A B C D E F G H I J K L M N O P Q R S T U V W

C

calculateAssemblySerial(int) - Method in class PIP.Core.Entry

calculateMaxDistance(Map<String, Map<String, Double>>, Atom, Atom, double) - Static method in class PIP.Domains.Interactions.DistanceInteraction

calculateRMSDforSetOfCoordinates(double[][], double[][]) - Static method in class PIP.IO.StampPackage.IRMSDCalc

Cath - Class in PIP.Domains.Family

Cath(String) - Constructor for class PIP.Domains.Family.Cath

Cath(int, int, int, int, int) - Constructor for class PIP.Domains.Family.Cath

CathReaderNew - Class in PIP.IO.MSD

CathReaderNew(Connection) - Constructor for class PIP.IO.MSD.CathReaderNew

centerOfGravity(double[][]) - Static method in class PIP.IO.StampPackage.IRMSDCalc

Chain - Class in PIP.Core

Chain(int) - Constructor for class PIP.Core.Chain

CheckAllOrientationFilesArePresent - Class in PIP.IO.CreatePeripheralData

CheckAllOrientationFilesArePresent() - Constructor for class PIP.IO.CreatePeripheralData.CheckAllOrientationFilesArePresent

classifyByInterfaceAndStoreResults(Collection<DomainInteraction>, FamilyType, int, File, boolean) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

ClassifyByOrientation - Class in PIP.Domains.Orientation

ClassifyByOrientation() - Constructor for class PIP.Domains.Orientation.ClassifyByOrientation

classifyInteractionsIntoThoseWithSameSequence(List<List<DomainInteraction>>, List<DomainInteraction>, int) - Static method in class PIP.Domains.SequenceSimilarity.SequenceClassifiedDIs

classifyIntoOrientations(Collection<DomainInteraction>, FamilyType, int) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

cleanAlignments(String, String, int, List<Domain>) - Static method in class PIP.IO.StampPackage.Alignments

cleanDomainDefsFile(String, String, List<Domain>) - Static method in class PIP.IO.StampPackage.RunStamp

cleanStampScanFile(String, String, List<Domain>) - Static method in class PIP.IO.StampPackage.RunStamp

clear() - Method in class PIP.Collections.Persistent.AbstractCollection

Removes all of the elements from this collection (optional operation).

clear() - Method in class PIP.Collections.Persistent.AbstractList

Removes all of the elements from this collection (optional operation).

clear() - Method in class PIP.Collections.Persistent.AbstractMap

Removes all mappings from this map (optional operation).

ClearLogs - Class in PIP.IO

The class is called ClearLogs because once the DB has be unlocked successfully there is no longer a Log file (File called same as DB but with extension .nlg) for the DB.

ClearLogs() - Constructor for class PIP.IO.ClearLogs

cloneListIterator(List<E>, ListIterator<E>) - Static method in class PIP.Collections.CollectionUtility

clusterDir() - Static method in class PIP.Core.App

clusterDir(String) - Static method in class PIP.Core.App

clusterDirSimple() - Static method in class PIP.Core.App

CollectionFactory - Class in PIP.Collections

CollectionSizeComparator - Class in PIP.Collections

CollectionSizeComparator() - Constructor for class PIP.Collections.CollectionSizeComparator

CollectionUtility - Class in PIP.Collections

CollectionUtility() - Constructor for class PIP.Collections.CollectionUtility

colourAtoms(Collection<Atom>, PrintStream, String) - Static method in class PIP.IO.PymolScript

colourChain(Chain, PrintStream, String) - Static method in class PIP.IO.PymolScript

colourResidues(Domain, PrintStream, String) - Static method in class PIP.IO.PymolScript

colourResidues(Collection<Residue>, PrintStream, String) - Static method in class PIP.IO.PymolScript

colourResiduesToRename(DomainInteraction, Domain, PrintStream) - Static method in class PIP.IO.PymolScript

ComparatorUtility - Class in PIP.Collections

ComparatorUtility() - Constructor for class PIP.Collections.ComparatorUtility

compare(Collection, Collection) - Method in class PIP.Collections.CollectionSizeComparator

compare(Integer, Integer) - Method in class PIP.Collections.IntegerComparator

compare(Map.Entry<K, V>, Map.Entry<K, V>) - Method in class PIP.Collections.Map.MapKeyComparator

compare(Map.Entry<K, V>, Map.Entry<K, V>) - Method in class PIP.Collections.Map.MapValueComparator

compare(Object, Object) - Method in class PIP.Domains.Family.FamilyComparator

compare(HierarchicalFamily, HierarchicalFamily) - Method in class PIP.Domains.Family.SubfamilyComparator

compare(Domain, Domain) - Method in class PIP.Domains.HighestResolutionDomainComp

compare(DomainInteraction, DomainInteraction) - Method in class PIP.Domains.HighestResolutionInteractionComp

compare(Map.Entry<Family, Collection<DomainInteraction>>, Map.Entry<Family, Collection<DomainInteraction>>) - Method in class PIP.Domains.Interactions.NumberOfUniqueDomainInteractionsComparator

compareAt(int, HierarchicalFamily, HierarchicalFamily) - Static method in class PIP.Domains.Family.HierarchicalFamily

compareOnKeyValue(Comparator) - Static method in class PIP.Collections.ComparatorUtility

compareOnMapValue(Comparator) - Static method in class PIP.Collections.ComparatorUtility

compareTo(Family) - Method in class PIP.Domains.Family.HierarchicalFamily

compressedObjectInputStream(String) - Static method in class PIP.IO.IOUtility

compressedObjectOutputStream(String) - Static method in class PIP.IO.IOUtility

ConnectionToJDODatabase - Class in PIP.ExampleCode

This class simply shows how to connect to the PIP database.

ConnectionToJDODatabase() - Constructor for class PIP.ExampleCode.ConnectionToJDODatabase

ConnectionTOMSDDatabase - Class in PIP.ExampleCode

This class simply shows an example of how to connect to the MSD and run a sql querry.

ConnectionTOMSDDatabase() - Constructor for class PIP.ExampleCode.ConnectionTOMSDDatabase

contains(Object) - Method in class PIP.Collections.Persistent.AbstractCollection

Returns true if this collection contains the specified element.

containsAll(Collection<?>) - Method in class PIP.Collections.Persistent.AbstractCollection

Returns true if this collection contains all of the elements in the specified collection.

containsDomainsOfDomainDefinition(Class) - Method in class PIP.Core.Entry

containsIndex(int) - Method in class PIP.Collections.Range

containsKey(Object) - Method in class PIP.Collections.Persistent.AbstractMap

Returns true if this map contains a mapping for the specified key.

containsNucAcids() - Method in class PIP.Domains.Domain

containsPQSInteractions() - Method in class PIP.Domains.Interactions.InteractionSourceType

containsSameOrientation(DomainInteraction, Collection<DomainInteraction>, FamilyType, double, String) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

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.

containsValue(Object) - Method in class PIP.Collections.Persistent.AbstractMap

Returns true if this map maps one or more keys to this value.

convert2DArrayTo1D(double[][], double[]) - Method in class PIP.Domains.Orientation.OrientatedDomInt

convertStampOutputToJalviewFormat(String, String, int, String) - Static method in class PIP.IO.StampPackage.Alignments

This fucntion takes in a Stamp output and removes all of the stuff that is not required....

copyIf(Collection<E>, Collection<E>, Predicate) - Static method in class PIP.Collections.CollectionUtility

create() - Method in class PIP.Collections.SArrayListFactory

create(Pair<Domain>) - Method in class PIP.Domains.Interactions.DistanceFactory

create(Pair<Domain>) - Method in interface PIP.Domains.Interactions.DomainInteractionFactory

CreateDB - Class in PIP.IO.CreateJDODatabase

This is a helper class which calls all the classes in the right order to create the database from scratch

CreateDB() - Constructor for class PIP.IO.CreateJDODatabase.CreateDB

createFormatDBFilesForBlast(FamilyType) - Static method in class PIP.IO.Blast.FormatDBFileCreator

createGroupsFiles(List<InteractionSurface>, Map<String, List<Character>>, String) - Static method in class PIP.IO.StampPackage.Alignments

createHmmerFiles(FamilyType) - Static method in class PIP.IO.Blast.FormatDBFileCreator

createIntList(Connection, String) - Static method in class PIP.IO.JDBCUtility

createOrdered(DomainInteraction, boolean) - Static method in class PIP.Domains.Interactions.DomainInteractionOrdered

CreatePDBFiles - Class in PIP.IO.CreatePeripheralData

CreatePDBFiles(String[]) - Constructor for class PIP.IO.CreatePeripheralData.CreatePDBFiles

createResultsFilesForSingleDomainInteractions(Domain, String, String) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

CSReaderNew - Class in PIP.IO.MSD

CSReaderNew(Connection, String) - Constructor for class PIP.IO.MSD.CSReaderNew