Re: [Rdkit-discuss] Substructure search

[Greg L. <gre...@gm...>]

On Sat, Nov 7, 2009 at 5:43 PM, Evgueni Kolossov <eko...@gm...> wrote:
>>are you doing the replace dummy for each fragment every time before
>>you do a search or do you do it just once?
> I am iterating through all the structures and all the fragments:
> so for each structure do
>                            for each fragment ( and need to replace dummy
> here)
>
> probably can do it another way:
> for each fragment do
>         for each structure
>
> In this case will need to do it only once for each fragment

yes, I imagine that will help a lot.

or:
for each fragment do: replace dummy atom
for each structure do
   for each fragment do something

-greg

-greg