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If we want to load PDB files with no connectivity data (such as those coming from PELE simulations) we need a method to assign the missing connectivity.
Solution
We can use an RDKit molecule representation with the correct connectivity assigned as the connectivity template. Then, the RDKit's method AllChem.AssignBondOrdersFromTemplate can be employed to assign the connectivity to a third molecular representation using the previous connectivity template.
The text was updated successfully, but these errors were encountered:
I just recently saw that MDAnalysis has added a to_rdkit method, and that they put some solid work into guessing valid connectivities + bond orders. It may be worth checking this out:
Description
If we want to load PDB files with no connectivity data (such as those coming from PELE simulations) we need a method to assign the missing connectivity.
Solution
We can use an
RDKit
molecule representation with the correct connectivity assigned as the connectivity template. Then, theRDKit
's methodAllChem.AssignBondOrdersFromTemplate
can be employed to assign the connectivity to a third molecular representation using the previous connectivity template.The text was updated successfully, but these errors were encountered: