Here are more details.
If I use
m = Chem.MolFromSmiles('ccc[nH]c', sanitize=False)
AllChem.Compute2DCoords(m)
It works.
But I get trouble with
>>> m = Chem.MolFromSmiles('C(=O)OCCO', sanitize=False)
>>> AllChem.Compute2DCoords(m)
I got
Pre-condition Violation
getNumImplic
Adrian,
I meet a weird case.
>>> import matplotlib.offsetbox
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> from rdkit.Chem import Draw
>>> m = Chem.MolFromSmiles('ccc[nH]c')
I got
non-ring atom 0 marked aromatic
>>> AllChem.Compute2DCoords(m)
Traceback (most recent call last)
Hi Toby and Greg,
Thanks a lot for your answers.
I'll use Toby's solution as it fits my situation better, as I'll have to do
this only for the compounds that will be used, and not on the reactants.
Best,
Christos
On 19 February 2014 10:40, Toby Wright wrote:
> Hi Christos,
>
> If you add hydr
Hi Christos,
The Hs are, by default, left in the query graph when you construct the
molecule from SMARTS.
They will only match when the molecule you are matching against also has an
H in the graph.
Chem.MolToSmarts() takes an optional "mergeHs" argument that will get you
the behavior you want:
In
Hi Christos,
If you add hydrogens to m3 after creating it in RDKit then both m1 and m2
are recognised as substructures of m3. See below for how I achieved this:
>>> from rdkit import Chem
>>> m1 = Chem.MolFromSmarts("[C:3][C:4](=[O:5])[O:6]([H:100])")
>>> m2 = Chem.MolFromSmarts("[C:3][C:4](=[O:5
Hi all,
At my current project I'm working on reaction based multiobjective de novo
design.
And I have a set of reactions that I have converted into SMIRKS and
reaction SMARTS..
The problem I have is that when I have a reactant pattern in SSMARTS, as
required by SMIRKS, that has explicit mapped Hy
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