CODEX Example

Question

CODEX Example

Closed this issue 3 years ago · 6 comments

While messing around with CODEX, I noticed it wants to compute ECFP4 fingerprints using a different method and this gives slightly different similarities. @geemi725 could you double-check the ECFP4 implementation we have is correct, or is the CODEX one correct?

Answer 1 · 2021-11-23T15:13:56.000Z

@whitead this is the reason. Not sure how to pick "what's the best" though.

Answer 2 · 2021-11-23T15:15:37.000Z

@whitead also codex is taking 1-similarity with the bit vectors but the output must be similarity, not distance?

Answer 3 · 2021-11-23T15:37:13.000Z

So which is more accepted?

Answer 4 · 2021-11-23T15:48:21.000Z

My understanding is that Morgan FPs by default uses the counts. If we use bit vectors we will be losing info pertaining to the counts. But I have seen bitvectors used more commonly (in the past few weeks).

Answer 5 · 2021-11-23T15:56:41.000Z

For future references: Visualizing which atoms contribute to similarity between two molecules.

Answer 6 · 2021-11-23T15:58:12.000Z

Interesting, maybe we could use that for @navneeth3005's project