open3dqsar: New package for pharmacophore detection.

QSAR is quantitative structure-activity relationships, which are used in
structure-based drug design to explain which atomic interactions are
important.

4 files changed, 187 insertions, 0 deletions

diff --git a/licenses/open3dqsar b/licenses/open3dqsar
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+Open3DQSAR version 1.x
+
+An open-source software aimed at high-throughput
+chemometric analysis of molecular interaction fields
+
+Copyright 2009, 2010 Paolo Tosco, Thomas Balle
+All rights reserved
+
+
+Open3DQSAR version 1.x SOFTWARE LICENSE AGREEMENT
+
+This License Agreement is a legal agreement between you, the end user
+(either an individual or an entity), and the copyright holders Paolo Tosco
+and Thomas Balle. This License Agreement is valid for Open3DQSAR version
+1.0 and all subsequent releases bearing "1" as the first version number,
+followed by any combination of alphanumeric characters, as collectively
+indicated by the "1.x" code.
+
+GRANT OF LICENSE
+
+The copyright holders of Open3DQSAR version 1.x, Paolo Tosco and Thomas
+Balle, grant, and you hereby accept, a non-exclusive license to use the
+Open3DQSAR version 1.x software product ("Software") to the extent of
+their rights and in accordance with the terms of this Agreement. This
+licensed copy of the Software may only be used on computers at your
+site by you and members of your organization at your site who have read
+and agreed to this license. You may install the Software on computers
+at your site for your own use or use by members of your organization
+at your site. You may not distribute copies of the Software to others
+outside of your site. You may make only those copies of the Software
+which are necessary to install and use it as permitted by this Agreement,
+or are for purposes of backup and archival records.
+
+LOCATION RESTRICTIONS
+
+The copyright holders of Open3DQSAR version 1.x, Paolo Tosco and Thomas
+Balle, explicitly forbid the use and distribution of the Software in
+the following countries:
+
+- Austria
+- Belgium
+- Denmark
+- France
+- Germany
+- Great Britain
+- Greece
+- Italy
+- Liechtenstein
+- Luxembourg
+- Netherlands
+- Sweden
+- Switzerland
+
+This geographical restriction is due to the existence in the
+aforementioned countries of a valid patent owned by a third-party
+which protects some of the methodologies used by the Software. Use and
+distribution of the Software in those countries may constitute patent
+infringement, and therefore is explicitly forbidden by the copyright
+holders.
+
+OWNERSHIP
+
+This ownership is protected by copyright laws and by international
+treaty provisions.
+
+MODIFICATIONS AND DERIVATIVE WORKS
+
+You may modify the software, and use it to create derivative works,
+for your internal use at the site covered by this License. You may not
+distribute such modified or derivative software to others outside of
+your site without written permission.
+
+REPORTS OF PUBLICATIONS
+
+You agree to acknowledge use of the Software in any reports or
+publications of results obtained with the Software, citing the following
+publication:
+Tosco, P.; Balle, T. "Open3DQSAR: a new open-source software aimed at
+high-throughput chemometric analysis of molecular interaction fields",
+J. Mol. Model. 2010, xx, yyy-zzz.
+
+ASSIGNMENT RESTRICTIONS
+
+You shall not use the Software (or any part thereof) in connection with
+the provision of consultancy, modeling or other services, whether for
+value or otherwise, on behalf of any third party who does not hold a
+current valid Open3DQSAR version 1.x Software License Agreement. You
+shall not use the Software to write other software that duplicates the
+functionality of the Software. You shall not rent, lease, or otherwise
+sublet the Software or any part thereof.
+
+LIMITED WARRANTY
+
+The Licensee acknowledges that Paolo Tosco and Thomas Balle (the
+Licensors) make no warranty, expressed or implied, that the program
+will function without error, or in any particular hardware environment,
+or so as to generate any particular function or result. This software is
+provided by the Licensors "as is" and any express or implied warranties,
+including, but not limited to, the implied warranties of merchantability
+and fitness for a particular purpose are disclaimed. In no event shall
+the Licensors be liable for any direct, indirect, incidental, special,
+exemplary, or consequential damages (including, but not limited to,
+procurement of substitute goods or services; loss of use, data, or
+profits; or business interruption) however caused and on any theory of
+liability, whether in contract, strict liability, or tort (including
+negligence or otherwise) arising in any way out of the use of this
+software, even if advised of the possibility of such damage.
+
+
+For further information, please contact:
+
+Paolo Tosco, PhD
+Dipartimento di Scienza e Tecnologia del Farmaco
+Universita' degli Studi di Torino
+Via Pietro Giuria, 9
+10125 Torino (Italy)
+Phone:  +39 011 670 7680
+Mobile: +39 348 553 7206
+Fax:    +39 011 670 7687
+E-mail: paolo.tosco@unito.it
diff --git a/sci-chemistry/open3dqsar/Manifest b/sci-chemistry/open3dqsar/Manifest
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+++ b/sci-chemistry/open3dqsar/Manifest
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+DIST open3dqsar-1.2.tar.gz 6423763 RMD160 5235b871873b45a01c9fe53c31bad99d163e4d08 SHA1 808c2130c82f0651771649f0407ee8758e80b948 SHA256 71a57e87a7e636d38033fc1e586341ea4f0bb63a65b7a5ad3c2a7ae530aa0e08
+EBUILD open3dqsar-1.2.ebuild 827 RMD160 f669a8810b55f0470b3e03509df46adfde6843f5 SHA1 e1f63996db4b62246ef56cc113d7c369a3334f9b SHA256 c6d2dbed063dedad414bceb9380bcd3bfe742d449e4881c6ef77acaad93c5323
+MISC open3dqsar-1.2.ebuild~ 470 RMD160 6cbbdd58c29cc83a54832122b68d33c9cc5c4abe SHA1 f3cb30507d088ade8b98b54afb03f742cfac6087 SHA256 942bf9073b84c873d59686251bcef69ddf2066df98350243415657429de4f2bf
diff --git a/sci-chemistry/open3dqsar/open3dqsar-1.2.ebuild b/sci-chemistry/open3dqsar/open3dqsar-1.2.ebuild
new file mode 100644
index 0000000..4c77d32
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+++ b/sci-chemistry/open3dqsar/open3dqsar-1.2.ebuild
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+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=2
+
+inherit autotools
+
+DESCRIPTION="Pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs)"
+HOMEPAGE="http://www.open3dqsar.org/"
+SRC_URI="${P}.tar.gz"
+LICENSE="${PN}"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+RESTRICT="fetch"
+RDEPEND="virtual/blas
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+pkg_nofetch() {
+	elog "Register at ${HOMEPAGE}, then download ${SRC_URI} and place it in ${DISTDIR}."
+}
+
+src_prepare () {
+	eautoreconf || die
+}
+
+src_configure() {
+	# --with-atlas just makes it look for a generic blas/cblas/lapack interface
+	econf \
+		--with-atlas \
+		|| die
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die
+	dodoc AUTHORS ChangeLog README || die
+}
diff --git a/sci-chemistry/open3dqsar/open3dqsar-1.2.ebuild~ b/sci-chemistry/open3dqsar/open3dqsar-1.2.ebuild~
new file mode 100644
index 0000000..b88ce8f
--- /dev/null
+++ b/sci-chemistry/open3dqsar/open3dqsar-1.2.ebuild~
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+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils
+
+DESCRIPTION=""
+HOMEPAGE=""
+SRC_URI="${P}.tar.gz"
+LICENSE=""
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+RESTRICT="fetch"
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+pkg_nofetch() {
+	elog "Register at ${HOMEPAGE}, then download ${SRC_URI} and place it in ${DISTDIR}."
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die
+	dodoc AUTHORS README || die
+}