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poloarol / peptide-descriptors

Structural and molecular descriptors for peptides
MIT License
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Use graphein for representation #4

Open poloarol opened 2 years ago

poloarol commented 2 years ago

Move to graphein to represent the peptides, as it is built on networkx and much more robust. Provides a good interface for Geometric Deep Learning downstream

poloarol commented 2 years ago

Tested it, and it does not model the interactions as I would have liked it. Would probably consider it, for an ML ready dataset.

a-r-j commented 1 year ago

Hi @poloarol - what did you not like? Happy to make improvements.

poloarol commented 1 year ago

@a-r-j - I was working with complexes and needed to separate them. However, I do not think graphein can do that hence opted for the biopython approach. Maybe I'm not just well versed with graphein and it is possible.