Ok, thanks. But the getOverlaps method returns *all* MCSS which can be
quite many. In my special case I am only interested in one and not even
in the structure but only in its size (molecule clustering).
I am playing with mcss in cdk from few months
I have implemented this mcss in my software molpharm.
where user can visualize the substructures found.
At this time i have only one fig. to show you(see last one)
Link: http://sushilronghe.tripod.com/cdk/index.html
(do you think result coming out is questionable.)
your purpose can be solved in two ways.
1) using mcss
Using Mcss you can determine the largest one from it's size.
But you want faster,and only the biggest one two determine.
2) Using substructure search.
Well this way it will be quite hard but interesting i think.
The substructure search in cdk actually check all the matches of each
atom and bond
if all the bond in query is matching with target molecule it will return
true.
Now, here you can put your code , here we go.
i) take a molecule and convert to smart (let's say this is our query and we
have to search
it against a
target molecule)
case 1: test whole molecule first against the query
case 2: (#challenging) see how many bonds are matching and then set
up a criteria for selecting
a hit.
well this is very simple logic you can make it better.
( But how can a molecule be converted to smarts,
with a best of my knowledge cdk don't have such converter.
so we can use smile for doing a substructure search.
at present the substrucutre search only take up smart this will not help
so a smile parser should have to be build (that will be very easy)
and then do substructure search.
If you think this will work for you
i can give you more information to proceed in this
way.
sorry for poor english.
On 5/4/07, Egon Willighagen <[EMAIL PROTECTED]> wrote:
On Friday 04 May 2007, Thorsten Meinl wrote:
> Ok, thanks. But the getOverlaps method returns *all* MCSS which can be
> quite many. In my special case I am only interested in one and not even
> in the structure but only in its size (molecule clustering). Is there a
> way to get this information faster than determining all MCSS?
No, I do not think so. To determine the biggest one, you have to determine
them all anyway.
Egon
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