org.strbio.app
Class CompareFolds

java.lang.Object
  org.strbio.app.CompareFolds

public class CompareFolds
extends java.lang.Object

Computes comparison scores for sets of sequences and folds. Run with no arguments to see valid command line options.

  Version 1.32, 1/11/00 - added UFSippl90 potential
  Version 1.31, 1/7/00 - added Sippl90 potential
  Version 1.3, 12/6/99 - added reverse test
  Version 1.28, 10/28/99 - precalculates dihedrals where needed
  Version 1.27, 9/29/99 - added avg psiblast, avg reverse psiblast
  Version 1.26, 9/28/99 - added reverse psiblast
  Version 1.25, 9/9/99 - ident is no longer scaled.  watch out
    for 9/9/99 bug!
  Version 1.24, 9/8/99 - describes parameters correctly.
  Version 1.23, 9/2/99 - added -eval option to evaluate with different
    parameters than used for calculating the alignments
  Version 1.22, 7/8/99 - added -saveparam option, -resume option
  Version 1.21, 6/14/99 - added optimizing for reciprocal weighted rank
  Version 1.2, 6/7/99 - added new statistics functions
  Version 1.13, 5/19/99 - added new scoring functions
  Version 1.12, 2/26/99 - adapted to new GapModel API
  Version 1.11, 8/3/98 - changed possible BackbonePotential reference states
  Version 1.1, 7/9/98 - added separate, sigma to BackbonePotential
  Version 1.0, 4/7/98 - adapted from compare (C++) 1.54
  

Version:

1.32, 1/11/00

Author:

JMC

See Also:

ThreadSet

Constructor Summary

CompareFolds()

Method Summary

static void

main(java.lang.String[] argv)

Methods inherited from class java.lang.Object

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

Constructor Detail

CompareFolds

public CompareFolds()

Method Detail

main

public static final void main(java.lang.String[] argv)