reinit the tree, so we can have metadata

5 files changed, 82 insertions, 0 deletions

diff --git a/sci-chemistry/pdbcat/Manifest b/sci-chemistry/pdbcat/Manifest
new file mode 100644
index 000000000000..a6b8d7f1e3bf
--- /dev/null
+++ b/sci-chemistry/pdbcat/Manifest
@@ -0,0 +1,7 @@
+AUX CMakeLists.txt 172 SHA256 f91b445bce562b3de8e82d593ad54960ed58e1c99bb3f9d908c159dcc4615894 SHA512 c8aa60098be10a25dcebf4c764e30f886f39a7d95da228d9d7fdcdedf3124ace32307197bbb2901b89ee3a8ce78411e61a4147eb395add65df6583683d3d5277 WHIRLPOOL 0345309440453b6827740e32f0e7f63b343caadfa8cf8b72214cc8a7d1d2584800d225e0b1eab34321a0062a890da8cdfae1d0e543db5f7e05ed2d9ff2e061e6
+AUX pdbcat-1.3-gcc.patch 423 SHA256 c42a7d4eaaa13c8bf253a786dc2ea5a1fb186c22c3684ab48ca36f8cf5e65347 SHA512 0a4b85ad2a4ec8014829e0c1449aecc90d65b57c4d0062ecd537991219c58c75dce138d901718a790c014d240afa9a063d46db5625d1e1c50727f1b1e468b032 WHIRLPOOL 1a33d959108dae3be74a1e6f518db55c723d504d7c64b0986e657db11f6f3882f3d97f0ab67f95115073fcb11c956890612eb83246f6ee91bcb1e1f6817c799d
+DIST pdbcat-1.3.tar.gz 12750 SHA256 a9c554c00b34e5131ca1be61aad9332ab26eca5a905b716c47f657521368babc SHA512 369ac0c4c1d8396eaa0450feb9852d2d75ebd9862a2e403ccd42a2801e924f99c28c5d71c0b66feb4588076a8948b503823d2c75420128dd04d020253f821f4c WHIRLPOOL ba6599d06814929bf23c83bb6df7084592fcc23603a8e3116e2661df3c9d97b335c627d09249be6c862466b2d83a0100d94b366df171e1c45ec6221a22b2ca78
+EBUILD pdbcat-1.3.ebuild 590 SHA256 afb4c1dc066e0ad2fd557791a5b2a8a7ee8e639e997d9eefc141e7ba194c6802 SHA512 d9a9734e6df0dd3773fab52b617a1dd6dff2aeaf3110903ba3af5d11644db1b14013371ba020bdae412c311648f72f955c358bd995c2ef2df659984ab6090077 WHIRLPOOL 43c3c260224f7e1af6385998bd113778c1ab19086c8e6a8575f404c7f38a16860736c760998452b0fa6778a3b3c65afb47b0ca01561c2d77ba91014ff2e00c6d
+MISC ChangeLog 2617 SHA256 bbbb971674500ca74e1f1626cff6f995d2dd6634ad776ee2a75dd44f06b143d4 SHA512 2cba87f9a17a513d8b6f32666213c4072f1f010bad9cefe2dcad62327c5b4becd848c2636b1c7fc47095fbf9425999b096f0ae4327edaef735b1bf5796700487 WHIRLPOOL 7395c37ff369c633b045733a813cc190fb174fa604517af3e8131e3d63353a8a53733e41cf650528222d8298f960ac7e392e1a5408d21f7e265aac117babad6c
+MISC ChangeLog-2015 651 SHA256 bccc631d4b77cd3c16f37c16f8389e7e283a5dc6847ed15142e0cc1e0faba922 SHA512 4e16b089ec80c7a6ae10865b412bafa7fda7b1b9468207c0086d06cd5e033d7bfda2329222ee29866591610f28b0f1a78d91b0c1dde40bd08d93c59608c3e44b WHIRLPOOL 00b1a861274324a9614d21298eca6cef5dacaf3af35bd12beb07ba03973685377d1ce2393613b6877ae794ae7053bbde072baa4d655c6d618c3ea36bfe30a0ae
+MISC metadata.xml 1145 SHA256 e0b0ff0a906bf4609dcfa891c5c6a1ec169d4100b0e19db7ee96b1d23877d6dc SHA512 4f4711173cdae81767ed2519c158fba751764b62f936d91a53ec0f275b6a52a9fc72c4dc4f6fa942376d81e741952c2e5c777465d520f2158b0bb125ba1b7ff0 WHIRLPOOL d0fb929e83d86689a47ee3410d23374296bc89118c557da37b8f4b633fd1c46fb4f20c9aa68964ed4d1ec783582d946c7702835e9ffbdc9b799827d8e937ae28
diff --git a/sci-chemistry/pdbcat/files/CMakeLists.txt b/sci-chemistry/pdbcat/files/CMakeLists.txt
new file mode 100644
index 000000000000..7a6f348f5929
--- /dev/null
+++ b/sci-chemistry/pdbcat/files/CMakeLists.txt
@@ -0,0 +1,11 @@
+cmake_minimum_required (VERSION 2.6)
+project (pdbcat)
+add_executable(pdbcat
+	Common.C
+	Common.h
+	pdbcat.C
+	PDBData.C
+	PDBData.h)
+
+install (TARGETS pdbcat DESTINATION bin)
+
diff --git a/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch b/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch
new file mode 100644
index 000000000000..b45c36bd8a8d
--- /dev/null
+++ b/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch
@@ -0,0 +1,17 @@
+ pdbcat.C | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/pdbcat.C b/pdbcat.C
+index 0786d9b..387edf9 100644
+--- a/pdbcat.C
++++ b/pdbcat.C
+@@ -17,7 +17,8 @@
+ #include <stdlib.h> // for exit
+ #include <stdio.h>  // for feof() and other file manip stuff
+ #include <string.h> // for strcasecmp
+-#include <iostream.h>
++#include <iostream>
++using namespace std;
+ #include "Common.h"
+ #include "PDBData.h"
+ 
diff --git a/sci-chemistry/pdbcat/metadata.xml b/sci-chemistry/pdbcat/metadata.xml
new file mode 100644
index 000000000000..29177ef0643c
--- /dev/null
+++ b/sci-chemistry/pdbcat/metadata.xml
@@ -0,0 +1,24 @@
+<?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>
+The Brookhaven Protein Data Bank stores atomic coordinate information
+for protein structures in a column based format.  This is designed to
+be read easily read by FORTRAN programs.  Indeed, if you get the
+format description (from anonymous ftp to ftp.pdb.bnl.gov, the file
+/pub/format.desc.ps) they show the single input line needed to read
+each record type.
+However, I am a C/C++ programmer in the Unix environment.  It is a
+easier for me to deal with field based input than column based ones.
+If the fields are white space delimited I can easily use awk and perl
+to manipulate the coordinate information.  So I needed some way to
+convert the ATOM and HETATM records of PDB files from the standard
+column based format to a field based one and back again.  It needed
+to denote missing fields if they exist.
+That converter is `pdbcat'.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-chemistry/pdbcat/pdbcat-1.3.ebuild b/sci-chemistry/pdbcat/pdbcat-1.3.ebuild
new file mode 100644
index 000000000000..ccdbd9928160
--- /dev/null
+++ b/sci-chemistry/pdbcat/pdbcat-1.3.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils
+
+DESCRIPTION="Manipulate and process PDB files using tools such as Perl, awk, etc"
+HOMEPAGE="http://www.ks.uiuc.edu/Development/MDTools/pdbcat/"
+SRC_URI="http://www.ks.uiuc.edu/Development/MDTools/${PN}/files/${P}.tar.gz"
+
+LICENSE="free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+PATCHES=( "${FILESDIR}"/${P}-gcc.patch )
+DOCS=( README )
+
+src_prepare() {
+	cp "${FILESDIR}"/CMakeLists.txt . || die
+	cmake-utils_src_prepare
+}