New upstream version (fixes bug #144329). Added pdb2caver script (fixes bug #141549). Added man page.

Package-Manager: portage-2.1-r2

5 files changed, 169 insertions, 5 deletions

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 <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
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<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/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