From bfc1825f3a8e673237107c649f9d053b6cc91eba Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Fri, 18 Aug 2006 16:48:41 +0000 Subject: New upstream version (fixes bug #144329). Added pdb2caver script (fixes bug #141549). Added man page. Package-Manager: portage-2.1-r2 --- sci-chemistry/caver/ChangeLog | 11 +++- sci-chemistry/caver/Manifest | 21 +++++-- sci-chemistry/caver/caver-0.99.4.ebuild | 64 +++++++++++++++++++++ sci-chemistry/caver/files/caver-0.99.4-001.patch | 72 ++++++++++++++++++++++++ sci-chemistry/caver/files/digest-caver-0.99.4 | 6 ++ 5 files changed, 169 insertions(+), 5 deletions(-) create mode 100644 sci-chemistry/caver/caver-0.99.4.ebuild create mode 100644 sci-chemistry/caver/files/caver-0.99.4-001.patch create mode 100644 sci-chemistry/caver/files/digest-caver-0.99.4 (limited to 'sci-chemistry') diff --git a/sci-chemistry/caver/ChangeLog b/sci-chemistry/caver/ChangeLog index 880f0f22197f..ee967bf50e2b 100644 --- a/sci-chemistry/caver/ChangeLog +++ b/sci-chemistry/caver/ChangeLog @@ -1,6 +1,15 @@ # ChangeLog for sci-chemistry/caver # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/ChangeLog,v 1.4 2006/08/05 05:05:18 dberkholz Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/ChangeLog,v 1.5 2006/08/18 16:48:41 ribosome Exp $ + +*caver-0.99.4 (18 Aug 2006) + + 18 Aug 2006; Olivier Fisette + +files/caver-0.99.4-001.patch, +caver-0.99.4.ebuild: + New upstream version; thanks to Richard Daigle for + his work (fixes bug #144329). Added pdb2caver script; thanks to Rossen + Apostolov for his work (fixes bug #141549). + Added man page. Ebuild clean-up. 05 Aug 2006; Donnie Berkholz ; metadata.xml: Remove myself as maintainer, anyone feel free to work on this, although I'll diff --git a/sci-chemistry/caver/Manifest b/sci-chemistry/caver/Manifest index 3e5b6c90e786..5d5ddfdf887a 100644 --- a/sci-chemistry/caver/Manifest +++ b/sci-chemistry/caver/Manifest @@ -1,6 +1,12 @@ +AUX caver-0.99.4-001.patch 1856 RMD160 4d2809d7ef0ba9a3205fca398ead887b4e104c67 SHA1 af85d449e94642b4b165507c2b699f3389430c29 SHA256 ebe19169d3db5b71a7c88dd2a22bae9f2095981b67cdd0308bfce4ed60b5c987 +MD5 c9ed0f57b4b34e1d99cf3a14709b59bd files/caver-0.99.4-001.patch 1856 +RMD160 4d2809d7ef0ba9a3205fca398ead887b4e104c67 files/caver-0.99.4-001.patch 1856 +SHA256 ebe19169d3db5b71a7c88dd2a22bae9f2095981b67cdd0308bfce4ed60b5c987 files/caver-0.99.4-001.patch 1856 DIST caverPLUG_unix_v0.99.2.tar.gz 81270 RMD160 58a5b2b7a1efe41a86d507831f754419ae912b12 SHA256 5b7ca30f26023e2ed9eda6a5430ca5db0ebef7b34f7f8d2391a49182ec0663b1 +DIST caverPLUG_unix_v0.99.4.tar.gz 81732 RMD160 5d2488d64077cfac0e81fdef53074149929aa558 SHA1 586037ad17f505e6eba739c8167982178edd86dc SHA256 61ac38fe2e9ae15af568d6eed19d7410599bc570fb0494793dff625c469b5b69 DIST caver_unix_v0.99.1.tar.gz 898765 DIST caver_unix_v0.99.2.tar.gz 1152263 RMD160 01b877bef15d0f0e1ccce8a3dbcda83826ba76c5 SHA256 9934b5e80f375159132c5327df1fa8bd19ce90682c04c4cd9b91e62476e0f98b +DIST caver_unix_v0.99.4.tar.gz 1084660 RMD160 c57c5b0c6259bb86fc844820d169a60d3895b2bd SHA1 b4a6a26651a20a1664ddfb96f36e89906dcc0bff SHA256 7aa8da882b8c7525164c4643e8feea2bb644bb5790400a21dcf8c70c40f0ea09 DIST pymolplug.tar.gz 81137 EBUILD caver-0.99.1.ebuild 1382 RMD160 93c178976bb98acebfaa94180d49e2b3e0d186c3 SHA1 2d7e2964f8952383a1f588c548521a1435b6f97b SHA256 eb2f5b4ee5f23c4a35ff3fceb4dd0cf75e134b06c1fa180121f14462391e2517 MD5 bb4a1218e09746c04c1f3da50f76eb66 caver-0.99.1.ebuild 1382 @@ -10,10 +16,14 @@ EBUILD caver-0.99.2.ebuild 1424 RMD160 dcbc74f15ede15298efaf8ce24e6dafeca4b9e04 MD5 52ba09a3550f24265d76eef093599850 caver-0.99.2.ebuild 1424 RMD160 dcbc74f15ede15298efaf8ce24e6dafeca4b9e04 caver-0.99.2.ebuild 1424 SHA256 8a82be54de34e816d03d241b0ed10ccbe28a00052ecc11357b9b753cf65364b5 caver-0.99.2.ebuild 1424 -MISC ChangeLog 1042 RMD160 eb9ad3f33eb33d2ea0b74d782ca3b4a6c58f4ec3 SHA1 47a03acd67b18fea90adc6f4e65f50bfc9badf34 SHA256 2921bd2e2b456af6ef2e7998e22c39eb5e94cc6b7b1622ce913ed6a8d3db4c3f -MD5 ab34de76a24df7ed1d1d6322cb4f150b ChangeLog 1042 -RMD160 eb9ad3f33eb33d2ea0b74d782ca3b4a6c58f4ec3 ChangeLog 1042 -SHA256 2921bd2e2b456af6ef2e7998e22c39eb5e94cc6b7b1622ce913ed6a8d3db4c3f ChangeLog 1042 +EBUILD caver-0.99.4.ebuild 1789 RMD160 92a237a30a9b776045ede92724b1a25b52e095e5 SHA1 4b0431921f394c0a26a35e7c393bb966a8d25549 SHA256 6e7697af6564548a64229542721ddce55dda144fbe5548fc7ea98820ebd4d226 +MD5 2bbd0a1c0845d254b3191df1aa432e8d caver-0.99.4.ebuild 1789 +RMD160 92a237a30a9b776045ede92724b1a25b52e095e5 caver-0.99.4.ebuild 1789 +SHA256 6e7697af6564548a64229542721ddce55dda144fbe5548fc7ea98820ebd4d226 caver-0.99.4.ebuild 1789 +MISC ChangeLog 1442 RMD160 dd707e6e8f9da084a7ef464a325b31087cc9a03d SHA1 0c6ed5a949cfbd188e3a60879e864f122bed51b0 SHA256 bbc1f90ba5952c6e541eb6fb2981e02d8114dea92af846575b1cc9e1330b037d +MD5 c5f43039250f6f06a20034072bf0c87e ChangeLog 1442 +RMD160 dd707e6e8f9da084a7ef464a325b31087cc9a03d ChangeLog 1442 +SHA256 bbc1f90ba5952c6e541eb6fb2981e02d8114dea92af846575b1cc9e1330b037d ChangeLog 1442 MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 MD5 8c623e53daafa025137077c6b65815bd metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 metadata.xml 156 @@ -24,3 +34,6 @@ SHA256 fb5d883d649a3227ef05372d785aa49851202133670d2199ac6aecdf11ecae08 files/di 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 580598ccf83086e940e96aacebfc1b45 files/digest-caver-0.99.4 524 +RMD160 38ce776a94ca93dd15522a7b4a6aca8ca2ef5781 files/digest-caver-0.99.4 524 +SHA256 633b07a25c8619cdc5e96b7d99ab69706403a67a4e3b0bb803749fcc29359e43 files/digest-caver-0.99.4 524 diff --git a/sci-chemistry/caver/caver-0.99.4.ebuild b/sci-chemistry/caver/caver-0.99.4.ebuild new file mode 100644 index 000000000000..0ca12c62f4e7 --- /dev/null +++ b/sci-chemistry/caver/caver-0.99.4.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2006 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/caver-0.99.4.ebuild,v 1.1 2006/08/18 16:48:41 ribosome Exp $ + +inherit multilib python eutils + +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_unpack() { + unpack ${A} + epatch "${FILESDIR}"/${P}-001.patch +} + +src_install() { + make DESTDIR="${D}" install + doman man/man1/* || die "Failed to install man page." + if use pymol; then + python_version + sed -e "s:^\(CAVER_BINARY_LOCATION\).*:\1 = \"${ROOT}usr/bin/caver\":g" \ + -i "${WORKDIR}"/${PLUG_P}/caver.py \ + || die "Failed setting caver location" + insinto /usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup + doins "${WORKDIR}"/${PLUG_P}/caver.py || die "Failed to install plugin" + fi + cd "${S}"/pdb2caver + dobin pdb2caver || die "Failed to install pdb2caver" + newdoc README README_pdb2caver || die "Failed to install pdb2caver readme." +} + +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/caver-0.99.4-001.patch b/sci-chemistry/caver/files/caver-0.99.4-001.patch new file mode 100644 index 000000000000..1ce570e9aed0 --- /dev/null +++ b/sci-chemistry/caver/files/caver-0.99.4-001.patch @@ -0,0 +1,72 @@ +diff -Naur caver_unix_v0.99.4/src/cav_io.cpp caver_unix_v0.99.4-patch001/src/cav_io.cpp +--- caver_unix_v0.99.4/src/cav_io.cpp 2006-01-15 11:41:49.000000000 +0100 ++++ caver_unix_v0.99.4-patch001/src/cav_io.cpp 2006-07-27 10:19:08.000000000 +0200 +@@ -2,6 +2,7 @@ + #include "StdAfx.h" + #include "cav_io.h" + ++//#define SHOWIOOPERATIONS + FILE *Fopen(const char *path, const char *mode) + { + +@@ -14,8 +15,10 @@ + exit(1); + + } else { +-// for (int i=0;i %p ('%s') mode: %s\n",f,path,mode); ++#ifdef SHOWIOOPERATIONS ++ for (int i=0;i %p ('%s') mode: %s no=%d\n",f,path,mode,nopenfiles); ++#endif + } + return f; + +@@ -24,9 +27,11 @@ + int Fclose(FILE *stream) + { + int res=fclose(stream); +-// for (int i=0;i %p\n",stream); ++ for (int i=0;i %p no=%d\n",stream,nopenfiles); ++#endif + return res; + } + +diff -Naur caver_unix_v0.99.4/src/CSearch.cpp caver_unix_v0.99.4-patch001/src/CSearch.cpp +--- caver_unix_v0.99.4/src/CSearch.cpp 2006-04-20 12:07:13.000000000 +0200 ++++ caver_unix_v0.99.4-patch001/src/CSearch.cpp 2006-07-27 10:37:13.000000000 +0200 +@@ -876,14 +876,7 @@ + } + clock.End (); + clock.Print (); +- printf +- ("-----------------------------------------------------------------\n"); +- fflush (stdout); +- } + +- +- Fclose (fout); +- Fclose (fin); + + if (Cfg.mEnableOutputVMD) { + +@@ -908,6 +901,15 @@ + + + } ++ ++ printf ++ ("-----------------------------------------------------------------\n"); ++ fflush (stdout); ++ } ++ ++ ++ Fclose (fout); ++ Fclose (fin); + // fclose (fout2); + + diff --git a/sci-chemistry/caver/files/digest-caver-0.99.4 b/sci-chemistry/caver/files/digest-caver-0.99.4 new file mode 100644 index 000000000000..e96852c5c9f9 --- /dev/null +++ b/sci-chemistry/caver/files/digest-caver-0.99.4 @@ -0,0 +1,6 @@ +MD5 581ef0d56b0c29b6da30908922d4eb90 caverPLUG_unix_v0.99.4.tar.gz 81732 +RMD160 5d2488d64077cfac0e81fdef53074149929aa558 caverPLUG_unix_v0.99.4.tar.gz 81732 +SHA256 61ac38fe2e9ae15af568d6eed19d7410599bc570fb0494793dff625c469b5b69 caverPLUG_unix_v0.99.4.tar.gz 81732 +MD5 95fee4b784716f0dd9bf39641f19de5b caver_unix_v0.99.4.tar.gz 1084660 +RMD160 c57c5b0c6259bb86fc844820d169a60d3895b2bd caver_unix_v0.99.4.tar.gz 1084660 +SHA256 7aa8da882b8c7525164c4643e8feea2bb644bb5790400a21dcf8c70c40f0ea09 caver_unix_v0.99.4.tar.gz 1084660 -- cgit v1.2.3-65-gdbad