On Apr 1, 2006, at 5:49 p, Bob Hanson wrote:
Tim, what's the story on this:
class AminoPolymer:
/*
* New code for assigning secondary structure based on
* phi-psi angles instead of hydrogen bond patterns.
*
* old code is commented below the new.
*
* molvisions 2005 10 12
*
*/
void calculateStructures() {
calcHydrogenBonds();
....
If hydrogen bonding is not used for the calculation anymore, why
calcHydrogenBonds()?
Is the comment wrong, or is the calculation unnecessary?
hi Bob,
the comment is correct. the hydrogen bond calculation is unnecessary
in the current implementation of calculateStructures().
my goal was to use a combination of phi-psi angles and hydrogen
bonding patterns to provide a more accurate secondary structure
assignment routine. as it turns out, the phi-psi angles do an
excellent job on their own.
it is possible that a future modification to calculateStructures()
might require hydrogen bonds, but I think for now it can be commented
out.
tim
--
Timothy Driscoll em: [EMAIL PROTECTED]
Virginia Bioinformatics Institute ph: 540-231-3007
Bioinformatics I im: molvisions
Washington St., Blacksburg, VA 24061
"Anyone who considers arithmetical methods of producing random digits
is, of course, in a state of sin." - J von Neumann
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