diff options
| -rw-r--r-- | sci-chemistry/acpype/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-chemistry/acpype/acpype-366.ebuild | 38 | ||||
| -rw-r--r-- | sci-chemistry/acpype/files/acpype.patch | 37 | ||||
| -rw-r--r-- | sci-chemistry/acpype/metadata.xml | 9 |
4 files changed, 94 insertions, 0 deletions
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> |