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cxcalc majorms removes disconnected components
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samseaver

Joined: 18 Nov 2011
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Link to postPosted: Thu Dec 01, 2011 4:35 pmPost subject: cxcalc majorms removes disconnected components Reply with quote

I've attached a mol file from KEGG that has several disconnected components.

When I run this file using cxcalc:

./cxcalc -N hi majorms -H 7 -f mol C12505.mol

I get an output that only contains the sulfate molecule and not the magnesium or any of the water.

I can't seem to find any options that will allow me to keep the all of the components.




 Filename: C12505.mol    Filesize: 1.29 KB    Downloaded: 29 Time(s)
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Zsolt
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Link to postPosted: Mon Dec 05, 2011 5:47 pmPost subject: Reply with quote

The major microspecies calculation is performend only on the largest fragment, all other fragments (magnesium, water) are removed by cxcalc. There is no option to change that.

Zsolt

samseaver

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Link to postPosted: Mon Dec 05, 2011 6:07 pmPost subject: Reply with quote

At my last count, of the 15K or so mol files released by KEGG, there are about 330 of them that have these multiple components.

I would like to be able to apply the majorms plugin to each of these components within a mol file, automatically.  Is there a way of using MarvinBeans to take these mol files, disconnect them into the respective components, run the majorms plugin on each component, and then re-connect the results?

Zsolt
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Link to postPosted: Wed Dec 07, 2011 2:26 pmPost subject: Reply with quote

It can be done using the Java API.

Steps:
 - convert the molecule to fragments,
 - generate the microspecies of all fragment,
 - fuse the microspecies of fragments.

Zsolt

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