Reply – Re: Filter PDB with COMPND Identifier
Your Name
Subject
Message
or Cancel
In Reply To
Re: Filter PDB with COMPND Identifier
— by Jack Shultz-2 Jack Shultz-2
This will get us out of our pickle!

#!/bin/csh
    set a=`grep END ${1} | wc -l`
    set b=`expr $a - 2`
    csplit -k -s -n 6 -f omega_ ${1} '/^END/+1' '{'$b'}'
    foreach f ( omega_[0-9][0-9][0-9] )
      mv $f $f.pdb
    end


On Sat, Nov 21, 2009 at 4:28 PM, Jack Shultz <[hidden email]> wrote:

> Noel,
>
> The main file is too big to send. Here is a file with 2 structures. I
> don't see any examples for using --seperate
> I tried doing this without and success
> babel test.pdb out.pdb --separate
>
> On Sat, Nov 21, 2009 at 2:59 PM, Noel O'Boyle <[hidden email]> wrote:
>> Your usage of babel --filter is correct, however it won't work on a
>> PDB file as the entire PDB file is regarded by OpenBabel as a single
>> "Molecule". It's a good idea though, and maybe something we should
>> think about implementing. Feel free to file a feature request at
>> http://sourceforge.net/tracker/?atid=428743&group_id=40728&func=browse
>>
>> You didn't attach the PDB file so I can't test this, but you might
>> want to try the --separate option to split the PDB into disconnected
>> fragments.
>>
>> - Noel
>>
>> 2009/11/20 Jack Shultz <[hidden email]>:
>>> Trying to filter a PDB file starting with this compound
>>>
>>> COMPND    omega_1
>>> HETATM    1  C1  UNL     1       1.852  -3.133   1.682  1.00  0.00           C
>>> HETATM    2  C2  UNL     1       0.996  -2.034   1.424  1.00  0.00           C
>>> HETATM    3  C3  UNL     1       2.869  -2.681   2.494  1.00  0.00           C
>>>
>>> I tried it two ways
>>>
>>> [boincadm@vps Ambinter_LL_3D_1-1]$ babel -ipdb Ambinter_LL.pdb -opdb
>>> omega_1.pdb --filter "COMPND='omega_1'"
>>> 0 molecules converted
>>> 52 info messages 12 audit log messages
>>> [boincadm@vps Ambinter_LL_3D_1-1]$ babel -ipdb Ambinter_LL.pdb -opdb
>>> omega_1.pdb --filter "title='omega_1'"
>>> 0 molecules converted
>>> 52 info messages 12 audit log messages
>>>
>>>
>>>
>>> --
>>> Jack
>>>
>>> http://drugdiscoveryathome.com
>>> http://hydrogenathome.org
>>>
>>> ------------------------------------------------------------------------------
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>>> trial. Simplify your report design, integration and deployment - and focus on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>
>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>



--
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss