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pierrepo / grodecoder

GroDecoder extracts and identifies the molecular components of a structure file (PDB or GRO) issued from a molecular dynamics simulation.
https://grodecoder.streamlit.app/
BSD 3-Clause "New" or "Revised" License
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Use biopython #33

Closed pierrepo closed 3 months ago

pierrepo commented 3 months ago

https://github.com/pierrepo/grodecoder/blob/e4e072758297926ea5a6a04b1ae9050a66e31b92/fasta_seq_into_PDBID.py#L6

Could you use biopython to read the fasta file?

pierrepo commented 3 months ago

Sorry @KarinDuong but why are you writing a FASTA file? Shouldn't you just read a fasta file?

KarinDuong commented 3 months ago

@pierrepo yes I read a fasta file to collect all the sequence, and re-write a fasta file to put the PDB ID in the line begin with ">" for each sequence

pierrepo commented 3 months ago

ok @KarinDuong No need to revrite the fasta with the PDB ID.

KarinDuong commented 3 months ago

@pierrepo so how to store these PDB ID ? and how we going to known to which sequence it's related ?

pierrepo commented 3 months ago

As discuss last time, we might have multiple PDB structures that match the target sequence. So it's better to just output in the terminal something like this:

FASTA sequence 1: <20-first-amino-acids> Putative structure: Putative PDB IDs: <5 or 10 best PDB IDs with best match>