Class AlternativeAlignment

Method Details

• 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()