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

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main(String[]) - Static method in class PIP.ExampleCode.ConnectionToJDODatabase

main(String[]) - Static method in class PIP.ExampleCode.ConnectionTOMSDDatabase

main(String[]) - Static method in class PIP.ExampleCode.IteratingThroughDataBasedOnDomainInteractions

main(String[]) - Static method in class PIP.ExampleCode.IteratingThroughDataBasedOnDomains

main(String[]) - Static method in class PIP.ExampleCode.IteratingThroughDataBasedOnEntryHeirarchy

main(String[]) - Static method in class PIP.IO.Blast.FormatDBFileCreator

main(String[]) - Static method in class PIP.IO.ClearLogs

main(String[]) - Static method in class PIP.IO.CreateJDODatabase.CreateDB

main(String[]) - Static method in class PIP.IO.CreateJDODatabase.PersistDatabase

main(String[]) - Static method in class PIP.IO.CreateJDODatabase.PersistDomainInteractions

This getiRMSD should be run after all of the data has been read in from the MSD i.e.

main(String[]) - Static method in class PIP.IO.CreateJDODatabase.PersistEntries

main(String[]) - Static method in class PIP.IO.CreateJDODatabase.PersistOritentationInteractions

main(String[]) - Static method in class PIP.IO.CreateJDODatabase.PersistPeripheral

main(String[]) - Static method in class PIP.IO.CreatePeripheralData.CheckAllOrientationFilesArePresent

main(String[]) - Static method in class PIP.IO.CreatePeripheralData.CreatePDBFiles

main(String[]) - Static method in class PIP.IO.CreatePeripheralData.GenerateOrientationFiles

main(String[]) - Static method in class PIP.IO.CreatePeripheralData.IdListCreator

main(String[]) - Static method in class PIP.IO.FixDatabases

main(String[]) - Static method in class PIP.IO.JoinResults

makeFamilyComparator() - Method in class PIP.Domains.Family.FamilyType

makeFamilyComparator() - Method in class PIP.Domains.Family.HFType

MapKeyComparator<K,V> - Class in PIP.Collections.Map

Just a useful class to compare the Keys of a Map

MapKeyComparator(Comparator<K>) - Constructor for class PIP.Collections.Map.MapKeyComparator

MapValueComparator<K,V> - Class in PIP.Collections.Map

Just a useful class to compare the Values of a Map

MapValueComparator(Comparator) - Constructor for class PIP.Collections.Map.MapValueComparator

MathUtility - Class in PIP.Core

MathUtility() - Constructor for class PIP.Core.MathUtility

MatrixFactory - Class in PIP.IO.StampPackage

MatrixFactory() - Constructor for class PIP.IO.StampPackage.MatrixFactory

Measure - Interface in PIP.Domains.Interactions

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

movePDBFilesIntoDifferentDirectory(List<DomainInteraction>, String, String) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

moveResultsToDifferentDirectory(List<Stamper>, String, String, String, String, String) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

moveScanFile(String, String, String) - Static method in class PIP.IO.StampPackage.RunStamp

MSDID - Interface in PIP.Core

MultiMap<K,V extends java.util.Collection> - Class in PIP.Collections

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

MultiMap(Factory) - Constructor for class PIP.Collections.MultiMap

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

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