Move sci-chemistry/caver to sci-chemistry/pymol-plugins-caver; removing caver

7 files changed, 0 insertions, 368 deletions

diff --git a/sci-chemistry/caver/ChangeLog b/sci-chemistry/caver/ChangeLog
deleted file mode 100644
index 8e5ec42b71f5..000000000000
--- a/sci-chemistry/caver/ChangeLog
+++ /dev/null
@@ -1,84 +0,0 @@
-# ChangeLog for sci-chemistry/caver
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/ChangeLog,v 1.18 2011/02/27 09:58:22 xarthisius Exp $
-
-  27 Feb 2011; Kacper Kowalik <xarthisius@gentoo.org> caver-2.1.1.ebuild:
-  Marked ~ppc wrt #321869
-
-*caver-2.1.1 (17 Jan 2011)
-
-  17 Jan 2011; Justin Lecher <jlec@gentoo.org> +caver-2.1.1.ebuild:
-  Version Bump
-
-  15 Jun 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
-  caver-0.99.4.ebuild:
-  Delete deprecation warnings.
-
-  22 Apr 2010; Justin Lecher <jlec@gentoo.org> -caver-0.99.2.ebuild,
-  -caver-2.0.003.ebuild:
-  REmoved old versions
-
-*caver-2.0.003-r1 (21 Feb 2010)
-
-  21 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
-  +caver-2.0.003-r1.ebuild:
-  EAPI=3, keywording for {amd64,x86}-linux
-
-*caver-2.0.003 (12 Feb 2010)
-
-  12 Feb 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +caver-2.0.003.ebuild:
-  Version bump
-
-  07 Jul 2009; Diego E. Pettenò <flameeyes@gentoo.org> caver-0.99.4.ebuild:
-  Use elog for fetch error.
-
-  06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml:
-  Add USE flag description to metadata wrt GLEP 56.
-
-  15 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> caver-0.99.2.ebuild,
-  caver-0.99.4.ebuild:
-  QA: Removed illegal use of ${ROOT}. Bug #168043
-
-  22 Feb 2007; Jeff Gardner <je_fro@gentoo.org> Manifest:
-  Updating for manifest2.
-
-  06 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -caver-0.99.1.ebuild:
-  QA: Removed unused versions.
-
-  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  (#148281) Change herd to sci-chemistry from sci.
-
-  20 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>; caver-0.99.2.ebuild:
-  Stable on x86/ppc.
-
-*caver-0.99.4 (18 Aug 2006)
-
-  18 Aug 2006; Olivier Fisette <ribosome@gentoo.org>
-  +files/caver-0.99.4-001.patch, +caver-0.99.4.ebuild:
-  New upstream version; thanks to Richard Daigle <rdaigle@rsvs.ulaval.ca> for
-  his work (fixes bug #144329). Added pdb2caver script; thanks to Rossen
-  Apostolov <rossen@protein.osaka-u.ac.jp> for his work (fixes bug #141549).
-  Added man page. Ebuild clean-up.
-
-  05 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
-  Remove myself as maintainer, anyone feel free to work on this, although I'll
-  continue to do so as well.
-
-  07 Jul 2006; Donnie Berkholz <spyderous@gentoo.org>; metadata.xml:
-  Update to my new email address.
-
-*caver-0.99.2 (14 May 2006)
-
-  14 May 2006; Donnie Berkholz <dberkholz@gentoo.org>; +caver-0.99.2.ebuild:
-  Bump. This version does a much better job of finding stuff, and the pymol
-  plugin's a lot more capable.
-
-*caver-0.99.1 (20 Dec 2005)
-
-  20 Dec 2005; Donnie Berkholz <dberkholz@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
deleted file mode 100644
index cc331f30529f..000000000000
--- a/sci-chemistry/caver/Manifest
+++ /dev/null
@@ -1,10 +0,0 @@
-AUX caver-0.99.4-001.patch 1856 RMD160 4d2809d7ef0ba9a3205fca398ead887b4e104c67 SHA1 af85d449e94642b4b165507c2b699f3389430c29 SHA256 ebe19169d3db5b71a7c88dd2a22bae9f2095981b67cdd0308bfce4ed60b5c987
-DIST Caver2_1_1_pymol_plugin.zip 5695137 RMD160 205cc36a040b7dcc1112e2e747d4d0c97806c285 SHA1 a7a2849c75074f596bb583d90679e96356622cda SHA256 367e3e37569219ef011d769e9109897c3e26a870a94e9132480768c027571da3
-DIST caver2_0-v003_pymol_plugin.zip 3605820 RMD160 ab937f9090c31dbf078b08fdf582d2cad7717658 SHA1 b18ae1b011c906fe7fe5d94f6ee3bac185c352c6 SHA256 af82aff17103d31385b401edd4fc2c5da91d5ddef7d96b41e0b6e37b5adaef08
-DIST caverPLUG_unix_v0.99.4.tar.gz 81732 RMD160 5d2488d64077cfac0e81fdef53074149929aa558 SHA1 586037ad17f505e6eba739c8167982178edd86dc SHA256 61ac38fe2e9ae15af568d6eed19d7410599bc570fb0494793dff625c469b5b69
-DIST caver_unix_v0.99.4.tar.gz 1084660 RMD160 c57c5b0c6259bb86fc844820d169a60d3895b2bd SHA1 b4a6a26651a20a1664ddfb96f36e89906dcc0bff SHA256 7aa8da882b8c7525164c4643e8feea2bb644bb5790400a21dcf8c70c40f0ea09
-EBUILD caver-0.99.4.ebuild 1706 RMD160 6242e201937924058ad474492547855748b728e4 SHA1 701c267d44e3ab26d37e538ea3c9a69a9201f86c SHA256 ca4ed0568bb7ef8ad517957a44213ab0c636347e7cb1a09ef2bfdf05d3f53829
-EBUILD caver-2.0.003-r1.ebuild 1784 RMD160 5e3262139d49085710e85d0d969fd5ab04921375 SHA1 fd3b9c1b1e1f7e45ba0bbaebd290094e69f540fa SHA256 481a985d8189625521251e71ce6cc793dc7ddd158b57abc4581d8ffe61f9ed98
-EBUILD caver-2.1.1.ebuild 1778 RMD160 e79a98ca807c7c36925de25f899913aea5892453 SHA1 016b423d7281c8152756ee2446bd8eb593486f14 SHA256 4639c7f4ec2b83ec5cb922f4c0e1bd5101dad2f984e0395de7ca2b529cdaae3e
-MISC ChangeLog 2968 RMD160 f9b1070d67bc084915251809605662fc72d02216 SHA1 8335e92b5479d4d1f7c4c6d6b5519cdcf3af7c99 SHA256 0e29394da736bc5641a04567eee18b5a76e1eec250c6e2ea2a6d30d0a95e6cc3
-MISC metadata.xml 270 RMD160 c173cba4fc9dd66e9c5f136819009c4571c36bb9 SHA1 8782ebcb086ea7e5f67c4895a46043f5478d66ba SHA256 907c1720b550d9f8332374f7ec880f422307a2495b180ee64218373d3551381a
diff --git a/sci-chemistry/caver/caver-0.99.4.ebuild b/sci-chemistry/caver/caver-0.99.4.ebuild
deleted file mode 100644
index 59a2a9476d30..000000000000
--- a/sci-chemistry/caver/caver-0.99.4.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2010 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 1.4 2010/06/15 12:36:32 arfrever 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() {
-	elog "Download ${MY_P}.tar.gz"
-	if use pymol; then
-		elog "and ${PLUG_P}.tar.gz"
-	fi
-	elog "from ${HOMEPAGE}. This requires registration."
-	elog "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
-		sed -e "s:^\(CAVER_BINARY_LOCATION\).*:\1 = \"usr/bin/caver\":g" \
-				-i "${WORKDIR}"/${PLUG_P}/caver.py \
-				|| die "Failed setting caver location"
-		insinto $(python_get_sitedir)/pmg_tk/startup
-		doins "${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_optimize $(python_get_sitedir)/pmg_tk/startup/caver.py
-	fi
-}
diff --git a/sci-chemistry/caver/caver-2.0.003-r1.ebuild b/sci-chemistry/caver/caver-2.0.003-r1.ebuild
deleted file mode 100644
index 7a952d60efa1..000000000000
--- a/sci-chemistry/caver/caver-2.0.003-r1.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/caver-2.0.003-r1.ebuild,v 1.2 2010/02/28 13:46:56 arfrever Exp $
-
-EAPI="3"
-SUPPORT_PYTHON_ABIS="1"
-
-inherit multilib python eutils versionator java-utils-2
-
-MY_PV="$(replace_version_separator 2 -v $(replace_version_separator 1 _ ${PV}))"
-MY_P="${PN}${MY_PV}_pymol_plugin"
-
-DESCRIPTION="Calculation of pathways from buried cavities to outside solvent in protein structures"
-HOMEPAGE="http://loschmidt.chemi.muni.cz/caver/"
-SRC_URI="${MY_P}.zip"
-
-LICENSE="CAVER"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=virtual/jre-1.6
-	sci-chemistry/pymol"
-DEPEND="app-arch/unzip"
-RESTRICT_PYTHON_ABIS="2.4 3.*"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/Caver${MY_PV}"/linux_mac
-
-pkg_nofetch() {
-	elog "Download ${MY_P}.tar.gz"
-	elog "from ${HOMEPAGE}. This requires registration."
-	elog "Place tarballs in ${DISTDIR}."
-}
-
-src_prepare() {
-	python_copy_sources
-}
-
-src_install() {
-	java-pkg_dojar Caver$(replace_all_version_separators _ ${PV})/*.jar
-
-	java-pkg_jarinto /usr/share/${PN}/lib/lib/
-	java-pkg_dojar Caver$(replace_all_version_separators _ ${PV})/lib/*.jar
-
-	installation() {
-	sed \
-		-e "s:directory/where/jar/with/plugin/is/located:${EPREFIX}/usr/share/${PN}/lib/:g" \
-		-i Caver$(replace_all_version_separators _ ${PV}).py || die
-
-		insinto $(python_get_sitedir)/pmg_tk/startup/
-		doins Caver$(replace_all_version_separators _ ${PV}).py || die
-	}
-	python_execute_function -s installation
-}
-
-pkg_postinst() {
-	python_mod_optimize pmg_tk/startup/Caver$(replace_all_version_separators _ ${PV}).py
-}
-
-pkg_postrm() {
-	python_mod_cleanup pmg_tk/startup/Caver$(replace_all_version_separators _ ${PV}).py
-}
diff --git a/sci-chemistry/caver/caver-2.1.1.ebuild b/sci-chemistry/caver/caver-2.1.1.ebuild
deleted file mode 100644
index f15103b91e81..000000000000
--- a/sci-chemistry/caver/caver-2.1.1.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/caver-2.1.1.ebuild,v 1.2 2011/02/27 09:58:22 xarthisius Exp $
-
-EAPI="3"
-
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="2.4 3.*"
-
-inherit multilib python eutils versionator java-utils-2
-
-MY_PV="$(replace_version_separator 2 -v $(replace_version_separator 1 _ ${PV}))"
-MY_P="Caver2_1_1_pymol_plugin"
-
-DESCRIPTION="Calculation of pathways from buried cavities to outside solvent in protein structures"
-HOMEPAGE="http://loschmidt.chemi.muni.cz/caver/"
-SRC_URI="${MY_P}.zip"
-
-LICENSE="CAVER"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	>=virtual/jre-1.6
-	sci-chemistry/pymol"
-DEPEND="app-arch/unzip"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/${MY_P}"/linux_mac
-
-pkg_nofetch() {
-	elog "Download ${MY_P}.tar.gz"
-	elog "from ${HOMEPAGE}. This requires registration."
-	elog "Place tarballs in ${DISTDIR}."
-}
-
-src_prepare() {
-	python_copy_sources
-}
-
-src_install() {
-	java-pkg_dojar Caver$(replace_all_version_separators _ ${PV})/*.jar
-
-	java-pkg_jarinto /usr/share/${PN}/lib/lib/
-	java-pkg_dojar Caver$(replace_all_version_separators _ ${PV})/lib/*.jar
-
-	installation() {
-	sed \
-		-e "s:directory/where/jar/with/plugin/is/located:${EPREFIX}/usr/share/${PN}/lib/:g" \
-		-i Caver$(replace_all_version_separators _ ${PV}).py || die
-
-		insinto $(python_get_sitedir)/pmg_tk/startup/
-		doins Caver$(replace_all_version_separators _ ${PV}).py || die
-	}
-	python_execute_function -s installation
-}
-
-pkg_postinst() {
-	python_mod_optimize pmg_tk/startup/Caver$(replace_all_version_separators _ ${PV}).py
-}
-
-pkg_postrm() {
-	python_mod_cleanup pmg_tk/startup/Caver$(replace_all_version_separators _ ${PV}).py
-}
diff --git a/sci-chemistry/caver/files/caver-0.99.4-001.patch b/sci-chemistry/caver/files/caver-0.99.4-001.patch
deleted file mode 100644
index 1ce570e9aed0..000000000000
--- a/sci-chemistry/caver/files/caver-0.99.4-001.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-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<nopenfiles;i++) fprintf(stderr,"  ");
--//    fprintf(stderr,"Opening -> %p ('%s') mode: %s\n",f,path,mode);
-+#ifdef SHOWIOOPERATIONS  
-+  for (int i=0;i<nopenfiles;i++) fprintf(stderr,"  ");
-+    fprintf(stderr,"Opening -> %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<nopenfiles;i++) fprintf(stderr,"  ");
--// fprintf(stderr,"Closing -> %p\n",stream);
-+ for (int i=0;i<nopenfiles;i++) fprintf(stderr,"  ");
-  nopenfiles--;
-+#ifdef SHOWIOOPERATIONS
-+ fprintf(stderr,"Closing -> %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/metadata.xml b/sci-chemistry/caver/metadata.xml
deleted file mode 100644
index 5f6488d5a9f0..000000000000
--- a/sci-chemistry/caver/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-chemistry</herd>
-<use>
-  <flag name='pymol'>Install the PyMol plugin (<pkg>sci-chemistry/pymol</pkg>)
-    </flag>
-</use>
-</pkgmetadata>