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initial files for POW python packages
- copied Mhp1/lib/python/Ligands/ghyd.py - copied some infra structure from GromacsWrapper UNTESTED...
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#!python | ||
"""Bootstrap setuptools installation | ||
If you want to use setuptools in your package's setup.py, just include this | ||
file in the same directory with it, and add this to the top of your setup.py:: | ||
from ez_setup import use_setuptools | ||
use_setuptools() | ||
If you want to require a specific version of setuptools, set a download | ||
mirror, or use an alternate download directory, you can do so by supplying | ||
the appropriate options to ``use_setuptools()``. | ||
This file can also be run as a script to install or upgrade setuptools. | ||
""" | ||
import sys | ||
DEFAULT_VERSION = "0.6c9" | ||
DEFAULT_URL = "http://pypi.python.org/packages/%s/s/setuptools/" % sys.version[:3] | ||
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md5_data = { | ||
'setuptools-0.6b1-py2.3.egg': '8822caf901250d848b996b7f25c6e6ca', | ||
'setuptools-0.6b1-py2.4.egg': 'b79a8a403e4502fbb85ee3f1941735cb', | ||
'setuptools-0.6b2-py2.3.egg': '5657759d8a6d8fc44070a9d07272d99b', | ||
'setuptools-0.6b2-py2.4.egg': '4996a8d169d2be661fa32a6e52e4f82a', | ||
'setuptools-0.6b3-py2.3.egg': 'bb31c0fc7399a63579975cad9f5a0618', | ||
'setuptools-0.6b3-py2.4.egg': '38a8c6b3d6ecd22247f179f7da669fac', | ||
'setuptools-0.6b4-py2.3.egg': '62045a24ed4e1ebc77fe039aa4e6f7e5', | ||
'setuptools-0.6b4-py2.4.egg': '4cb2a185d228dacffb2d17f103b3b1c4', | ||
'setuptools-0.6c1-py2.3.egg': 'b3f2b5539d65cb7f74ad79127f1a908c', | ||
'setuptools-0.6c1-py2.4.egg': 'b45adeda0667d2d2ffe14009364f2a4b', | ||
'setuptools-0.6c2-py2.3.egg': 'f0064bf6aa2b7d0f3ba0b43f20817c27', | ||
'setuptools-0.6c2-py2.4.egg': '616192eec35f47e8ea16cd6a122b7277', | ||
'setuptools-0.6c3-py2.3.egg': 'f181fa125dfe85a259c9cd6f1d7b78fa', | ||
'setuptools-0.6c3-py2.4.egg': 'e0ed74682c998bfb73bf803a50e7b71e', | ||
'setuptools-0.6c3-py2.5.egg': 'abef16fdd61955514841c7c6bd98965e', | ||
'setuptools-0.6c4-py2.3.egg': 'b0b9131acab32022bfac7f44c5d7971f', | ||
'setuptools-0.6c4-py2.4.egg': '2a1f9656d4fbf3c97bf946c0a124e6e2', | ||
'setuptools-0.6c4-py2.5.egg': '8f5a052e32cdb9c72bcf4b5526f28afc', | ||
'setuptools-0.6c5-py2.3.egg': 'ee9fd80965da04f2f3e6b3576e9d8167', | ||
'setuptools-0.6c5-py2.4.egg': 'afe2adf1c01701ee841761f5bcd8aa64', | ||
'setuptools-0.6c5-py2.5.egg': 'a8d3f61494ccaa8714dfed37bccd3d5d', | ||
'setuptools-0.6c6-py2.3.egg': '35686b78116a668847237b69d549ec20', | ||
'setuptools-0.6c6-py2.4.egg': '3c56af57be3225019260a644430065ab', | ||
'setuptools-0.6c6-py2.5.egg': 'b2f8a7520709a5b34f80946de5f02f53', | ||
'setuptools-0.6c7-py2.3.egg': '209fdf9adc3a615e5115b725658e13e2', | ||
'setuptools-0.6c7-py2.4.egg': '5a8f954807d46a0fb67cf1f26c55a82e', | ||
'setuptools-0.6c7-py2.5.egg': '45d2ad28f9750e7434111fde831e8372', | ||
'setuptools-0.6c8-py2.3.egg': '50759d29b349db8cfd807ba8303f1902', | ||
'setuptools-0.6c8-py2.4.egg': 'cba38d74f7d483c06e9daa6070cce6de', | ||
'setuptools-0.6c8-py2.5.egg': '1721747ee329dc150590a58b3e1ac95b', | ||
'setuptools-0.6c9-py2.3.egg': 'a83c4020414807b496e4cfbe08507c03', | ||
'setuptools-0.6c9-py2.4.egg': '260a2be2e5388d66bdaee06abec6342a', | ||
'setuptools-0.6c9-py2.5.egg': 'fe67c3e5a17b12c0e7c541b7ea43a8e6', | ||
'setuptools-0.6c9-py2.6.egg': 'ca37b1ff16fa2ede6e19383e7b59245a', | ||
} | ||
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import sys, os | ||
try: from hashlib import md5 | ||
except ImportError: from md5 import md5 | ||
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def _validate_md5(egg_name, data): | ||
if egg_name in md5_data: | ||
digest = md5(data).hexdigest() | ||
if digest != md5_data[egg_name]: | ||
print >>sys.stderr, ( | ||
"md5 validation of %s failed! (Possible download problem?)" | ||
% egg_name | ||
) | ||
sys.exit(2) | ||
return data | ||
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def use_setuptools( | ||
version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir, | ||
download_delay=15 | ||
): | ||
"""Automatically find/download setuptools and make it available on sys.path | ||
`version` should be a valid setuptools version number that is available | ||
as an egg for download under the `download_base` URL (which should end with | ||
a '/'). `to_dir` is the directory where setuptools will be downloaded, if | ||
it is not already available. If `download_delay` is specified, it should | ||
be the number of seconds that will be paused before initiating a download, | ||
should one be required. If an older version of setuptools is installed, | ||
this routine will print a message to ``sys.stderr`` and raise SystemExit in | ||
an attempt to abort the calling script. | ||
""" | ||
was_imported = 'pkg_resources' in sys.modules or 'setuptools' in sys.modules | ||
def do_download(): | ||
egg = download_setuptools(version, download_base, to_dir, download_delay) | ||
sys.path.insert(0, egg) | ||
import setuptools; setuptools.bootstrap_install_from = egg | ||
try: | ||
import pkg_resources | ||
except ImportError: | ||
return do_download() | ||
try: | ||
pkg_resources.require("setuptools>="+version); return | ||
except pkg_resources.VersionConflict, e: | ||
if was_imported: | ||
print >>sys.stderr, ( | ||
"The required version of setuptools (>=%s) is not available, and\n" | ||
"can't be installed while this script is running. Please install\n" | ||
" a more recent version first, using 'easy_install -U setuptools'." | ||
"\n\n(Currently using %r)" | ||
) % (version, e.args[0]) | ||
sys.exit(2) | ||
else: | ||
del pkg_resources, sys.modules['pkg_resources'] # reload ok | ||
return do_download() | ||
except pkg_resources.DistributionNotFound: | ||
return do_download() | ||
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def download_setuptools( | ||
version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir, | ||
delay = 15 | ||
): | ||
"""Download setuptools from a specified location and return its filename | ||
`version` should be a valid setuptools version number that is available | ||
as an egg for download under the `download_base` URL (which should end | ||
with a '/'). `to_dir` is the directory where the egg will be downloaded. | ||
`delay` is the number of seconds to pause before an actual download attempt. | ||
""" | ||
import urllib2, shutil | ||
egg_name = "setuptools-%s-py%s.egg" % (version,sys.version[:3]) | ||
url = download_base + egg_name | ||
saveto = os.path.join(to_dir, egg_name) | ||
src = dst = None | ||
if not os.path.exists(saveto): # Avoid repeated downloads | ||
try: | ||
from distutils import log | ||
if delay: | ||
log.warn(""" | ||
--------------------------------------------------------------------------- | ||
This script requires setuptools version %s to run (even to display | ||
help). I will attempt to download it for you (from | ||
%s), but | ||
you may need to enable firewall access for this script first. | ||
I will start the download in %d seconds. | ||
(Note: if this machine does not have network access, please obtain the file | ||
%s | ||
and place it in this directory before rerunning this script.) | ||
---------------------------------------------------------------------------""", | ||
version, download_base, delay, url | ||
); from time import sleep; sleep(delay) | ||
log.warn("Downloading %s", url) | ||
src = urllib2.urlopen(url) | ||
# Read/write all in one block, so we don't create a corrupt file | ||
# if the download is interrupted. | ||
data = _validate_md5(egg_name, src.read()) | ||
dst = open(saveto,"wb"); dst.write(data) | ||
finally: | ||
if src: src.close() | ||
if dst: dst.close() | ||
return os.path.realpath(saveto) | ||
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def main(argv, version=DEFAULT_VERSION): | ||
"""Install or upgrade setuptools and EasyInstall""" | ||
try: | ||
import setuptools | ||
except ImportError: | ||
egg = None | ||
try: | ||
egg = download_setuptools(version, delay=0) | ||
sys.path.insert(0,egg) | ||
from setuptools.command.easy_install import main | ||
return main(list(argv)+[egg]) # we're done here | ||
finally: | ||
if egg and os.path.exists(egg): | ||
os.unlink(egg) | ||
else: | ||
if setuptools.__version__ == '0.0.1': | ||
print >>sys.stderr, ( | ||
"You have an obsolete version of setuptools installed. Please\n" | ||
"remove it from your system entirely before rerunning this script." | ||
) | ||
sys.exit(2) | ||
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req = "setuptools>="+version | ||
import pkg_resources | ||
try: | ||
pkg_resources.require(req) | ||
except pkg_resources.VersionConflict: | ||
try: | ||
from setuptools.command.easy_install import main | ||
except ImportError: | ||
from easy_install import main | ||
main(list(argv)+[download_setuptools(delay=0)]) | ||
sys.exit(0) # try to force an exit | ||
else: | ||
if argv: | ||
from setuptools.command.easy_install import main | ||
main(argv) | ||
else: | ||
print "Setuptools version",version,"or greater has been installed." | ||
print '(Run "ez_setup.py -U setuptools" to reinstall or upgrade.)' | ||
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def update_md5(filenames): | ||
"""Update our built-in md5 registry""" | ||
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import re | ||
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for name in filenames: | ||
base = os.path.basename(name) | ||
f = open(name,'rb') | ||
md5_data[base] = md5(f.read()).hexdigest() | ||
f.close() | ||
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data = [" %r: %r,\n" % it for it in md5_data.items()] | ||
data.sort() | ||
repl = "".join(data) | ||
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import inspect | ||
srcfile = inspect.getsourcefile(sys.modules[__name__]) | ||
f = open(srcfile, 'rb'); src = f.read(); f.close() | ||
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match = re.search("\nmd5_data = {\n([^}]+)}", src) | ||
if not match: | ||
print >>sys.stderr, "Internal error!" | ||
sys.exit(2) | ||
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src = src[:match.start(1)] + repl + src[match.end(1):] | ||
f = open(srcfile,'w') | ||
f.write(src) | ||
f.close() | ||
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if __name__=='__main__': | ||
if len(sys.argv)>2 and sys.argv[1]=='--md5update': | ||
update_md5(sys.argv[2:]) | ||
else: | ||
main(sys.argv[1:]) | ||
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,28 @@ | ||
# POW package __init__.py | ||
# Copyright (c) 2010 Oliver Beckstein <[email protected]> | ||
# Released under the GNU Public License 3 (or higher, your choice) | ||
# See the file COPYING for details. | ||
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""" | ||
:mod:`pow` --- Computing the octanol/water partitioning coefficient | ||
=================================================================== | ||
The :mod:`pow` module helps in setting up and analyzing absolute free | ||
energy calculations of small molecules. By computing the hydration | ||
free energy and the solvation free energy in octanol one can compute | ||
the octanol/water partitioning coefficient, and important quantity | ||
that is used to characterize drug-like compounds. | ||
The simulations are performed with Gromacs_ 4.x | ||
.. _Gromacs: http://www.gromacs.org | ||
""" | ||
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__all__ = ['ghyd', 'config'] | ||
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import log | ||
logger = log.create('pow', 'pow.log') | ||
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import ghyd | ||
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