PIP.IO.StampPackage
Class IRMSDCalc

java.lang.Object
  PIP.IO.StampPackage.IRMSDCalc

public class IRMSDCalc
extends java.lang.Object

Constructor Summary

IRMSDCalc()

Method Summary

static double	calculateRMSDforSetOfCoordinates(double[][] c1, double[][] c2)
static double[]	centerOfGravity(double[][] positions)
static double[][]	getCoordinates(Domain d)
static double[][]	getCoordinatesAroundCenterOfGravity(double[] cog)
static double[][]	getCoordinatesForOverlappingParts(Domain d0, java.util.List<java.lang.Character> alignmentReference, java.util.List<java.lang.Character> alignmentAlternative)
static double	getIRMSD(RMSDComponents RefA_AltA_A_Matrix, RMSDComponents RefB_AltB_A_Matrix, RMSDComponents RefA_AltA_B_Matrix, RMSDComponents RefB_AltB_B_Matrix)
static double	getiRMSDForPairOfDomainInteractions(DomainInteraction di0, DomainInteraction di1, FamilyType ft)
static double[]	getiRMSDForPairOfDomainInteractions(DomainInteraction di0, DomainInteraction di1, java.util.List<Transform> transformsA, java.util.List<Transform> transformsB, java.util.Map<java.lang.String,java.util.List<java.lang.Character>> alignmentsA, java.util.Map<java.lang.String,java.util.List<java.lang.Character>> alignmentsB, FamilyType ft, boolean isHomodimer)
static double[][]	getPositionsCAlphaAtoms(Domain d)
static double[][]	getRepresentativeCoordinates(double[][] positions)
static java.util.List<RMSDComponents>	getRMSDComponents(Domain referenceA, Domain referenceB, Domain alternativeA, Domain alternativeB, java.util.List<Transform> transformsA, java.util.List<Transform> transformsB, java.util.Map<java.lang.String,java.util.List<java.lang.Character>> alignmentA, java.util.Map<java.lang.String,java.util.List<java.lang.Character>> alignmentB)
static double[][]	getTransform(java.util.List<Transform> transforms, Domain reference, Domain alternative)
static double[][]	getTransform(java.util.List<Transform> transforms, java.lang.String id)
static double[][]	transformCoordinates(double[][] matrix, double[][] co)
static void	writeOutDomainInteractionsInSameCoordinateSpace(DomainInteraction di0, FamilyType ft, double[][] transform, DomainInteraction di1)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IRMSDCalc

public IRMSDCalc()

Method Detail

getiRMSDForPairOfDomainInteractions

public static double[] getiRMSDForPairOfDomainInteractions(DomainInteraction di0,
                                                           DomainInteraction di1,
                                                           java.util.List<Transform> transformsA,
                                                           java.util.List<Transform> transformsB,
                                                           java.util.Map<java.lang.String,java.util.List<java.lang.Character>> alignmentsA,
                                                           java.util.Map<java.lang.String,java.util.List<java.lang.Character>> alignmentsB,
                                                           FamilyType ft,
                                                           boolean isHomodimer)

Parameters:

di0 - - this is the reference domain interaction

di1 - - this is the alternative domain interaction

transformsA -

transformsB -

alignmentsA -

alignmentsB -

ft -

isHomodimer -

Returns:

an array of two elements - first one is the iRMSD score. The second one is the order of the alternative domain in comparison to the reference. If the order is 0 then the domains are already in the same order otherwise if the order is 1 then the alternative domain is in a different order.

getRMSDComponents

public static java.util.List<RMSDComponents> getRMSDComponents(Domain referenceA,
                                                               Domain referenceB,
                                                               Domain alternativeA,
                                                               Domain alternativeB,
                                                               java.util.List<Transform> transformsA,
                                                               java.util.List<Transform> transformsB,
                                                               java.util.Map<java.lang.String,java.util.List<java.lang.Character>> alignmentA,
                                                               java.util.Map<java.lang.String,java.util.List<java.lang.Character>> alignmentB)

getTransform

public static double[][] getTransform(java.util.List<Transform> transforms,
                                      Domain reference,
                                      Domain alternative)

getTransform

public static double[][] getTransform(java.util.List<Transform> transforms,
                                      java.lang.String id)

getIRMSD

public static double getIRMSD(RMSDComponents RefA_AltA_A_Matrix,
                              RMSDComponents RefB_AltB_A_Matrix,
                              RMSDComponents RefA_AltA_B_Matrix,
                              RMSDComponents RefB_AltB_B_Matrix)

transformCoordinates

public static double[][] transformCoordinates(double[][] matrix,
                                              double[][] co)

calculateRMSDforSetOfCoordinates

public static double calculateRMSDforSetOfCoordinates(double[][] c1,
                                                      double[][] c2)

getPositionsCAlphaAtoms

public static double[][] getPositionsCAlphaAtoms(Domain d)

getRepresentativeCoordinates

public static double[][] getRepresentativeCoordinates(double[][] positions)

getCoordinatesForOverlappingParts

public static double[][] getCoordinatesForOverlappingParts(Domain d0,
                                                           java.util.List<java.lang.Character> alignmentReference,
                                                           java.util.List<java.lang.Character> alignmentAlternative)

getCoordinatesAroundCenterOfGravity

public static double[][] getCoordinatesAroundCenterOfGravity(double[] cog)

centerOfGravity

public static double[] centerOfGravity(double[][] positions)

getCoordinates

public static double[][] getCoordinates(Domain d)

getiRMSDForPairOfDomainInteractions

public static double getiRMSDForPairOfDomainInteractions(DomainInteraction di0,
                                                         DomainInteraction di1,
                                                         FamilyType ft)
                                                  throws java.lang.Exception

Throws:

java.lang.Exception

writeOutDomainInteractionsInSameCoordinateSpace

public static void writeOutDomainInteractionsInSameCoordinateSpace(DomainInteraction di0,
                                                                   FamilyType ft,
                                                                   double[][] transform,
                                                                   DomainInteraction di1)
                                                            throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException