From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1Qmhx6-0000Ve-5y for garchives@archives.gentoo.org; Fri, 29 Jul 2011 07:57:48 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 23AEE21C14E; Fri, 29 Jul 2011 07:57:41 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id D550521C14E for ; Fri, 29 Jul 2011 07:57:40 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 449681B401C for ; Fri, 29 Jul 2011 07:57:40 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 4E55E8003D for ; Fri, 29 Jul 2011 07:57:39 +0000 (UTC) From: "Alexey Shvetsov" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Alexey Shvetsov" Message-ID: Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/acpype/files/, sci-chemistry/acpype/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/acpype/acpype-366.ebuild sci-chemistry/acpype/files/acpype.patch sci-chemistry/acpype/metadata.xml X-VCS-Directories: sci-chemistry/acpype/files/ sci-chemistry/acpype/ X-VCS-Committer: alexxy X-VCS-Committer-Name: Alexey Shvetsov X-VCS-Revision: d4b19911fbd85815587db0bb1a61891417a6e73d Date: Fri, 29 Jul 2011 07:57:39 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: b086f38dd80bc2f9a857f09559d8b187 commit: d4b19911fbd85815587db0bb1a61891417a6e73d Author: Alexey Shvetsov gentoo org> AuthorDate: Fri Jul 29 07:56:39 2011 +0000 Commit: Alexey Shvetsov gentoo org> CommitDate: Fri Jul 29 07:57:11 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3Dd4b19911 [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/acpyp= e/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=3D3 + +inherit eutils python +PYTHON_DEPEND=3D"2:2.5" + +DESCRIPTION=3D"AnteChamber PYthon Parser interfacE" +HOMEPAGE=3D"http://code.google.com/p/acpype/" +SRC_URI=3D"mirror://gentoo/${P}.tar.xz" + +LICENSE=3D"GPL-3" +SLOT=3D"0" +KEYWORDS=3D"~amd64 ~x86" +IUSE=3D"" + +DEPEND=3D"sci-chemistry/ambertools" +RDEPEND=3D"${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/acpy= pe/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 +=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D +--- acpype.py (revision 366) ++++ acpype.py (working copy) +@@ -3020,32 +3020,6 @@ + acMol2FileName =3D '%s_%s_%s.mol2' % (base, chargeType, atomTyp= e) + self.acMol2FileName =3D acMol2FileName + self.charmmBase =3D '%s_CHARMM' % base +- # check for which version of antechamber +- if 'amber10' in self.acExe: +- if qprog =3D=3D 'sqm': +- self.printWarn("SQM is not implemented in AmberTools 1.= 2") +- self.printWarn("Setting mopac for antechamber") +- qprog =3D 'mopac' +- elif qprog =3D=3D '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 =3D 'mopac' +- elif 'amber11' in self.acExe: +- if qprog =3D=3D 'divcon': +- self.printWarn("DIVCON is not implemented in AmberTools= 1.3 anymore") +- self.printWarn("Setting sqm for antechamber") +- qprog =3D 'sqm' +- elif qprog =3D=3D '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 =3D 'sqm' +- else: +- self.printWarn("Old version of antechamber. Strongly consid= er upgrading to AmberTools") +- self.printWarn("Setting mopac for antechamber") +- qprog =3D 'mopac' + self.qFlag =3D qDict[qprog] + self.outTopols =3D [outTopol] + if outTopol =3D=3D 'all': diff --git a/sci-chemistry/acpype/metadata.xml b/sci-chemistry/acpype/met= adata.xml new file mode 100644 index 0000000..b2558d8 --- /dev/null +++ b/sci-chemistry/acpype/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-chemistry + + alexxy@gentoo.org + Alexey Shvetsov + +