Hi Quyen,
It's been a few years since I wrote that but here is what I recall:
D0 is a constant cutoff that represents the upper bound of dissimilarity
for the difference of two distance matrices A_i and B_j, rooted at
subsequences i to i+8 and j to j+8, respectively. Raising this value allows
for sloppier fragments being considered.
D1 is a constant cutoff that represents the upper bound of dissimilarity
for the entire path being considered. In fact, it's equal to path_score /
(window_size * path_length).
So, D0 ensure that incoming fragments are still good. D1 ensures that as
we extend the current alignment the total quality of the current alignment
remains good.
After this, all N top scoring paths are stored in the path cache and the
best path is returned.
Cheers,
-- Jason
On Wed, Apr 17, 2013 at 3:34 AM, QT <rdirect...@gmail.com> wrote:
> 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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--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
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