Search script and OMG database

[rakeshr10]

Hi,

Is there a python script for search and retrieval tasks which could be used without the server? How to do residue level and sequence level retrieval as shown in the paper.

Also I don't see the OMG database related weights or faiss index file. Would be glad if you could comment on this.

Regards
Rakesh

[LTEnjoy]

Hi Rakesh,

Is there a python script for search and retrieval tasks which could be used without the server? How to do residue level and sequence level retrieval as shown in the paper.

We don't directly provide a python script for retrieval tasks. However you could easily implement it by yourself! You could follow below steps:

1. Load the ProTrek model and calculate your query embedding. See here.
2. Directly load faiss index. If you have already downloaded the faiss index files from here, you could dive into the folder and see .index files and corresponding ids.tsv files. An example for your retrieval would be:

import faiss

# Load model and get query embedding
...

# Load faiss index
path  = "/your/path/to/***.index"
index = faiss.read_index(path)
index.metric_type = faiss.METRIC_INNER_PRODUCT

# Start retrieval
topk = 10
scores, ranks = index.search(query_embedding, topk)

# Once you get ranks, you could load "ids.tsv" to get the information of retrieved candidates
...

For more details about the usage of the faiss library, please refer to the official github repo here. If you want to perform residue-level or sequence-level retrieval, you only need to load corresponding .index file and follow the above steps.

I don't see the OMG database related weights or faiss index file. Would be glad if you could comment on this.

Yes. Currently we don't upload other database index files due to their large size (~hundreds of GB). You could use our online server to access these databases. We are working hard on making it more handy and efficient :)

Best regards,
Jin