Thank you Jason.
Quyen
On Wed, Apr 17, 2013 at 10:18 AM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> 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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