> as an example you use this file (silica glass SiO2 with 3000 atoms in PDB 
> format, written using Babel):
> Is this the reason why it is so slow for this kind of coordinates is because 
> Babel looking for bonds ?

My guess, based on your example, is ring / aromaticity perception.

In PDB, while bonds (CONECT) records can be stored, bond orders are not. So by 
default, Open Babel performs bond order perception 

At the moment, this includes a process to detect aromaticity and perform Kekule 
assignment. This gets slowed by perception over multiple fused rings 
(nanotubes, graphene, .. silica glass). On most molecules, it’s not a huge 
issue, but for materials and nanostructures, its. very. . slooww. . .

I’m not sure how you’re using your code, but I’d make sure that 
PerceiveBondOrders() is not called.

Finding bonds with ConnectTheDots() is usually reasonably fast, but this can 
also be an impact that you’re describing.

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