[sci-chemistry/acpype] Initial import

Package-Manager: portage-2.2.0_alpha47/cvs/Linux x86_64

diff --git a/sci-chemistry/acpype/ChangeLog b/sci-chemistry/acpype/ChangeLog
new file mode 100644 (file)
index 0000000..57f2cc6
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+++ 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/Manifest b/sci-chemistry/acpype/Manifest
new file mode 100644 (file)
index 0000000..bde9fc6
--- /dev/null
+++ b/sci-chemistry/acpype/Manifest
@@ -0,0 +1,25 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
+AUX acpype.patch 1807 RMD160 5404c733dd5839d10fc2eb597185475a05ca1160 SHA1 ed67c2d809437bcbcb32a997ed693dbb3517acde SHA256 35c05cb04fdc97937b93cc71eb05aaba2a2b09b2b91cee3318648b7fc79fdcf5
+DIST acpype-366.tar.xz 539408 RMD160 295d38f499865f4ca2ea5618841eddc12221e9b0 SHA1 2d8672a6ab069532acd4fa8a5c79a56ec66f405b SHA256 f0c77abea0a5680ecbbecadc1a95c8f851159b7c84d079f6f527336d447e1e9d
+EBUILD acpype-366.ebuild 832 RMD160 f9f1d59ac3a3caa1e7e206f507139334c53eeb41 SHA1 7810c8450471fc5f358a0b5688d22311a2f580d3 SHA256 d58f51ae3dd08c73d81bbcceb24f866c6ec734806f72af0e44ed411070e7ae0c
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+MISC metadata.xml 262 RMD160 abf0b35c0af8e943f7fcb083b2b244e56fd5ee02 SHA1 89729eb37958dd5256d7661f12185026a18ca12e SHA256 3545a7acb49dae4eeb1e9934f6ab2a1dfbe2e1b772fe9a503cf0b6fa1f5457de
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diff --git a/sci-chemistry/acpype/acpype-366.ebuild b/sci-chemistry/acpype/acpype-366.ebuild
new file mode 100644 (file)
index 0000000..2515c89
--- /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 (file)
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 (file)
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@gentoo.org</email>
+               <name>Alexey Shvetsov</name>
+       </maintainer>
+</pkgmetadata>