Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

LMDB Support for FoldComp databases. #286

Open
a-r-j opened this issue Mar 27, 2023 · 0 comments
Open

LMDB Support for FoldComp databases. #286

a-r-j opened this issue Mar 27, 2023 · 0 comments
Labels
enhancement New feature or request help wanted Extra attention is needed ML

Comments

@a-r-j
Copy link
Owner

a-r-j commented Mar 27, 2023

Assuming the worst case scenario (using all of the uniprot predictions, approx 200m structures iirc), mapping graph/node labels into Data/Protein objects would have to be done when we get a structure so they're not stored in memory (200m node label tensors seems.. prohibitive). I think the way to go is to connect this to an (optional) LMDB which could also store additional pre-computed features. Thus when we get a structure we pull in these additional data and store them in the returned Data/Protein.

FWIW, I see this functionality as complementary to the other strand of dataset creation we've been doing in #272 . Essentially, I think a model workflow looks like: make a dataset selection with a Manager -> Instantiate a FoldCompDataset -> wrap it in a LightningModule (optional).

I also saw as of 0.0.3 FoldComp supports multi-chain structures. I'm not sure if this now expands support to "real" (i.e. from the PDB) PDB files, but if it does this is something to strongly consider in #272 as an export option.

Originally posted by @a-r-j in #284

@a-r-j a-r-j added enhancement New feature or request help wanted Extra attention is needed ML labels Mar 27, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request help wanted Extra attention is needed ML
Projects
None yet
Development

No branches or pull requests

1 participant