The other answers on this thread have been right on point with the
exception of neglecting to explicitly encourage you to call
Chem.SanitizeMol() on your joined molecule before you do anything else with
it. In your case you'd call:
Chem.SanitizeMol(back)
This will lead to the error that Nik explain
Hi Per,
I can think of 2 approaches to solve this.
The 1st is to have fragments of molecules that have an explicit connection
point, i.e. OH[*] and C[*], and use RDKit's functionality of combining
fragments.
The 2nd is to use define a reaction for this using SMIRKS or Reaction
SMILES, i.e. [O
Hi Nikolaus and Ling,
Thanks for your help (the atom numbe shouldnt be 43 but it still gives the
error I will clarify)- yes Nikolaus you are right it is a sanitization
issue and in this case I am trying to use it as a molecular editor to build
a model molecule (a transition state model to be exact
Hi Per
Just by looking at your code I would assume you have a sanitization issue. You
create your pentane molecule and then add H’s. This will saturate each single
carbon. When you then add a bond between the two fragments your atom 3 will
have a valence of 5 and this causes issues.
Maybe do the
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