org.biojava.nbio.structure.align.pairwise

Class AlternativeAlignment

java.lang.Object

org.biojava.nbio.structure.align.pairwise.AlternativeAlignment

All Implemented Interfaces:

Serializable

public class AlternativeAlignment
extends Object
implements Serializable

Implements a class which handles one possible (alternative) solution. Alternative alignments arise from different seed alignments or seed FPairs. The AltAlg class contains methods for refinement (Dynamic Programming based) and filtering (i.e. removing probably wrongly matched APairs). In the refinement phase, different seed alignments can converge to the same solution.

Since:

3:04:26 PM

Version:

%I% %G%

Author:

Andreas Prlic,, Peter Lackner (original Python and C code)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static Logger	logger

Constructor Summary

Constructors

Constructor and Description
AlternativeAlignment()

Method Summary

Methods

Modifier and Type	Method and Description
void	apairs_from_idxlst(JointFragments jf) Set apairs according to a list of (i,j) tuples.
void	apairs_from_seed(int l, int i, int j) Set apairs according to a seed position.
void	calcScores(Atom[] ca1, Atom[] ca2) calculates scores for this alignment ( %id )
void	calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)
void	finish(StrucAligParameters params, Atom[] ca1, Atom[] ca2)
Structure	getAlignedStructure(Structure s1, Structure s2) create an artifical Structure object that contains the two structures superimposed onto each other.
int	getAltAligNumber() returns the sequential number of this alternative alignment
int	getCluster() get the number of the cluster this alignment belongs to
Matrix	getDistanceMatrix() The distance matrix this alignment is based on
static Matrix	getDistanceMatrix(Atom[] ca1, Atom[] ca2)
int	getEqr() returns the number of euqivalent residues in this alignment
int	getGaps() return the number of gaps in this alignment
int[]	getIdx1() the positions of the structure equivalent positions in atom set 1
int[]	getIdx2() the positions of the structure equivalent atoms in atom set 2
IndexPair[]	getPath()
String[]	getPDBresnum1()
String[]	getPDBresnum2()
int	getPercId()
double	getRmsd()
Matrix	getRotationMatrix() returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
float	getScore() the alignment score
Atom	getShift() returns the shift vector that has to be applied on structure to to shift on structure one
void	refine(StrucAligParameters params, Atom[] ca1, Atom[] ca2) Refinement procedure based on superposition and dynamic programming.
void	setAltAligNumber(int fromia)
void	setCluster(int cluster) set the number of the cluster this alignment belongs to.
void	setDistanceMatrix(Matrix distanceMatrix) The distance matrix this alignment is based on
void	setPDBresnum1(String[] pdbresnum1)
void	setPDBresnum2(String[] pdbresnum2)
void	setPercId(int percId)
void	setRms(double rms) the rms in the structurally equivalent regions
void	setScore(float score)
String	toPDB(Structure s1, Structure s2) converts the alignment to a PDB file each of the structures will be represented as a model.
String	toString() print the idx positions of this alignment

Methods inherited from class java.lang.Object

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

Field Detail

logger

public static Logger logger

Constructor Detail

AlternativeAlignment

public AlternativeAlignment()

Method Detail

toString

public String toString()

print the idx positions of this alignment

Overrides:

toString in class Object

Returns:

a String representation

getCluster

public int getCluster()

get the number of the cluster this alignment belongs to

Returns:

an int giving the number of the cluster

setCluster

public void setCluster(int cluster)

set the number of the cluster this alignment belongs to. All alignments in a cluster are quite similar.

Parameters:

cluster - the number of the cluster

getRmsd

public double getRmsd()

setRms

public void setRms(double rms)

the rms in the structurally equivalent regions

Parameters:

rms -

getScore

public float getScore()

the alignment score

Returns:

the score of this alignment

setScore

public void setScore(float score)

getGaps

public int getGaps()

return the number of gaps in this alignment

Returns:

the number of Gaps

getEqr

public int getEqr()

returns the number of euqivalent residues in this alignment

Returns:

the number of equivalent residues

getIdx1

public int[] getIdx1()

the positions of the structure equivalent positions in atom set 1

Returns:

the array of the positions

getIdx2

public int[] getIdx2()

the positions of the structure equivalent atoms in atom set 2

Returns:

the array of the positions

getPercId

public int getPercId()

setPercId

public void setPercId(int percId)

apairs_from_seed

public void apairs_from_seed(int l,
                    int i,
                    int j)

Set apairs according to a seed position.

Parameters:

l -

i -

j -

apairs_from_idxlst

public void apairs_from_idxlst(JointFragments jf)

Set apairs according to a list of (i,j) tuples.

Parameters:

jf - a JoingFragment

getAltAligNumber

public int getAltAligNumber()

returns the sequential number of this alternative alignment

Returns:

the sequential number of this alternative alignment

setAltAligNumber

public void setAltAligNumber(int fromia)

finish

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

Throws:

StructureException

getDistanceMatrix

public static Matrix getDistanceMatrix(Atom[] ca1,
                       Atom[] ca2)

refine

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

Refinement procedure based on superposition and dynamic programming. Performs an iterative refinement. Several methods apply such a procedure, e.g. CE or ProSup. Here we additionally test for circular permutation, which are in the same frame of superposition as the optimal alignment. This feature may be switched off by setting permsize to -1.

Parameters:

params - the parameters

ca1 - atoms of structure 1

ca2 - atoms of structure 2

Throws:

StructureException

getPDBresnum1

public String[] getPDBresnum1()

setPDBresnum1

public void setPDBresnum1(String[] pdbresnum1)

getPDBresnum2

public String[] getPDBresnum2()

setPDBresnum2

public void setPDBresnum2(String[] pdbresnum2)

calculateSuperpositionByIdx

public void calculateSuperpositionByIdx(Atom[] ca1,
                               Atom[] ca2)
                                 throws StructureException

Throws:

StructureException

getRotationMatrix

public Matrix getRotationMatrix()

returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1

Returns:

the rotation Matrix

getShift

public Atom getShift()

returns the shift vector that has to be applied on structure to to shift on structure one

Returns:

the shift vector

calcScores

public void calcScores(Atom[] ca1,
              Atom[] ca2)

calculates scores for this alignment ( %id )

Parameters:

ca1 - set of Atoms for molecule 1

ca2 - set of Atoms for molecule 2

getAlignedStructure

public Structure getAlignedStructure(Structure s1,
                            Structure s2)

create an artifical Structure object that contains the two structures superimposed onto each other. Each structure is in a separate model. Model 1 is structure 1 and Model 2 is structure 2.

Parameters:

s1 - the first structure. its coordinates will not be changed

s2 - the second structure, it will be cloned and the cloned coordinates will be rotated according to the alignment results.

Returns:

composite structure containing the 2 aligned structures as a models 1 and 2

toPDB

public String toPDB(Structure s1,
           Structure s2)

converts the alignment to a PDB file each of the structures will be represented as a model.

Parameters:

s1 -

s2 -

Returns:

a PDB file as a String

getDistanceMatrix

public Matrix getDistanceMatrix()

The distance matrix this alignment is based on

Returns:

a Matrix object.

setDistanceMatrix

public void setDistanceMatrix(Matrix distanceMatrix)

The distance matrix this alignment is based on

Parameters:

distanceMatrix -

getPath

public IndexPair[] getPath()