Hey,
I have a question regarding the valency property of Atom.
Consider this example in which methyl radical is constructed with a
SingleElectron at the carbon position. Then a hydrogen is added, bonded to
the carbon, the SingleElectron is removed, making the methylradical a
methane
Hi,
If I remember correctly the Murcko framework code in the CDK is broken.
I would be *very* useful if the people interested in this
functionality could set up (e.g. in the wiki) a set if molecules with
the expected murcko hits for those molecules...
Done:
On Wed, Oct 6, 2010 at 9:10 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
Hi, what is the preferred way to check whether a bond is in a ring?
The SpanningTree.
Egon
--
Dr E.L. Willighagen
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog:
Hi, I've been debugging some of my code and I could you determine how
many frameworks should be identified from
C1(c2c2)(CC(CC1)CCc1c1)CC1C=CC=C1
I know that that the 6-ring and 5-ring joined by a single bond (zero
atom linker) correspond to 2 separate ring systems, but would the
On Wed, Oct 6, 2010 at 4:03 PM, gilleain torrance
gilleain.torra...@gmail.com wrote:
Hi,
This isn't really relevant to fragments as defined in the Murko paper,
but it could be interesting to fragment ring systems and linkers in
other ways.
Say we label the rings as A-D. Then you're asking
Given that a framework is a combination of ring systems and linkers, I
there are quite a few frameworks - (ABCD), (AB) (ABC) (ABD) (CBD)
Hah. Right. Guess I should have actually read, and not just skimmed,
the paper :)
gilleain
OK - but then should I go via getCyclicFragmentsContainer()? Or via
the getAllRings()?
On Wed, Oct 6, 2010 at 3:16 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Wed, Oct 6, 2010 at 9:10 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
Hi, what is the preferred way to check whether a
Hi, looking at some of your examples, I came across ZINC00051216
The full molecule is CCC(=O)c...@](c1c1)(C(F)(F)F)O and you note
the framework (non-hetero) as c1c1
But according to the paper referenced, a framework must be a
combination of ring system + linkers, which this does not
Another example: You have
c1cc(ccc1C(=O)Nc2ccc3c(c2)nc(o3)c4ccncc4)F ZINC00037772
Visually this should have 3 frameworks - but you list one.
It seems that all combinations of ring systems and linkers are valid
frameworks - or maybe I have misunderstood.
Could you explain how you arrived at
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