recreate pdbs after generate?

[paoslaos]

Dear authors,

thanks a lot for this great pipeline! I was able to run some tests without many problems! I have a question though, is it possible to create the actual PDBs behind the pickle files within ProteinFlow?

Maybe I missed it but the filtering seems to indicate nicely how many structures were removed for what reason but not as obviously how many we had initially / in the end?

Great appreciation for your work! Thank you!

[linear[bot]]

ENG-1568 recreate pdbs after generate?

[elkoz]

Hey! We're very glad that it was useful for you, sorry for the long response time.

You can generate a PDB file from a ProteinEntry instance by running protein.to_pdb(PATH). It will not be exactly the same file as it was created from since some information is lost in the process but it will contain the same amino acid sequence and structure under the same chain names.

It's a good point about the filtering, the idea is that you can see the number of resulting files and the number of files in the PDB snapshot, but you're right, it would make sense to write it in the log. We will add it next time we do changes, otherwise please feel free to make a PR.