Hi Steven,
The PDB reader in the RDKit doesn’t determine any bond orders - everything
is read as a single bond.
In order to set the bond orders, you need to call the
AssignBondOrdersFromTemplate() function using a reference molecule
generated from SMILES (or SDF).
Here is some example code from
Hi Steven,
The PDB reader in the RDKit doesn’t determine any bond orders - everything is
read as a single bond.
In order to set the bond orders, you need to call the
AssignBondOrdersFromTemplate() function using a reference molecule generated
from SMILES (or SDF).
Here is some example code
Hello!
I have a pdb block that I am working with, which is attached to this email.
The ligand has aromatic ring structures in it; however, when it is read
into RDKit and converted into a smiles string, the aromatic rings are
converted into aliphatic rings. Any thoughts?
Here is the python code:
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