Re: [Rdkit-discuss] postgres cartridge not parsing a SMILES

Ah, should have checked in the shell first! Thanks for the pointer On Sat, Jan 13, 2018 at 5:07 PM, Andrew Dalke wrote: > Hi Rajarshi, > > Here's what RDKit says from the interactive shell: > > >>> from rdkit import Chem > >>>

Re: [Rdkit-discuss] postgres cartridge not parsing a SMILES

On 13/01/2018 18:52, Rajarshi Guha wrote: Hi, I'm using RDKit 2017.09 with Postgres 9.5 and a substructure query is failing when the query SMILES is C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3 Within [] the formal charge must be specified:

Re: [Rdkit-discuss] postgres cartridge not parsing a SMILES

Hi Rajarshi, Here's what RDKit says from the interactive shell: >>> from rdkit import Chem >>> Chem.MolFromSmiles("C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3") [23:02:36] Explicit valence for atom # 6 N, 4, is greater than permitted RDKit is pretty strict about accepting

[Rdkit-discuss] postgres cartridge not parsing a SMILES

Hi, I'm using RDKit 2017.09 with Postgres 9.5 and a substructure query is failing when the query SMILES is C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3 The error reported from Postgres is PSQLException: ERROR: could not create molecule from SMILES