Just an FYI on this one: I just merged a Python DP and DT implementation onto master. Here's the github issue referencing the commits: https://github.com/rdkit/rdkit/issues/574
I will try to get a C++ version done in time for the next release. On Wed, Jul 15, 2015 at 11:02 AM, Greg Landrum <[email protected]> wrote: > Hi Michael, > > On Tuesday, July 14, 2015, Michael Reutlinger <[email protected]> wrote: > >> Hi Greg, >> >> thanks for your answer. I also figured that the invariant feature of the >> AtomPair functions should be well suited. Initially, I thought that the >> pi-electron and neighbouring atom count would always be added, but this is >> clearly not the case. >> > > It shouldn't be the case for the AP fingerprint. It *does*, however, look > like there will be a problem with the TT fingerprints if you provide your > own invariants (this is based on a skim of the code, so I'm not sure that's > correct). > > The definition of the pharmacophoric patterns was initially described in >> the PATTY paper (Bush & Sheridan, J. Chem. Inf. Comput. Sci., 1993) and as >> far as I know the definitions are still valid. >> >> Luckily, there is a SMARTS based version floating around (allegedly based >> on an early OpenBabel version): >> http://tripod.nih.gov/files/patty.rules >> >> I compared those to the original definitions from the paper and they seem >> to match and overall make sense. >> > > Thanks for that pointer. That is really helpful! If I manage to make the > time to do so, I will incorporate this into the next RDKit release. > > I implemented a quick Typer based on this definition, taking into account >> the fact that only the first atom in the SMARTS is typed. >> >> I attached a ipython notebook containing a small example, including the >> example molecule from the paper. >> >> Btw. is the hashing method used for creating the hashed fingerprint still >> valid / suitable if only a small number of the >> maximal numAtomPairFingerprintBits / codeSize is actually used? >> > > The quick read-through I did of the code makes me believe that it should > be fine. I will confirm over the next day or so and let you know. > > Best, > -greg >
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