Dear all,
I have a question regarding CEalign d0 and d1 parameter. What exactly are
their functions?
I don't know enough C++ to decipher the algorithm but they are used
findPath() in ccealignmodule.cpp. It seems that that d0 controls a
similarity matrix and d1 the path length. A d1 below a certain number does
indeed make cealign return RMSD over smaller set of residues and there is a
lower bound for d1 where cealign will fail to align. D0 behaves
similarly. The default is 2 and 3 for d0 and d1. I'm going to guess that
those numbers are also dimensionless.
Will it be useful to tune the parameter d0 and d1?
Best,
Quyen
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