Hi all,
I'm currently in the process of trying to port a Daylight application to RDKit.
Unfortunately, the application relies heavily on the Daylight function:
dt_fp_partfp. The function takes an atom or bond from a molecule object and
"generates an atom or bond partial fingerprint. A partial fingerprint is a
normal fingerprint, where bits are set only for paths which contain the atom or
bond 'ab'." (see the Daylight website -
http://www.daylight.com/dayhtml/doc/man/man3/dt_fp_partfp.html).
I was wondering if it's possible to implement the function in RDKit with the
current functionality and how difficult its likely to be. Having a quick think
about the likely algorithm to generate it - I would need to generate all the
path/sub-graphs of the input molecule, loop through these to see which contain
the atom/bond I'm interested in. The relevant paths/subgraphs would then need
to be put through the hashing method to generate the bits set for the partial
fingerprint for the atom/bond. I'm sure there are other (more clever) ways to
generate the partial FP but that was the obvious way I could think of. Would
this be possible with the current RDKit functionality (from python -
unfortunately my python is much better than my C++) ? Or can anyone think of a
way to generate a partial fp for an atom in a molecule using the existing RDKit
functionality ?
Thanks for your help.
Thanks
Jameed
GSK
Computational Chemistry
CSC, PTS
Ext: (Stevenage) 8401
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