org.strbio.mol.lib
Class ScorePairwiseDistance

java.lang.Object
  org.strbio.mol.lib.ScorePairwiseDistance

All Implemented Interfaces:

ScoreFunction

public class ScorePairwiseDistance
extends java.lang.Object
implements ScoreFunction

A scoring function based on the CA distance between 2 residues. This could be used to get an alignment from a structural superposition of 2 proteins.

  Version 1.1, 3/9/99 - subtract 100 from all scores so < 0
  Version 1.0, 3/4/99 - original version
  

Version:

1.1, 3/9/99

Author:

JMC

Constructor Summary

ScorePairwiseDistance()

Method Summary

double	score(Monomer a, Monomer b) This function should return a score for aligning two monomers of a polymer, preferably with low = good, high = bad.
double	score(Residue a, Residue b) Score is the distance between the residues' CA atoms.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ScorePairwiseDistance

public ScorePairwiseDistance()

Method Detail

score

public double score(Residue a,
                    Residue b)

Score is the distance between the residues' CA atoms.

score

public double score(Monomer a,
                    Monomer b)

Description copied from interface: ScoreFunction

This function should return a score for aligning two monomers of a polymer, preferably with low = good, high = bad. If this is not the case, be sure to comment it as such! If monomer order matters to your scoring function, the first monomer should be from the sequence (unknown structure), and the second monomer should be from the fold (known structure).

Specified by:

score in interface ScoreFunction