Oh, I got confused by lack of error message when using MolFromSmiles with a
Smarts string. But I see the problem and can now make it work.
SOLVED, thank you!
On Thursday, October 3, 2019, 9:02:04 PM GMT+2, Andrew Dalke
wrote:
On Oct 3, 2019, at 20:34, Ondrej Gutten via Rdkit-discuss
On Oct 3, 2019, at 20:34, Ondrej Gutten via Rdkit-discuss
wrote:
> # MCS is a benzene
> my_mcs = Chem.MolFromSmiles(res.smarts)
The res.smarts (or res.smartsString if you use the rdFMCS module) returns a
SMARTS string, not a SMILES string. You should be using Chem.MolFromSmarts() in
the code
Hi,
I am new to rdkit, sorry if I am missing something obvious.
I am trying to pair matching substructures for a list of molecules. The plan is
to:1) do MCS on a list of molecules2) use GetSubstructMatch to get pairing for
each molecule and MCS result
However, GetSubstructMatch returns empty tupl
Dear Greg,
Leaving cycle/non-cycle atoms aside let's try to figure out how to reduce
the number of maps allowing only 1 overlap between matches:
Can you please suggest the best approach to do that?
Example:
vMatches:
[0][5]((0,1),(1,2),(2,3),(3,4),(4,5))
[1][5]((0,1),(1,2),(2,3),(3,8),(4
I cannot agree about default behaviour - at IDBS we have done different way
and this why fragment-based models based on IDBS fragment-structure mapping
was so good...
looking like I will need to write my own mapping...
Regards,
Evgueni
2009/12/1 Adrian Schreyer
> You need to provide a more spec
You need to provide a more specific query. * is very generic and hits
everything in the molecule except the sulfur and the imidazole. I am not
sure about 17 hits but I can count at least 15. This is the default
behaviour in every toolkit, by the way.
You should try the SMARTS tester from Dayli
>I will repeat myself: please provide a specific match that you
>consider to be wrong.
I can investigate if it make sense
>Comments like this do not improve my motivation to continue to be helpful.
I am sorry - I have no intention to offend you. I just cannot understand the
purpose of this functio
On Tue, Dec 1, 2009 at 12:31 PM, Evgueni Kolossov wrote:
> I can investigate but even without this cyclic/non-cyclic problem there
> cannot be 17 matches! Especially with uniquify set to true.
I will repeat myself: please provide a specific match that you
consider to be wrong.
> So, this functio
I can investigate but even without this cyclic/non-cyclic problem there
cannot be 17 matches! Especially with uniquify set to true.
So, this function is actually useless.
2009/12/1 Greg Landrum
> On Tue, Dec 1, 2009 at 12:01 PM, Evgueni Kolossov
> wrote:
> > I believe none of them if take in ac
I believe none of them if take in account cyclic and non-cyclic atoms
2009/12/1 Greg Landrum
> Evgueni,
>
> Please provide specific maps that don't make sense.
>
> -greg
>
>
> On Tue, Dec 1, 2009 at 11:50 AM, Evgueni Kolossov
> wrote:
> > Fragment: *
> > Structure: S=C(CC1C1)N1CCC(c2nc[
On Tue, Dec 1, 2009 at 12:01 PM, Evgueni Kolossov wrote:
> I believe none of them if take in account cyclic and non-cyclic atoms
That's definitely the case. If you want to include that information in
your query, you have to explicitly do so. In order to do this, you are
going to have to either ex
Evgueni,
Please provide specific maps that don't make sense.
-greg
On Tue, Dec 1, 2009 at 11:50 AM, Evgueni Kolossov wrote:
> Fragment: *
> Structure: S=C(CC1C1)N1CCC(c2nc[nH]c2)CC1
>
> Code
> //
> void CFragmentation::Rep
If you've looked at the matches and found specific ones that don't
make sense, please post them, the exact query and molecule you used
(including the atom numbering), and the code you are using to do the
matching and I will take a look.
-greg
On Tue, Dec 1, 2009 at 10:52 AM, Evgueni Kolossov wr
Yes, Greg,
I believe that result 17 matches for this fragment does not make any sense
2009/12/1 Greg Landrum
> Dear Evgueni,
>
> On Tue, Dec 1, 2009 at 10:21 AM, Evgueni Kolossov
> wrote:
> >
> > I have enclosed 2 files - images for structure and fragment. When using
> > unsigned int Substruct
Dear Evgueni,
On Tue, Dec 1, 2009 at 10:21 AM, Evgueni Kolossov wrote:
>
> I have enclosed 2 files - images for structure and fragment. When using
> unsigned int SubstructMatch() I am getting value = 17!!! Looking like
> function is not taking in account atom types and flag uniquify is not
> work
Hi Greg,
I have enclosed 2 files - images for structure and fragment. When using
unsigned int SubstructMatch() I am getting value = 17!!! Looking like
function is not taking in account atom types and flag uniquify is not
working at all - or may be I am missing something? Can you please comment on
16 matches
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