sci-chemistry/pdbcat: New addition

(Portage version: 2.2.0_alpha137/cvs/Linux x86_64)

6 files changed, 92 insertions, 0 deletions

diff --git a/sci-chemistry/pdbcat/ChangeLog b/sci-chemistry/pdbcat/ChangeLog
new file mode 100644
index 000000000000..98fd3744d55d
--- /dev/null
+++ b/sci-chemistry/pdbcat/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/pdbcat
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdbcat/ChangeLog,v 1.1 2012/10/12 11:32:58 jlec Exp $
+
+*pdbcat-1.3 (12 Oct 2012)
+
+  12 Oct 2012; Justin Lecher <jlec@gentoo.org> +pdbcat-1.3.ebuild,
+  +files/pdbcat-1.3-gcc.patch, +files/CMakeLists.txt, +metadata.xml:
+  New addition
+
diff --git a/sci-chemistry/pdbcat/Manifest b/sci-chemistry/pdbcat/Manifest
new file mode 100644
index 000000000000..b3be4323a531
--- /dev/null
+++ b/sci-chemistry/pdbcat/Manifest
@@ -0,0 +1,6 @@
+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 608 SHA256 e051ce89292682c6af3b4970ae65ad724383ca0001fe8e0991c1684aa4684313 SHA512 732c5987946b9800941875e95df5494c390334209a720f88b6b67e9bcfd87c35094c98f2c100f96e1b93497173e6e076efe567fc71cf10caa7553122b711aded WHIRLPOOL ac1a5a3c36f3d783a49b7d2a827003e2d163614859c04342be14215dadff719342def7165375367efae12f3db1d1c3124db8a77f0dbc6c3a773e2708d43c4120
+MISC ChangeLog 300 SHA256 ba6b35323602c24ea3550f23d515280632bbdc716ba18f0f1d65305222ee1060 SHA512 0d20c78531124322094236fdb77e821e01c1bb285152c31d64b9d210826f6885544835fcfa5f2f4728cc47e0bfdab8dee0b6ea68913526023c9d452ef2e5afb4 WHIRLPOOL 0ccdfdb5a69cd2d7ae6d99a2a7fcc9252120e18da2bbc5b3f8f427032b28add844eb2bcbe9fe54a9ddb1d77f824bd1d78de7d174bad3eb3b306bd69d3f1f014a
+MISC metadata.xml 1102 SHA256 d8271d6b0e9c4ccf80242606b85aa1bafef9687d1bf2266c823772518e839a22 SHA512 65805dbe70d493739a61ed79973c3756dfa0d4cf286b76b4b1c2fbaa68035ff5653e6c0f9f1927cf88cd40ca9b6df8d3f924f6ab2cf64c6cd1dd5564fd849ce4 WHIRLPOOL 9dfa06261f536f2adf2f011f0dc816d16cb6bc1b25c9c68a348ccb7958b59f550350390a47b14aa46f3b1e9a0819a7c427744d842062bf7af507a768d04e7500
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..a83752041b17
--- /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>
+	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>jlec@gentoo.org</email>
+	</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..b868dc63528c
--- /dev/null
+++ b/sci-chemistry/pdbcat/pdbcat-1.3.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdbcat/pdbcat-1.3.ebuild,v 1.1 2012/10/12 11:32:58 jlec Exp $
+
+EAPI=4
+
+inherit cmake-utils
+
+DESCRIPTION="Manipulate and process PDB files using commonly available 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"
+
+SLOT="0"
+LICENSE="as-is"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+PATCHES=( "${FILESDIR}"/${P}-gcc.patch )
+DOCS=( README )
+
+src_prepare() {
+	cp "${FILESDIR}"/CMakeLists.txt . || die
+	base_src_prepare
+}