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Hi, I am trying to see if I can use R to perform more rigorous regression analysis. I wonder if the fingerprint package is able to handle pipeline pilot fingerprints (ECFC6 etc) now. Thank you, Eric [[alternative HTML version deleted]]

...Asuming they output fp's for a single molecule on a single row, you could implement your own line parse and supply it via the lf argument in fp.read. See cdk.lf, moe.lf or bci.lf for examples) The other issue is how one evaluates similarity between variable length feature fingerprints, such as ECFPs. One approach is to map the features into a fixed length bit string. Another approach is to just look at intersections and unions of features to evaluate the Tanimoto score. It seems to me that the former leads to loss of resolution and that the latter could lead to generally low Tanimoto scores....