Installing Decoy Finder under Mac OS X
DecoyFinder is a graphical tool which helps finding sets of decoy molecules for a given group of active ligands. It does so by finding molecules which have a similar number of rotational bonds, hydrogen bond acceptors, hydrogen bond donors, logP value and molecular weight, but are chemically different, which is defined by a maximum Tanimoto value threshold between active ligand and decoy molecule MACCS fingerprints. Optionally, a maximum Tanimoto value threshold can be set between decoys in order to assure chemical diversity in the decoy set.
- Python >= 2.5, < 3
- OpenBabel >= 2.3.0 with python bindings
- pybel (usually included with OpenBabel python bindings; also part of cinfony)
- PySide >= 1.0 (or PyQt4 >= 4.6 for PyQt4 version)
- Qt >= 4.5 (sometimes included with PySide or PyQt, depending on your platform; it might work with older versions of Qt)
I’m using Mac OS X 10.8 which comes with Python 2.7 installed, you also need to check where it is installed, you can check by typing
chrismacbookpro:~ swain$ python Python 2.7.2 (default, Oct 11 2012, 20:14:37) [GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import sys >>> print sys.path ['', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages', '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload', '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyObjC', '/Library/Python/2.7/site-packages’].
To do all the installation you need Xcode and the optional command line tools installed.
To install OpenBabel with python bindings you need to download the source code and follow these instructions. When I did this it installed the three files openbabel.py, pybel.py and _openbabel.so into usr/local/bin but I think they should be in the site-packages folder so I copied them there.
You can check is all OK by opening a python session in a Terminal window and typing
chrismacbookpro swain$ python Python 2.7.2 (default, Oct 11 2012, 20:14:37) [GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> >>> import openbabel >>> >>> import pybel >>>
If you get no errors then all should be OK.
PySide can be downloaded as a Mac OS X bianary and installed in the same location as Pybel.py etc. To install PySide in Mac OS X, you need to install both PySide and the appropriate Qt version. Qt should be installed in usr/local.
Once you have everything installed, download DecoyFinder from here, extract the contents of the archive to wherever you want.
swain$ python decoy_finder.py
I used this structure as the my “lead” and used the chembridge catalogue as a local file for the source of decoys.
You can follow the process in the Terminal window.
chrismacbookpro:~ swain$ python /Users/swain/Downloads/DecoyFinder-1.1/decoy_finder.py No icon theme set, using default: Tango starting thread started Looking for decoys! 1 decoys found 2 decoys found 3 decoys found 4 decoys found 5 decoys found 6 decoys found 7 decoys found 8 decoys found 9 decoys found 10 decoys found 11 decoys found 12 decoys found 13 decoys found 14 decoys found 15 decoys found 16 decoys found 17 decoys found 18 decoys found 19 decoys found 20 decoys found 21 decoys found 22 decoys found 23 decoys found 24 decoys found 25 decoys found 26 decoys found 27 decoys found 28 decoys found 29 decoys found 30 decoys found 31 decoys found 32 decoys found 33 decoys found 34 decoys found 35 decoys found 36 decoys found ('Decoy set completed for ', 'TestCompund1') All decoy sets complete Completed 1 of 1 decoy sets Found all wanted decoys