org.biojava.bio.structure.align
Class StructurePairAligner

java.lang.Object
  org.biojava.bio.structure.align.StructurePairAligner

public class StructurePairAligner
extends Object

Constructor Summary

StructurePairAligner()

Method Summary

void	align(Atom[] ca1, Atom[] ca2, StrucAligParameters params) calculate the actual protein structure superimposition.
void	align(Structure s1, Structure s2)
void	align(Structure s1, Structure s2, StrucAligParameters params)
AlternativeAlignment[]	getAlignments() return the alternative alignments that can be found for the two structures
Matrix	getDistMat() return the difference of distance matrix between the two structures
FragmentPair[]	getFragmentPairs() get the results of step 1 - the FragmentPairs used for seeding the alignment
StrucAligParameters	getParams() get the parameters.
static void	main(String[] args) example usage of this class
void	setFragmentPairs(FragmentPair[] fragPairs)
void	setParams(StrucAligParameters params) set the parameters to be used for the algorithm

Methods inherited from class java.lang.Object

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

Constructor Detail

StructurePairAligner

public StructurePairAligner()

Method Detail

main

public static void main(String[] args)

example usage of this class

Parameters:

args -

getFragmentPairs

public FragmentPair[] getFragmentPairs()

get the results of step 1 - the FragmentPairs used for seeding the alignment

Returns:

a FragmentPair[] array

setFragmentPairs

public void setFragmentPairs(FragmentPair[] fragPairs)

getAlignments

public AlternativeAlignment[] getAlignments()

return the alternative alignments that can be found for the two structures

Returns:

AlternativeAlignment[] array

getDistMat

public Matrix getDistMat()

return the difference of distance matrix between the two structures

Returns:

a Matrix

getParams

public StrucAligParameters getParams()

get the parameters.

Returns:

the Parameters.

setParams

public void setParams(StrucAligParameters params)

set the parameters to be used for the algorithm

Parameters:

params - the Parameter object

align

public void align(Structure s1,
                  Structure s2)
           throws StructureException

Throws:

StructureException

align

public void align(Structure s1,
                  Structure s2,
                  StrucAligParameters params)
           throws StructureException

Throws:

StructureException

align

public void align(Atom[] ca1,
                  Atom[] ca2,
                  StrucAligParameters params)
           throws StructureException

calculate the actual protein structure superimposition.

Parameters:

ca1 - set of Atoms of structure 1

ca2 - set of Atoms of structure 2

params - the parameters to use for the alignment

Throws:

StructureException