ProGAL.proteins.beltaStructure.sheet
Class SheetAlignment

java.lang.Object
  ProGAL.proteins.beltaStructure.sheet.SheetAlignment

public class SheetAlignment
extends java.lang.Object

Field Summary

int[]	alignmentPairs The entire alignment is specified by sTop.strandPairs.size() residue indices.
SheetTopology	sTop

Constructor Summary

SheetAlignment(SheetTopology sTop)
Construct an alignment of strands in the given topology.

SheetAlignment(SheetTopology sTop, PDBFile f)

Method Summary

static void	main(java.lang.String[] args)
void	setAligned(int res1, int res2) Aligns the strand with residue res1 with another strand containing res2 such that res1 and res2 are aligned.

Methods inherited from class java.lang.Object

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

Field Detail

sTop

public SheetTopology sTop

alignmentPairs

public int[] alignmentPairs

The entire alignment is specified by sTop.strandPairs.size() residue indices. There is an entry for each StrandPair in sTop.strandPairs. Each entry is a residue-index indicating which residue in the latter strand is paired to the first residue in the first strand. Notice that this residue might be outside the actual strand. TODO: Explain better.

Constructor Detail

SheetAlignment

public SheetAlignment(SheetTopology sTop)

Construct an alignment of strands in the given topology. Strands are aligned such that their centers align.

SheetAlignment

public SheetAlignment(SheetTopology sTop,
                      PDBFile f)

Method Detail

main

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

setAligned

public void setAligned(int res1,
                       int res2)

Aligns the strand with residue res1 with another strand containing res2 such that res1 and res2 are aligned.