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* remove all of the "from __future__" imports * remove the first batch of rdkit.six imports/uses * next step of rdkit.six removal * removing xrange, range, and some maps * next round of removals * next round of cleanups * fix inchi test * last bits of "from rdkit.six" are gone * and the last of the six stuff is gone * strange importlib problem
Glare Algorithm.
Implementation of
GLARE: A New Approach for Filtering Large Reagent Lists in
Combinatorial Library Design Using Product Properties
Jean-Francois Truchon* and Christopher I. Bayly
http://pubs.acs.org/doi/pdf/10.1021/ci0504871
Usage:
# somehow make sidechains1/2 with props [mw, alogp, tpsa]
r1 = RGroups(sidechains1)
r2 = RGroups(sidechains2)
lib = Library([r1, r2])
props = [
Property("mw", 0, 0, 500),
Property("alogp", 1, -2.4, 5),
Property("tpsa", 2, 0, 90)
]
glare = Glare()
glare.optimize(lib, props)
Notes:
Some nomenclature:
A Libary is made of RGroups
RGroups are a collection of sidechains (the paper uses Fragments)
that can populate the rgroup position.
We desire to optimize the Library so that we have a good chance
of making the desired products.
From the testing code, using Fake data:
r1 = RGroups(makeFakeSidechains("aldehydes", num=1000))
r2 = RGroups(makeFakeSidechains("boronic_acids", num=1500))
libs = Library([r1,r2])
props = [
Property("mw", propIdx=0, minValue=0, maxValue=500),
Property("alogp", propIdx=1, minValue=-2.4, maxValue=5),
Property("tpsa", propIdx=2, minValue=0, maxValue=90)
]
glare = Glare()
# optimize the library...
glare.optimize(libs, props)