How do I use the molecule_matcher function?

It seems that even though I have downloaded both openbabel and pybel, I still can’t use the molecule_matcher function. Did I do anything wrong

Hi @Jump_viriyavaree,

This error is most likely due to a problem in how you’ve constructed your molecule1 object. Could you please show how you’ve defined molecule1?


Hi Sam,

I figured it out. There are two main problems. The first one is that I use the ‘Imolecule’ to construct the molecule. The second one is that the latest version of open babel has bugged in it.


Hi Jump,

Glad to hear it. Yes, I suggest you stick with Openbabel 2.4.1 as the latest version 3.0 seems to have some issues, as you’ve seen. Please let me know if you encounter any further problems.


Hello I still have a problem with this molecule matcher. I am using openbabel3.1.1.1 and I wish to find (pull out) unique molecules from files of different molecules.
When I try to match two molecule to find out whether they are identical (, mol2 )) I get the following error, mol2 )
TypeError: fit() missing 1 required positional argument: ‘mol2’

Can you please provide me with some help on how to fix this?
Many thanks