Filter PDB with COMPND Identifier

Next Topic
 
classic Classic list List threaded Threaded
10 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Filter PDB with COMPND Identifier

Jack Shultz-2
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
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Filter PDB with COMPND Identifier

Jack Shultz-2
Another thing I did was replace all the COMPND strings with title.
Still no luck filtering.

On Fri, Nov 20, 2009 at 2:23 PM, Jack Shultz <[hidden email]> wrote:

> 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
>



--
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
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Filter PDB with COMPND Identifier

Noel O'Boyle
Administrator
In reply to this post by Jack Shultz-2
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
>

------------------------------------------------------------------------------
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
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Filter PDB with COMPND Identifier

Jack Shultz-2
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

------------------------------------------------------------------------------
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

test.pdb (12K) Download Attachment
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Filter PDB with COMPND Identifier

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
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

John

Smitha469
In reply to this post by Jack Shultz-2
I truly prize your function, Wonderful post. bfcegkdcbdkdckee
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Good info

Pharma714
In reply to this post by Jack Shultz-2
Very nice site!  [url=http://apeyixo2.com/ysyaxvs/2.html]cheap goods[/url]
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

John

Smithk795
In reply to this post by Jack Shultz-2
You completed a number of fine points there. I did a search on the theme and found the majority of folks will agree with your blog. aggbekbdedfddeec
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

John

Smithg559
In reply to this post by Jack Shultz-2
Real nice design and great articles, nothing else we want  bdddkfedadfdfbkk
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

viagra online pharmacy

online
In reply to this post by Jack Shultz-2
You actually make it seem really easy together with your presentation but I in finding this matter to be really something that I feel I would by no means understand. It sort of feels too complex and extremely broad for me. I'm looking forward for your next publish, Ill try to get the cling of it!
Loading...