reinit the tree, so we can have metadata

4 files changed, 119 insertions, 0 deletions

diff --git a/sci-chemistry/numbat/Manifest b/sci-chemistry/numbat/Manifest
new file mode 100644
index 000000000000..d02a8970421c
--- /dev/null
+++ b/sci-chemistry/numbat/Manifest
@@ -0,0 +1,6 @@
+AUX numbat-0.999-gnuplot.patch 2048 SHA256 689e9690e92f531ffbbdfbb7620c5ba4f9f2cb2531c6b3267aac502bd541e5aa SHA512 dd646e8f6652a63cb4e1c97830a755629e45d20fa13431f628b66fe8a5062b7bd7ebacddb3dbcca5aeeac3ae0d89f59c61036c1a3639d25fe0426ada77a888bb WHIRLPOOL 18248ba1654f499af5c4ba22e9a03ba010b3d3c359976014bf1a0e3a584f424e61e5be868a941b1e0dd842d20ee671634c67d661114258467ff2d6492dd67b6a
+DIST Numbat-0.999.tar.gz 1791471 SHA256 aef72903f262c5a25e542429f3cc7aca4d2dbc920c08b59847d5cb325855e9ab SHA512 0887f77905bbb476b0d12a7015d5d5745023740acc974ea9cd452de7d38a75a92e6090015127588b38ba62353d38c2be20f57be5df3011b51050c4934dfd206c WHIRLPOOL 8282bf5481a93d17a833f809c28d927d681d6d5016552a07b9267bdb78e99fc568370321567d7d6a87a84f31eea8fae9494c1ae8c0109157fca779c7c06805d9
+EBUILD numbat-0.999-r1.ebuild 1075 SHA256 43ffd2cfb44d6ccfa0efe6d0ee874d7493bd8cf07c59e26dbbea9795409882bf SHA512 28df0153d08c7656c59212ced742ab2d6c8e3eaefaa96c5f62d44beb2e56e39cc60d51a8dc284187e90b3eb57322f7352137908294508b53b13e79e7e0719a30 WHIRLPOOL d97c4042f3163e15d2b0970056bf1fea02732d9d7804c25acc504916e31d489e1e03a239235f6e84034e766ba983fee440cc675aebdae85da9367b47e5d9600c
+MISC ChangeLog 2610 SHA256 356de4f5f73d5180dcb84f3edf86fe38a24241a536b20265008ee605d05aa83e SHA512 742eea54775960ebd7b6f0ec66ebc6214cb53375e953bed1e17c602bb88bae18643deac578459f3c99fa60369b2865c441f32a0c9e1d77e77cb3fe7e33f9428b WHIRLPOOL a5c4324a0cd0fe606bfc700340b632fdd09641d7260705df3cd3b900f6481611d7999c7a6399972a9e7c8cdd70ea5ea85f5812450e4314747e1dec0b0622b500
+MISC ChangeLog-2015 695 SHA256 7a057f9001163360fe83457617413cca318326a1b6a704d6d58fbec64d58dcb7 SHA512 8eb3d41d769d0be4f2b8fc8d49c58ed682b81e615535c5bce482165aecf910b3434d7009fb55d26375a0c78b20dc534e0a5ac9367dbd8ac8c76a93cfe858b8ba WHIRLPOOL f33a3a491ed15f04491bc30328ac563a78ea017806aa0f6c70ce1929b9c3304fe21d644fa3ab9ee7ca27e5b04a2ba2702c3a4ddaaa5fcd655237addfd487aa12
+MISC metadata.xml 852 SHA256 00c4cc1301e237e514595470acd436d91c2c5095b972c40e1ac25c9f4b139e37 SHA512 64e5552a677fc7370f68f7f811734ac17144fcb95e23503c962b678a1678dccf22a2d19991eb69dcdf8d4c1c97448d35d7f34654245ebe3fee8b30a0a8fa586c WHIRLPOOL 99bc5bfa27a4c358c8c4df4671651256907cdd50e63e9051551191a8be5be8844ddb5c1866de819e4b5fdf1353635c894dc9cf7b0c0c49d5a05d9bd98b0e5148
diff --git a/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch b/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch
new file mode 100644
index 000000000000..942f5871e50b
--- /dev/null
+++ b/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch
@@ -0,0 +1,42 @@
+ src/error_analysis.c | 20 ++++++++++----------
+ 1 file changed, 10 insertions(+), 10 deletions(-)
+
+diff --git a/src/error_analysis.c b/src/error_analysis.c
+index eb86a6f..c0edf5f 100644
+--- a/src/error_analysis.c
++++ b/src/error_analysis.c
+@@ -848,11 +848,11 @@ void write_sanson_mac(FILE * F, char * name_plot, char * name_world, int number_
+     }
+ 
+     fprintf(F, "reset\n");
+-    fprintf(F, "set noxtics\n");
+-    fprintf(F, "set noytics\n");
++    fprintf(F, "unset xtics\n");
++    fprintf(F, "unset ytics\n");
+     fprintf(F, "set angles degrees\n");
+-    fprintf(F, "set nogrid\n");
+-    fprintf(F, "set noborder\n");
++    fprintf(F, "unset grid\n");
++    fprintf(F, "unset border\n");
+     //fprintf(F, "width=40\n");
+     //fprintf(F, "height=width*(3./4.)\n");
+     //fprintf(F, "set xrange [-width : width]\n");
+@@ -867,12 +867,12 @@ void write_sanson_mac(FILE * F, char * name_plot, char * name_world, int number_
+     fprintf(F, "YC(lat,lon)=(lon-long0)*cos(lat)\n");
+     fprintf(F, "plot '%s'  using (YC($2,$1)):(XC($2,$1)) t '' with lines lw 0.1 lt -1", name_world);
+     for(i = 0; i < number_of_tensor; i++){
+-        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot,
+-                6*i+2, 6*i+1, 6*i+2, 6*i+1, 3*i+1);
+-        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot,
+-                6*i+4, 6*i+3, 6*i+4, 6*i+3, 3*i+2);
+-        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot,
+-                6*i+6, 6*i+5, 6*i+6, 6*i+5, 3*i+3);
++        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot,
++                6*i+2, 6*i+1, 6*i+2, 6*i+1);
++        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot,
++                6*i+4, 6*i+3, 6*i+4, 6*i+3);
++        fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot,
++                6*i+6, 6*i+5, 6*i+6, 6*i+5);
+     }
+     fprintf(F, "\n");
+     //fprintf(F, "pause 2\n");
diff --git a/sci-chemistry/numbat/metadata.xml b/sci-chemistry/numbat/metadata.xml
new file mode 100644
index 000000000000..0f4399d7df6d
--- /dev/null
+++ b/sci-chemistry/numbat/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+  <longdescription>
+Numbat is a user friendly software that fits dX-tensor to a set of PCS 
+measurements and a structure from a PDB file. It has also been designed to 
+assist in the semi automatic process of PCS assignment. A detailed description 
+of the software can be found in this publication: 
+
+Christophe Schmitz, Mitchell J. Stanton-Cook, Xun-Cheng Su, Gottfried Otting, 
+and Thomas Huber (2008). Numbat: an interactive software tool for fitting 
+Δχ-tensors to molecular coordinates using pseudocontact shifts. Journal of 
+Biomolecular NMR. 41:179-189.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-chemistry/numbat/numbat-0.999-r1.ebuild b/sci-chemistry/numbat/numbat-0.999-r1.ebuild
new file mode 100644
index 000000000000..66f5b2ae0652
--- /dev/null
+++ b/sci-chemistry/numbat/numbat-0.999-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+MY_PN="Numbat"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="new user-friendly method built for automatic dX-tensor determination"
+HOMEPAGE="http://www.nmr.chem.uu.nl/~christophe/numbat.html"
+SRC_URI="http://comp-bio.anu.edu.au/private/downloads/Numbat/${MY_P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+CDEPEND="
+	gnome-base/libglade:2.0
+	sci-libs/gsl
+	x11-libs/gtk+:2"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+RDEPEND="${CDEPEND}
+	sci-chemistry/molmol
+	sci-chemistry/pymol
+	sci-visualization/gnuplot"
+
+S="${WORKDIR}"/${MY_P}
+
+PATCHES=(
+#	"${FILESDIR}"/${P}-glade.patch
+	"${FILESDIR}"/${P}-gnuplot.patch )
+
+src_prepare() {
+	sed \
+		-e '/COPYING/d' \
+		-e "s:doc/numbat:share/doc/${PF}:g" \
+		-i Makefile.am src/common.h || die
+	rm missing
+	emake distclean
+	autotools-utils_src_prepare
+}
+
+src_install() {
+	docompress -x /usr/share/doc/${PF}
+	autotools-utils_src_install
+}