Re: [OpenBabel-Devel] Fragmentation

[erapp <er...@mi...>]

Noel,

For this task I must find all unique fragments.  For example, C(CCCC)O 
1-hydroxy-pentane, when I set levels = 1 (and delete hydrogens just to make 
this simpler), I get the following fragments using mna:

-C(-C-O)
-C(-C-C)
-C(-C-C)
-C(-C-C)
-C(-C)
-O(-C)

There are three instances of -C(-C-C), what makes each of those three 
unique?  In this view (using the GUI) they look identical.  I can't see what 
other bonds they have.  For example, in one instance does the first C atom 
have only one bond or two?  How many bonds does the second C atom have?

Using another program the results for this molecule look like (just a small 
example):

O(C(X)(X)X)X OHC(X)(X)X OHC(C(X)(X)X)(X)X OHCH(C(X)(X)X)X OHCH2C(X)(X)X 
OHCH2C(C(X)(X)X)(X)X

So, we can see the bonds on each element to distinguish one CC or CCC from 
another.

I apologize if I am missing something but I am somewhat new to OpenBabel and 
couldn't find what I was looking for in the documentation.

Thanks for your response!

Elliot

-- 
View this message in context: http://forums.openbabel.org/Fragmentation-tp3159761p3160803.html
Sent from the openbabel-devel mailing list archive at Nabble.com.