[gentoo-commits] proj/sci:master commit in: sci-chemistry/acpype/files/, sci-chemistry/acpype/

[Alexey Shvetsov]

commit:     d4b19911fbd85815587db0bb1a61891417a6e73d
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 29 07:56:39 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Jul 29 07:57:11 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d4b19911

[sci-chemistry/acpype] Initial import

(Portage version: 2.2.0_alpha47/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/acpype/acpype-366.ebuild  |   38 +++++++++++++++++++++++++++++++
 sci-chemistry/acpype/files/acpype.patch |   37 ++++++++++++++++++++++++++++++
 sci-chemistry/acpype/metadata.xml       |    9 +++++++
 3 files changed, 84 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/acpype/acpype-366.ebuild b/sci-chemistry/acpype/acpype-366.ebuild
new file mode 100644
index 0000000..f0babda
--- /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: $
+
+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 0000000..9354527
--- /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 0000000..b2558d8
--- /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@g.o</email>
+		<name>Alexey Shvetsov</name>
+	</maintainer>
+</pkgmetadata>