From 8b83eb890b6e05ab687e95dc8d38b399d02ea053 Mon Sep 17 00:00:00 2001
From: Alexey Shvetsov <alexxy@gentoo.org>
Date: Fri, 29 Jul 2011 08:27:31 +0000
Subject: [sci-chemistry/acpype] Initial import

(Portage version: 2.2.0_alpha47/cvs/Linux x86_64)
---
 sci-chemistry/acpype/ChangeLog          | 10 +++++++++
 sci-chemistry/acpype/acpype-366.ebuild  | 38 +++++++++++++++++++++++++++++++++
 sci-chemistry/acpype/files/acpype.patch | 37 ++++++++++++++++++++++++++++++++
 sci-chemistry/acpype/metadata.xml       |  9 ++++++++
 4 files changed, 94 insertions(+)
 create mode 100644 sci-chemistry/acpype/ChangeLog
 create mode 100644 sci-chemistry/acpype/acpype-366.ebuild
 create mode 100644 sci-chemistry/acpype/files/acpype.patch
 create mode 100644 sci-chemistry/acpype/metadata.xml

(limited to 'sci-chemistry')

diff --git a/sci-chemistry/acpype/ChangeLog b/sci-chemistry/acpype/ChangeLog
new file mode 100644
index 000000000000..57f2cc65a93e
--- /dev/null
+++ b/sci-chemistry/acpype/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/acpype
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/acpype/ChangeLog,v 1.1 2011/07/29 08:27:31 alexxy Exp $
+
+*acpype-366 (29 Jul 2011)
+
+  29 Jul 2011; Alexey Shvetsov <alexxy@gentoo.org> +acpype-366.ebuild,
+  +files/acpype.patch, +metadata.xml:
+  Initial import
+
diff --git a/sci-chemistry/acpype/acpype-366.ebuild b/sci-chemistry/acpype/acpype-366.ebuild
new file mode 100644
index 000000000000..2515c8947a78
--- /dev/null
+++ b/sci-chemistry/acpype/acpype-366.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/acpype/acpype-366.ebuild,v 1.1 2011/07/29 08:27:31 alexxy Exp $
+
+EAPI=3
+
+inherit eutils python
+PYTHON_DEPEND="2:2.5"
+
+DESCRIPTION="AnteChamber PYthon Parser interfacE"
+HOMEPAGE="http://code.google.com/p/acpype/"
+SRC_URI="mirror://gentoo/${P}.tar.xz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="sci-chemistry/ambertools"
+RDEPEND="${DEPEND}"
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	epatch "${FILESDIR}/${PN}.patch"
+	python_convert_shebangs -r 2 .
+}
+
+src_install() {
+	newbin ${PN}.py ${PN}
+	newbin CcpnToAcpype.py CcpnToAcpype
+	dodoc NOTE.txt README.txt
+	insinto /usr/share/${PN}
+	doins -r ffamber_additions test
+}
diff --git a/sci-chemistry/acpype/files/acpype.patch b/sci-chemistry/acpype/files/acpype.patch
new file mode 100644
index 000000000000..9354527cc8a9
--- /dev/null
+++ b/sci-chemistry/acpype/files/acpype.patch
@@ -0,0 +1,37 @@
+Index: acpype.py
+===================================================================
+--- acpype.py	(revision 366)
++++ acpype.py	(working copy)
+@@ -3020,32 +3020,6 @@
+         acMol2FileName = '%s_%s_%s.mol2' % (base, chargeType, atomType)
+         self.acMol2FileName = acMol2FileName
+         self.charmmBase = '%s_CHARMM' % base
+-        # check for which version of antechamber
+-        if 'amber10' in self.acExe:
+-            if qprog == 'sqm':
+-                self.printWarn("SQM is not implemented in AmberTools 1.2")
+-                self.printWarn("Setting mopac for antechamber")
+-                qprog = 'mopac'
+-            elif qprog == 'divcon':
+-                if not os.path.exists(os.path.join(os.path.dirname(self.acExe), qprog)):
+-                    self.printWarn("DIVCON is not installed")
+-                    self.printWarn("Setting mopac for antechamber")
+-                    qprog = 'mopac'
+-        elif 'amber11' in self.acExe:
+-            if qprog == 'divcon':
+-                self.printWarn("DIVCON is not implemented in AmberTools 1.3 anymore")
+-                self.printWarn("Setting sqm for antechamber")
+-                qprog = 'sqm'
+-            elif qprog == 'mopac':
+-                if not os.path.exists(os.path.join(os.path.dirname(self.acExe), qprog)):
+-                    self.printWarn("MOPAC is not installed")
+-                    self.printWarn("Setting sqm for antechamber")
+-                    return None
+-                    qprog = 'sqm'
+-        else:
+-            self.printWarn("Old version of antechamber. Strongly consider upgrading to AmberTools")
+-            self.printWarn("Setting mopac for antechamber")
+-            qprog = 'mopac'
+         self.qFlag = qDict[qprog]
+         self.outTopols = [outTopol]
+         if outTopol == 'all':
diff --git a/sci-chemistry/acpype/metadata.xml b/sci-chemistry/acpype/metadata.xml
new file mode 100644
index 000000000000..b2558d8c6282
--- /dev/null
+++ b/sci-chemistry/acpype/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>alexxy@gentoo.org</email>
+		<name>Alexey Shvetsov</name>
+	</maintainer>
+</pkgmetadata>
-- 
cgit v1.2.3-65-gdbad