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

W

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

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

withLevels(int) - Method in class PIP.Domains.Family.HierarchicalFamily

write(Collection<Residue>, int, String) - Method in class PIP.IO.CreatePeripheralData.PDBFileChainBased

Core getiRMSD of this class which takes in a list of residues and writes them out in PDB file format to the PrintStream ps using residue position numbering which starts at count.

write(Collection<Residue>, int, String, Domain) - Method in class PIP.IO.CreatePeripheralData.PDBFileDomainBased

Core getiRMSD of this class which takes in a list of residues and writes them out in PDB file format to the PrintStream ps using residue position numbering which starts at count.

writeInteractingResiduesPlusNeighbours(Domain, int, Collection<Residue>) - Method in class PIP.IO.CreatePeripheralData.PDBFileChainBased

This getiRMSD was written to create templates of interaction sites, initally for the program Multiprot which needs the interacting residue (residue interacting with a residue in another domain) in addition to the residues at a distance of one residue upstream and one residue downstream of the interacting residue.

writeInteractingResiduesPlusNeighbours(Domain, int, Collection<Residue>, String) - Method in class PIP.IO.CreatePeripheralData.PDBFileDomainBased

This function was written to create templates of interaction sites, initally for the program Multiprot which needs the interacting residue (residue interacting with a residue in another domain) in addition to the residues at a distance of one residue upstream and one residue downstream of the interacting residue.

writeOutAtom(Atom, Residue, int, String, String[]) - Method in class PIP.IO.CreatePeripheralData.PDBFileChainBased

writeOutAtom(Atom, Residue, int, String, Domain, String[]) - Method in class PIP.IO.CreatePeripheralData.PDBFileDomainBased

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

writeOutRepresentativeCoordinates(double[][], String) - Method in class PIP.IO.CreatePeripheralData.PDBFile

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

writeResidues(List<Residue>) - Method in class PIP.IO.CreatePeripheralData.PDBFileChainBased

This is just a helper getiRMSD which essentially just calls the write(Collection residues, int count) getiRMSD using the default value of 0 for the count parameter.

writeResidues(List<Residue>, int) - Method in class PIP.IO.CreatePeripheralData.PDBFileChainBased

This is just a helper getiRMSD which essentially just calls the write(Collection residues, int count) getiRMSD using the count parameter.

writeResidues(List<Residue>, int, String) - Method in class PIP.IO.CreatePeripheralData.PDBFileChainBased

writeResidues(List<Residue>, Domain, String) - Method in class PIP.IO.CreatePeripheralData.PDBFileDomainBased

This is just a helper getiRMSD which essentially just calls the write(Collection residues, int count) getiRMSD using the default value of 0 for the count parameter.

writeResidues(Domain, String) - Method in class PIP.IO.CreatePeripheralData.PDBFileDomainBased

writeResidues(Domain) - Method in class PIP.IO.CreatePeripheralData.PDBFileDomainBased

writeResidues(List<Residue>, Domain, String, int) - Method in class PIP.IO.CreatePeripheralData.PDBFileDomainBased

writeTransformedCoordinates(Collection<Residue>, int, String, double[][]) - Method in class PIP.IO.CreatePeripheralData.PDBFileChainBased

writeTransformedCoordinates(Collection<Residue>, String, Domain, double[][], int) - Method in class PIP.IO.CreatePeripheralData.PDBFileDomainBased