ADL: Lamarckian Algorithm reference

Arneh Babakhani ababakha at mccammon.ucsd.edu
Mon Oct 8 10:27:40 PDT 2007


Does anybody have a good copy of this reference:
Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, W. E., 
Belew, R. K. and Olson, A. J. (1998), Automated Docking Using a 
Lamarckian Genetic Algorithm and and Empirical Binding Free Energy 
Function 
<http://www3.interscience.wiley.com/cgi-bin/abstract/76804/ABSTRACT> /J. 
Computational Chemistry/, *19*: 1639-1662.

(The pdf from the journal's site lacks a lot of the subscripts, for some 
reason.),

Thanks,

Arneh



Jack Shultz wrote:
> Hello AutoDockers!
>
> I got some advice on this issue, but still don't understand how to import
> MolKit module into python. I've tried it several ways first with pyinstaller
> then with cx Freeze
> 1) Pyinstaller I tried it first with python and using path=directory of
> MolKit, then I tried it using pythonsh because I figured that would do all
> the necessary imports. It generated the error bellow.
> 2) Then I tried Sargis suggestion on cx freeze, but I ended up with the
> familare message about "ImportError: No module named MolKit"
>
> Any suggestions appreciated!
>
> Jack
>
> setting PYTHONHOME environment
> I: computing EXE_dependencies
> I: Finding TCL/TK...
> I: found TCL/TK version 8.4
> I: testing for Zlib...
> I: ... Zlib available
> I: Testing for Unicode support...
> I: ... Unicode available
> I: testing for UPX...
> sh: upx: command not found
> I: ...UPX unavailable
> I: computing PYZ dependencies...
> [root at vps pyinstaller-1.3]# pythonsh Makespec.py --onefile
> /usr/local/MGLTools-1.4.6
> /mgltools_i86Linux2_1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py
> setting PYTHONHOME environment
> wrote /root/pyinstaller-1.3/prepare_ligand4/prepare_ligand4.spec
> now run Build.py to build the executable
> [root at vps pyinstaller-1.3]# pythonsh Build.py /root/pyinstaller-1.3
> /prepare_ligand4/prepare_ligand4.spec
> setting PYTHONHOME environment
> checking Analysis
> building because support/useUnicode.py changed
> running Analysis out0.toc
> Analyzing: support/_mountzlib.py
> Analyzing: support/useUnicode.py
> Analyzing: /usr/local/MGLTools-1.4.6
> /mgltools_i86Linux2_1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py
> Syntax error in /usr/local/MGLTools-1.4.6
> /mgltools_i86Linux2_1.4.6/MGLToolsPckgs/DejaVu/MaterialEditor.py
> ('invalid syntax',
> ('/usr/local/MGLTools-1.4.6/mgltools_i86Linux2_1.4.6/MGLToolsPckgs/DejaVu/MaterialEditor.py',
> 22, 1, '\r\n'))
> Traceback (most recent call last):
>   File "Build.py", line 839, in ?
>     build(sys.argv[1])
>   File "Build.py", line 76, in build
>     exec open(spec, 'r').read()+'\n'
>   File "<string>", line 2, in ?
>   File "Build.py", line 112, in __init__
>     self.__postinit__()
>   File "Build.py", line 94, in __postinit__
>     self.assemble()
>   File "Build.py", line 182, in assemble
>     analyzer.analyze_script(script)
>   File "/root/pyinstaller-1.3/mf.py", line 379, in analyze_script
>     return self.analyze_r('__main__')
>   File "/root/pyinstaller-1.3/mf.py", line 299, in analyze_r
>     newnms = self.analyze_one(name, nm, imptyp)
>   File "/root/pyinstaller-1.3/mf.py", line 333, in analyze_one
>     mod = self.doimport(nm, ctx, fqname)
>   File "/root/pyinstaller-1.3/mf.py", line 392, in doimport
>     mod = parent.doimport(nm)
>   File "/root/pyinstaller-1.3/mf.py", line 515, in doimport
>     mod = self.subimporter.getmod(nm)
>   File "/root/pyinstaller-1.3/mf.py", line 216, in getmod
>     mod = owner.getmod(nm)
>   File "/root/pyinstaller-1.3/mf.py", line 71, in getmod
>     co = compile(open(py[0], 'r').read()+'\n', py[0], 'exec')
>   File "/usr/local/MGLTools-1.4.6/mgltools_i86Linux2_1.4.6/MGLToolsPckgs/DejaVu/MaterialEditor.py",
> line 22
>
>     ^
> SyntaxError: invalid syntax
> ________________________________________________
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>
>   

-- 
--------------------------------------
Arneh Babakhani
McCammon Lab
Department of Chemistry & Biochemistry
University of California at San Diego
9500 Gilmand Dr MC 0365
La Jolla, CA 92093-0365
(619)895-6540
(858)534-4974 (FAX)
ababakha at mccammon.ucsd.edu
http://mccammon.ucsd.edu/~ababakha/



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