemistry/mpqc. + + 02 Oct 2004; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.2.2-r1.ebuild, + mpqc-2.2.2.ebuild: + Add some die()'s (#54595). + + 23 Sep 2004; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.2.2-r1.ebuild: + Add previous KEYWORDS as ~arch. + +*mpqc-2.2.2-r1 (23 Sep 2004) + + 23 Sep 2004; Donnie Berkholz <spyderous@gentoo.org>; +mpqc-2.2.2-r1.ebuild: + Update blas and lapack dependencies to the virtuals. This requires a revision + bump to fix some issues (#54596, #64200). + + 23 Sep 2004; Donnie Berkholz <spyderous@gentoo.org>; -mpqc-2.1.2.ebuild, + -mpqc-2.2.0.ebuild: + Pull old versions. + + 21 Sep 2004; Danny van Dyk <kugelfang@gentoo.org> mpqc-2.2.2.ebuild: + Marked stable on amd64. + + 27 Jul 2004; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.2.2.ebuild: + x86. + + 05 Jun 2004; David Holm <dholm@gentoo.org> mpqc-2.2.2.ebuild: + Added to ~ppc. + +*mpqc-2.2.2 (03 Jun 2004) + + 03 Jun 2004; Donnie Berkholz <spyderous@gentoo.org>; +mpqc-2.2.2.ebuild: + Version bump (#52646). Should now work on ppc. + + 30 Mar 2004; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.1.2.ebuild, + mpqc-2.2.0.ebuild: + Change x11-base/xfree dependency to virtual/x11. + + 24 Dec 2003; Donnie Berkholz <spyderous@gentoo.org>; : + Bad digest. Closing bug #36425. + +*mpqc-2.2.0 (14 Dec 2003) + + 14 Dec 2003; Donnie Berkholz <spyderous@gentoo.org>; mpqc-2.2.0.ebuild: + Version bump. + + 02 Nov 2002; Hannes Mehnert <hannes@gentoo.org> mpqc-2.1.2.ebuild: + marked stable for x86 + +*mpqc-2.1.2 (31 Oct 2002) + + 31 Oct 2002; Hannes Mehnert <hannes@gentoo.org> mpqc-2.1.2.ebuild, + ChangeLog: Initial ebuild. diff --git a/sci-chemistry/mpqc/Manifest b/sci-chemistry/mpqc/Manifest new file mode 100644 index 0000000..00705f7 --- /dev/null +++ b/sci-chemistry/mpqc/Manifest @@ -0,0 +1,24 @@ +MD5 c68b2c8bf315900df6b742527ea91baa ChangeLog 2790 +RMD160 a2a00124bf0bf524ab124158fdac9a61fc4d2646 ChangeLog 2790 +SHA256 22a3072f0b8e5ee650c0f681ef2eeed44b85e4929606f1cc390b791c4a548b18 ChangeLog 2790 +MD5 ef8f7cc3214e84dfd6bec6d38eacb3a6 files/digest-mpqc-2.2.2 129 +RMD160 c64d3d28a7e28dca50d6dfec3896da2c9f7eb465 files/digest-mpqc-2.2.2 129 +SHA256 6e476007b6bb43d49a3b6ea3faa9966c5993db1a6533a3c4fa76fbb0d000ac71 files/digest-mpqc-2.2.2 129 +MD5 4a8b0c0ea1bc3bafc4302eceff353d0f files/digest-mpqc-2.2.3 131 +RMD160 30931d6bfdd3313f4bbdccdfe1c2eba11a387caf files/digest-mpqc-2.2.3 131 +SHA256 1fead6a0addeb7ea4b67a05dddbb250b76920e612b8db2661fee602f350169a1 files/digest-mpqc-2.2.3 131 +MD5 cdcd9f41ec0e4f8816b9fddf98827723 files/digest-mpqc-2.3.0 64 +RMD160 4ae35f6b7d267a399942757299fef1251094512f files/digest-mpqc-2.3.0 64 +SHA256 621bc9e20c5f2ca9601825d7bb3b6b30498d48b0cc1e6a9493fcd09eade5464c files/digest-mpqc-2.3.0 64 +MD5 df166a2ae1cb64196abc394d4fa522ed metadata.xml 272 +RMD160 42331a21c1e7a31cfe105f705fe3073de14b6b14 metadata.xml 272 +SHA256 36ae23839abbf283daf51b7f9585af067c0504484f5ca61e2f08113912becb77 metadata.xml 272 +MD5 e9d844071c64f7af1c83acc43ca9e81b mpqc-2.2.2.ebuild 1410 +RMD160 7dfdf2696d1acd6dfc118782fb177f584bbc2dab mpqc-2.2.2.ebuild 1410 +SHA256 d41bec4f18a51b3d1d5efeadc902be7d2d0c383da66d8c562d230fbb5a0533c1 mpqc-2.2.2.ebuild 1410 +MD5 a23ed54c567aeb218b58c4ebd4bb851e mpqc-2.2.3.ebuild 1446 +RMD160 7e0ba5b1ea804d6d7b30ed21c57760ecbdf30784 mpqc-2.2.3.ebuild 1446 +SHA256 29ac57f509d587ff8b9673ae0d115d83918ec9cff35c90b69abb4fb1c75cb08d mpqc-2.2.3.ebuild 1446 +MD5 e91e2b63a729ccc4d3ef98103c194a8e mpqc-2.3.0.ebuild 2538 +RMD160 76c729f3aaf34d79376ba63c908da738552b9ca1 mpqc-2.3.0.ebuild 2538 +SHA256 acf798dcd6068b2bcdc3f682cbf47342a997b41918967989b91747f5b6ddd36c mpqc-2.3.0.ebuild 2538 diff --git a/sci-chemistry/mpqc/files/digest-mpqc-2.2.2 b/sci-chemistry/mpqc/files/digest-mpqc-2.2.2 new file mode 100644 index 0000000..86aa626 --- /dev/null +++ b/sci-chemistry/mpqc/files/digest-mpqc-2.2.2 @@ -0,0 +1,2 @@ +MD5 7f5d2e6340aa9eba76a6e37cebc5fb9d mpqc-2.2.2.tar.gz 2061755 +MD5 2602c914c9181e92c77153ce21e13116 mpqc-man-2.2.2.tar.gz 166450 diff --git a/sci-chemistry/mpqc/files/digest-mpqc-2.2.3 b/sci-chemistry/mpqc/files/digest-mpqc-2.2.3 new file mode 100644 index 0000000..782b4a7 --- /dev/null +++ b/sci-chemistry/mpqc/files/digest-mpqc-2.2.3 @@ -0,0 +1,2 @@ +MD5 893a104bc6119058a6fe102803d0bdb9 mpqc-2.2.3.tar.bz2 1615558 +MD5 4048680d977d336096e57f7721f21c0e mpqc-man-2.2.3.tar.bz2 105008 diff --git a/sci-chemistry/mpqc/files/digest-mpqc-2.3.0 b/sci-chemistry/mpqc/files/digest-mpqc-2.3.0 new file mode 100644 index 0000000..228a600 --- /dev/null +++ b/sci-chemistry/mpqc/files/digest-mpqc-2.3.0 @@ -0,0 +1 @@ +MD5 91da0edb46e0416e730ae871b2ea57fa mpqc-2.3.0.tar.bz2 2446415 diff --git a/sci-chemistry/mpqc/metadata.xml b/sci-chemistry/mpqc/metadata.xml new file mode 100644 index 0000000..f866028 --- /dev/null +++ b/sci-chemistry/mpqc/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>markusle@gentoo.org</email> + <name>Markus Dittrich</name> + </maintainer> + <herd>sci</herd> +</pkgmetadata> diff --git a/sci-chemistry/mpqc/mpqc-2.2.2.ebuild b/sci-chemistry/mpqc/mpqc-2.2.2.ebuild new file mode 100644 index 0000000..ebf8814 --- /dev/null +++ b/sci-chemistry/mpqc/mpqc-2.2.2.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2004 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mpqc/mpqc-2.2.2.ebuild,v 1.2 2004/12/29 16:30:31 ribosome Exp $ + +DESCRIPTION="The Massively Parallel Quantum Chemistry Program" +HOMEPAGE="http://www.mpqc.org/" +SRC_URI="mirror://sourceforge/mpqc/${P}.tar.gz + doc? ( mirror://sourceforge/mpqc/${PN}-man-${PV}.tar.gz )" + +LICENSE="GPL-2" +SLOT="0" +# Should work on x86, amd64 and ppc, at least +KEYWORDS="x86 ~ppc amd64" +IUSE="doc X" + +DEPEND="sys-devel/flex + sci-libs/blas + sci-libs/lapack + dev-lang/perl + X? ( virtual/x11 )" + +src_compile() { + CFLAGS_SAVE=${CFLAGS}; CXXFLAGS_SAVE=${CXXFLAGS} + myconf="${myconf} --prefix=/usr" + use X && myconf="${myconf} --x-includes=/usr/X11R6/include \ + --x-libraries=/usr/X11R6/lib" + ./configure ${myconf} || die "configure failed" + sed -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS_SAVE}:" \ + -e "s:^FFLAGS =.*$:FFLAGS=${CFLAGS_SAVE}:" \ + -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS_SAVE}:" \ + lib/LocalMakefile > lib/LocalMakefile.foo + mv lib/LocalMakefile.foo lib/LocalMakefile + emake || die "emake failed" +} + +src_install() { + sed -e "s:^prefix=.*$:prefix=${D}/usr:" lib/LocalMakefile \ + > lib/LocalMakefile.foo + mv lib/LocalMakefile.foo lib/LocalMakefile + use doc && doman ${WORKDIR}/${PN}-man-${PV}/man3/* + make install install_devel install_inc || die "install failed" +} diff --git a/sci-chemistry/mpqc/mpqc-2.2.3.ebuild b/sci-chemistry/mpqc/mpqc-2.2.3.ebuild new file mode 100644 index 0000000..574eff1 --- /dev/null +++ b/sci-chemistry/mpqc/mpqc-2.2.3.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mpqc/mpqc-2.2.3.ebuild,v 1.3 2005/06/11 16:24:38 corsair Exp $ + +inherit fortran + +DESCRIPTION="The Massively Parallel Quantum Chemistry Program" +HOMEPAGE="http://www.mpqc.org/" +SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2 + doc? ( mirror://sourceforge/mpqc/${PN}-man-${PV}.tar.bz2 )" + +LICENSE="GPL-2" +SLOT="0" +# Should work on x86, amd64 and ppc, at least +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" +IUSE="doc X threads" + +DEPEND="sys-devel/flex + virtual/blas + virtual/lapack + dev-lang/perl + >=sys-apps/sed-4" + +src_compile() { + CFLAGS_SAVE=${CFLAGS}; CXXFLAGS_SAVE=${CXXFLAGS} + myconf="${myconf} --prefix=/usr" + use X \ + && myconf="${myconf} --x-includes=/usr/X11R6/include \ + --x-libraries=/usr/X11R6/lib" + + # only shared will work on ppc64 - bug #62124 + if use ppc64; then + myconf="${myconf} --enable-shared" + fi + + ./configure \ + $(use_enable threads) \ + ${myconf} || die "configure failed" + sed -i -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS_SAVE}:" \ + -e "s:^FFLAGS =.*$:FFLAGS=${CFLAGS_SAVE}:" \ + -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS_SAVE}:" \ + lib/LocalMakefile + emake || die "emake failed" +} + +src_install() { + sed -i -e "s:^prefix=.*$:prefix=${D}/usr:" lib/LocalMakefile + use doc && doman ${WORKDIR}/${PN}-man-${PV}/man3/* + make install install_devel install_inc || die "install failed" +} diff --git a/sci-chemistry/mpqc/mpqc-2.3.0.ebuild b/sci-chemistry/mpqc/mpqc-2.3.0.ebuild new file mode 100644 index 0000000..65737cc --- /dev/null +++ b/sci-chemistry/mpqc/mpqc-2.3.0.ebuild @@ -0,0 +1,104 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mpqc/mpqc-2.3.0.ebuild,v 1.3 2006/01/09 22:29:30 mr_bones_ Exp $ + +inherit fortran + +DESCRIPTION="The Massively Parallel Quantum Chemistry Program" +HOMEPAGE="http://www.mpqc.org/" +SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +# Should work on x86, amd64 and ppc, at least +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" +IUSE="doc threads tcltk" + +DEPEND="sys-devel/flex + virtual/blas + virtual/lapack + dev-lang/perl + >=sys-apps/sed-4 + tcltk? ( dev-lang/tk ) + doc? ( app-doc/doxygen + media-gfx/graphviz )" + +src_unpack() { + unpack ${A} + cd "${S}" + + # do not install tkmolrender if not requested + if ! use tcltk; then + sed -e "s:.*/bin/molrender/tkmolrender.*::" \ + -e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \ + -e "s:/bin/rm -f tkmolrender::" \ + -i "./src/bin/molrender/Makefile" \ + || die "failed to disable tkmolrender" + fi +} + + +src_compile() { + CFLAGS_SAVE=${CFLAGS}; CXXFLAGS_SAVE=${CXXFLAGS} + myconf="${myconf} --prefix=/usr" + + # only shared will work on ppc64 - bug #62124 + if use ppc64; then + myconf="${myconf} --enable-shared" + fi + + econf \ + $(use_enable threads) \ + ${myconf} || die "configure failed" + + sed -i -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS_SAVE}:" \ + -e "s:^FFLAGS =.*$:FFLAGS=${CFLAGS_SAVE}:" \ + -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS_SAVE}:" \ + lib/LocalMakefile + emake || die "emake failed" +} + + +src_test() { + cd "${S}"/src/bin/mpqc/validate + + # we'll only run the small test set, since the + # medium and large ones take >10h and >24h on my + # 1.8Ghz P4M + make check0 || die "failed in test routines" +} + + + +src_install() { + make installroot="${D}" install install_devel install_inc \ + || die "install failed" + + dodoc CHANGES CITATION README || die "failed to install docs" + + # make extended docs + if use doc; then + cd "${S}"/doc + make all || die "failed to generate documentation" + doman man/man1/* && doman man/man3/* || \ + die "failed to install man pages" + dohtml -r html/ + fi +} + +pkg_postinst() { + echo + einfo "MPQC can be picky with regard to compilation flags." + einfo "If during mpqc runs you have trouble converging or " + einfo "experience oscillations during SCF interations, " + einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS." + einfo "Particularly, replacing -march=pentium4 by -march=pentium3" + einfo "might help if you encounter problems with correlation " + einfo "consistent basis sets." + echo +} + + + + + diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog new file mode 100644 index 0000000..83da192 --- /dev/null +++ b/sci-chemistry/pymol/ChangeLog @@ -0,0 +1,99 @@ +# ChangeLog for sci-chemistry/pymol +# Copyright 2002-2005 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.10 2005/12/19 18:55:11 spyderous Exp $ + + 19 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; pymol-0.98.ebuild: + virtual/glut, not media-libs/glut. + + 13 Aug 2005; Michael Hanselmann <hansmi@gentoo.org> pymol-0.98.ebuild: + Stable on ppc. + + 25 Jun 2005; Olivier Fisette <ribosome@gentoo.org> -pymol-0.88.ebuild, + pymol-0.98.ebuild: + Added to x86. Removed obsolete version. + + 17 Jun 2005; Michael Hanselmann <hansmi@gentoo.org> pymol-0.97.ebuild: + Stable on ppc. + +*pymol-0.98 (18 May 2005) + + 18 May 2005; Olivier Fisette <ribosome@gentoo.org> -pymol-0.90.ebuild, + -pymol-0.95.ebuild, +pymol-0.98.ebuild: + New version: 0.98. Removed obsolete versions. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> pymol-0.97.ebuild: + Fixed multilib issue (bug #92103). + + 04 May 2005; David Holm <dholm@gentoo.org> pymol-0.97.ebuild: + Readded to ~ppc. Please don't remove it without filing a proper bug report. + + 06 Feb 2005; Simon Stelling <blubb@gentoo.org> pymol-0.97.ebuild: + added ~amd64 + +*pymol-0.97 (24 Dec 2004) + + 24 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/header_order.patch, +files/nosplash-gentoo.patch, + +files/pymol-gentoo.diff, +files/setup.py-gentoo.patch, + +files/setup2.py-gentoo.patch, +pymol-0.88.ebuild, +pymol-0.90.ebuild, + +pymol-0.95.ebuild, +pymol-0.97.ebuild: + Moved from app-sci/pymol to sci-chemistry/pymol. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> pymol-0.97.ebuild: + Added to x86. + +*pymol-0.97 (26 Jul 2004) + + 26 Jul 2004; Olivier Fisette <ribosome@gentoo.org> pymol-0.97.ebuild: + Version bump suggested by Stéphane Gagné <sgagne@rsvs.ulaval.ca> (bug #58097). + Removed header order patch since it is no longer needed. + +*pymol-0.95 (20 Apr 2004) + + 20 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> pymol-0.95.ebuild, + files/header_order.patch: + Version bump. Needed a little patch and a change to the setup2.py call (if it + does not find the modules, it will create no python.com) + + 19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> pymol-0.82.ebuild, + pymol-0.86.ebuild, pymol-0.88.ebuild, pymol-0.90.ebuild: + Adding IUSE, cleanup + + 03 Mar 2004; Peter Bienstman <pbienst@gentoo.org> pymol-0.90: + marked stable on x86 + + 02 Sep 2003; Alastair Tse <liquidx@gentoo.org> pymol-0.82.ebuild, + pymol-0.86.ebuild, pymol-0.88.ebuild, pymol-0.90.ebuild: + moved dev-python/Numeric to dev-python/numeric + +*pymol-0.90 (23 Jul 2003) + + 23 Jul 2003; George Shapovalov <george@gentoo.org> pymol-0.90, files/setup.py-gentoo.patch : + new version + fix for setup.py, (#24967) + thanks to Ben Cornett <acornet@emory.edu> for the update + +*pymol-0.88 (29 Jun 2003) + + 19 Jun 2003; George Shapovalov <george@gentoo.org> pymol-0.88.ebuild, files/{digest-pymol-0.88,nosplash-gentoo.patch,setup2.py-gentoo.patch} : + new version (#22235) + now uses distutils for python + thanks to Todd Geders <geders@purdue.edu> for update notification + and Ben Cornett <acornet@emory.edu> for "distutilized" ebuild submission + +*pymol-0.86 (05 Feb 2003) + + 05 Feb 2003; George Shapovalov <george@gentoo.org> pymol-0.86.ebuild, files/digest-pymol-0.86 : + new version, (#13531) + removed -funroll-loops from CFLAGS + +*pymol-0.82 (17 July 2002) + + 19 Oct 2002; Daniel Ahlberg <aliz@gentoo.org> pymol-0.82.ebuild : + Updated to mirror://sourceforge in SRC_URI. + + 17 July 2002; George Shapovalov <george@gentoo.org> pymol-0.82.ebuild, files/digest-pymol-0.82, ChangeLog : + + Inital release, + molecular visualization package + + ebuild submitted by Ben Cornett <acornet@emory.edu> diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest new file mode 100644 index 0000000..40dcc55 --- /dev/null +++ b/sci-chemistry/pymol/Manifest @@ -0,0 +1,27 @@ +MD5 b6605c26bd0098518434bb02aec53a68 ChangeLog 3719 +RMD160 520116b287065463171c79202250eab0d14644ce ChangeLog 3719 +SHA256 a50073ea82a1685ba15d39a2c5c06e3e45c7541b85cbd06c72899200ca3ac9fd ChangeLog 3719 +MD5 925dc45d0ae6070f5506dffc1d100975 files/digest-pymol-0.99_rc6 247 +RMD160 505a34a7bebbbdd2c60913ea3ec7cd41164eeaff files/digest-pymol-0.99_rc6 247 +SHA256 c6ec27d34304ab8e1d2d24f80537f9b63d14e6e915776434e158eecfa1060aac files/digest-pymol-0.99_rc6 247 +MD5 1a6ba582a7928c370c8dfe44c8867e7c files/header_order.patch 905 +RMD160 0a4e2b2f95e2ace2ad21d27740bef5308a4990d5 files/header_order.patch 905 +SHA256 1f181350c2d99e31c59baea2f31b5ce27b16bae61ce6c9438d2f0e1e903b4cce files/header_order.patch 905 +MD5 929741dc2da6577e6e99c5542d68dbd5 files/nosplash-gentoo.patch 332 +RMD160 2280fbe9daba8a0d3ca81a3aacfcc55bd06fc7d3 files/nosplash-gentoo.patch 332 +SHA256 5e0761591eeea90bcaa06a72c210a80ba46f2542ff985f8dd893af112254a890 files/nosplash-gentoo.patch 332 +MD5 34d172ef31b5038e071b634d4e645cf1 files/pymol-gentoo.diff 1566 +RMD160 6a566cd0105ba94f9b06be8219c5fbe644281ab9 files/pymol-gentoo.diff 1566 +SHA256 15bdd116551022045c57743f21337c14ca368211a68a2a9763a1a7950f9af9d3 files/pymol-gentoo.diff 1566 +MD5 e42746bf581479c61ff1e7cc5b978edd files/setup.py-gentoo.patch 311 +RMD160 483f63778aa928bf2ce4de99edbc45af98abab8c files/setup.py-gentoo.patch 311 +SHA256 850bae1aef6007f159abf8d2f3ba3342ea5a7aaff8f4798c6829fc879d08d5ed files/setup.py-gentoo.patch 311 +MD5 af2da92225ab57969d18d16ed60324ce files/setup2.py-gentoo.patch 493 +RMD160 2d6bbabc01f6e4eb8ddafb9b0215ece50a639923 files/setup2.py-gentoo.patch 493 +SHA256 dc721d4d3fd557c684ddb1ec43e07e05c38f13750393cd1665148e18c5e6a959 files/setup2.py-gentoo.patch 493 +MD5 8c623e53daafa025137077c6b65815bd metadata.xml 156 +RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 metadata.xml 156 +SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 metadata.xml 156 +MD5 3662c250200ff906c5f280082f8e24a4 pymol-0.99_rc6.ebuild 1717 +RMD160 94ab430d50ce8c8f40184ebbfe16619c306d7c9f pymol-0.99_rc6.ebuild 1717 +SHA256 1e78941c363700b90d4d0ab2d55df003f3a454b929932e9265b9a5499a870416 pymol-0.99_rc6.ebuild 1717 diff --git a/sci-chemistry/pymol/files/digest-pymol-0.99_rc6 b/sci-chemistry/pymol/files/digest-pymol-0.99_rc6 new file mode 100644 index 0000000..3a46209 --- /dev/null +++ b/sci-chemistry/pymol/files/digest-pymol-0.99_rc6 @@ -0,0 +1,3 @@ +MD5 cb29385ab523f648d4db47a222b1d03e pymol-0_99rc6-src.tgz 4198816 +RMD160 e9dc568dd38fffd37f306adf7e7a109d81dd4477 pymol-0_99rc6-src.tgz 4198816 +SHA256 d56bebc1316fd3442c54dee5bc4b2979041943bf50a9b34b44839595fd1b9a59 pymol-0_99rc6-src.tgz 4198816 diff --git a/sci-chemistry/pymol/files/header_order.patch b/sci-chemistry/pymol/files/header_order.patch new file mode 100644 index 0000000..e11f31b --- /dev/null +++ b/sci-chemistry/pymol/files/header_order.patch @@ -0,0 +1,36 @@ +--- layer0/MyPNG.c 2004-01-30 00:40:33.000000000 +0100 ++++ layer0/MyPNG.c.new 2004-04-20 16:05:35.399498139 +0200 +@@ -14,17 +14,8 @@ + Z* ------------------------------------------------------------------- + */ + +-#include"os_predef.h" +-#include"os_std.h" +- +-#include"Base.h" +-#include "MyPNG.h" +-#include"MemoryDebug.h" +-#include "Setting.h" +- + #ifdef _HAVE_LIBPNG +-#include<png.h> +- ++#include <png.h> + /* The png_jmpbuf() macro, used in error handling, became available in + * libpng version 1.0.6. If you want to be able to run your code with older + * versions of libpng, you must define the macro yourself (but only if it +@@ -37,6 +28,14 @@ + + #endif + ++#include"os_predef.h" ++#include"os_std.h" ++ ++#include"Base.h" ++#include "MyPNG.h" ++#include"MemoryDebug.h" ++#include "Setting.h" ++ + int MyPNGWrite(char *file_name,unsigned char *p,unsigned int width,unsigned int height) + { + #ifdef _HAVE_LIBPNG diff --git a/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch new file mode 100644 index 0000000..202a7cf --- /dev/null +++ b/sci-chemistry/pymol/files/nosplash-gentoo.patch @@ -0,0 +1,8 @@ +--- modules/pymol/invocation.py.orig 2003-06-11 13:40:13.000000000 -0400 ++++ modules/pymol/invocation.py 2003-06-11 13:40:29.000000000 -0400 +@@ -179,5 +179,3 @@ + + else: + options.deferred.append(a) +- if options.show_splash and not options.no_gui: +- options.deferred.insert(0,"_do__ cmd.splash(1)") diff --git a/sci-chemistry/pymol/files/pymol-gentoo.diff b/sci-chemistry/pymol/files/pymol-gentoo.diff new file mode 100644 index 0000000..8b4b2ba --- /dev/null +++ b/sci-chemistry/pymol/files/pymol-gentoo.diff @@ -0,0 +1,53 @@ +--- Rules.linux Sun Mar 31 03:06:22 2002 ++++ Rules.make Tue May 21 15:42:31 2002 +@@ -12,14 +12,13 @@ + XLIB_DIR = -L/usr/X11R6/lib + XINC_DIR = -I/usr/X11R6/include + #--- Python +-PYTHON_EXE = $(PYMOL_PATH)/ext/bin/python ++PYTHON_EXE = /usr/bin/python + PYTHON_LIB = + PYTHON_LIB_DIR = +-PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.1 \ +- -I$(PYMOL_PATH)/ext/include/python2.1/Numeric ++PYTHON_INC_DIR = -I/usr/include/python2.2 -I/usr/include/python2.2/Numeric + #--- Other external dependencies +-EXT_INC_DIR = -I$(PYMOL_PATH)/ext/include +-EXT_LIB_DIR = -L$(PYMOL_PATH)/ext/lib ++EXT_INC_DIR = ++EXT_LIB_DIR = + #--------------------------------------------------------------------- + # + #- Build for LINUX as an importable module --------------------------- +@@ -48,7 +47,7 @@ + # + #- Choose One -------------------------------------------------------- + #--- Workaround for XFree86/DRI linux dll problem for module build +-BUGS = -D_DRI_WORKAROUND ++DEFS += -D_DRI_WORKAROUND + #--- + #BUGS = + #--------------------------------------------------------------------- +@@ -58,7 +57,7 @@ + #PNG = -D_HAVE_LIBPNG + #ZLIB = + #--- Libpng2 available but needs zlib +-PNG = -D_HAVE_LIBPNG ++DEFS += -D_HAVE_LIBPNG + ZLIB = -lz + #--- Libpng2 not available + #PNG = +@@ -77,12 +76,7 @@ + PYMOL_INC_DIRS = -I../layer0 -I../layer1 -I../layer2 \ + -I../layer3 -I../layer4 -I../layer5 + +-C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \ +- $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) +- +-CFLAGS = $(C_FLAGS) +- +- ++C_FLAGS := $(CFLAGS) $(PYTHON_INC_DIR) $(XINC_DIR) $(DEFS) + + + diff --git a/sci-chemistry/pymol/files/setup.py-gentoo.patch b/sci-chemistry/pymol/files/setup.py-gentoo.patch new file mode 100644 index 0000000..d675596 --- /dev/null +++ b/sci-chemistry/pymol/files/setup.py-gentoo.patch @@ -0,0 +1,10 @@ +--- pymol-0.90/setup.py 2003-04-26 21:22:14.000000000 -0400 ++++ pymol-0.90.new/setup.py 2003-07-21 09:39:51.000000000 -0400 +@@ -71,6 +71,7 @@ + "layer0/Map.c", + "layer0/Match.c", + "layer0/Matrix.c", ++ "layer0/MemoryCache.c", + "layer0/MemoryDebug.c", + "layer0/MyPNG.c", + "layer0/Parse.c", diff --git a/sci-chemistry/pymol/files/setup2.py-gentoo.patch b/sci-chemistry/pymol/files/setup2.py-gentoo.patch new file mode 100644 index 0000000..1d387ea --- /dev/null +++ b/sci-chemistry/pymol/files/setup2.py-gentoo.patch @@ -0,0 +1,17 @@ +--- setup2.py.orig 2003-06-10 19:12:35.000000000 -0400 ++++ setup2.py 2003-06-10 19:11:46.000000000 -0400 +@@ -12,6 +12,14 @@ + import sys + from distutils import dir_util,file_util + ++import os.path ++pmlibs = os.path.join(os.environ['D'], ++ sys.prefix[1:], ++ 'lib/python%s' % sys.version[:3], ++ 'site-packages') ++sys.path.insert(0, pmlibs) ++ ++ + if sys.platform=='win32': + launch_script = "pymol.bat" + elif sys.platform=='cygwin': diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml new file mode 100644 index 0000000..b229aec --- /dev/null +++ b/sci-chemistry/pymol/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +</pkgmetadata> diff --git a/sci-chemistry/pymol/pymol-0.99_rc6.ebuild b/sci-chemistry/pymol/pymol-0.99_rc6.ebuild new file mode 100644 index 0000000..d1827c5 --- /dev/null +++ b/sci-chemistry/pymol/pymol-0.99_rc6.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.98.ebuild,v 1.4 2005/12/19 18:55:11 spyderous Exp $ + +inherit distutils eutils multilib + +MY_PV=${PV/_} +MY_S_P="${PN}-${MY_PV}" +MY_PV=${MY_PV/./_} +MY_P="${PN}-${MY_PV}" +DESCRIPTION="A Python-extensible molecular graphics system." +HOMEPAGE="http://pymol.sourceforge.net/" +SRC_URI="mirror://sourceforge/pymol/${MY_P}-src.tgz" + +LICENSE="PSF-2.2" +IUSE="" +SLOT="0" +KEYWORDS="~amd64 ppc x86" + +DEPEND="dev-lang/python + dev-python/pmw + dev-python/numeric + dev-lang/tk + media-libs/libpng + sys-libs/zlib + virtual/glut" +S="${WORKDIR}/${MY_S_P}" + +src_unpack() { + unpack ${A} + cd ${S} + # Turn off splash screen. Please do make a project contribution + # if you are able though. + [[ -n "$WANT_NOSPLASH" ]] && epatch ${FILESDIR}/nosplash-gentoo.patch + + # Respect CFLAGS + sed -i \ + -e "s:\(ext_comp_args=\).*:\1[]:g" \ + ${S}/setup.py +} + +src_install() { + python_version + + distutils_src_install + cd ${S} + + #The following three lines probably do not do their jobs and should be + #changed + PYTHONPATH="${D}/usr/$(get_libdir)/site-packages" ${python} setup2.py + + # Make our own wrapper +cat >> ${T}/pymol << EOF +#!/bin/sh +PYMOL_PATH=/usr/lib/python${PYVER}/site-packages/pymol +PYMOL_DATA="/usr/share/pymol/data" +PYMOL_SCRIPTS="/usr/share/pymol/scripts" +export PYMOL_PATH PYMOL_DATA PYMOL_SCRIPTS +${python} \${PYMOL_PATH}/__init__.py \$* +EOF + + exeinto /usr/bin + doexe ${T}/pymol + dodoc DEVELOPERS CHANGES + + mv examples ${D}/usr/share/doc/${PF}/ + + dodir /usr/share/pymol + mv test ${D}/usr/share/pymol/ + mv data ${D}/usr/share/pymol/ + mv scripts ${D}/usr/share/pymol/ +} diff --git a/sci-chemistry/schakal/Manifest b/sci-chemistry/schakal/Manifest new file mode 100644 index 0000000..7ebd355 --- /dev/null +++ b/sci-chemistry/schakal/Manifest @@ -0,0 +1,6 @@ +MD5 e9eff222fc8bc0a9417e209b974cea89 files/digest-gtk-gamess-1.04.1 253 +RMD160 26dac9544c8b0a3e9c5e4ce7136d7ad70c81fe1e files/digest-gtk-gamess-1.04.1 253 +SHA256 f4be243d027c7527ed0fdca0af8f8b3b188bb96ef32fda23aaad0d8d6f2c9ef8 files/digest-gtk-gamess-1.04.1 253 +MD5 a1daae598930e217f99793d7ddeda5af gtk-gamess-1.04.1.ebuild 672 +RMD160 ce67c36f994fa85f64f3cae5b651c1daf8fd8929 gtk-gamess-1.04.1.ebuild 672 +SHA256 8aa9a3a50ddc725acd162bab6192fbb5788d645f2dd14b72f2bb1fac309f618d gtk-gamess-1.04.1.ebuild 672 diff --git a/sci-chemistry/schakal/schakal-99.ebuild b/sci-chemistry/schakal/schakal-99.ebuild new file mode 100644 index 0000000..ac9dada --- /dev/null +++ b/sci-chemistry/schakal/schakal-99.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +# This is an incredibly ugly UI, but it can create beautiful graphics. +# Ebuild not yet in a working state, but very close. src_install() just needs +# finishing. + +inherit fortran toolchain-funcs + +DESCRIPTION="Program for the graphical representation of molecular and solid-state structure models" +HOMEPAGE="http://www.krist.uni-freiburg.de/ki/Mitarbeiter/Keller/schakal.html" +SRC_URI="http://www.krist.uni-freiburg.de/ki/Mitarbeiter/Keller/sch${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86" +IUSE="" + +RDEPEND="|| ( ( x11-libs/libXaw + x11-terms/xterm + ) + virtual/x11 + )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +FORTRAN="gfortran" + +src_unpack() { + unpack ${A} + sed -i \ + -e "s:^\(MACHINE=\).*:\1LINUX:g" \ + -e "s:^\(F77=\).*:\1${FORTRANC}:g" \ + -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ + -e "s:^\(C_FLAGS = \).*:\1${CFLAGS} -DFILEPROMPT:g" \ + ${S}/makefile.x + sed -i \ + -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ + ${S}/makefile.fsb + sed -i \ + -e 's~^jot.*~xterm -e ${EDITOR:-/bin/nano} $*~g' \ + ${S}/editt.sh + epatch ${FILESDIR}/fix-xs-character-escapes.patch +} + +src_compile() { + emake -f makefile.x || die "make.x failed" + + # Do file selection box by hand -- taken from mfilepr script + mkdir file_selection_box + cd file_selection_box + mv ../file*.* . + mv ../makefile.fsb . + emake -f makefile.fsb || die "make.fsb failed" + cp fileprompt ../ + cd .. + +} + +src_install() { + doexe ${S}/uschak ${S}/sch99x ${S}/fileprompt ${S}/printm + + insinto /usr/lib/schakal + # create all the dat, scf, sif etc dirs with stuff in them +} + +pkg_postinst() { + einfo "You may also wish to download the tutorial from" + einfo "http://www.krist.uni-freiburg.de/ki/Mitarbeiter/Keller/tutorial.pdf" +} diff --git a/sci-chemistry/tinker/ChangeLog b/sci-chemistry/tinker/ChangeLog new file mode 100644 index 0000000..2300ccb --- /dev/null +++ b/sci-chemistry/tinker/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for sci-chemistry/tinker +# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/ChangeLog,v 1.2 2005/12/03 20:29:18 spyderous Exp $ + + 03 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; tinker-4.2.ebuild: + Note that tinker script has hardcoded blackdown in it. This is needed + because java-config's exit codes return 0, even on failure. + +*tinker-4.2 (03 Dec 2005) + + 03 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; +metadata.xml, + +tinker-4.2.ebuild: + (#35945) New molecular mechanics package. Heavily modified ebuild based on + that of Jeremy Warren <jwarren@cheesefoam.dyndns.org>. + diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest new file mode 100644 index 0000000..54d514d --- /dev/null +++ b/sci-chemistry/tinker/Manifest @@ -0,0 +1,12 @@ +MD5 8bb9b767a5eb6c8e9b18e4956f614744 ChangeLog 679 +RMD160 4fdd4abd2cf01a883c0103fbe79fab82a629f751 ChangeLog 679 +SHA256 0c538893547f95ecb36d0b826d9d9d6c7bb61eab5446fc58c756df1a551a7c65 ChangeLog 679 +MD5 c336619e5cd4eb1ef174a15514c99a88 files/digest-tinker-4.2 59 +RMD160 417dc19396cb5a4a4b6ffb67fbbd2f75dc58f0d5 files/digest-tinker-4.2 59 +SHA256 85b0f4ec639f8ec3037abd8ea96cef7747983ee1252b105fb9c848c654c950ce files/digest-tinker-4.2 59 +MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248 +RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248 +SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248 +MD5 0ff4f27045feca24fdc0d7ef4d0eed6f tinker-4.2.ebuild 3538 +RMD160 f1522c64af702e4d9fd9e7f0fc10516035fe954c tinker-4.2.ebuild 3538 +SHA256 6f493b1f8f3f35814f6e91729e8d7e131ba65bcc66966fa6955ad54daf1329d3 tinker-4.2.ebuild 3538 diff --git a/sci-chemistry/tinker/files/digest-tinker-4.2 b/sci-chemistry/tinker/files/digest-tinker-4.2 new file mode 100644 index 0000000..3381b74 --- /dev/null +++ b/sci-chemistry/tinker/files/digest-tinker-4.2 @@ -0,0 +1 @@ +MD5 5618d8a373896f00e452b137200223fd tinker.tar.gz 8177555 diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml new file mode 100644 index 0000000..211b8bd --- /dev/null +++ b/sci-chemistry/tinker/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<maintainer> +<email>spyderous@gentoo.org</email> +<name>Donnie Berkholz</name> +</maintainer> +</pkgmetadata> diff --git a/sci-chemistry/tinker/tinker-4.2.ebuild b/sci-chemistry/tinker/tinker-4.2.ebuild new file mode 100644 index 0000000..d3adad8 --- /dev/null +++ b/sci-chemistry/tinker/tinker-4.2.ebuild @@ -0,0 +1,135 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/tinker-4.2.ebuild,v 1.2 2005/12/03 20:29:18 spyderous Exp $ + +inherit fortran toolchain-funcs + +FORTRAN="ifc g77" + +DESCRIPTION="TINKER is a molecular modeling package that includes force fields for handing large molecules and large systems, such as AMBER and CHARMM. A Java based visualization front end is included." +HOMEPAGE="http://dasher.wustl.edu/tinker/" +SRC_URI="ftp://dasher.wustl.edu/pub/tinker.tar.gz" +IUSE="X" +LICENSE="Tinker" +SLOT="0" +KEYWORDS="~x86" + +DEPEND="X? ( + || ( dev-java/blackdown-java3d-bin + dev-java/sun-java3d-bin ) + )" +S="${WORKDIR}/tinker/source" + +src_compile() { + if use X; then + COMPGUI="./compgui.make" + LINK="./linkgui.make" + if use ppc-macos; then + cp ../jar/macosx/sockets.c . + else + cp ../jar/linux/sockets.c . + fi + else + LINK="./link.make" + fi + + COMPILE="./compile.make" + LIBRARY="./library.make" + + # Need to make sure all of the appropriate config files are in place + # for the build. + # This should be easily customizable for other Fortran compilers, e.g. pg77. + if use ppc-macos; then + cp ../apple/gnu/* . + elif [ "${FORTRANC}" = "ifc" ]; then + cp ../linux/intel/* . + elif [ "${FORTRANC}" = "g77" ]; then + cp ../linux/gnu/* . + fi + + cp ../make/* . + + # Prep build scripts + if use X; then + sed -i \ + -e "s:-O3:${CFLAGS}:" \ + -e "s:gcc:$(tc-getCC):" \ + ${COMPGUI} + local JAVA_HOME=$(java-config --jdk-home) + local JAVA_LIB_PATH="${JAVA_HOME}/jre/lib/i386/client" + ln -s ${JAVA_LIB_PATH}/libjvm.so + sed -i -e "s:/local/java/j2sdk1.4.2_05:${JAVA_HOME}:g" ${COMPGUI} + sed -i -e "s:g77:${FORTRANC}:g" ${LINK} + fi + # Default to -O2 if FFLAGS is unset + sed -i -e "s:-O3 -ffast-math:${FFLAGS:- -O2}:" ${COMPILE} + sed -i -e "s:g77:${FORTRANC}:g" ${COMPILE} + + # Prep executable script - the one packaged with the distro is b0rked + if use X; then + echo 'java -jar /usr/lib/tinker/ffe.jar -Djava.library.path=$(java-config -i blackdown-java3d-bin) -cp $(java-config -p blackdown-java3d-bin)' > tinker + fi + + einfo "Compiling ..." + if use X; then + ${COMPGUI} || die "GUI compile failed" + fi + ${COMPILE} || die "compile failed" + einfo "Building libraries ..." + ${LIBRARY} || die "library creation failed" + einfo "Linking ..." + ${LINK} || die "link failed" +} + +src_install() { + exeinto /usr/bin + + dodoc \ + ${WORKDIR}/tinker/doc/*.txt \ + ${WORKDIR}/tinker/doc/release-4.2 \ + ${WORKDIR}/tinker/doc/*.pdf + + if use X; then + if use ppc-macos; then + dolib.so ${WORKDIR}/tinker/jar/macosx/libffe.jnilib + else + dolib.so ${WORKDIR}/tinker/jar/linux/libffe.so + fi + fi + + dolib.a libtinker.a + + insinto /usr/lib/tinker + if use X; then + doins ${WORKDIR}/tinker/jar/ffe.jar + fi + + for EXE in *.x; do + newexe ${EXE} ${EXE%.x} + done + + # superpose overlaps with ccp4, so don't install it locally + rm -f ${D}/usr/bin/superpose + + if use X; then + doexe tinker + fi + + docinto example + dodoc ${WORKDIR}/tinker/example/* + docinto test + dodoc ${WORKDIR}/tinker/test/* + + doexe ${WORKDIR}/tinker/perl/mdavg + + insinto /usr/share/tinker/params + doins ${WORKDIR}/tinker/params/* +} + +pkg_postinst() { + einfo "Tinker binaries installed to ${ROOT}usr/bin." + einfo "Parameter files installed to ${ROOT}usr/share/tinker/params." + einfo "Call the Java X front-end, Force-Field Explorer, with 'tinker.'" + einfo "It doesn't seem to detect installed Java3D yet, fixes welcome." + einfo "You must edit ${ROOT}usr/bin/tinker if you aren't using Blackdown." +} diff --git a/sci-chemistry/yaehmop/Manifest b/sci-chemistry/yaehmop/Manifest new file mode 100644 index 0000000..7ebd355 --- /dev/null +++ b/sci-chemistry/yaehmop/Manifest @@ -0,0 +1,6 @@ +MD5 e9eff222fc8bc0a9417e209b974cea89 files/digest-gtk-gamess-1.04.1 253 +RMD160 26dac9544c8b0a3e9c5e4ce7136d7ad70c81fe1e files/digest-gtk-gamess-1.04.1 253 +SHA256 f4be243d027c7527ed0fdca0af8f8b3b188bb96ef32fda23aaad0d8d6f2c9ef8 files/digest-gtk-gamess-1.04.1 253 +MD5 a1daae598930e217f99793d7ddeda5af gtk-gamess-1.04.1.ebuild 672 +RMD160 ce67c36f994fa85f64f3cae5b651c1daf8fd8929 gtk-gamess-1.04.1.ebuild 672 +SHA256 8aa9a3a50ddc725acd162bab6192fbb5788d645f2dd14b72f2bb1fac309f618d gtk-gamess-1.04.1.ebuild 672 diff --git a/sci-chemistry/yaehmop/files/digest-gtk-gamess-1.04.1 b/sci-chemistry/yaehmop/files/digest-gtk-gamess-1.04.1 new file mode 100644 index 0000000..410cbec --- /dev/null +++ b/sci-chemistry/yaehmop/files/digest-gtk-gamess-1.04.1 @@ -0,0 +1,3 @@ +MD5 b15544b8d4f20c0e39f9c4577b80f2a4 gtk-gamess-1.04.1.tar.gz 110334 +RMD160 da36f5b7270e0589dcc94982fc92f206aea0fbb4 gtk-gamess-1.04.1.tar.gz 110334 +SHA256 37304b864ec4cc00a7d70ec65e85e1a867a24e0787406676d4d801fe0ae867b9 gtk-gamess-1.04.1.tar.gz 110334 diff --git a/sci-chemistry/yaehmop/gtk-gamess-1.04.1.ebuild b/sci-chemistry/yaehmop/gtk-gamess-1.04.1.ebuild new file mode 100644 index 0000000..611ff42 --- /dev/null +++ b/sci-chemistry/yaehmop/gtk-gamess-1.04.1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $ + +DESCRIPTION="GTK+ frontend to GAMESS" +HOMEPAGE="http://www.uiowa.edu/~ghemical/gtk-gamess.shtml" +SRC_URI="mirror://sourceforge/gtk-gamess/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86" +IUSE="" + +RDEPEND="=gnome-base/libglade-0*" +DEPEND="${RDEPEND}" + +src_unpack() { + unpack ${A} + sed -i -e "s:/usr/local/gamess/rungms:/usr/bin/rungms:g" \ + ${S}/src/gg_config.cpp +} + +src_install() { + make DESTDIR="${D}" install || die "install failed" +} |