ADL: how to install from CVS??

Savani Anbalagan savani1987 at gmail.com
Tue Oct 30 04:01:52 PDT 2007


---------- Forwarded message ----------
From: Savani Anbalagan <savani1987 at gmail.com>
Date: 30 Oct 2007 16:16
Subject: how to install from CVS??
To: 4725EBCB.2060907 at scripps.edu


hi..

ok fine.. cvs i dint understant wat it means.. googled it got it meaning..
gr8....

How to update ADT in my sys?? how to install from CVS?

googling out ADT and cvs i got tis link
http://www.scripps.edu/~sanner/python/FAQ.html#cvsu<http://www.scripps.edu/%7Esanner/python/FAQ.html#cvsu>

which says

*Updating platform independent packages:*
To update packages under sys.prefix,
%cd sys.prefix/python2.3/site-packages
%cvs -d:pserver:anonymous at moses.scripps.edu: /export/cvs login
%cvs -z3 -d:pserver:anonymous at moses.scripps.edu:/export/cvs update packname
(for eg:packnames like DejaVu,Pmv,AutoDockTools,Vision etc)

*Updating platform dependent packages:*
To update packages under sys.exec_prefix you have to cvs checkout
packnameDIST as given below,
%cvs -d:pserver:anonymous at moses.scripps.edu: /export/cvs login
%cvs -z3 -d:pserver:anonymous at moses.scripps.edu:/export/cvs co packnameDIST
(for eg: packnames like opengltk,sff,mslib,stride etc)
And build and install them by yourself,
%cd packnameDIST
%python2.3 setup.py build
%python2.3 setup.py install --install-purelib="puredir"
--install-platlib="platdir"
puredir="sys.prefix/python2.3/site-packages"
platdir="sys.exec_prefix/python2.3/site-packages"



the system in which i hav installed is not connected to net... :-(
is there any patch which i can download and install in my system..

(my system config PIV 32bit OS: Open SUSE 10.0  )


Thanks..


With Regards,

Savani Anbalagan


Date: Mon, 29 Oct 2007 07:18:51 -0700
From: Ruth Huey <rhuey at scripps.edu>
Subject: Re: ADL: ADT 1.4.6 error
To: autodock at scripps.edu
Message-ID: <4725EBCB.2060907 at scripps.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Savani,
This problem was caused by a bug in MolKit/interactionDescriptor.py
which occurred in the case where the ligand had no hydrogen bonding atoms.
I have just repaired the problem and checked the correction into cvs.

Thank you  very much for your feedback and your patience!

        Ruth


Savani Anbalagan wrote:
> Hi autodockers...
>
> I am using ADT 1.4.6..
>
> my OS SUSE 10.0
>
> When i tried to analyze the rsults of docking by  option SHOW
INTERACTION..
>
>
>
> Python 2.4.2 (#2, Jan  6 2006, 13:20:42)
> [GCC 3.2.3 20030422 (Red Hat Linux 3.2.3-6)] on linux2
> Type "copyright", "credits" or "license()" for more information.
>
>     ****************************************************************
>     Personal firewall software may warn about the connection IDLE
>     makes to its subprocess using this computer's internal loopback
>     interface.  This connection is not visible on any external
>     interface and no data is sent to or received from the Internet.
>     ****************************************************************
>
> IDLE 1.1.2      ==== No Subprocess ====
>
>>>> ERROR *********************************************
>>>>
> Traceback (most recent call last):
>   File "/usr/local/MGLTOOLSS/MGLTools-1.4.6
/MGLToolsPckgs/ViewerFramework/VF.py",
> line 714, in tryto
>     result = apply( command, args, kw )
>   File "/usr/local/MGLTOOLSS/MGLTools-1.4.6
/MGLToolsPckgs/AutoDockTools/autoanalyzeCommands.py",
> line 1922, in doit
>     self.build()
>   File "/usr/local/MGLTOOLSS/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/autoanalyzeCommands.py",

> line 1759, in build
>     self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)
>   File "/usr/local/MGLTOOLSS/MGLTools-1.4.6
/MGLToolsPckgs/MolKit/interactionDescriptor.py",
> line 44, in __init__
>     self.build(detect_pi=detect_pi)
>   File "/usr/local/MGLTOOLSS/MGLTools-1.4.6
/MGLToolsPckgs/MolKit/interactionDescriptor.py",
> line 51, in build
>     self.buildHydrogenBonds()           #
>   File "/usr/local/MGLTOOLSS/MGLTools-1.4.6
/MGLToolsPckgs/MolKit/interactionDescriptor.py",
> line 117, in buildHydrogenBonds
>     lig_gly_res = d['lig_hb_gly_res'] = lig_hb_res.get(lambda x:
> x.type=='GLY')
> UnboundLocalError: local variable 'lig_hb_res' referenced before
assignment
> Plz help..
>
>
>
>
> WIth Regards,
>
>
> Savani Anbalagan
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>

-- 
Take Care,
Savani Anbalagan
http://del.icio.us/savani1987/?setcount=100
http://savaniabel.blogspot.com


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