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java.lang.Objectorg.biojava.bio.structure.align.pairwise.AlternativeAlignment
public class AlternativeAlignment
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.
Field Summary | |
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static Logger |
logger
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Constructor Summary | |
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AlternativeAlignment()
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Method Summary | |
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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)
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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()
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String[] |
getPDBresnum1()
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String[] |
getPDBresnum2()
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int |
getPercId()
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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)
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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)
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void |
setPDBresnum2(String[] pdbresnum2)
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void |
setPercId(int percId)
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static Logger logger
Constructor Detail |
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public AlternativeAlignment()
Method Detail |
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public String toString()
toString
in class Object
public int getCluster()
public void setCluster(int cluster)
cluster
- the number of the clusterpublic double getRmsd()
public void setRms(double rms)
rms
- public float getScore()
public void setScore(float score)
public int getGaps()
public int getEqr()
public int[] getIdx1()
public int[] getIdx2()
public int getPercId()
public void setPercId(int percId)
public void apairs_from_seed(int l, int i, int j)
l
- i
- j
- public void apairs_from_idxlst(JointFragments jf)
jf
- a JoingFragmentpublic int getAltAligNumber()
public void setAltAligNumber(int fromia)
public void finish(StrucAligParameters params, Atom[] ca1, Atom[] ca2) throws StructureException
StructureException
public static Matrix getDistanceMatrix(Atom[] ca1, Atom[] ca2)
public void refine(StrucAligParameters params, Atom[] ca1, Atom[] ca2) throws StructureException
params
- the parametersca1
- atoms of structure 1ca2
- atoms of structure 2
StructureException
public String[] getPDBresnum1()
public void setPDBresnum1(String[] pdbresnum1)
public String[] getPDBresnum2()
public void setPDBresnum2(String[] pdbresnum2)
public void calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2) throws StructureException
StructureException
public Matrix getRotationMatrix()
public Atom getShift()
public void calcScores(Atom[] ca1, Atom[] ca2)
ca1
- set of Atoms for molecule 1ca2
- set of Atoms for molecule 2public Structure getAlignedStructure(Structure s1, Structure s2)
s1
- the first structure. its coordinates will not be changeds2
- the second structure, it will be cloned and the cloned coordinates will be rotated according to the alignment results.
public String toPDB(Structure s1, Structure s2)
s1
- s2
-
public Matrix getDistanceMatrix()
public void setDistanceMatrix(Matrix distanceMatrix)
distanceMatrix
- public IndexPair[] getPath()
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