PIP.Domains.Orientation
Class ClassifyByOrientation

java.lang.Object
  PIP.Domains.Orientation.ClassifyByOrientation

public class ClassifyByOrientation
extends java.lang.Object

Constructor Summary

ClassifyByOrientation()

Method Summary

static void	alterStampOutputToKeepInfoOnDomainInteractions(java.util.List<Stamper> stampers, java.util.List<DomainInteraction> domIntsToKeep, java.lang.String jalviewA, java.lang.String jalviewB, java.lang.String groupsA, java.lang.String groupsB)
static void	analyseDomainInteractionSuperposition(FamilyType ft, DomainInteraction di0, DomainInteraction di1, java.util.List<Transform> transformA, boolean isHomodimer)
static void	classifyByInterfaceAndStoreResults(java.util.Collection<DomainInteraction> domainInteractions, FamilyType hft, int iRMSDThreshold, java.io.File clsification, boolean isHomodimer)
static java.util.List<java.util.List<DomainInteraction>>	classifyIntoOrientations(java.util.Collection<DomainInteraction> domainInteractions, FamilyType ft, int stampRMSD)
static boolean	containsSameOrientation(DomainInteraction di0, java.util.Collection<DomainInteraction> domainInteractions, FamilyType ft, double iRMSDThreshold, java.lang.String dir) This function checks to see if any of the domainInteractions in the list passed in are of the same orientation of the single domain interaction passed in.
static void	createResultsFilesForSingleDomainInteractions(Domain d, java.lang.String dir, java.lang.String fileName)
static java.util.List<Stamper>	generateSameOrientationsIntoList(java.util.List<java.util.List<DomainInteraction>> sameList, java.util.List<DomainInteraction> startingList, FamilyType ft, double iRMSDThreshold, boolean isHomodimer) The sameList passed in is added to by one List of Domain interactions each time this function is called untill the starting list has no more elements and they have all been classified into the sameList by orientation similarity.
static java.util.List<DomainInteraction>	getDomainInteractionsWithSameOrientation(java.util.List<DomainInteraction> domainInteractions, FamilyType ft, double iRMSDThreshold, boolean isHomodimer)
static java.util.List<Domain>	getListFirstDomains(java.util.List<DomainInteraction> domainInteractions)
static java.util.List<InteractionSurface>	getListFirstInterfaceSurfaces(java.util.List<DomainInteraction> domainInteractions)
static java.util.List<Domain>	getListSecondDomains(java.util.List<DomainInteraction> domainInteractions)
static java.util.List<InteractionSurface>	getListSecondInterfaceSurfaces(java.util.List<DomainInteraction> domainInteractions)
static void	movePDBFilesIntoDifferentDirectory(java.util.List<DomainInteraction> domIntsToKeep, java.lang.String dirDest, java.lang.String dir)
static void	moveResultsToDifferentDirectory(java.util.List<Stamper> stampers, java.lang.String dirDest, java.lang.String jalviewA, java.lang.String jalviewB, java.lang.String groupsA, java.lang.String groupsB)
static void	printOutSummaryDomainInteractionsToKeep(java.util.List<DomainInteraction> di, java.lang.String dirDest, java.lang.String nameOfFile)
static java.util.List<Domain>	removeDuplicateDomains(java.util.List<Domain> domToKeepWithDuplicates)
static java.util.List<InteractionSurface>	removeDuplicateISurfaces(java.util.List<InteractionSurface> iSurfaceToKeepWithDuplicates)

Methods inherited from class java.lang.Object

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

Constructor Detail

ClassifyByOrientation

public ClassifyByOrientation()

Method Detail

classifyByInterfaceAndStoreResults

public static void classifyByInterfaceAndStoreResults(java.util.Collection<DomainInteraction> domainInteractions,
                                                      FamilyType hft,
                                                      int iRMSDThreshold,
                                                      java.io.File clsification,
                                                      boolean isHomodimer)
                                               throws java.lang.Exception

Throws:

java.lang.Exception

printOutSummaryDomainInteractionsToKeep

public static void printOutSummaryDomainInteractionsToKeep(java.util.List<DomainInteraction> di,
                                                           java.lang.String dirDest,
                                                           java.lang.String nameOfFile)
                                                    throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

removeDuplicateDomains

public static java.util.List<Domain> removeDuplicateDomains(java.util.List<Domain> domToKeepWithDuplicates)

removeDuplicateISurfaces

public static java.util.List<InteractionSurface> removeDuplicateISurfaces(java.util.List<InteractionSurface> iSurfaceToKeepWithDuplicates)

movePDBFilesIntoDifferentDirectory

public static void movePDBFilesIntoDifferentDirectory(java.util.List<DomainInteraction> domIntsToKeep,
                                                      java.lang.String dirDest,
                                                      java.lang.String dir)
                                               throws java.io.IOException,
                                                      java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

moveResultsToDifferentDirectory

public static void moveResultsToDifferentDirectory(java.util.List<Stamper> stampers,
                                                   java.lang.String dirDest,
                                                   java.lang.String jalviewA,
                                                   java.lang.String jalviewB,
                                                   java.lang.String groupsA,
                                                   java.lang.String groupsB)
                                            throws java.io.IOException,
                                                   java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

alterStampOutputToKeepInfoOnDomainInteractions

public static void alterStampOutputToKeepInfoOnDomainInteractions(java.util.List<Stamper> stampers,
                                                                  java.util.List<DomainInteraction> domIntsToKeep,
                                                                  java.lang.String jalviewA,
                                                                  java.lang.String jalviewB,
                                                                  java.lang.String groupsA,
                                                                  java.lang.String groupsB)
                                                           throws java.io.IOException,
                                                                  java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

getListFirstInterfaceSurfaces

public static java.util.List<InteractionSurface> getListFirstInterfaceSurfaces(java.util.List<DomainInteraction> domainInteractions)

getListSecondInterfaceSurfaces

public static java.util.List<InteractionSurface> getListSecondInterfaceSurfaces(java.util.List<DomainInteraction> domainInteractions)

getListFirstDomains

public static java.util.List<Domain> getListFirstDomains(java.util.List<DomainInteraction> domainInteractions)

getListSecondDomains

public static java.util.List<Domain> getListSecondDomains(java.util.List<DomainInteraction> domainInteractions)

getDomainInteractionsWithSameOrientation

public static java.util.List<DomainInteraction> getDomainInteractionsWithSameOrientation(java.util.List<DomainInteraction> domainInteractions,
                                                                                         FamilyType ft,
                                                                                         double iRMSDThreshold,
                                                                                         boolean isHomodimer)
                                                                                  throws java.lang.Exception

Parameters:

domainInteractions -

ft -

iRMSDThreshold -

isHomodimer -

Returns:

A sublist of the original domain interactions passed in which are all at the same orientation based on the iRMSDThreshold. The list of domain interactions returned is ordered so that all of the domain interactions within the list are the same way round as the reference domain interaction (first domain interaction in the list). I.E if the first domain interaction is ordered by domain from family a.1.2.3 being the first domain and b.4.7.6 being the second domain then so are all of the alternative domain interactions in the list.

Throws:

java.lang.Exception

generateSameOrientationsIntoList

public static java.util.List<Stamper> generateSameOrientationsIntoList(java.util.List<java.util.List<DomainInteraction>> sameList,
                                                                       java.util.List<DomainInteraction> startingList,
                                                                       FamilyType ft,
                                                                       double iRMSDThreshold,
                                                                       boolean isHomodimer)
                                                                throws java.lang.Exception

The sameList passed in is added to by one List of Domain interactions each time this function is called untill the starting list has no more elements and they have all been classified into the sameList by orientation similarity. Each list of domain interactions added to smaeList is ordered so that all of the domain interactions within the list are the same way round as the reference domain interaction (first domain interaction in the list). I.E if the first domain interaction is ordered by domain from family a.1.2.3 being the first domain and b.4.7.6 being the second domain then so are all of the alternative domain interactions in the list.

Parameters:

sameList -

startingList -

ft -

iRMSDThreshold -

isHomodimer -

Returns:

Throws:

java.lang.Exception

analyseDomainInteractionSuperposition

public static void analyseDomainInteractionSuperposition(FamilyType ft,
                                                         DomainInteraction di0,
                                                         DomainInteraction di1,
                                                         java.util.List<Transform> transformA,
                                                         boolean isHomodimer)
                                                  throws java.io.IOException

Throws:

java.io.IOException

createResultsFilesForSingleDomainInteractions

public static void createResultsFilesForSingleDomainInteractions(Domain d,
                                                                 java.lang.String dir,
                                                                 java.lang.String fileName)
                                                          throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

classifyIntoOrientations

public static java.util.List<java.util.List<DomainInteraction>> classifyIntoOrientations(java.util.Collection<DomainInteraction> domainInteractions,
                                                                                         FamilyType ft,
                                                                                         int stampRMSD)
                                                                                  throws java.lang.Exception,
                                                                                         java.lang.InterruptedException

Throws:

java.lang.Exception

java.lang.InterruptedException

containsSameOrientation

public static boolean containsSameOrientation(DomainInteraction di0,
                                              java.util.Collection<DomainInteraction> domainInteractions,
                                              FamilyType ft,
                                              double iRMSDThreshold,
                                              java.lang.String dir)
                                       throws java.lang.Exception

This function checks to see if any of the domainInteractions in the list passed in are of the same orientation of the single domain interaction passed in.

Parameters:

di0 -

domainInteractions -

ft -

iRMSDThreshold -

dir -

Returns:

Throws:

java.lang.Exception