The molecule has been constructed without problems, but the jupyter
rendering code is failing.
This isn't particularly surprising, that code is really set up to render
non-query molecules, not things constructed from SMARTS.
If you want to get a rendering of a molecule build from SMARTS in the
notebook, try:
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1ccccc1)c1ccccc1'
mol =Chem.MolFromSmarts(sa)
Draw.MolToImage(mol,kekulize=False)
Best,
-greg
On Wed, Jul 12, 2017 at 5:10 PM, Chicago Ji <chicago...@gmail.com> wrote:
> the code :
> ----------------------------
> from rdkit import Chem
> from rdkit.Chem.Draw import IPythonConsole
> sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1ccccc1)c1ccccc1'
> mol =Chem.MolFromSmarts(sa)
> mol
> -----------------------------
>
> The error information:
>
> RDKit ERROR: [16:07:15]
> RDKit ERROR:
> RDKit ERROR: ****
> RDKit ERROR: Pre-condition Violation
> RDKit ERROR: getExplicitValence() called without call to calcExplicitValence()
> RDKit ERROR: Violation occurred on line 162 in file
> ....soft/rdkit/Code/GraphMol/Atom.cpp
> RDKit ERROR: Failed Expression: d_explicitValence > -1
> RDKit ERROR: ****
> RDKit ERROR:
> RDKit ERROR: [16:07:15] Can't kekulize mol. Unkekulized atoms: 4 5 6 7 8 9
> RDKit ERROR:
>
>
> -----------------------
>
>
> On Wed, Jul 12, 2017 at 2:27 PM, Greg Landrum <greg.land...@gmail.com>
> wrote:
>
>>
>>
>> On Tue, Jul 11, 2017 at 6:53 PM, Chicago Ji <chicago...@gmail.com> wrote:
>>
>>> Thanks a lot for your code.
>>>
>>> I met another error. I don't know whether it's Normal.
>>>
>>> I have a correct SMILES, and read it through MolFromSmarts:
>>>
>>> --------------------------------------------------------
>>> sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1ccccc1)c1ccccc1'
>>> Chem.MolFromSmarts(sa)
>>> --------------------------------------------------------
>>>
>>>
>>> Is there something wrong with my input?
>>>
>>
>> Looks fine to me:
>>
>> In [9]: sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1ccccc1)c1ccccc1'
>>
>> In [10]: m = Chem.MolFromSmarts(sa)
>>
>> In [11]: m.GetNumAtoms()
>> Out[11]: 35
>>
>>
>> What error do you see?
>>
>> -greg
>>
>>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
