The SMILES strings are not correct, rings should be enumerated. In the first
string for example, all four rings are labelled with '1' but it should look
like this: c1ccc(c(c1)C2CC(=NN2c3ccccc3F)c4ccc(cc4)Br)Cl. That is why RDKit
is throwing an error. Which software did you use to create the SMILES
strings?
Adrian
On Thu, Nov 19, 2009 at 11:48, bouille <[email protected]> wrote:
> Dear Greg
>
> Thank you Adrian Schreyer for his quick answer
>
> now I have the following error on some structures
> rdkit.Chem.rdMolDescriptors._CalcMolWt(NoneType)
> did not match C++ signature:
> _CalcMolWt(RDKit::ROMol mol, bool onlyHeavy=False)
>
> I have written
> AvailDescriptors.descDict['MolWt'](mol,onlyHeavy=False) to repair ???
>
> Is it not clear ?
>
> I read other alternative to handle heavy structure
>
> print 'embed: ',i
> AllChem.EmbedMolecule(mol)
> print 'optimize: ',i
> AllChem.UFFOptimizeMolecule(mol)
> mols.append(mol)
>
> As example 3 compounds with difficulties why ?
>
> bad molecule Fc1ccccc1N1N=C(CC1c1ccccc1Cl)c1ccc(Br)cc1 |c:9|
> bad molecule NC1=C(C#N)C2=CCCCC2C2(C(=O)Nc3ccccc23)C1(C#N)C#N |c:1,t:5|
> bad molecule
> CCOC(=O)C1=C(C)N(c2ccc(OC)cc2)C(C)=C(C1c1ccc(Cl)cc1)C(=O)OCC |c:5,19|
>
> Thank you to clarify
>
> Best Regards
> Bouille
>
>
>
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