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

R

Range<E> - Class in PIP.Collections

Range(List<E>, int, int) - Constructor for class PIP.Collections.Range

rangePresent(Domain, Chain, int, int) - Method in class PIP.IO.MSD.CSReaderNew

read(Assembly) - Method in class PIP.IO.MSD.DomainReader

read(int) - Method in class PIP.IO.MSD.EntryReader

Reads in Entry information from the MSD

read(Assembly) - Method in class PIP.IO.MSD.PfamReader

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

readInTransformations(String, String) - Static method in class PIP.IO.StampPackage.Transformations

readInts(Collection<Integer>, String) - Static method in class PIP.IO.IOUtility

readInVanDerWals() - Static method in class PIP.Domains.Interactions.DistanceInteraction

record(F, double) - Method in class PIP.Collections.Distribution.Distribution

record(F) - Method in class PIP.Collections.Distribution.Distribution

record(F, double) - Method in class PIP.Collections.Distribution.Histogram

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

remove() - Method in class PIP.Collections.PairsIterator

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

Removes a single instance of the specified element from this collection, if it is present (optional operation).

remove(int) - Method in class PIP.Collections.Persistent.AbstractList

Removes the element at the specified position in this list (optional operation).

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

Removes the mapping for this key from this map if present (optional operation).

remove(int) - Method in class PIP.Collections.Persistent.SArrayList

remove() - Method in class PIP.Collections.UniformSamplerIterator

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

Removes from this collection all of its elements that are contained in the specified collection (optional operation).

removeDuplicateDomains(List<Domain>) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

removeDuplicateISurfaces(List<InteractionSurface>) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

removeDuplicatesInSameAssembly(Collection<DomainInteraction>, FamilyType, boolean) - Static method in class PIP.Collections.General

This makes sure that the PDB interactions are added first and then the PQS interactions that are not in the same assembly as the PDB interactions!

removeDuplicatesInSameEntry(Collection<DomainInteraction>, FamilyType, boolean) - Static method in class PIP.Collections.General

This makes sure that the PDB interactions are added first and then the PQS interactions that are not in the same assembly as the PDB interactions!

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

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

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

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

removeInteractionsSameAssembly(List<DomainInteraction>, FamilyType) - Static method in class PIP.Collections.General

removeInteractionsSameEntry(List<DomainInteraction>, FamilyType) - Static method in class PIP.Collections.General

removeInteractionsSameOrientationWithinSameEntry(List<DomainInteraction>, FamilyType) - Static method in class PIP.Collections.General

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

Residue - Class in PIP.Core

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

ResidueName - Class in PIP.Core

ResidueName(String) - Constructor for class PIP.Core.ResidueName

ResidueNames - Class in PIP.Core

ResidueNames(boolean) - Constructor for class PIP.Core.ResidueNames

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

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

Retains only the elements in this collection that are contained in the specified collection (optional operation).

reversed() - Method in class PIP.Collections.Pair

RMSDComponents - Class in PIP.IO.StampPackage

RMSDComponents(Domain, List<Character>, Domain, List<Character>, double[][]) - Constructor for class PIP.IO.StampPackage.RMSDComponents

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

run() - Method in class PIP.IO.PymolScript

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

runCmd(String) - Static method in class PIP.IO.Bash

runCmd(String, String[]) - Static method in class PIP.IO.Bash

This getiRMSD runs stamp on the command line and deals with the fact that if the output of the program is over a certain size.

runCmd(String, String[], File) - Static method in class PIP.IO.Bash

RunStamp - Class in PIP.IO.StampPackage

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