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 $f.pdb
end
On Sat, Nov 21, 2009 at 4:28 PM, Jack Shultz <[email protected]>
wrote:
> Noel,
>
> The main file is too big to send. Here is a file with 2 structures. I
> don't see any examples for using --seperate
> I tried doing this without and success
> babel test.pdb out.pdb --separate
>
> On Sat, Nov 21, 2009 at 2:59 PM, Noel O'Boyle <[email protected]> wrote:
>> Your usage of babel --filter is correct, however it won't work on a
>> PDB file as the entire PDB file is regarded by OpenBabel as a single
>> "Molecule". It's a good idea though, and maybe something we should
>> think about implementing. Feel free to file a feature request at
>> http://sourceforge.net/tracker/?atid=428743&group_id=40728&func=browse
>>
>> You didn't attach the PDB file so I can't test this, but you might
>> want to try the --separate option to split the PDB into disconnected
>> fragments.
>>
>> - Noel
>>
>> 2009/11/20 Jack Shultz <[email protected]>:
>>> Trying to filter a PDB file starting with this compound
>>>
>>> COMPND omega_1
>>> HETATM 1 C1 UNL 1 1.852 -3.133 1.682 1.00 0.00
>>> C
>>> HETATM 2 C2 UNL 1 0.996 -2.034 1.424 1.00 0.00
>>> C
>>> HETATM 3 C3 UNL 1 2.869 -2.681 2.494 1.00 0.00
>>> C
>>>
>>> I tried it two ways
>>>
>>> [boinc...@vps Ambinter_LL_3D_1-1]$ babel -ipdb Ambinter_LL.pdb -opdb
>>> omega_1.pdb --filter "COMPND='omega_1'"
>>> 0 molecules converted
>>> 52 info messages 12 audit log messages
>>> [boinc...@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
>>>
>>> ------------------------------------------------------------------------------
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>>
>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>
--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
------------------------------------------------------------------------------
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