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Pipeline pilot fingerprint package
3 messages · Rajarshi Guha, Eric Hu
On Tue, Oct 12, 2010 at 8:54 PM, Eric Hu <Eric.Hu at gilead.com> wrote:
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.
Currently no - does Pipeline Pilot out put their ECFP's in a standard format? if so can you send me an example file? (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. Do you know what Pipeline Pilot does?
Rajarshi Guha NIH Chemical Genomics Center
Hi Rajarshi, Here is a post I found from Pipeline pilot community help pages: https://community.accelrys.com/message/3466 Eric -----Original Message----- From: Rajarshi Guha [mailto:rajarshi.guha at gmail.com] Sent: Wednesday, October 13, 2010 7:52 AM To: Eric Hu Cc: r-help at r-project.org Subject: Re: Pipeline pilot fingerprint package
On Tue, Oct 12, 2010 at 8:54 PM, Eric Hu <Eric.Hu at gilead.com> wrote:
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.
Currently no - does Pipeline Pilot out put their ECFP's in a standard format? if so can you send me an example file? (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. Do you know what Pipeline Pilot does?
Rajarshi Guha NIH Chemical Genomics Center