Hi Jan,
Thanks for catching the problem.
Your proposed solution looks reasonable to me.
As an aside: I believe that assigning an RWMol to another like you did in
your first attempt should work. The fact that it doesn't is a separate bug
that I will go ahead and fix.
-greg
On Thu, Nov 15, 2018
Dear Paolo,
Thanks for your reply. I tried your suggestion and aligned the conformers
with either AlignMol and AlignMolConformers. However I got the same
results. I attach the test I performed on aspirin. The atoms I actually
freeze are the O of the ester function and the O of the OH of the
Hi Francis,
I think that parameter has been exposed to Python in the latest 2018.09
release:
>>> import rdkit
>>> from rdkit.Chem import MolFromSmiles
>>> from rdkit.Chem.AllChem import ReactionFromSmarts
>>> mol = MolFromSmiles('OCC(O)CCCO')
>>> rxn = ReactionFromSmarts('[O:1]>>[S:1]')
>>>
Hi,
I have an issue with the cartridge - mol_to_svg() changes the input
molecule so I want to make MolGetSVG() to work on a copy of the input
molecule instead.
In Code/PgSQL/rdkit/adapter.cpp:
extern "C" char *MolGetSVG(CROMol i, unsigned int w, unsigned int h,
On 11/15/2018 11:41 AM, Francis Atkinson wrote:
> products = rxn.RunReactants([mol], maxProducts=1)
> Boost.Python.ArgumentError: Python argument types in
> ChemicalReaction.RunReactants(ChemicalReaction, list)
> did not match C++ signature:
> RunReactants(RDKit::ChemicalReaction*,
Hi Shaozhen,
that parameter can be accessed from Python, it is called maxProducts,
and it defaults to 1000 as described in the Python API docs:
http://www.rdkit.org/docs/source/rdkit.Chem.rdChemReactions.html?highlight=runreactants#rdkit.Chem.rdChemReactions.ChemicalReaction.RunReactants
I don't know how you access that parameter from Pythonn, I'm afraid.
Maybe someone else here can help?
On 15/11/2018 12:47, ?? wrote:
Dear Atkinson:
From rdkit document, I found there is a parameter named numProducts in
RunReactants function, this parameter can limit the products number,
I’ve written a program that does this: https://github.com/jensengroup/xyz2mol
You need to set "charged_fragments = False” to work with radicals
Best regards, Jan
On 15 Nov 2018, at 15:05, Peter St. John
mailto:peterc.stj...@gmail.com>> wrote:
Makes sense, apologies for the lack of details --
Hi Peter,
a few weeks ago I wrote something very close to what you describe:
https://gist.github.com/ptosco/4844d3635cf14d11e5e14381993915c1
which takes coordinates from a XYZ block (which is what you get from
Gaussian) and assigns them to an RDKit molecule generated from a SMILES
string. I
> Essentially I'm taking the result of a Gaussian optimization (for a radical);
> constructing an SDF file with OpenBabel (via cclib), and then trying to read
> the result in RDKit.
> I have the SMILES string of the radical, but the connectivity is lost in the
> gaussian output file. So the SDF
Makes sense, apologies for the lack of details -- it was a bit of a
convoluted process to get to that molecule.
Attached is a python script that hopefully reproduces it.
Essentially I'm taking the result of a Gaussian optimization (for a
radical); constructing an SDF file with OpenBabel (via
Shaozen,
?0?2?0?2?0?2 I have successfully used the solution outlined in this SO answer
...
https://stackoverflow.com/questions/2281850/timeout-function-if-it-takes-too-long-to-finish
?0?2?0?2?0?2 It uses Posix signals so it wouldn't work on older versions of
Windows (I don't know about
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