How do you keep "comment-type" information ? (from an SDF file)

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

How do you keep "comment-type" information ? (from an SDF file)

ashika
Hello all,

I am in the possession of an SDF file containing a chemical library. In this file, each molecule is identified by and id number. I am wondering if this information can be kept when splitting or acting upon this file. So far I have not found a way.

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

Re: How do you keep "comment-type" information ? (from an SDF file)

Fredrik Wallner
Hi,

The information is key within open babel, so whether you see it in the end depends on the output format. If you keep the files as SDFiles the information should be preserved. If there are a few properties you would like to keep, you can also add them to the title with the option --append, see http://openbabel.org/wiki/--append

Kind regards,
Fredrik

> 2 dec. 2015 kl. 16:55 skrev ashika <[hidden email]>:
>
> Hello all,
>
> I am in the possession of an SDF file containing a chemical library. In this
> file, each molecule is identified by and id number. I am wondering if this
> information can be kept when splitting or acting upon this file. So far I
> have not found a way.
>
> Thanks,
> Ashika
>
>
>
> --
> View this message in context: http://forums.openbabel.org/How-do-you-keep-comment-type-information-from-an-SDF-file-tp4659076.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss


------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
_______________________________________________
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: How do you keep "comment-type" information ? (from an SDF file)

Phil Evans
(Apologies to list, my first response was accidentally off-list)

Ashika sent me a sample, which is below.  If the tag of interest is "mol.id" (i.e. dot in string), babel hangs with 
*** Open Babel Error  in GetValues

  mol not recognized as a property or a descriptor


But if the tag is changed to "mol_id", -m and -append "mol_id" produce the expected results.


I (quickly, not exhaustively) tried some different quoting and escaping of "mol.id" but got no joy.  Didn't see anything with cursory read of bug list.


Best,

Phil





SAMPLE SDF


      -IDBS-   120620101130

  5  4  0  0  0  0  0  0  0  0999 V2000
    0.2500   -6.3375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9625   -5.9208    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6750   -6.3333    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3875   -5.9167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1000   -5.5000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0     0  0
  1  2  2  0     0  0
  3  4  1  0     0  0
  4  5  3  0     0  0
M  END
>  <mol.id>
AB-00010674

>  <mol.weight>

68.07734


$$$$


On Thu, Dec 3, 2015 at 11:29 PM, Fredrik Wallner <[hidden email]> wrote:
Hi,

The information is key within open babel, so whether you see it in the end depends on the output format. If you keep the files as SDFiles the information should be preserved. If there are a few properties you would like to keep, you can also add them to the title with the option --append, see http://openbabel.org/wiki/--append

Kind regards,
Fredrik
> 2 dec. 2015 kl. 16:55 skrev ashika <[hidden email]>:
>
> Hello all,
>
> I am in the possession of an SDF file containing a chemical library. In this
> file, each molecule is identified by and id number. I am wondering if this
> information can be kept when splitting or acting upon this file. So far I
> have not found a way.
>
> Thanks,
> Ashika
>
>
>
> --
> View this message in context: http://forums.openbabel.org/How-do-you-keep-comment-type-information-from-an-SDF-file-tp4659076.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss


------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss


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

_______________________________________________
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

you can try these out

robertfcrocker
This post has NOT been accepted by the mailing list yet.
What a fantabulous post this has been. Never seen this kind of useful post. I am grateful to you and expect more number of posts like these. Thank you very much.
you can try these out
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: How do you keep "comment-type" information ? (from an SDF file)

signage
This post has NOT been accepted by the mailing list yet.
In reply to this post by Fredrik Wallner
I am a signage designer.As a signage designer i loved your post.In my opinion your post is very good platform to get valid information.Thank you for posting this.I hope more post from you.Thank You.
Loading...