On Thu, Sep 14, 2017 at 12:05 PM, Michał Nowotka wrote:
> Using
>
> params = AdjustQueryParameters()
> params.makeAtomsGeneric = True
> params.makeBondsGeneric = True
> pattern = AdjustQueryProperties(pattern, params)
>
> Seems to solve my problem - I'm getting a match now (but I
Using
params = AdjustQueryParameters()
params.makeAtomsGeneric = True
params.makeBondsGeneric = True
pattern = AdjustQueryProperties(pattern, params)
Seems to solve my problem - I'm getting a match now (but I haven't yet
verified if the match is correct and I don't understand why
This isn't a really straightforward one.
One solution (and I think the best one) is to change the aromaticity model
used to match whatever is generating the hits (in your case it's the Symyx
cartridge).
The RDKit has functionality to do this already when you call the
SetAromaticity() function:
In
I'm afraid it won't work in the general case (i.e. you can make it work for
some classes of compounds, but not without unwanted side effects on others)
if the aromaticity model of the other cartridge is different - and it seems
to be the case here...
On Wednesday, 13 September 2017, Michał Nowotka
OK, so what I have is some substructure results from other (non-rdkit)
cartridge and I want to use rdkit to generate images of all results
with the query substracture highlighed and aligned.
So I have two things: a list of compounds and a query compound.
Now I need to highlight the query compound f
Your course of action depends upon just what you are really trying to do.
If it's only aspirin, then why wouldn't you just do it manually? If it goes
beyond aspirin, you have to start by defining in general terms exactly what
you want to match to what.
For example, given a query molecule (aspirin
Is there any flag in RDkit to match both 'normal' aspirin and embedded
aromatic analogues?
The problem is that I can't modify user queries by hand in real time :)
On Wed, Sep 13, 2017 at 2:12 PM, Chris Earnshaw wrote:
> Hi
>
> The problem is due to RDkit perceiving the embedded pyranone in
> CHEM
Hi
The problem is due to RDkit perceiving the embedded pyranone in
CHEMBL1999443 as an aromatic system, which is probably correct. However, in
the structure of aspirin the carboxyl carbon and singly bonded oxygen are
non-aromatic, so if you just use the SMILES of aspirin as a query it won't
match
Hi,
This problem is probably due to my lack of chemistry knowledge but
plese have a look:
If I do a substructure search in ChEMBL using aspirin (CHEMBL25) as a
query (ChEMBL API uses the Symix catridge):
from chembl_webresource_client.new_client import new_client
res = new_client.substru
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