Complete Fragmentation

Is it possible to fragment a molecule into every possible piece of all the length and branches and so on?





When I try


[*1][*2]>>[*1].[*2]


it splits up the molecule into single atoms but I want also ALL the fragments with size 2 3 4 etc.





thanks for answers

Have you tried the extensive fragmentation, e.g. by specifying the -e option flag in the command line?





fragment -c ~/work/Test/FragmenterAll.xml "CCCCCCC"


C |$C_{Q:1}$|





fragment -c ~/work/Test/FragmenterAll.xml "CCCCCCC" -e


C |$C_{Q:1}$|


CC |$C_{Q:2};$|


CCC |$C_{Q:2};;$|


CCCC |$C_{Q:2};;;$|


CCCCC |$C_{Q:2};;;;$|


CCCCCC |$C_{Q:2};;;;;$|


CCCCCCC |$;;;;;;$|





Is this what you mean?


Regards,


Miklos

mvargyas wrote:

fragment -c ~/work/Test/FragmenterAll.xml "CCCCCCC" -e C |$C_{Q:1}$| CC |$C_{Q:2};$| CCC |$C_{Q:2};;$| CCCC |$C_{Q:2};;;$| CCCCC |$C_{Q:2};;;;$| CCCCCC |$C_{Q:2};;;;;$| CCCCCCC |$;;;;;;$|

Looks good! Could you show me the FragmenterAll.xml file?


And does this also work with rings, branched molecules and double bonds?

Actually, FragmentAll.xml did not contain anything else than your rule with a minor modification, namely the only transformation looked like this:

Code:

[*:1][*:2]>>[*:1].[*:2]

But I did not experiment with various bond types, chains etc. Shall I do this for you?





Regards,


Miklos

Eh... Sorry for the delay, I was in holiday.

mvargyas wrote:

But I did not experiment with various bond types, chains etc. Shall I do this for you? Regards, Miklos

Thanks, I would very appreciate that (because I think it has difficulties with rings...)

You are right, C - C ring bonds are not cut. We need to implement this feature!





Btw: did you try to experiment with the CutRingHetero option? See http://www.chemaxon.com/jchem/doc/user/Fragmenter.html#config for details.





Regards,


Miklos