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Open Multiple Compounds with MarvinSketch
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Ben

Joined: 11 Sep 2009
Posts: 19

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Link to postPosted: Mon Oct 19, 2009 9:33 pmPost subject: Open Multiple Compounds with MarvinSketch Reply with quote

Hello,

Is there a way to open a list of comounds in sdf format with MarvinSketch?  I mean open all the compounds at once in one MarvinSketch window.

I have an sdf file with all the sulfonyl chlorides available from Maybridge (209 compounds).  I would like to use these as a user_defined_homology group but I need to define where the attachment point is.  Based on the way the other homology groups are done, I assume I need all the compounds in one MarvinSketch file with attachment points.  209 is alot of compounds I dont want to have to copy paste by hand.  Is there anyway I can do this in a more automated way?

Thank you,

Ben Chittick

Nora
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Joined: 25 Jun 2004
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Link to postPosted: Tue Oct 20, 2009 2:28 pmPost subject: Re: Open Multiple Compounds with MarvinSketch Reply with quote

This functionality is not yet available but we will implement it in the next major Marvin release (5.3).

However, it is possible even now, with Marvin 5.2, after a conversion with molconvert which fuses the fragments into one molecule. Example:

 

molconvert sdf e.sdf -R frags.sdf -o unionFrags.sdf
msketch unionFrags.sdf

unionFrags.sdf will contain the fragments in frags.sdf in a single molecule. Unfortunately currently you have to specify an empty molecule (e.sdf) to fuse the fragments to, but this difficulty will be eliminated in Marvin 5.3. From Marvin 5.3, the above will be available in this simpler form:

molconvert sdf frags.sdf -U -o unionFrags.sdf
msketch unionFrags.sdf

 

If you have a file with R-group definition members with attachment points already set, then it is possible to fuse them as R-group definition members to a scaffold. Example:

 

molconvert sdf scaffold.sdf -R1 frags.sdf -o rmol.sdf
msketch rmol.sdf

In both cases it is possible to specify a range of molecule indexes. In case of the R-group definition members, you can filter the input by accepting only 1 or only 2 attachment molecules. Refer to the MolConverter guide for details.




 Filename: scaffold.sdf    Filesize: 749 Bytes    Downloaded: 203 Time(s)
 Description:  scaffold file

 Filename: frags.sdf    Filesize: 3.35 KB    Downloaded: 221 Time(s)
 Description:  fragment file

 Filename: e.sdf    Filesize: 87 Bytes    Downloaded: 198 Time(s)
 Description:  the auxiliary empty molecule
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