On Fri, Jul 23, 2021 at 4:53 AM Paolo Tosco
wrote:
>
> # here there seems to a be a bug with the 2D depiction, but that's another
> story
>
> template
>
> [image: image.png]
>
>
Just a quick thing: I don't know if this is supposed to be a bug or a
feature, but I noticed that this seems to be
Thanks a lot!
--
Gustavo Seabra.
On Fri, Jul 23, 2021 at 12:18 PM Paolo Tosco
wrote:
> Hi Gustavo,
>
> Chem.Atom.HasQuery() and Chem.Bond.HasQuery() return True when the
> underlying atom (or bond) is an instance of Chem.QueryAtom (or Chem.
> QueryBond).
> Query atoms and bonds can either be
Hi Gustavo,
Chem.Atom.HasQuery() and Chem.Bond.HasQuery() return True when the
underlying atom (or bond) is an instance of Chem.QueryAtom (or Chem.
QueryBond).
Query atoms and bonds can either be defined through SMARTS expressions...
from rdkit import Chem
from rdkit.Chem import rdqueries
a =
This works perfectly!
I could understand most of what you did there ;-), but what does the
".HasQuery()" mean? The RDKit API is not very clear about it: "Returns
whether or not the atom has an associated query". Is this described
anywhere else?
Thank you so much!
--
Gustavo Seabra.
On Fri, Jul
Hi Gustavo,
you should be able to address this with a custom AtomCompare (and
BondCompare, if you want to use bond queries too) class, that now is also
supported from Python.
You can take a look at Code/GraphMol/FMCS/Wrap/testFMCS.py for inspiration
how to use it; here's something that seems to
On Jul 23, 2021, at 06:42, Andrew Dalke wrote:
>
> No, there's no way to do that.
>
> The best I can suggest is to go back to the original Python implementation
> and change the code leading up to
Alternatively, since your template is small, you can brute-force enumerate all
possible
On Jul 23, 2021, at 01:01, Gustavo Seabra wrote:
> I actually want the sulfone to be found, if it is there. My problem is that I
> also want flexibility to change the ring atoms and still find the ring as a
> match, while considering a match on the sulfone only if it really is there.
> (e.g.,
Hi,
Thanks a lot for the reply! However, in this case, it looks like I would
have to somehow label the isotope in every query molecule, right? For
example:
```
template =
Chem.MolFromSmarts('[c]1(-[2S](=[3O])(=[3O])(-C)):[c]:[c]:[c]:[c]:[c]:1')
mol1 =
Hi Gustavo,
> template =
> Chem.MolFromSmarts('[a]1(-[S](-*)(=[O])=[O]):[a]:[a]:[a]:[a]:[a]:1')
Unless things have changed since I last looked at the algorithm, you can't
meaningfully pass a SMARTS-based query molecule into the MCS program, outside
of a few simple cases.
It generates a
Hi all,,
I would appreciate some pointers on how it would be possible to find the
maximum common substructure of 2 molecules, where in the template structure
some atoms may be *any*, but some other atoms must be fixed.
Currently, I'm trying to use rdFMCS module. For example:
from rdkit import
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