On Wed, Mar 5, 2014 at 4:03 PM, Toby Wright wrote:
>
> This is probably related to the above so I thought I'd post it on this
> thread. I am noticing inconsistent behaviour when a molecule created via
> SMARTS that contains an 'or' statement has HasSubstructMatch called on it,
> as opposed to it
Thanks Jan.
The fix and pull request have both been integrated.
-greg
On Wed, Mar 5, 2014 at 7:35 PM, Jan Holst Jensen wrote:
> Hi Greg,
>
> Thanks for the explanation.
>
> I added this to rdkit_io.c in mol_from_ctab():
>
> + bool keepConformer = PG_GETARG_BOOL(1);
> - mol = parseMolCTAB(da
Hi Greg,
Thanks for the explanation.
I added this to rdkit_io.c in mol_from_ctab():
+ bool keepConformer = PG_GETARG_BOOL(1);
- mol = parseMolCTAB(data,false,true);
+ mol = parseMolCTAB(data,keepConformer,true);
and then I can get the expected behavior and have my tests complete
successful
Hi,
This is probably related to the above so I thought I'd post it on this
thread. I am noticing inconsistent behaviour when a molecule created via
SMARTS that contains an 'or' statement has HasSubstructMatch called on it,
as opposed to it being the argument to HasSubstructMatch. A simple example
Hi Jan,
The below behavior is the result of a bug (
https://github.com/rdkit/rdkit/issues/229).
mol_from_ctab() takes an (undocumented) optional argument that is supposed
to determine whether or not the molecule's conformation is stored in the
database. The default is to not store the conformation
Thanks all for informative and helpful responses, the behaviour I was
struggling to understand now makes perfect sense.
Toby Wright
--
InhibOx Ltd
On 4 March 2014 04:06, Greg Landrum wrote:
> Bob hit the nail on the head.
>
> The first case, "N1N=CC=C1", is aromatic because the RDKit sees tha
Hi Greg,
Thanks a lot for the explanation.
It makes things clearer now.
Well the reason I'm doing SMARTS-SMARTS match is because I would like to
match functional groups with the reactants in reactions.
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob
Hi,
About ready to push a changeset for implementing mol_to_ctab(), but I
would like it to play nice and preserve input depictions.
Ideally I would like the following
select mol_to_ctab(mol_from_ctab());
to output a molfile where the coordinates of "input-molfile" are preserved.
If I do
On Wednesday, March 5, 2014, James Davidson wrote:
> Thanks Greg - that did the trick!
> (I still see pythonTestDbCLI - as previously posted)
Those problems are due to windows not being able to delete files that it
has just closed. I need to put the deletion bit in a try..except block. The
fail
Thanks Greg - that did the trick!
(I still see pythonTestDbCLI - as previously posted)
Kind regards
James
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