ProGAL.proteins.belta
Class SheetTopology

java.lang.Object
  extended by ProGAL.proteins.belta.SheetTopology

public class SheetTopology
extends java.lang.Object

Representation of the topology of a single sheet. Where the BetaTopology is represented using a pairing matrix, the sheet topology uses a list of strand pairs that can be accessed via the public strandPairs field. The list of strand pairs is ordered such that the pairs follow the order along the sheet, and the first strand from the N-terminal is in the first half of the list. getStrandOrder and getStrandOrientation are alternative methods to access the topology. The following example shows the relationship between the pairing- matrix in the beta-topology and the order and orientation-arrays.

   SecondaryStructure ss = new SecondaryStructure(" EE EE EE EE ");
   //Beta-topology with a single sheet
   BetaTopology bTop = new BetaTopology(ss);
   bTop.setPaired(1,0);
   bTop.setPaired(2,0);
   bTop.setPaired(2,3);
   SheetTopology sTop = new SheetTopology(bTop,0);
   System.out.println(sTop.getStrandOrderString());       //Prints "1 0 2 3"
   System.out.println(sTop.getStrandOrientationString()); //Prints "1110"
 

Author:
R.Fonseca

Nested Class Summary
static class SheetTopology.StrandPair
          A pair of strands specified by two strand-indices (i.e.
 
Field Summary
 SecondaryStructure secondaryStructure
          The secondary structure that the sheet-topology is related to
 java.util.List<SheetTopology.StrandPair> strandPairs
          An ordered list of strand-pairs.
 java.util.List<java.lang.Integer> strands
          A sorted list of strand-indices.
 
Constructor Summary
SheetTopology(BetaTopology bTop, int strand)
          Construct the sheet containing the specified strand.
 
Method Summary
 boolean containsStrand(int strand)
          Return true if the specified strand is in this sheet.
 int[] getNormalizedStrandOrder()
          Return an array indicating the normalized strand order.
 int[] getStrandOrder()
          Return an array indicating the strand order.
 java.lang.String getStrandOrderString()
          String representation of strand order.
 int[] getStrandOrientation()
          Return an array indicating orientation of strands.
 java.lang.String getStrandOrientationString()
          String representation of strand orientation.
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

secondaryStructure

public final SecondaryStructure secondaryStructure
The secondary structure that the sheet-topology is related to


strandPairs

public final java.util.List<SheetTopology.StrandPair> strandPairs
An ordered list of strand-pairs. The order follows the order of pairs when "climbing" the sheet-ladder from one end to the other. The first strand from the N-terminal is in the first half of this list. If it is in the middle, then the second strand is in the first half. This corresponds to the convention in Ruczinskis paper.


strands

public final java.util.List<java.lang.Integer> strands
A sorted list of strand-indices. A strand-index is used in the secondaryStructure.getStrands()-array.

Constructor Detail

SheetTopology

public SheetTopology(BetaTopology bTop,
                     int strand)
Construct the sheet containing the specified strand. The order of the strandPairs list will be such that the lowest index strand will be in the first half of the list. If it is in the center the second-lowest index strand will be in the first part of the list.

Method Detail

containsStrand

public boolean containsStrand(int strand)
Return true if the specified strand is in this sheet.

Parameters:
strand - A strand-index (i.e. an index in the secondaryStructure.getStrands()-array).

getStrandOrder

public int[] getStrandOrder()
Return an array indicating the strand order. This method can be more convenient than traversing the strand-pairs in order.


getNormalizedStrandOrder

public int[] getNormalizedStrandOrder()
Return an array indicating the normalized strand order. Members of the normalized order refers to indexes in the SheetTopology.this.strands-array and not to SheetTopology.this.secondaryStructure.getStrands() as strand- indices usually do.


getStrandOrientation

public int[] getStrandOrientation()
Return an array indicating orientation of strands. A 1-entry indicates the strand is pointing up and a 0-entry down.


toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

getStrandOrderString

public java.lang.String getStrandOrderString()
String representation of strand order.


getStrandOrientationString

public java.lang.String getStrandOrientationString()
String representation of strand orientation.