Commit 26c1b801 authored by Andreas Tille's avatar Andreas Tille

New upstream version 1.5.7

parent 21b4c4d4
This package was debianized by Steffen Moeller <moeller@debian.org> on
Thu, 10 Jul 2008 00:03:24 +0200
It was downloaded from http://mgltools.scripps.edu
Upstream Authors:
The main development is performed by the researchers
and developers at the
Molecular Graphics Laboratory <mgltools@scripps.edu>
led by
Michael F. Sanner <sanner@scripps.edu>
with contributions by
Anna Omelchenko <annao@scripps.edu>
Guillaume Vareille <vareille@scripps.edu>
Copyright:
The respective authors and the Scripps Research Institute
Copyright 1989-2013 Michael Sanner <sanner@scripps.edu>
License:
All files distributed or redistributed in this package are subject
to the here presented license, regardless of the information
that is explicitly stated or omitted in the respective files
themselves. The original copyright holders have made respective
agreements regarding this redistribution.
This software is copyrighted by Michel F. Sanner (sanner@scripps.edu) and TSRI.
The following terms apply to all files associated with the software
unless explicitly disclaimed in individual files.
MGLTOOLS SOFTWARE LICENSE AGREEMENT.
1. Grant Of Limited License; Software Use Restrictions. The programs
received by you will be used only for NON COMMERCIAL purposes.
......@@ -41,11 +13,11 @@ agreements regarding this redistribution.
For any question regarding license agreements, please contact
Michel Sanner:
TSRI, Molecular Biology Department, TCP 26,
10550 North Torrey Pines Road, La Jolla, CA 92037
sanner@scripps.edu
tel (858) 784-7742
fax (858) 784-2341
TSRI, Molecular Biology Department, TCP 26,
10550 North Torrey Pines Road, La Jolla, CA 92037
sanner@scripps.edu
tel (858) 784-7742
fax (858) 784-2341
2. COMMERCIAL USAGE is defined as revenues generating activities. These
include using this software for consulting activities and selling
......@@ -73,36 +45,3 @@ agreements regarding this redistribution.
IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE
NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
MODIFICATIONS.
The Debian packaging is Copyright (C) 2007-2008,
Steffen Moeller <moeller@debian.org>
and is licensed under the GPL, see '/usr/share/common-licenses/GPL'.
In addition to the license above, the Debian project also got the explicit
permission from the copyright owner to distribute the software:
Date: Mon, 20 May 2013 10:07:13 -0700
From: Michel Sanner <sanner@scripps.edu>
To: Thorsten Alteholz <debian-med@alteholz.de>
Cc: "annao >> Anna Omelchenko" <annao@scripps.edu>
Subject: Re: mgltools license
Hello Thorsten
Sorry for not following up this earlier. We are delighted to have Debian
include the MGLTools in their distribution.
So you need us to amend the License text or will this email suffice ?
Thanks
--
-----------------------------------------------------------------------
o
/ Michel F. Sanner Ph.D. The Scripps Research Institute
o Associate Professor Department of Molecular Biology
\ 10550 North Torrey Pines Road
o Tel. (858) 784-7742 La Jolla, CA 92037, TPC 26
/ Fax. (858) 784-2341
o sanner@scripps.edu http://www.scripps.edu/~sanner
-----------------------------------------------------------------------
include MANIFEST.in
include version.py
include bhtree/*.i
include src/*
exclude bhtree/bhtreelib.py
include CVS/*
include bhtree/CVS/*
include bhtree/Tests/CVS/*
include src/CVS/*
include bhtree/doc.tar.gz
include LICENSE
This package contains a Distutils interface for building bhtree Python
extension and creating a source distribution.
SWIG (version 1.3.20 or higher) is used for generating a C wrapper code
(can be downloaded from www.swig.org).
To build and install the extension:
python2.4 setup.py install
This creates bhtreelib.py (python shadow classes) and
_bhtreelib.so in build/lib.<platform_specifier>/bhtree .
bhtree/Tests is copied to build/lib.<platform_specifier>/bhtree.
The bhtree package is then installed in
sys.exec_prefix/lib/python2.4/site-packages.
To specify the install directory use --install-platlib option:
python2.4 setup.py install --install-platlib=INSTALL_DIR
To build the extension only:
python2.4 setup.py build
this will build bhtree python extension in build/lib.<platform_specifier>/bhtree.
To build the distribution:
python2.4 setup.py sdist
Testing of the installed package:
tester bhtree
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# x,y,z and bondOrderRadius for cv.pdb
pts = [
(0.601000, -1.594000, -0.306000, 0.676000),
(-0.339000, -1.512000, -1.485000, 0.762000),
(-0.759000, -0.072000, -1.891000, 0.762000),
(0.513000, 0.787000, -2.119000, 0.762000),
(1.489000, 0.746000, -0.907000, 0.762000),
(2.782000, 1.566000, -1.187000, 0.762000),
(3.854000, 1.494000, -0.069000, 0.762000),
(4.885000, 2.443000, -0.013000, 0.762000),
(5.866000, 2.353000, 0.972000, 0.762000),
(5.834000, 1.320000, 1.901000, 0.762000),
(4.820000, 0.369000, 1.854000, 0.762000),
(3.831000, 0.440000, 0.870000, 0.762000),
(2.689000, -0.609000, 0.878000, 0.762000),
(1.840000, -0.720000, -0.439000, 0.762000),
(4.964000, 3.475000, -0.916000, 0.640000),
(-1.672000, 0.597000, -0.912000, 0.676000),
(-3.162000, 0.169000, -0.819000, 1.053000),
(-3.261000, -1.094000, -0.408000, 0.640000),
(-3.727000, 0.205000, -2.026000, 0.640000),
(-3.960000, 1.089000, 0.162000, 0.676000),
(-4.589000, 0.000000, 2.337000, 0.762000),
(-3.626000, 0.955000, 1.623000, 0.762000),
(-4.169000, 2.509000, -0.278000, 0.762000),
(-5.547000, 3.062000, 0.117000, 0.762000),
(0.805000, -3.010000, 0.163000, 0.762000),
(-0.334000, -3.935000, -0.316000, 0.762000),
(-0.149000, -5.389000, 0.134000, 0.762000),
(-5.635000, 0.355000, 2.282000, 0.352000),
(-4.559000, -1.020000, 1.911000, 0.352000),
(-4.332000, -0.090000, 3.408000, 0.352000),
(-3.651000, 1.931000, 2.144000, 0.352000),
(-2.588000, 0.593000, 1.743000, 0.352000),
(-3.365000, 3.160000, 0.115000, 0.352000),
(-4.079000, 2.579000, -1.377000, 0.352000),
(-5.681000, 3.095000, 1.214000, 0.352000),
(-5.682000, 4.093000, -0.257000, 0.352000),
(-6.369000, 2.453000, -0.302000, 0.352000),
(1.783000, -3.397000, -0.185000, 0.352000),
(0.870000, -3.073000, 1.262000, 0.352000),
(-1.305000, -3.563000, 0.061000, 0.352000),
(-0.410000, -3.911000, -1.420000, 0.352000),
(-0.978000, -6.025000, -0.226000, 0.352000),
(0.790000, -5.823000, -0.258000, 0.352000),
(-0.123000, -5.477000, 1.236000, 0.352000),
(0.146000, -1.992000, -2.358000, 0.352000),
(-1.237000, -2.132000, -1.306000, 0.352000),
(-1.294000, -0.132000, -2.857000, 0.352000),
(1.036000, 0.416000, -3.022000, 0.352000),
(0.238000, 1.832000, -2.359000, 0.352000),
(0.969000, 1.250000, -0.067000, 0.352000),
(3.245000, 1.216000, -2.130000, 0.352000),
(2.502000, 2.620000, -1.374000, 0.352000),
(6.660000, 3.085000, 1.017000, 0.352000),
(6.597000, 1.257000, 2.664000, 0.352000),
(3.130000, -1.594000, 1.119000, 0.352000),
(2.018000, -0.380000, 1.727000, 0.352000),
(2.487000, -1.176000, -1.215000, 0.352000),
(4.808000, -0.421000, 2.592000, 0.352000),
(-1.198000, 0.611000, -0.002000, 0.352000),
(5.728000, 4.017000, -0.706000, 0.352000),
]
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#
#################################################################
# Author: Sowjanya Karnati
#################################################################
#
#Purpose:To update dependencies list
#
# $Id: test_dependencies.py,v 1.2 2006/03/15 21:38:58 sowjanya Exp $
from mglutil.TestUtil.Tests.dependenciestest import DependencyTester
import unittest
d = DependencyTester()
result_expected =[]
class test_dep(unittest.TestCase):
def test_dep_1(self):
result = d.rundeptester('bhtree')
if result !=[]:
print "\nThe Following Packages are not present in CRITICAL or NONCRITICAL DEPENDENCIES of bhtree :\n %s" %result
self.assertEqual(result,result_expected)
else:
self.assertEqual(result,result_expected)
if __name__ == '__main__':
unittest.main()
from bhtreelib import *
__MGLTOOLSVersion__ = '1-4alpha3'
CRITICAL_DEPENDENCIES = ['mglutil']
NONCRITICAL_DEPENDENCIES = []
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autodocktools and other modules of MGLtools for Debian
======================================================
This package aims at providing the complete infrastructure for ligand
screening with Debian Linux. It is part of the MGL (Molecular Graphics
Labs at Scripps) Python tools set for the computational and visual
interaction of protein structures and their ligands.
The Debian community shall thank Sargis Dallakyan <sargis@scripps.edu>
for his help in easing the compatibility with Debian by accepting our
patches and providing more himself. Also, the leader of the Molecular
Graphics Labs, Prof. Michael Sanner, is thanked for his support.
Please be continuously reminded that that closer a software gets towards
identifying or further describing functional compounds in medicine,
the harder it is to get access to free (as in beer) solutions. And it
certainly does not get much closer than with the AutoDockToolkit. To
have the AutoDockToolkit with Debian is special and good for the world
as it spawns the development of new drugs. We will need to wait a bit
longer for a DFSG compatible license, though.
If you are a regular user of this package, your feedback to us
packagers would much appreciated. The packaging is organised
via the Debian-Med alioth project that has its own portal on
http://debian-med.alioth.debian.org.
-- Steffen Moeller <moeller@debian.org> Sun, 20 Jul 2008 00:33:11 +0200
Any package of the MGLtools suite
=================================
The URL presented in debian/watch guides to a tar file
as the source distribution of the MGLtools set. That tar file
has a subdirectory MGLPACKS that comprises many tar files
itself, each representing a distinguished Python module.
For the packaging of the AutoDockTool kit, the maintainers
have decided to package each module individually, to foster
the collaboration between similar applications.
The maintainers of the Debian package may decide to release
interim version from the upstream CVS source repository,
instead of waiting for an official release by the upstream
developers.
For further details on how to prepare the source for the
packaging, please refer to
http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/BUILD?op=file&rev=0&sc=0
-- Steffen Moeller <moeller@debian.org>
mgltools-bhtree (1.5.7-1) unstable; urgency=medium
* New upstream version (Closes: #767144,#783547,
lp:#821299,lp:1386091,lp:#1386163,lp:#1492762)
-- Steffen Moeller <moeller@debian.org> Fri, 08 Jul 2016 17:53:57 +0200
mgltools-bhtree (1.5.7~rc1+cvs.20140424-1) unstable; urgency=medium
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Thu, 24 Apr 2014 17:40:44 +0200
mgltools-bhtree (1.5.7~rc1~cvs.20130917-1) unstable; urgency=low
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Tue, 17 Sep 2013 14:47:39 +0200
mgltools-bhtree (1.5.7~rc1~cvs.20130519-1) unstable; urgency=low
* New upstream version.
* debian/control: remove DM-Upload-Allowed
* debian/copyright: add permission for debian to distribute mgltools
-- Thorsten Alteholz <debian@alteholz.de> Sun, 19 May 2013 12:00:00 +0200
mgltools-bhtree (1.5.6~rc3~cvs.20120601-1) unstable; urgency=low
* New upstream version.
* debian/rules: add call to dh_numpy
* debian/control: bump standard to 3.9.3
-- Thorsten Alteholz <debian@alteholz.de> Fri, 01 Jun 2012 18:00:00 +0200
mgltools-bhtree (1.5.6~rc3~cvs.20120206-1) unstable; urgency=low
* New upstream version.
* debian/control: vcs fields corrected
-- Thorsten Alteholz <debian@alteholz.de> Mon, 06 Feb 2012 18:00:00 +0100
mgltools-bhtree (1.5.6~rc2+cvs.20111222-1) unstable; urgency=low
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Thu, 22 Dec 2011 17:10:07 +0100
mgltools-bhtree (1.5.6~rc2+cvs.20110926-1) unstable; urgency=low
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Tue, 27 Sep 2011 10:58:09 +0200
mgltools-bhtree (1.5.6~rc1+cvs.20110617-1) unstable; urgency=low
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Fri, 17 Jun 2011 01:20:15 +0200
mgltools-bhtree (1.5.6~rc1+cvs.20110615-1) unstable; urgency=low
* New upstream version.
* debian/control:
- add myself to Uploaders:
- Standards-Version: 3.9.2 (no changes needed)
* debian/copyright: word copyright needed in text
-- Thorsten Alteholz <debian@alteholz.de> Wed, 15 Jun 2011 21:43:36 +0200
mgltools-bhtree (1.5.4.cvs.20100912-3) unstable; urgency=low
* debian/control: XS-Python-Version: >= 2.6
Closes: #623907
-- Andreas Tille <tille@debian.org> Tue, 26 Apr 2011 15:40:55 +0200
mgltools-bhtree (1.5.4.cvs.20100912-2) unstable; urgency=low
* Debhelper 8 (control+compat)
* debian/source/format: 3.0 (quilt)
* debian/control: Build-Depends: python-all-dev (>= 2.6) to enable
python-support2
* debian/rules: switch to short dh syntax which makes
dh_python2 easy
Closes: #616887
* debian/rules: Iterate over Python versions
-- Andreas Tille <tille@debian.org> Thu, 07 Apr 2011 12:27:24 +0200
mgltools-bhtree (1.5.4.cvs.20100912-1) unstable; urgency=low
* New upstream version.
* Adjusted dependencies (Closes: #596318).
-- Steffen Moeller <moeller@debian.org> Sun, 12 Sep 2010 00:20:31 +0200
mgltools-bhtree (1.5.4.cvs.20090603-2) UNRELEASED; urgency=low
* debian/control:
- Enhances: autodocktools
- debhelper 7
- Standards-Version: 3.8.3 (no changes needed)
-- Andreas Tille <tille@debian.org> Fri, 16 Oct 2009 22:36:21 +0200
mgltools-bhtree (1.5.4.cvs.20090603-1) unstable; urgency=low
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Wed, 03 Jun 2009 11:48:19 +0200
mgltools-bhtree (1.5.4.cvs.20090528-1) unstable; urgency=low
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Thu, 28 May 2009 21:41:39 +0200
mgltools-bhtree (1.5.4.cvs.20090514-1) unstable; urgency=low
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Thu, 14 May 2009 21:46:31 +0200
mgltools-bhtree (1.5.4.cvs.20081126-1) unstable; urgency=low
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Wed, 26 Nov 2008 14:43:09 +0100
mgltools-bhtree (1.5.2.cvs.20081109-1) unstable; urgency=low
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Sun, 09 Nov 2008 15:02:29 +0100
mgltools-bhtree (1.5.2.cvs.20080731-1) unstable; urgency=low
* Initial release, contributes to closing ITP #458811.
-- Steffen Moeller <moeller@debian.org> Thu, 31 Jul 2008 21:59:55 +0200
Source: mgltools-bhtree
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>,
Andreas Tille <tille@debian.org>,
Thorsten Alteholz <debian@alteholz.de>
Section: non-free/science
XS-Autobuild: yes
Priority: optional
Build-Depends: debhelper (>= 9),
python-all-dev,
python-numpy,
swig,
dh-python
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/mgltools/bhtree/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mgltools/bhtree/trunk/
Homepage: http://mgltools.scripps.edu/
X-Python-Version: >= 2.5
Package: mgltools-bhtree
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
${python:Depends}
Enhances: autodocktools
Description: Bhtree library extension module
This package is part of the mgltools set of Python libraries which
provide an infrastructure for the analysis of protein structures and
their docking of chemical compounds.
.
Python binding for looking Barnes-Hut tree code used for finding
neighboring points (e.g. when building bonds by distance).
#!/usr/bin/make -f
# -*- makefile -*-
# debian/rules for mgltools-bhtree
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
BRANCH=`cat debian/get-orig-source/current-branch`
RCVERSION=`cat debian/get-orig-source/rc-version`
SRC=bhtreeDIST
PYVERS := $(shell pyversions -vs)
%:
dh $@ --with python2
override_dh_clean:
dh_clean
find . -name CVS -a -type d| xargs -r rm -r
rm -rf build build-stamp debian/Pmv
rm -rf debian/tmpbuild
rm -rf bhtree/bhtreelib.py bhtree/bhtreelib_wrap.c
override_dh_auto_build:
for i in $(PYVERS); do \
python$$i setup.py install --install-platlib=`pwd`/debian/tmpbuild; \
done
override_dh_install:
dh_install
dh_numpy
get-orig-source:
./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION)
version=3
http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz
# setup.py - Distutils interface for building Bhtree Python extension and
# creating a distribution.
from distutils.core import setup, Extension
from distutils.command.build import build
from distutils.command.sdist import sdist
import sys
from os import path
pack_name = "bhtree"
ext_name = "_bhtreelib"
#source = [path.join(pack_name, "bhtreelib.i"), path.join(pack_name, "bhtree.c")]
source = [path.join(pack_name, "bhtreelib.i"), path.join("src", "bhtree.c")]
#include_dirs = [path.join(".",pack_name)]
import numpy
numpy_include = numpy.get_include()
include_dirs = [path.join(".", "src"), numpy_include]
#if sys.platform == "darwin":
#include_dirs.append("/usr/include/sys") # for malloc.h
# Change the order of commands that are called by "build"
# so that "build_py" command is called after "build_ext". In this case
# "build_py" will install (copy to the build directory) python
# modules generated by "build_ext'.
class modified_build(build):
sub_commands = [('build_clib', build.has_c_libraries),
('build_ext', build.has_ext_modules),
('build_py', build.has_pure_modules),
('build_scripts', build.has_scripts),
]
# Overwrite the prune_file_list method of sdist to not
# remove automatically the RCS/CVS directory from the distribution.
class modified_sdist(sdist):
def prune_file_list(self):
build = self.get_finalized_command('build')
base_dir = self.distribution.get_fullname()
self.filelist.exclude_pattern(None, prefix=build.build_base)
self.filelist.exclude_pattern(None, prefix=base_dir)
try:
from version import VERSION
except:
VERSION = "1.0"
# setup()
dist = setup(name="bhtree",
version=VERSION,
description = "Bhtree library extension module",
author = "Molecular Graphics Laboratory",
author_email = "mgltools@scripps.edu",
url = "http://www.scripps.edu/~sanner/python/packager.html",
py_modules = ['bhtree.bhtreelib', 'bhtree.__init__'],
packages = ["bhtree.Tests"],
cmdclass = {"build" : modified_build,
'sdist' : modified_sdist},
ext_package = pack_name,
ext_modules = [Extension (ext_name, source,
include_dirs = include_dirs,
#define_macros = [('UNIX', None),],
) ] ,)
# cp built .so from ./build/lib.platform to ./pack_name/ - for testing.
## from distutils.util import get_platform
## from distutils.file_util import copy_file
## plat_specifier = ".%s-%s" % (get_platform(), sys.version[0:3])
## orig_ext = path.join(".", "build", "lib"+plat_specifier , pack_name, ext_name+".so")
## cp_ext = path.join(pack_name, ext_name+".so")
## if path.isfile(orig_ext):
## copy_file(orig_ext, cp_ext, update=1)
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VERSION="1.5.6"
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