org.biojava.nbio.structure.align

Class StructurePairAligner

java.lang.Object

org.biojava.nbio.structure.align.StructurePairAligner

public class StructurePairAligner
extends Object

Perform a pairwise protein structure superimposition.

The algorithm is a distance matrix based, rigid body protein structure superimposition. It is based on a variation of the PSC++ algorithm provided by Peter Lackner (Peter.Lackner@sbg.ac.at, personal communication) .

Example

  public void run(){

                // first load two example structures
                InputStream inStream1 = this.getClass().getResourceAsStream("/files/5pti.pdb");
                InputStream inStream2 = this.getClass().getResourceAsStream("/files/1tap.pdb");

                Structure structure1 = null;
                Structure structure2 = null;

                PDBFileParser pdbpars = new PDBFileParser();
                structure1 = pdbpars.parsePDBFile(inStream1) ;
                structure2 = pdbpars.parsePDBFile(inStream2);


                // calculate structure superimposition for two complete structures
                StructurePairAligner aligner = new StructurePairAligner();


                        // align the full 2 structures with default parameters.
                        // see StructurePairAligner for more options and how to align
                        // any set of Atoms
                        aligner.align(structure1,structure2);

                        AlternativeAlignment[] aligs = aligner.getAlignments();
                        AlternativeAlignment a = aligs[0];
                        System.out.println(a);

                        //display the alignment in Jmol

                        // first get an artificial structure for the alignment
                        Structure artificial = a.getAlignedStructure(structure1, structure2);


                        // and then send it to Jmol (only will work if Jmol is in the Classpath)

                        BiojavaJmol jmol = new BiojavaJmol();
                        jmol.setTitle(artificial.getName());
                        jmol.setStructure(artificial);

                        // color the two structures


                        jmol.evalString("select *; backbone 0.4; wireframe off; spacefill off; " +
                                        "select not protein and not solvent; spacefill on;");
                        jmol.evalString("select *"+"/1 ; color red; model 1; ");


                        // now color the equivalent residues ...

                        String[] pdb1 = a.getPDBresnum1();
                        for (String res : pdb1 ){
                                jmol.evalString("select " + res + "/1 ; backbone 0.6; color white;");
                        }

                        jmol.evalString("select *"+"/2; color blue; model 2;");
                        String[] pdb2 = a.getPDBresnum2();
                        for (String res :pdb2 ){
                                jmol.evalString("select " + res + "/2 ; backbone 0.6; color yellow;");
                        }


                        // now show both models again.
                        jmol.evalString("model 0;");

        }
  

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic, Peter Lackner

Constructor Summary

Constructors

Constructor and Description
StructurePairAligner()

Method Summary

Modifier and Type	Method and Description
void	addProgressListener(AlignmentProgressListener li)
void	align(Atom[] ca1, Atom[] ca2, StrucAligParameters params) calculate the protein structure superimposition, between two sets of atoms.
void	align(Structure s1, String chainId1, Structure s2, String chainId2) Align two chains from the structures.
void	align(Structure s1, String chainId1, Structure s2, String chainId2, StrucAligParameters params) Aligns two chains from the structures using user provided parameters.
void	align(Structure s1, Structure s2) Calculate the alignment between the two full structures with default parameters
void	align(Structure s1, Structure s2, StrucAligParameters params) Calculate the alignment between the two full structures with user provided parameters
void	clearListeners()
Atom[]	getAlignmentAtoms(Structure s) Returns the atoms that are being used for the alignment.
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.
boolean	isDebug() Deprecated.
static void	main(String[] args) example usage of this class
void	setDebug(boolean debug) Deprecated.
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

addProgressListener

public void addProgressListener(AlignmentProgressListener li)

clearListeners

public void clearListeners()

main

public static void main(String[] args)
                 throws Exception

example usage of this class

Parameters:

args -

Throws:

Exception

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

isDebug

@Deprecated
public boolean isDebug()

Deprecated.

check if debug mode is set on

Returns:

debug flag

setDebug

@Deprecated
public void setDebug(boolean debug)

Deprecated.

set the debug flag

Parameters:

debug - flag

align

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

Calculate the alignment between the two full structures with default parameters

Parameters:

s1 -

s2 -

Throws:

StructureException

align

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

Calculate the alignment between the two full structures with user provided parameters

Parameters:

s1 -

s2 -

params -

Throws:

StructureException

align

public void align(Structure s1,
                  String chainId1,
                  Structure s2,
                  String chainId2)
           throws StructureException

Align two chains from the structures. Uses default parameters.

Parameters:

s1 -

chainId1 -

s2 -

chainId2 -

Throws:

StructureException

align

public void align(Structure s1,
                  String chainId1,
                  Structure s2,
                  String chainId2,
                  StrucAligParameters params)
           throws StructureException

Aligns two chains from the structures using user provided parameters.

Parameters:

s1 -

chainId1 -

s2 -

chainId2 -

params -

Throws:

StructureException

getAlignmentAtoms

public Atom[] getAlignmentAtoms(Structure s)

Returns the atoms that are being used for the alignment. (E.g. Calpha only, etc.)

Parameters:

s -

Returns:

an array of Atoms objects

align

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

calculate the protein structure superimposition, between two sets of atoms.

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