AlternativeAlignment (biojava 5.0.0 API)

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

Fields
Modifier and Type	Field and Description
`static Logger`	`logger`

Constructor Summary

Constructors
Constructor and Description

AlternativeAlignment()

Constructors
Constructor and Description
`AlternativeAlignment()`

Method Summary

All Methods Static Methods Instance Methods Concrete 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()
```

Class AlternativeAlignment

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

logger

Constructor Detail

AlternativeAlignment

Method Detail

toString

getCluster

setCluster

getRmsd

setRms

getScore

setScore

getGaps

getEqr

getIdx1

getIdx2

getPercId

setPercId

apairs_from_seed

apairs_from_idxlst

getAltAligNumber

setAltAligNumber

finish

getDistanceMatrix

refine

getPDBresnum1

setPDBresnum1

getPDBresnum2

setPDBresnum2

calculateSuperpositionByIdx

getRotationMatrix

getShift

calcScores

getAlignedStructure

toPDB

getDistanceMatrix

setDistanceMatrix

getPath