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tbepler / protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019
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1s in contact map? #5

Closed thomas-a-neil closed 5 years ago

thomas-a-neil commented 5 years ago

Hi,

Looking at how the contact map .pngs are loaded, I noticed that there seem to be two classes corresponding to pixel intensities 0 (no contact) and 255 (contact). There seems to be an additional class for pixel intensity = 1. All of those pixels are masked out (i.e. set to -1) https://github.com/tbepler/protein-sequence-embedding-iclr2019/blob/master/eval_contact_scop.py#L45

What did this class correspond to?

Thank you for your help!

tbepler commented 5 years ago

Those are residues that were missing from the structure.

thomas-a-neil commented 5 years ago

I see, thank you!