edu.sdsc.mbt.util
Class DerivedInformation

java.lang.Object
  edu.sdsc.mbt.util.DerivedInformation

public class DerivedInformation

extends java.lang.Object

DerivedInformation is a class that encapsulates methods that produce information derivable from data in the source file. Example: secondary structures. This implementation is based on the one in Molscript by Per Kraulis and the original paper by Kabsch and Sander Kabsch W and Sander C, "Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features" Byopolymers, Vol. 22, pp 2577-2637 (1983).

Author:

Apostol Gramada

Constructor Summary

DerivedInformation(Structure structure)

DerivedInformation(Structure structure, StructureMap structureMap)

Method Summary

int	getChain(int[] fragment)
java.awt.Color	getColor(int[] fragment)
boolean	getDisjointFragments(java.util.Vector fragments, java.util.Vector conformationType)
boolean	getFragments(java.util.Vector fragments, java.util.Vector conformationType)
int	getNumberOfChains()
char[]	getSsFlags()
void	setConformationType(java.util.Vector residues) Given a RangeMap object, it sets its Value according to the set of Secondary Structures as derived via the Kabsch-Sander algorithm.
java.lang.Object[]	setSsExtendedFlags()

Methods inherited from class java.lang.Object

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

Constructor Detail

DerivedInformation

public DerivedInformation(Structure structure)

DerivedInformation

public DerivedInformation(Structure structure,
                          StructureMap structureMap)

Method Detail

setSsExtendedFlags

public java.lang.Object[] setSsExtendedFlags()

getSsFlags

public char[] getSsFlags()

getNumberOfChains

public int getNumberOfChains()

getChain

public int getChain(int[] fragment)

getColor

public java.awt.Color getColor(int[] fragment)

getFragments

public boolean getFragments(java.util.Vector fragments,
                            java.util.Vector conformationType)

getDisjointFragments

public boolean getDisjointFragments(java.util.Vector fragments,
                                    java.util.Vector conformationType)

setConformationType

public void setConformationType(java.util.Vector residues)

Given a RangeMap object, it sets its Value according to the set of Secondary Structures as derived via the Kabsch-Sander algorithm.