Index (singa-structure 0.3.3 API)

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

A

AbstractRepresentationScheme - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations: This abstract implementation provide a fallback solution to compute the centroid of a LeafSubstructure, iff the specified representation fails.
AbstractRepresentationScheme() - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.AbstractRepresentationScheme
ACTINIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
add(Quantity<MolarMass>) - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
addAtom(OakAtom) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
addAtom(String, String, Vector3D) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure: Adds an Atom to the Structure FIXME: atom serial overflow may happen (if exceeds 9999)
addBondBetween(OakBond, OakAtom, OakAtom) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure: Adds a bond connecting the the given atoms.
addBondBetween(OakAtom, OakAtom) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
addBondBetween(OakAtom, OakAtom, BondType) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
addChain(OakChain) - Method in class de.bioforscher.singa.structure.model.oak.OakModel
addEdgeBetween(int, MoleculeAtom, MoleculeAtom) - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraph
addEdgeBetween(MoleculeAtom, MoleculeAtom) - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraph
addEdgeBetween(MoleculeAtom, MoleculeAtom, MoleculeBondType) - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraph
addExchangeableFamily(FamilyType) - Method in interface de.bioforscher.singa.structure.model.oak.Exchangeable: Adds an exchangeable StructuralFamily.
addExchangeableFamily(FamilyType) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
addExchangeableFamily(LeafIdentifier, MatcherFamily) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif: For a given LeafIdentifier a possible exchange is added.
addExchangeableFamily(LeafIdentifier, NucleotideFamily) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif: For a given LeafIdentifier a possible exchange is added.
addExchangeableFamily(LeafIdentifier, AminoAcidFamily) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif: For a given LeafIdentifier a possible exchange is added.
addExchangeableFamilyToAll(AminoAcidFamily) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif: Assigns an AminoAcidFamily to all members of this motif as exchange.
addExchangeableFamilyToAll(NucleotideFamily) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif: Assigns an NucleotideFamily to all members of this motif as exchange.
addExchangeableFamilyToAll(MatcherFamily) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif: Assigns each member of a MatcherFamily to all members of this motif as exchange.
addInteraction(Interaction) - Method in class de.bioforscher.singa.structure.parser.plip.InteractionContainer: Adds an interaction to this container.
addLeafSubstructure(OakLeafSubstructure, boolean) - Method in class de.bioforscher.singa.structure.model.oak.OakChain
addLeafSubstructure(OakLeafSubstructure) - Method in class de.bioforscher.singa.structure.model.oak.OakChain
addLeafSubstructure(LeafSubstructure) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif
addModel(OakModel) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
addNeighbour(OakAtom) - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
addNextAtom(char) - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraph
addNextAtom(String) - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraph
addNextAtom(Element) - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraph
addNextAtom(Element, int) - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraph
addNextAtom(Element, int, int) - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraph
addToConsensusDistance(double) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
AffinityAlignment - Class in de.bioforscher.singa.structure.algorithms.superimposition.affinity: An affinity alignment of same-sized StructuralMotifs can be used to cluster them according their geometric similarity in a multi-structure alignment manner.
AffinityAlignment.AtomStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.affinity
AffinityAlignment.Builder - Class in de.bioforscher.singa.structure.algorithms.superimposition.affinity
AffinityAlignment.InputStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.affinity
AffinityAlignment.ParameterStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.affinity
ALANINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
alignWithinClusters(boolean) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.Builder
alignWithinClusters(boolean) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.ParameterStep
alignWithinClusters(boolean) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.Builder
alignWithinClusters(boolean) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.ParameterStep
all() - Method in class de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder
all() - Method in interface de.bioforscher.singa.structure.parser.pfam.PfamParser.ChainStep: Parse all chains annotated in Pfam.
ALL_AMINO_ACIDS - Static variable in enum de.bioforscher.singa.structure.model.families.MatcherFamily
allChains() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiChainStep: Parses all chains.
allChains() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.SingleChainStep: Parses all chains.
allModels() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiBranchStep: Short cut to parse all models.
allModels() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.SingleBranchStep: Short cut to parse all models.
AlphaCarbonRepresentationScheme - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations: An implementation to represent a given LeafSubstructure by its alpha carbon.
AlphaCarbonRepresentationScheme() - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.AlphaCarbonRepresentationScheme
ALUMINIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
AMERICIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
AminoAcid - Interface in de.bioforscher.singa.structure.model.interfaces: A specific type of LeafSubstructure, representing amino acids.
aminoAcid(int) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.ResidueStep
aminoAcid(int) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
AminoAcidFamily - Enum in de.bioforscher.singa.structure.model.families: A AminoAcidFamily contains the general information of a type of amino acid.
AminoAcids - Class in de.bioforscher.singa.structure.model.oak: Utility methods for AminoAcids.
ANTIMONY - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
applyTo(List<LeafSubstructure<?>>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition
ARGININE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
ARGON - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
ARSENIC - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
asAnion(int) - Method in class de.bioforscher.singa.structure.elements.Element: Converts this element into an ion (anion) by increasing its electron count.
asCation(int) - Method in class de.bioforscher.singa.structure.elements.Element: Converts this element into an ion (cation) by decreasing its electron count.
asIon(int) - Method in class de.bioforscher.singa.structure.elements.Element: Converts this element into an ion (cation) by decreasing its electron count.
asIsotope(int) - Method in class de.bioforscher.singa.structure.elements.Element: Converts this element into an isotope by adjusting its neutron count.
ASPARAGINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
ASPARTIC_ACID_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
assembleAtom(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.AtomToken
assemblePDBLine(LeafSubstructure) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.AtomToken
assemblePDBLine(LeafSubstructure) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ChainTerminatorToken: Creates a terminate record from the last leaf in the consecutive part of a chain.
assemblePDBLine(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.HeaderToken
assemblePDBLines(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.TitleToken
assignComplexExchanges(StructuralMotif, EnumSet<MatcherFamily>) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralMotifs: Assigns the given EnumSet of exchanges to the specified StructuralMotif.
ASTATINE - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
asType(Class<T>) - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
Atom - Interface in de.bioforscher.singa.structure.model.interfaces: An Atom is the physical instance of an atom in three dimensional space.
atom(int) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.AtomStep
atom(int) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
AtomConditions() - Constructor for class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphismFinder.AtomConditions
AtomContainer - Interface in de.bioforscher.singa.structure.model.interfaces: Everything that contains Atoms.
atomContainer(int) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.ResidueStep
atomContainer(int) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
atomFilter(Predicate<Atom>) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.AtomStep: Defines the StructuralEntityFilter.AtomFilter to be used for the computed alignments.
atomFilter(Predicate<Atom>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.Builder
atomFilter(Predicate<Atom>) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.AtomStep: Defines the StructuralEntityFilter.AtomFilter to be used during consensus calculation.
atomFilter(Predicate<Atom>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.Builder
atomFilter(Predicate<Atom>) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.AtomStep: Defines a StructuralEntityFilter.AtomFilter filter to be used for the Fit3D alignment (e.g.
atomFilter(Predicate<Atom>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
AtomFilter() - Constructor for class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
AtomName - Enum in de.bioforscher.singa.structure.model.oak: Most (some) of the AtomNames in the PDB.
AtomToken - Enum in de.bioforscher.singa.structure.parser.pdb.structures.tokens: The atom and hetatm token.

B

BARIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
BERKELIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
BERYLLIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
BetaCarbonRepresentationScheme - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations: An implementation to represent a given LeafSubstructure by its beta carbon.
BetaCarbonRepresentationScheme() - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.BetaCarbonRepresentationScheme
BISMUTH - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
BOHRIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
BondConditions() - Constructor for class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphismFinder.BondConditions
BondType - Enum in de.bioforscher.singa.structure.model.oak
BORON - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
BROMINE - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
Builder() - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.Builder
Builder() - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
Builder() - Constructor for class de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder

C

CADMIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
CALCIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
calculateAtomDistanceMatrix(AtomContainer) - Static method in class de.bioforscher.singa.structure.model.oak.Structures: Returns the distance matrix of the given Atoms.
calculateAtomDistanceMatrix(List<Atom>) - Static method in class de.bioforscher.singa.structure.model.oak.Structures: Returns the distance matrix of the given Atoms.
calculateDistanceMatrix(LeafSubstructureContainer) - Static method in class de.bioforscher.singa.structure.model.oak.Structures: Returns the distance matrix of the given LeafSubstructureContainer.
calculateExtent(LeafSubstructureContainer) - Static method in class de.bioforscher.singa.structure.model.oak.Structures: Returns the maximal extent of the given LeafSubstructureContainer.
calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>, Predicate<Atom>) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>, RepresentationScheme) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateIdealSubstructureSuperimposition(LeafSubstructureContainer, LeafSubstructureContainer) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateIdealSubstructureSuperimposition(LeafSubstructureContainer, LeafSubstructureContainer, Predicate<Atom>) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateIdealSubstructureSuperimposition(LeafSubstructureContainer, LeafSubstructureContainer, RepresentationScheme) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>, SubstitutionMatrix, boolean) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>, Predicate<Atom>, SubstitutionMatrix, boolean) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>, RepresentationScheme, SubstitutionMatrix, boolean) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer, LeafSubstructureContainer, SubstitutionMatrix, boolean) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer, LeafSubstructureContainer, Predicate<Atom>, SubstitutionMatrix, boolean) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer, LeafSubstructureContainer, RepresentationScheme, SubstitutionMatrix, boolean) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculatePvalues(List<Fit3DMatch>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.FofanovEstimation
calculatePvalues(List<Fit3DMatch>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.StarkEstimation
calculatePvalues(List<Fit3DMatch>) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.StatisticalModel
calculateRmsdMatrix(List<StructuralMotif>, boolean) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralMotifs: Performs a superimposition of given StructuralMotifs using arbitrary atoms and returns the RMSD distance matrix between all elements.
calculateRmsdMatrix(List<StructuralMotif>, Predicate<Atom>, boolean) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralMotifs: Performs a superimposition of given StructuralMotifs using the specified StructuralEntityFilter.AtomFilter and returns the RMSD distance matrix between all elements.
calculateSquaredDistanceMatrix(LeafSubstructureContainer) - Static method in class de.bioforscher.singa.structure.model.oak.Structures: Returns the squared distance matrix of the given LeafSubstructureContainer.
calculateSquaredExtent(LeafSubstructureContainer) - Static method in class de.bioforscher.singa.structure.model.oak.Structures: Returns the maximal squared extent of the given LeafSubstructureContainer.
calculateSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.FragmentSubstructureSuperimposer
calculateSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>, BiFunction<MoleculeAtom, MoleculeAtom, Boolean>, BiFunction<MoleculeBond, MoleculeBond, Boolean>) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.FragmentSubstructureSuperimposer
calculateSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>, Predicate<Atom>) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateSubstructureSuperimposition(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>, RepresentationScheme) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateSubstructureSuperimposition(LeafSubstructureContainer, LeafSubstructureContainer) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateSubstructureSuperimposition(LeafSubstructureContainer, LeafSubstructureContainer, Predicate<Atom>) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateSubstructureSuperimposition(LeafSubstructureContainer, LeafSubstructureContainer, RepresentationScheme) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
calculateSuperimposition() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer: Finds the superimposition for a list of LeafSubstructure according to their input order
CALIFORNIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
candidate - Variable in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
CARBON - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
CentroidRepresentationScheme - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations: An implementation to represent a given LeafSubstructure by its centroid EXCLUDING hydrogen.
CentroidRepresentationScheme() - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.CentroidRepresentationScheme
CERIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
CESIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
Chain - Interface in de.bioforscher.singa.structure.model.interfaces: Chains that represent one continuous macro molecule (most often the biggest macro molecules and its ligands are collected in one model).
chain(String) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiChainStep: If only a single chain should be parsed, choose it here.
chain(String) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.ChainStep
chain(String) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
CHAIN_TERMINATOR - Static variable in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.TerminatorTokens
ChainContainer - Interface in de.bioforscher.singa.structure.model.interfaces: Everything that contains Chains.
ChainFilter() - Constructor for class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.ChainFilter
chainIdentifier(String) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.SingleChainStep: If only a single chain should be parsed, choose it here.
chainList(Path) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.AdditionalLocalSourceStep: Reads the provided chainIdentifier list from a file.
chainList(Path, String) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.AdditionalLocalSourceStep: Reads the provided chainIdentifier list from a file.
chainList(Path) - Method in class de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder
chainList(Path, String) - Method in class de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder
chainList(Path) - Method in interface de.bioforscher.singa.structure.parser.pfam.PfamParser.ChainStep: Parse all chains annotated in Pfam and listed in the given chain list.
chainList(Path, String) - Method in interface de.bioforscher.singa.structure.parser.pfam.PfamParser.ChainStep: Parse all chains annotated in Pfam and listed in the given chain list with the custom separator.
chains() - Method in class de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder
chains() - Method in interface de.bioforscher.singa.structure.parser.pfam.PfamParser.DomainStep: Parse all chains carrying one Pfam domain with the desired Pfam-ID.
ChainTerminatorToken - Enum in de.bioforscher.singa.structure.parser.pdb.structures.tokens
characters(char[], int, int) - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
characters(char[], int, int) - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
CHLORINE - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
CHROMIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
CifFileParser - Class in de.bioforscher.singa.structure.parser.pdb.ligands
clusterCutoff(double) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.Builder
clusterCutoff(double) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.ParameterStep
COBALT - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
compareTo(Fit3DMatch) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
compareTo(LigandFamily) - Method in class de.bioforscher.singa.structure.model.families.LigandFamily
compareTo(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
compareTo(UniqueAtomIdentifer) - Method in class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
composePdbRepresentation(Structure) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureRepresentation: Creates a pdb representation of the given structure.
composePdbRepresentation(List<LeafSubstructure<?>>) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureRepresentation: Creates a pdb representation of the given structure.
composePdbRepresentation(OakModel) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureRepresentation: Creates a representation of the given model.
connectChainBackbone() - Method in class de.bioforscher.singa.structure.model.oak.OakChain
connectHydrogens(boolean) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option to true will try to connect hydrogen atom tho their respective partners.

Default value: false
connectNucleotideBonds(OakNucleotide, OakNucleotide) - Method in class de.bioforscher.singa.structure.model.oak.OakChain
connectPeptideBonds(OakAminoAcid, OakAminoAcid) - Method in class de.bioforscher.singa.structure.model.oak.OakChain: Connects two residues, using the Backbone Carbon (C) of the source residue and the Backbone Nitrogen (N) of the target residue.
connectsAtom(OakAtom) - Method in class de.bioforscher.singa.structure.model.oak.OakBond
ConsensusAlignment - Class in de.bioforscher.singa.structure.algorithms.superimposition.consensus: A consensus alignment of same-sized StructuralMotifs can be used to cluster them according their geometric similarity in a multi-structure alignment manner as described in:
ConsensusBuilder - Class in de.bioforscher.singa.structure.algorithms.superimposition.consensus: A builder that guides through the creation of a ConsensusAlignment.
ConsensusBuilder.AtomStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.consensus
ConsensusBuilder.Builder - Class in de.bioforscher.singa.structure.algorithms.superimposition.consensus
ConsensusBuilder.InputStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.consensus
ConsensusBuilder.ParameterStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.consensus
ConsensusContainer - Class in de.bioforscher.singa.structure.algorithms.superimposition.consensus: A container encapsulating a StructuralMotif with a BinaryTree that represents its associated consensus tree.
ConsensusContainer(StructuralMotif, boolean) - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
ConsensusException - Exception in de.bioforscher.singa.structure.algorithms.superimposition.consensus
ConsensusException(String) - Constructor for exception de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusException
containsAtomWithName(String) - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure
containsAtomWithName(String) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
containsAtomWithName(String) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
containsExpectedAtoms(List<Atom>, AminoAcidFamily) - Method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily: Returns true if the set of AtomFilter contains only Atom names, that can occur in the given residue type.
convertToSpheres(AtomContainer) - Static method in class de.bioforscher.singa.structure.model.oak.Structures
COPPER - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
countAtomsOfElement(MoleculeGraph, Element) - Static method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraphs
create() - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment
create() - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder: Creates a new instance of the actual ConsensusBuilder.Builder.
create() - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder: Creates a new instance of the actual Fit3DBuilder.Builder.
create() - Static method in class de.bioforscher.singa.structure.parser.pfam.PfamParser
createAminoAcidFromAtoms(LeafIdentifier, AminoAcidFamily, Map<String, OakAtom>, StructureParserOptions) - Static method in class de.bioforscher.singa.structure.model.oak.LeafSubstructureFactory
createEdges(boolean) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option true will connect the molecule with bonds.
createLeafSubstructure(LeafIdentifier, StructuralFamily) - Static method in class de.bioforscher.singa.structure.model.oak.LeafSubstructureFactory
createMoleculeGraphFromStructure(OakLeafSubstructure<?>) - Static method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraphs
createNucleotideFromAtoms(LeafIdentifier, NucleotideFamily, Map<String, OakAtom>, StructureParserOptions) - Static method in class de.bioforscher.singa.structure.model.oak.LeafSubstructureFactory
createRepresentationScheme(RepresentationSchemeType) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.RepresentationSchemeFactory: Creates a RepresentationScheme for the given RepresentationSchemeType.
createVirtualCBAtom(AminoAcid) - Static method in class de.bioforscher.singa.structure.model.oak.AminoAcids: This creates a virtual beta carbon for glycine by superimposing alanine.
CSV_HEADER - Static variable in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
CURIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
cutoffScore(double) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
cutoffScore(double) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.SiteParameterConfigurationStep: The cutoff score that should be used when extending the site alignment.
CYSTEINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName

D

de.bioforscher.singa.structure.algorithms.gyration - package de.bioforscher.singa.structure.algorithms.gyration
de.bioforscher.singa.structure.algorithms.molecules - package de.bioforscher.singa.structure.algorithms.molecules
de.bioforscher.singa.structure.algorithms.superimposition - package de.bioforscher.singa.structure.algorithms.superimposition
de.bioforscher.singa.structure.algorithms.superimposition.affinity - package de.bioforscher.singa.structure.algorithms.superimposition.affinity
de.bioforscher.singa.structure.algorithms.superimposition.consensus - package de.bioforscher.singa.structure.algorithms.superimposition.consensus
de.bioforscher.singa.structure.algorithms.superimposition.fit3d - package de.bioforscher.singa.structure.algorithms.superimposition.fit3d
de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations - package de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations
de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics - package de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics
de.bioforscher.singa.structure.algorithms.superimposition.scores - package de.bioforscher.singa.structure.algorithms.superimposition.scores
de.bioforscher.singa.structure.elements - package de.bioforscher.singa.structure.elements
de.bioforscher.singa.structure.features.molarmass - package de.bioforscher.singa.structure.features.molarmass
de.bioforscher.singa.structure.model.families - package de.bioforscher.singa.structure.model.families
de.bioforscher.singa.structure.model.identifiers - package de.bioforscher.singa.structure.model.identifiers
de.bioforscher.singa.structure.model.interfaces - package de.bioforscher.singa.structure.model.interfaces
de.bioforscher.singa.structure.model.mmtf - package de.bioforscher.singa.structure.model.mmtf
de.bioforscher.singa.structure.model.molecules - package de.bioforscher.singa.structure.model.molecules
de.bioforscher.singa.structure.model.oak - package de.bioforscher.singa.structure.model.oak
de.bioforscher.singa.structure.parser.pdb.ligands - package de.bioforscher.singa.structure.parser.pdb.ligands
de.bioforscher.singa.structure.parser.pdb.rest - package de.bioforscher.singa.structure.parser.pdb.rest
de.bioforscher.singa.structure.parser.pdb.rest.cluster - package de.bioforscher.singa.structure.parser.pdb.rest.cluster
de.bioforscher.singa.structure.parser.pdb.structures - package de.bioforscher.singa.structure.parser.pdb.structures
de.bioforscher.singa.structure.parser.pdb.structures.tokens - package de.bioforscher.singa.structure.parser.pdb.structures.tokens
de.bioforscher.singa.structure.parser.pfam - package de.bioforscher.singa.structure.parser.pfam
de.bioforscher.singa.structure.parser.pfam.tokens - package de.bioforscher.singa.structure.parser.pfam.tokens
de.bioforscher.singa.structure.parser.plip - package de.bioforscher.singa.structure.parser.plip
de.bioforscher.singa.structure.parser.sifts - package de.bioforscher.singa.structure.parser.sifts
DEFAULT_ALTERNATIVE_POSITION_CODE - Static variable in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
DEFAULT_CHAIN_IDENTIFIER - Static variable in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
DEFAULT_INSERTION_CODE - Static variable in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
DEFAULT_LEAF_IDENTIFIER - Static variable in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
DEFAULT_MODEL_IDENTIFIER - Static variable in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
DEFAULT_PDB_IDENTIFIER - Static variable in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
DEFAULT_REFERENCE_SIZE - Static variable in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.FofanovEstimation: The number of chains in the BLASTe-80 nrpdb dataset according to VAST as of 2017-10-17.
defaultBoundingBox - Static variable in class de.bioforscher.singa.structure.model.molecules.MoleculeGraphs
defineAtoms() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.FragmentSubstructureSuperimposer
defineAtoms() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer: Method to define the intersecting Atoms that should be used for the alignment.
determine(StructuralMotif) - Static method in enum de.bioforscher.singa.structure.model.oak.StructuralMotif.Type
determineEpsilon(StructuralMotif, double) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.FofanovEstimation: This calculates the cutoff epsilon up to which the RMSD distribution should be sampled for a desired model correctness.
determineEpsilon(int, double) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.FofanovEstimation: This calculates the cutoff epsilon up to which the RMSD distribution should be sampled for a desired model correctness.
determineRepresentingAtom(LeafSubstructure<?>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.AlphaCarbonRepresentationScheme
determineRepresentingAtom(LeafSubstructure<?>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.BetaCarbonRepresentationScheme
determineRepresentingAtom(LeafSubstructure<?>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.CentroidRepresentationScheme
determineRepresentingAtom(LeafSubstructure<?>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.LastHeavySidechainRepresentationScheme
determineRepresentingAtom(LeafSubstructure<?>) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.RepresentationScheme: Determined the representing Atom for the concrete implementation.
determineRepresentingAtom(LeafSubstructure<?>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.SideChainCentroidRepresentationScheme
DEUTERIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
distanceTolerance(double) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
distanceTolerance(double) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.ParameterStep: Defines the distance tolerance that is accepted when extracting local environments.
divide(Quantity<?>) - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
divide(Number) - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
domains() - Method in class de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder
domains() - Method in interface de.bioforscher.singa.structure.parser.pfam.PfamParser.DomainStep: Parse only the domains.
DUBNIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
DYSPROSIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider

E

EINSTEINIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
ElectronConfiguration - Class in de.bioforscher.singa.structure.elements
ElectronConfiguration() - Constructor for class de.bioforscher.singa.structure.elements.ElectronConfiguration
ElectronConfiguration.AtomicOrbital - Enum in de.bioforscher.singa.structure.elements
Element - Class in de.bioforscher.singa.structure.elements: A chemical element or element is a species of atoms having the same number of protons.
Element(String, String, int, Quantity<MolarMass>, String) - Constructor for class de.bioforscher.singa.structure.elements.Element: Creates a new Element with name, symbol, proton number and atomic weight.
Element(String, String, int, double, String, double) - Constructor for class de.bioforscher.singa.structure.elements.Element: Creates a new Element with name, symbol, proton number and atomic weight in g/mol.
Element(String, String, int, double, String) - Constructor for class de.bioforscher.singa.structure.elements.Element
ElementProvider - Class in de.bioforscher.singa.structure.elements: This library provides Elements 1 (Hydrogen) to 111 (Roentgenium) with their names, symbols, atomic numbers, and atomic mass.
ElementProvider() - Constructor for class de.bioforscher.singa.structure.elements.ElementProvider
endDocument() - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
endDocument() - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
endElement(String, String, String) - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
endElement(String, String, String) - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
endLine(String) - Static method in interface de.bioforscher.singa.structure.parser.pdb.structures.tokens.PDBToken
endPrefixMapping(String) - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
endPrefixMapping(String) - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
equals(Object) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
equals(Object) - Method in class de.bioforscher.singa.structure.elements.Element
equals(Object) - Method in class de.bioforscher.singa.structure.model.families.LigandFamily
equals(Object) - Method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
equals(Object) - Method in class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
equals(Object) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
equals(Object) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
equals(Object) - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
equals(Object) - Method in class de.bioforscher.singa.structure.model.oak.OakBond
equals(Object) - Method in class de.bioforscher.singa.structure.model.oak.OakChain
equals(Object) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
equals(Object) - Method in class de.bioforscher.singa.structure.model.oak.OakModel
equals(Object) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
ERBIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
EUROPIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
everything() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiChainStep: Shortcut to parse all chains.
everything() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.SingleChainStep: Shortcut to parse all chains.
Exchangeable<FamilyType extends StructuralFamily> - Interface in de.bioforscher.singa.structure.model.oak: Exchangeable defines an entity that is exchangeable in terms of mapping another label or a set of other labels to that entity.
exchangeableFamilies - Variable in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure: The families to which the LeafSubstructure can be exchanged.
exhaustive() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
exhaustive() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.SiteConfigurationStep: Guarantees to find the ideal alignment of the input sites.
extract(String) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.tokens.PDBToken: Extracts a value from pdb line.
extract(String) - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.TitleToken
extract(String) - Method in interface de.bioforscher.singa.structure.parser.pfam.tokens.PfamToken
extractFirst(String) - Static method in class de.bioforscher.singa.structure.model.identifiers.PDBIdentifier: Extracts the first occurrence of any PDB identifier from a string.
extractValueFromPDBLine(String, PDBToken) - Static method in interface de.bioforscher.singa.structure.parser.pdb.structures.tokens.PDBToken: Extracts a value from a pdb line, given a token and line to extract from.
extractValueFromPfamLine(String, PfamToken) - Static method in interface de.bioforscher.singa.structure.parser.pfam.tokens.PfamToken

F

family - Variable in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure: The structural family of this entity
FERMIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
file(File) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalSourceStep: The file to parse.
fileLocation(String) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalSourceStep: The location of a file as a sting.
fileLocations(List<String>) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalSourceStep: The location of files as strings.
files(List<File>) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalSourceStep: The files to parse.
filterEnvironments() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
filterEnvironments() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.ParameterStep: Enables pre-filtering of extracted environments, i.e.
findAromaticPath(MoleculeGraph) - Static method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculePathFinder
findMultiPathInMolecule(MoleculeGraph, LinkedList<Set<Element>>) - Static method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculePathFinder
findMultiPathOfElements(MoleculeGraph, LinkedList<Set<Element>>) - Static method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraphs
findPathInMolecule(MoleculeGraph, LinkedList<Element>) - Static method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculePathFinder
findPathOfElements(MoleculeGraph, LinkedList<Element>) - Static method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraphs
Fit3D - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d: Represents an instance of the Fit3D algorithm.
Fit3DAlignment - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d: An implementation of the Fit3D algorithm for substructure search.
Fit3DAlignmentBatch - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d: A parallel version of the Fit3DAlignment for substructure search in a set of target structures.
Fit3DBuilder - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d: A builder that guides through the creation of a Fit3D alignment.
Fit3DBuilder.AtomStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d
Fit3DBuilder.BatchParameterStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d
Fit3DBuilder.Builder - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d
Fit3DBuilder.ParameterStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d
Fit3DBuilder.QueryStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d
Fit3DBuilder.SiteConfigurationStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d
Fit3DBuilder.SiteParameterConfigurationStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d
Fit3DBuilder.SiteStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d
Fit3DBuilder.TargetStep - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d
Fit3DException - Exception in de.bioforscher.singa.structure.algorithms.superimposition.fit3d: An uncaught exception that may occur during a Fit3D calculation.
Fit3DException(String) - Constructor for exception de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DException
Fit3DMatch - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d: A data object encapsulating a match of the Fit3D algorithms.
Fit3DSiteAlignment - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d: An implementation of an algorithm for pairwise comparision of structure sites (e.g.
Fit3DSiteAlignment(Fit3DBuilder.Builder) - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DSiteAlignment
flatToString() - Method in interface de.bioforscher.singa.structure.model.interfaces.Atom: Returns the flat String representation of this atom in the form:
flatToString() - Method in interface de.bioforscher.singa.structure.model.interfaces.Chain
flatToString() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure: Returns the flat String representation of this leaf substructure in the form:
flatToString() - Method in interface de.bioforscher.singa.structure.model.interfaces.Model
flatToString() - Method in interface de.bioforscher.singa.structure.model.interfaces.Structure
flatToString() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfNucleotide
FLUORINE - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
FofanovEstimation - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics: An estimation method of the statistical significance of matches produced by the Fit3D algorithm.
FofanovEstimation(double) - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.FofanovEstimation
FofanovEstimation(double, int, double) - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.FofanovEstimation
FragmentSubstructureSuperimposer - Class in de.bioforscher.singa.structure.algorithms.superimposition: A special version of the SubstructureSuperimposer that uses subgraph isomorphism to align a candidate against a given reference fragment.
FRANCIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
from(GenericGraph<LeafSubstructure<?>>, GenericNode<LeafSubstructure<?>>) - Method in enum de.bioforscher.singa.structure.parser.plip.PlipShellGenerator.InteractionShell
fromLeafIdentifiers(Structure, List<LeafIdentifier>) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralMotif: Creates a StructuralMotif by extracting the given residues identified by a list of LeafIdentifiers.
fromLeafSubstructures(List<LeafSubstructure<?>>) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralMotif: Forms a StructuralMotif out of the given LeafSubstructures.
fromSimpleString(String) - Static method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier: Constructs a LeafIdentifier from the given simple string.
FUNCTIONAL - Static variable in enum de.bioforscher.singa.structure.model.families.MatcherFamily: The following types are grouped according to functional chemical groups:

G

GADOLINIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
GALLIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
GERMANIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
getAcceptor() - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
getAcceptor() - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
getAcceptor() - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
getAcceptorAngle() - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
getAlignedSequence() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
getAlignmentString() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3D: Returns a string that represents the alignment.
getAlignmentString() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DSiteAlignment
getAlignmentTrace() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusAlignment
getAllAminoAcids() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Returns all AminoAcids.
getAllAtoms() - Method in interface de.bioforscher.singa.structure.model.interfaces.AtomContainer: Returns all Atoms.
getAllAtoms() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Returns all Atoms.
getAllAtoms() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
getAllAtoms() - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
getAllChainIdentifiers() - Method in interface de.bioforscher.singa.structure.model.interfaces.Model: Returns A set of all chin identifiers referenced in th model.
getAllChainIdentifiers() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getAllChainIdentifiers() - Method in class de.bioforscher.singa.structure.model.oak.OakModel
getAllChains() - Method in interface de.bioforscher.singa.structure.model.interfaces.ChainContainer: Returns all Chains.
getAllChains() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getAllChains() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getAllChains() - Method in class de.bioforscher.singa.structure.model.oak.OakModel
getAllChains() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getAllLeafSubstructures() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Returns all LeafSubstructures.
getAllLeafSubstructures() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
getAllLeafSubstructures() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getAllLeafSubstructures() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getAllLeafSubstructures() - Method in class de.bioforscher.singa.structure.model.oak.OakChain
getAllLeafSubstructures() - Method in class de.bioforscher.singa.structure.model.oak.OakModel
getAllLeafSubstructures() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getAllLeafSubstructures() - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif
getAllLigands() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Returns all Ligands.
getAllModelIdentifiers() - Method in interface de.bioforscher.singa.structure.model.interfaces.Structure: Returns all model identifiers referenced in the model.
getAllModelIdentifiers() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getAllModelIdentifiers() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getAllModels() - Method in interface de.bioforscher.singa.structure.model.interfaces.Structure: Returns all Models.
getAllModels() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getAllModels() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getAllNucleotides() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Returns all Nucleotides.
getAllowedAtoms() - Method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily
getAminoAcid(LeafIdentifier) - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Returns an Optional of the AminoAcid with the given identifier.
getAminoAcidTypeByOneLetterCode(char) - Static method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily
getAminoAcidTypeByOneLetterCode(String) - Static method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily
getAminoAcidTypeByThreeLetterCode(String) - Static method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily
getAngle() - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
getAngle() - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
getAssignedFamily() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton
getAtom(Integer) - Method in interface de.bioforscher.singa.structure.model.interfaces.AtomContainer: Returns an Optional of the Atom with the given identifier.
getAtom(int) - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Returns an Optional of the Atom with the given identifier.
getAtom(Integer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
getAtom(Integer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
getAtom(Integer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getAtom(Integer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getAtom(Integer) - Method in class de.bioforscher.singa.structure.model.oak.OakChain
getAtom(Integer) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
getAtom(Integer) - Method in class de.bioforscher.singa.structure.model.oak.OakModel
getAtom(Integer) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getAtom(Integer) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif
getAtom1() - Method in class de.bioforscher.singa.structure.parser.plip.HydrophobicInteraction
getAtom1() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
getAtom2() - Method in class de.bioforscher.singa.structure.parser.plip.HydrophobicInteraction
getAtom2() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
getAtomByName(String) - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure
getAtomByName(String) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
getAtomByName(String) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
getAtomicMass() - Method in class de.bioforscher.singa.structure.elements.Element: Returns the atomic mass.
getAtomicOrbital(String) - Static method in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital
getAtomIdentifier() - Method in interface de.bioforscher.singa.structure.model.interfaces.Atom: Returns the atom identifier, an integer greater or equal to 1.
getAtomIdentifier() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfAtom
getAtomIdentifier() - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
getAtomName() - Method in interface de.bioforscher.singa.structure.model.interfaces.Atom: Returns a short atom name.
getAtomName() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfAtom
getAtomName() - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
getAtomNameFromString(String) - Static method in enum de.bioforscher.singa.structure.model.oak.AtomName
getAtomNameString() - Method in enum de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.RepresentationSchemeType
getAtomPairs(MoleculeGraph) - Method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphism
getAtoms() - Method in class de.bioforscher.singa.structure.algorithms.gyration.Gyration: Returns the atoms the gyration has been calculated from.
getAtoms1() - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
getAtoms1() - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
getAtoms1() - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
getAtoms2() - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
getAtoms2() - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
getAtoms2() - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
getAtomSerial() - Method in class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
getBondForSMILESSymbol(char) - Static method in enum de.bioforscher.singa.structure.model.molecules.MoleculeBondType
getBonds() - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
getBonds() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton
getBondType() - Method in class de.bioforscher.singa.structure.model.oak.OakBond
getBondTypeByCifName(String) - Static method in enum de.bioforscher.singa.structure.model.oak.BondType
getCandidate() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition
getCandidateMotif() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
getCentroid() - Method in class de.bioforscher.singa.structure.algorithms.gyration.Gyration: Returns the centroid of this gyration.
getChain(String) - Method in interface de.bioforscher.singa.structure.model.interfaces.Model: Returns an Optional of the Chain with the given identifier.
getChain(int, String) - Method in interface de.bioforscher.singa.structure.model.interfaces.Structure: Returns an Optional of the Chain with the given identifier from the model with the given identifier.
getChain(String) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getChain(int, String) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getChain(String) - Method in class de.bioforscher.singa.structure.model.oak.OakModel
getChain(int, String) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getChainIdentifier() - Method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
getChainIdentifier() - Method in class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
getChainIdentifier() - Method in interface de.bioforscher.singa.structure.model.interfaces.Chain: Returns the chain identifier, a short sequence of alphabetic characters.
getChainIdentifier() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure
getChainIdentifier() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
getChainIdentifier() - Method in class de.bioforscher.singa.structure.model.oak.OakChain
getChainIdentifier() - Method in class de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceClusterMember
getChains() - Method in class de.bioforscher.singa.structure.parser.pfam.PfamParser
getCharge() - Method in class de.bioforscher.singa.structure.elements.Element: Returns the charge of this Element.
getCifName() - Method in enum de.bioforscher.singa.structure.model.oak.BondType
getClusterMembers() - Method in class de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceCluster
getClusters() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment
getClusters() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusAlignment
getColumn() - Method in interface de.bioforscher.singa.structure.parser.pfam.tokens.PfamToken
getColumn() - Method in enum de.bioforscher.singa.structure.parser.pfam.tokens.PfamToken.IdentifierToken
getColumn() - Method in enum de.bioforscher.singa.structure.parser.pfam.tokens.PfamToken.PDBToken
getColumns() - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.AtomToken
getColumns() - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ChainTerminatorToken
getColumns() - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.HeaderToken
getColumns() - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ModelToken
getColumns() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.tokens.PDBToken: Gets the columns (the staring and ending index) where a value can be extracted.
getColumns() - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.TitleToken
getCompatibleRepresentationScheme() - Method in enum de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.RepresentationSchemeType
getComplexnum() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
getConfiguration() - Method in class de.bioforscher.singa.structure.elements.ElectronConfiguration
getConsecutivePart() - Method in class de.bioforscher.singa.structure.model.oak.OakChain
getConsensusDistance() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
getConsensusScore() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusAlignment: Returns the consensus score of this ConsensusAlignment, i.e.
getConsensusTree() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
getConsensusTrees() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusAlignment: Returns all trees that were constructed during this alignment.
getContainingFamilies() - Method in interface de.bioforscher.singa.structure.model.oak.Exchangeable: Returns all StructuralFamily types that are defined, this is the concrete type of the Exchangeable itself plus all exchangeable types.
getCoordination() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
getCopy() - Method in interface de.bioforscher.singa.structure.model.interfaces.Atom
getCopy() - Method in interface de.bioforscher.singa.structure.model.interfaces.Chain: Returns a copy of this chain.
getCopy() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure: Returns a copy of this LeafSubstructure.
getCopy() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer
getCopy() - Method in interface de.bioforscher.singa.structure.model.interfaces.Model: Returns a copy of this model.
getCopy() - Method in interface de.bioforscher.singa.structure.model.interfaces.Structure: Returns a copy of this structure.
getCopy() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfAminoAcid
getCopy() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfAtom
getCopy() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
getCopy() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLigand
getCopy() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getCopy() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfNucleotide
getCopy() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getCopy() - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeAtom
getCopy() - Method in class de.bioforscher.singa.structure.model.oak.OakAminoAcid
getCopy() - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
getCopy() - Method in class de.bioforscher.singa.structure.model.oak.OakBond
getCopy() - Method in class de.bioforscher.singa.structure.model.oak.OakChain
getCopy() - Method in class de.bioforscher.singa.structure.model.oak.OakLigand
getCopy() - Method in class de.bioforscher.singa.structure.model.oak.OakModel
getCopy() - Method in class de.bioforscher.singa.structure.model.oak.OakNucleotide
getCopy() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getCopy() - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif
getCurrentChainIdentifier() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiParser: Returns the chain identifier of the next structure, if it can be accessed prior to parsing.
getCurrentPdbIdentifier() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiParser: Returns the pdb identifier of the next structure, if it can be accessed prior to parsing.
getCurrentPdbIdentifier() - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
getDescription() - Method in enum de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.RepresentationSchemeType
getDescription() - Method in enum de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilterType
getDescription() - Method in enum de.bioforscher.singa.structure.model.oak.StructuralMotif.Type
getDistance() - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
getDistance() - Method in class de.bioforscher.singa.structure.parser.plip.HydrophobicInteraction
getDistance() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
getDistance() - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
getDistance() - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
getDistance() - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
getDistanceAW() - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
getDistanceDA() - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
getDistanceDW() - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
getDistanceHA() - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
getDistanceMatrix() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment
getDomains() - Method in class de.bioforscher.singa.structure.parser.pfam.PfamParser
getDonor() - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
getDonor() - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
getDonor() - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
getDonorAngle() - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
getDonorAngle() - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
getEcNumbers() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
getElectronNumber() - Method in class de.bioforscher.singa.structure.elements.Element: Returns the electron number.
getElement() - Method in interface de.bioforscher.singa.structure.model.interfaces.Atom: Returns the Element.
getElement() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfAtom
getElement() - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeAtom
getElement() - Method in enum de.bioforscher.singa.structure.model.oak.AtomName
getElement() - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
getElementBySymbol(String) - Static method in class de.bioforscher.singa.structure.elements.ElementProvider: Retrieves an Optional of an Element by ity symbol.
getElements() - Static method in class de.bioforscher.singa.structure.elements.ElementProvider: Contains all the elements of this library.
getEndpoint() - Method in class de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceCluster
getEndpoint() - Method in class de.bioforscher.singa.structure.parser.pdb.rest.PDBRestEndpoint
getExchangeableFamilies() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
getExchangeableFamilies() - Method in interface de.bioforscher.singa.structure.model.oak.Exchangeable: Returns the StructuralFamilys to which this entity is exchangeable.
getExchangeableFamilies() - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
getFamily() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
getFamily() - Method in interface de.bioforscher.singa.structure.model.oak.Exchangeable: Returns the StructuralFamily of this entity.
getFamily() - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
getFeatureContent() - Method in class de.bioforscher.singa.structure.model.identifiers.PDBIdentifier
getFilter() - Method in enum de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilterType
getFilter() - Method in enum de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.LeafFilterType
getFirstChain() - Method in interface de.bioforscher.singa.structure.model.interfaces.ChainContainer: Returns the first Chain.
getFirstChain() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getFirstChain() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getFirstChain() - Method in class de.bioforscher.singa.structure.model.oak.OakModel
getFirstChain() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getFirstLeafSubstructure() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer
getFirstLeafSubstructure() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
getFirstLeafSubstructure() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getFirstLeafSubstructure() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getFirstLeafSubstructure() - Method in class de.bioforscher.singa.structure.model.oak.OakChain
getFirstLeafSubstructure() - Method in class de.bioforscher.singa.structure.model.oak.OakModel
getFirstLeafSubstructure() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getFirstLeafSubstructure() - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif
getFirstModel() - Method in interface de.bioforscher.singa.structure.model.interfaces.Structure: Returns the first Model (with the smallest identifier).
getFirstModel() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getFirstModel() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getFirstSourceAtom() - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
getFirstSourceAtom() - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
getFirstSourceAtom() - Method in class de.bioforscher.singa.structure.parser.plip.HydrophobicInteraction
getFirstSourceAtom() - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
getFirstSourceAtom() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex: For MetalComplexes the first source atom is the atom identifier of the metal ion.
getFirstSourceAtom() - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
getFirstSourceAtom() - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
getFirstSourceAtom() - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
getFirstSourceAtom() - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
getFirstTargetAtom() - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
getFirstTargetAtom() - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
getFirstTargetAtom() - Method in class de.bioforscher.singa.structure.parser.plip.HydrophobicInteraction
getFirstTargetAtom() - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
getFirstTargetAtom() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex: For MetalComplexes the first target atom is the atom identifier of the interaction partner (possibly ligand or residue).
getFirstTargetAtom() - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
getFirstTargetAtom() - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
getFirstTargetAtom() - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
getFirstTargetAtom() - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
getFraction() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3D: Returns the fraction of residues that were aligned.
getFraction() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DAlignment: Returns the fraction of aligned residues, which is always 1.0 for this kind of alignment.
getFraction() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DAlignmentBatch: Returns the fraction of aligned residues, which is always 1.0 for this kind of alignment.
getFraction() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DSiteAlignment: Returns the fraction of aligned residues, in respect to the smaller site.
getFullMatches() - Method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphism
getGeometry() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
getGraph() - Method in class de.bioforscher.singa.structure.parser.plip.PlipShellGenerator
getIdentifier() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure: Returns the complete leaf identifier.
getIdentifier() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
getIdentifier() - Method in class de.bioforscher.singa.structure.model.oak.OakBond
getIdentifier() - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
getIdentity() - Method in enum de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceCluster.PDBSequenceClusterIdentity
getIncompleteShells() - Method in class de.bioforscher.singa.structure.elements.ElectronConfiguration
getInsertionCode() - Method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
getInsertionCode() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure
getInteractionClass() - Method in enum de.bioforscher.singa.structure.parser.plip.InteractionType
getInteractionContainer() - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
getInteractions() - Method in class de.bioforscher.singa.structure.parser.plip.InteractionContainer: Retuens all interactions from this container.
getInteractionsBetween(LeafIdentifier, LeafIdentifier) - Method in class de.bioforscher.singa.structure.parser.plip.InteractionContainer: Returns all Interactions between two leaves (i.e.
getInteractionShellsForLigand(Chain, LeafSubstructure<?>, InteractionContainer, InteractionContainer) - Static method in class de.bioforscher.singa.structure.parser.plip.PlipShellGenerator
getLastAddedAtomIdentifier() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getLeafInsertionCode() - Method in class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
getLeafSerial() - Method in class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
getLeafSubstructure(LeafIdentifier) - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Returns an Optional of the LeafSubstructure with the given identifier.
getLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
getLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.oak.OakChain
getLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.oak.OakModel
getLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif
getLigand(LeafIdentifier) - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Returns an Optional of the Ligand with the given identifier.
getLigandCoordinate() - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
getLigandGroup() - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
getLigandGroup() - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
getLigandInteractions() - Method in class de.bioforscher.singa.structure.parser.plip.InteractionContainer
getLocalPdbPath() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalPDB: Returns the path to the local pdb.
getLocation() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
getMappedCandidate() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition
getMappedFullCandidate() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition
getMapping() - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
getMassNumber() - Method in class de.bioforscher.singa.structure.elements.Element
getMatches() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3D: Returns the matches that were found by this Fit3D search.
getMatches() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DAlignment: Returns the computed matches of this Fit3D search.
getMatches() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DAlignmentBatch: Returns all matches of this Fit3D batch calculation.
getMatches() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DSiteAlignment
getMatchType() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
getMatrix() - Method in enum de.bioforscher.singa.structure.algorithms.superimposition.scores.SubstitutionMatrix
getMaximalElectrons() - Method in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital
getMembers() - Method in enum de.bioforscher.singa.structure.model.families.MatcherFamily
getMetalType() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
getModel(int) - Method in interface de.bioforscher.singa.structure.model.interfaces.Structure: Returns an Optional of the Model with the given identifier.
getModel(int) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getModel(int) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getModelCorrectnessCutoff() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.FofanovEstimation
getModelIdentifier() - Method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
getModelIdentifier() - Method in class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
getModelIdentifier() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure
getModelIdentifier() - Method in interface de.bioforscher.singa.structure.model.interfaces.Model: Returns the model identifier, an integer greater or equal to 1.
getModelIdentifier() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getModelIdentifier() - Method in class de.bioforscher.singa.structure.model.oak.OakModel
getName() - Method in class de.bioforscher.singa.structure.elements.Element: Returns the name.
getName() - Method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily
getName() - Method in enum de.bioforscher.singa.structure.model.oak.AtomName
getName() - Method in class de.bioforscher.singa.structure.model.oak.OakLigand
getNeighbours() - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
getNeutronNumber() - Method in class de.bioforscher.singa.structure.elements.Element: Returns the neutron number.
getNextEdgeIdentifier() - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
getNextLeafIdentifier() - Method in class de.bioforscher.singa.structure.model.oak.OakChain
getNonConsecutivePart() - Method in class de.bioforscher.singa.structure.model.oak.OakChain
getNormalizedConsensusScore() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusAlignment: Returns the consensus score normalized by number of iterations and the size of the input structures:
getNormalizedScore() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.scores.XieScore
getNucleotide(char) - Static method in enum de.bioforscher.singa.structure.model.families.NucleotideFamily
getNucleotide(LeafIdentifier) - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Returns an Optional of the Nucleotide with the given identifier.
getNucleotideByThreeLetterCode(String) - Static method in enum de.bioforscher.singa.structure.model.families.NucleotideFamily
getNumberOfLeafSubstructures() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer
getNumberOfLeafSubstructures() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
getNumberOfLeafSubstructures() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
getNumberOfLeafSubstructures() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getNumberOfPotentialBonds() - Method in class de.bioforscher.singa.structure.elements.Element: Estimates the Number of potential bonds this element forms.
getNumberOfQueuedStructures() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiParser: Returns the number of structures totally queued.
getNumberOfRemainingStructures() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiParser: Returns the number of structures remaining.
getNumberOfValenceElectrons() - Method in class de.bioforscher.singa.structure.elements.ElectronConfiguration
getOffset() - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
getOffset() - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
getOneLetterCode() - Method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily
getOneLetterCode() - Method in class de.bioforscher.singa.structure.model.families.LigandFamily
getOneLetterCode() - Method in enum de.bioforscher.singa.structure.model.families.MatcherFamily
getOneLetterCode() - Method in enum de.bioforscher.singa.structure.model.families.NucleotideFamily
getOneLetterCode() - Method in interface de.bioforscher.singa.structure.model.families.StructuralFamily
getOrbitalsOfShell(int) - Method in class de.bioforscher.singa.structure.elements.ElectronConfiguration
getOuterMostShell() - Method in class de.bioforscher.singa.structure.elements.ElectronConfiguration
getParent() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton
getPathForPdbIdentifier(String) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalPDB: Returns the full path of a given PDB-ID in respect to the local PDB copy.
getPdbIdentifier() - Method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
getPdbIdentifier() - Method in class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
getPdbIdentifier() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure
getPdbIdentifier() - Method in interface de.bioforscher.singa.structure.model.interfaces.Structure: Returns the PDB identifier, a 4 character code, where the first character is any number followed by three alphanumeric characters.
getPdbIdentifier() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getPdbIdentifier() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getPdbIdentifier() - Method in class de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceClusterMember
getPdbLines() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure
getPfamIdentifiers() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
getPlipIdentifier() - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
getPosition() - Method in interface de.bioforscher.singa.structure.model.interfaces.Atom: Returns the position in three dimensional space.
getPosition() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure
getPosition() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfAminoAcid
getPosition() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfAtom
getPosition() - Method in class de.bioforscher.singa.structure.model.oak.OakAminoAcid
getPosition() - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
getProteinCoordinate() - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
getProtonNumber() - Method in class de.bioforscher.singa.structure.elements.Element: Returns the proton number.
getPrototype() - Method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily: Returns a prototype of the AminoAcid that are deposited in the project resources.
getPsScore() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3D: Returns the PsScore of aligned residues (only available for Fit3DSiteAlignment.
getPsScore() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DSiteAlignment
getPvalue() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
getRadius() - Method in class de.bioforscher.singa.structure.algorithms.gyration.Gyration: Returns the radius of this gyration.
getRank() - Method in class de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceClusterMember
getRecordNamePattern() - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.AtomToken
getRecordNamePattern() - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ChainTerminatorToken
getRecordNamePattern() - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.HeaderToken
getRecordNamePattern() - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ModelToken
getRecordNamePattern() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.tokens.PDBToken: Returns the record name for this token.
getRecordNamePattern() - Method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.TitleToken
getReference() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition
getRepresentative() - Method in class de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceCluster: Returns the representative for this cluster as an array containing the PDB-ID and the chain-ID.
getRms() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
getRmsd() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
getRmsd() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition
getRotation() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition
getScore() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.scores.PsScore
getScore() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.scores.XieScore
getSelfDissimilarity() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment
getSerial() - Method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
getSerial() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure
getShell() - Method in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital
getShells() - Method in class de.bioforscher.singa.structure.parser.plip.PlipShellGenerator
getSignificance() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.scores.PsScore
getSignificance() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.scores.XieScore
getSilhouetteCoefficient() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment
getSmilesRepresentation() - Method in enum de.bioforscher.singa.structure.model.molecules.MoleculeBondType
getSource() - Method in class de.bioforscher.singa.structure.model.oak.OakBond
getSource() - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
getStringRepresentation() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition: Returns a string representation of the SubstructureSuperimposition, that is:
getStructuralMotif() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
getStructureTitle() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
getSubShell() - Method in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital
getSubstructureSuperimposition() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
getSuperimposition() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
getSymbol() - Method in class de.bioforscher.singa.structure.elements.Element: Returns the symbol.
getSymbol() - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
getTarget() - Method in class de.bioforscher.singa.structure.model.oak.OakBond
getTarget() - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
getThreeLetterCode() - Method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily
getThreeLetterCode() - Method in class de.bioforscher.singa.structure.model.families.LigandFamily
getThreeLetterCode() - Method in enum de.bioforscher.singa.structure.model.families.MatcherFamily
getThreeLetterCode() - Method in enum de.bioforscher.singa.structure.model.families.NucleotideFamily
getThreeLetterCode() - Method in interface de.bioforscher.singa.structure.model.families.StructuralFamily
getThreeLetterCode() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure: Returns the three letter code of the chemical compound represented by this leaf substructure.
getThreeLetterCode() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
getThreeLetterCode() - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
getThreeLetterCode() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton
getThreeLetterCode(Class<? extends Interaction>) - Static method in enum de.bioforscher.singa.structure.parser.plip.InteractionType
getThreeLetterCode() - Method in enum de.bioforscher.singa.structure.parser.plip.InteractionType
getTitle() - Method in interface de.bioforscher.singa.structure.model.interfaces.Structure: Returns the title.
getTitle() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
getTitle() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getTopConsensusTree() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusAlignment: Returns the top-level tree of this consensus alignment.
getTotalNumberOfElectrons() - Method in class de.bioforscher.singa.structure.elements.ElectronConfiguration
getTranslation() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition
getType() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.AlphaCarbonRepresentationScheme
getType() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.BetaCarbonRepresentationScheme
getType() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.CentroidRepresentationScheme
getType() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.LastHeavySidechainRepresentationScheme
getType() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.RepresentationScheme: Returns the actual RepresentationSchemeType of this RepresentationScheme.
getType() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.SideChainCentroidRepresentationScheme
getType() - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeBond
getType() - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
getUniProtIdentifiers() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
getUniqueAtomEntry(int) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
getUnit() - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
getValenceElectronNumber() - Method in class de.bioforscher.singa.structure.elements.Element: Returns the number of valence electrons.
getValidAlignments() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.ValidAlignmentGenerator
getValidCandidates() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.ValidCandidateGenerator
getValue() - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
getVanDerWaalsRadius() - Method in class de.bioforscher.singa.structure.elements.Element
getWaterAngle() - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
getXieScore() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3D: Returns the XieScore of aligned residues (only available for Fit3DSiteAlignment.
getXieScore() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DSiteAlignment
GLUTAMIC_ACID_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
GLUTAMINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
GLYCINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
GOLD - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
GRAM_PER_MOLE - Static variable in class de.bioforscher.singa.structure.features.molarmass.MolarMass
GUTTERIDGE - Static variable in enum de.bioforscher.singa.structure.model.families.MatcherFamily: The following types are grouped according to
Gyration - Class in de.bioforscher.singa.structure.algorithms.gyration: An implementation of the gyration radius measurement for the compactness of molecules.

H

HAFNIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
HalogenBond - Class in de.bioforscher.singa.structure.parser.plip
HalogenBond(int) - Constructor for class de.bioforscher.singa.structure.parser.plip.HalogenBond
hasAtomName(String) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
hasAtomName(AtomName) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
hasAtomNames(String...) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
hashCode() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
hashCode() - Method in class de.bioforscher.singa.structure.elements.Element
hashCode() - Method in class de.bioforscher.singa.structure.model.families.LigandFamily
hashCode() - Method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
hashCode() - Method in class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
hashCode() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
hashCode() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
hashCode() - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
hashCode() - Method in class de.bioforscher.singa.structure.model.oak.OakBond
hashCode() - Method in class de.bioforscher.singa.structure.model.oak.OakChain
hashCode() - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
hashCode() - Method in class de.bioforscher.singa.structure.model.oak.OakModel
hashCode() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
hasIdentifier(int) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
hasIdentifier(Object) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.LeafFilter
hasInteractions(LeafIdentifier, LeafIdentifier) - Method in class de.bioforscher.singa.structure.parser.plip.InteractionContainer: Returns true if any interaction between the two leaves is annotated in this container.
hasNext() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiParser
HASSIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
HeaderToken - Enum in de.bioforscher.singa.structure.parser.pdb.structures.tokens
HELIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
heteroAtoms(boolean) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions
HISTIDINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
HOLMIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
HYDROGEN - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
HydrogenBond - Class in de.bioforscher.singa.structure.parser.plip
HydrogenBond(int) - Constructor for class de.bioforscher.singa.structure.parser.plip.HydrogenBond
HydrophobicInteraction - Class in de.bioforscher.singa.structure.parser.plip
HydrophobicInteraction(int) - Constructor for class de.bioforscher.singa.structure.parser.plip.HydrophobicInteraction

I

idealSuperimposition(boolean) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.Builder
idealSuperimposition(boolean) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.ParameterStep
idealSuperimposition(boolean) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.Builder
idealSuperimposition(boolean) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.ParameterStep
ignorableWhitespace(char[], int, int) - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
ignorableWhitespace(char[], int, int) - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
ignoreSpecifiedExchanges() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
ignoreSpecifiedExchanges() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.SiteConfigurationStep: Ignores the specified exchanges of the input sites and allows alignment of any type against any type using a heuristic that does not necessarily yield the best alignment possible.
incrementGs() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.FofanovEstimation
incrementNs() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.FofanovEstimation
INDIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
inferIdentifierFromFileName(boolean) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option to true will try parse any pdb identifier from the file name.
inferTitleFromFileName(boolean) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option to true will set the title of the structure to the file name.
inputStream(InputStream) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalSourceStep: Parses a structure from an input stream of a pdb file.
inputStructuralMotifs(List<StructuralMotif>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.Builder
inputStructuralMotifs(List<StructuralMotif>) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.InputStep
inputStructuralMotifs(List<StructuralMotif>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.Builder
inputStructuralMotifs(List<StructuralMotif>) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.InputStep: Defines the input StructuralMotifs for the ConsensusAlignment.
Interaction - Class in de.bioforscher.singa.structure.parser.plip
Interaction(int) - Constructor for class de.bioforscher.singa.structure.parser.plip.Interaction
InteractionContainer - Class in de.bioforscher.singa.structure.parser.plip: The interaction container takes all interactions in a PLIP xml-file that was generated using the inter-chain interaction annotation feature.
InteractionContainer() - Constructor for class de.bioforscher.singa.structure.parser.plip.InteractionContainer: Creates a new empty interaction container.
InteractionType - Enum in de.bioforscher.singa.structure.parser.plip
inverse() - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
IODINE - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
IRIDIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
IRON - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
isAlphaCarbon() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isAlphaCarbonStructure(Structure) - Static method in class de.bioforscher.singa.structure.model.oak.Structures: Returns true iff the given Structure consists only of alpha carbon atoms (this may include hydrogen atoms).
isAminoAcid() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.LeafFilter
isAnion() - Method in class de.bioforscher.singa.structure.elements.Element: Returns true if this Element is an anion (excess of electrons) and false otherwise.
isAnnotatedAsHeteroAtom() - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructure
isAnnotatedAsHeteroAtom() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfAminoAcid
isAnnotatedAsHeteroAtom() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLigand
isAnnotatedAsHeteroAtom() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfNucleotide
isAnnotatedAsHeteroAtom() - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
isArbitrary() - Static method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphismFinder.AtomConditions
isArbitrary() - Static method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphismFinder.BondConditions
isArbitrary() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isBackbone() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isBackboneCarbon() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isBackboneNitrogen() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isBackboneOxygen() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isBackboneStructure(Structure) - Static method in class de.bioforscher.singa.structure.model.oak.Structures: Returns true iff the given Structure consists only of backbone atoms (this may include beta carbon and hydrogen atoms).
isBetaCarbon() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isCarbon() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isCation() - Method in class de.bioforscher.singa.structure.elements.Element: Returns true if this Element is an cation (shortage of electrons) and false otherwise.
isConnectingHydrogens() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option to true will try to connect hydrogen atom tho their respective partners.

Default value: false
isConsensus() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer: Returns true if the associated StructuralMotif is an artificial consensus.
isCreatingEdges() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option true will connect the molecule with bonds.
isElement(Element) - Static method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraphs
isHeteroAtoms() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions
isHydrogen() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isInChain(String) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.ChainFilter
isInferringIdentifierFromFileName() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option to true will try parse any pdb identifier from the file name.
isInferringTitleFromFileName() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option to true will set the title of the structure to the file name.
isIon() - Method in class de.bioforscher.singa.structure.elements.Element: Returns true if this Element is an ion and false otherwise.
isIsotope() - Method in class de.bioforscher.singa.structure.elements.Element: Returns true if this Element is an isotope and false otherwise.
isLigand() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.LeafFilter
isNitrogen() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isNucleotide() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.LeafFilter
ISOLEUCINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
isOmittingHydrogen() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option to true will omit all hydrogen (and eventually deuterium) atoms in amino acids and nucleotides.
isOneOfElements(Set<Element>) - Static method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraphs
isOxygen() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isPhosphorus() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isProtcharged() - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
isProtIsDon() - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
isProtIsDon() - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
isProtIsPos() - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
isRetrievingLigandInformation() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option to true will retrieve additional information from cif files from the PDB.
isSameElement() - Static method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphismFinder.AtomConditions
isSameType() - Static method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphismFinder.BondConditions
isSideChain() - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isSidechain() - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
isWithinRange(int, int) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilter
isWithinRange(int, int) - Static method in class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.LeafFilter

J

Justification - Enum in de.bioforscher.singa.structure.parser.pdb.structures.tokens

K

KRYPTON - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
kuhnMunkres(SubstitutionMatrix, boolean) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
kuhnMunkres(SubstitutionMatrix, boolean) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.SiteConfigurationStep: Assigns the alignment using Kuhn-Munkres optimization and scoring derived from the specified substitution matrix.

L

LANTHANUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
LastHeavySidechainRepresentationScheme - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations: An implementation to represent a given LeafSubstructure by its last heavy sidechain atom (the atom most far from the alpha carbon).
LastHeavySidechainRepresentationScheme() - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.LastHeavySidechainRepresentationScheme
LAWRENCIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
LEAD - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
LeafFilter() - Constructor for class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.LeafFilter
LeafIdentifier - Class in de.bioforscher.singa.structure.model.identifiers: The leaf identifier consists of the PDB identifer, the model identifier, the chain identifier, the serial of a leaf substructure and optionally its insertion code.
LeafIdentifier(String, int, String, int, char) - Constructor for class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
LeafIdentifier(String, int, String, int) - Constructor for class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
LeafIdentifier(String, int, char) - Constructor for class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
LeafIdentifier(String, int) - Constructor for class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
LeafIdentifier(int) - Constructor for class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
LeafIdentifiers - Class in de.bioforscher.singa.structure.model.identifiers
LeafIdentifiers() - Constructor for class de.bioforscher.singa.structure.model.identifiers.LeafIdentifiers
LeafSkeleton - Class in de.bioforscher.singa.structure.parser.pdb.structures.tokens
LeafSkeleton(String, String, LeafSkeleton.AssignedFamily, Map<Pair<String>, BondType>) - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton
LeafSkeleton.AssignedFamily - Enum in de.bioforscher.singa.structure.parser.pdb.structures.tokens
LeafSubstructure<FamilyType extends StructuralFamily> - Interface in de.bioforscher.singa.structure.model.interfaces: A leaf substructure is a collection of atoms with meta data assigned to it.
LeafSubstructureContainer - Interface in de.bioforscher.singa.structure.model.interfaces: Everything that contains leaf substructures.
LeafSubstructureFactory - Class in de.bioforscher.singa.structure.model.oak: The residue factory is used to create residues from a set of AtomFilter with their AtomNames.
leafSubstructures - Variable in class de.bioforscher.singa.structure.model.oak.StructuralMotif
LEUCINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
Ligand - Interface in de.bioforscher.singa.structure.model.interfaces: A specific type of LeafSubstructure, representing ligands.
LigandFamily - Class in de.bioforscher.singa.structure.model.families
LigandFamily(String) - Constructor for class de.bioforscher.singa.structure.model.families.LigandFamily
LigandFamily(String, String) - Constructor for class de.bioforscher.singa.structure.model.families.LigandFamily
LigandParserService - Class in de.bioforscher.singa.structure.parser.pdb.ligands
LigandParserService() - Constructor for class de.bioforscher.singa.structure.parser.pdb.ligands.LigandParserService
limitedParallelism(int) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.BatchParameterStep: Defines for a batch search the level of parallelism (number of cores) that should be used by Fit3D.
limitedParallelism(int) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
LITHIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
local() - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser: Structures will be retrieved from a local source.
LocalPDB(String, SourceLocation) - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalPDB: Creates a new reference for a local pdb installation.
localPDB(StructureParser.LocalPDB) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalSourceStep: The location of a local PDB installation.
localPDB(StructureParser.LocalPDB, String) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalSourceStep: The location of a local PDB installation in addition to the structure, that is to be parsed.
localPDB(StructureParser.LocalPDB, List<String>) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalSourceStep: The location of a local PDB installation in addition to a list of structures, that are to be parsed.
logger - Static variable in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3D
logger - Static variable in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.AbstractRepresentationScheme
logger - Static variable in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.RepresentationSchemeFactory
LUTETIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
LYSINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName

M

MAGNESIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
MANGANESE - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
map(String) - Static method in class de.bioforscher.singa.structure.parser.sifts.PDBEnzymeMapper
map(String) - Static method in class de.bioforscher.singa.structure.parser.sifts.PDBPfamMapper
map(String) - Static method in class de.bioforscher.singa.structure.parser.sifts.PDBUniProtMapper
mapECNumbers() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
mapECNumbers() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.ParameterStep: Enables mapping of each chain of a Fit3DMatch to an ECNumber using the SIFTS project.
mapPfamIdentifiers() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
mapPfamIdentifiers() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.ParameterStep: Enables mapping of each chain of a Fit3DMatch to a PfamIdentifier using the SIFTS project.
mapping - Variable in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
mapToPseudoAtoms(OakStructure) - Method in class de.bioforscher.singa.structure.parser.plip.InteractionContainer: Adds the interactions in this container to a structure as pseudo atoms.
mapUniProtIdentifiers() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
mapUniProtIdentifiers() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.ParameterStep: Enables mapping of each chain of a Fit3DMatch to a UniProtIdentifier using the SIFTS project.
MatcherFamily - Enum in de.bioforscher.singa.structure.model.families: This is a StructuralFamily that groups others.
MAX_ELECTRONS_D - Static variable in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital
MAX_ELECTRONS_F - Static variable in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital
MAX_ELECTRONS_P - Static variable in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital
MAX_ELECTRONS_S - Static variable in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital
maximalParallelism() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.BatchParameterStep: Allows Fit3D in search mode to use all available cores for processing.
maximalParallelism() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
MENDELEVIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
MERCURY - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
mergeWith(SaltBridge) - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
MetalComplex - Class in de.bioforscher.singa.structure.parser.plip
MetalComplex(int) - Constructor for class de.bioforscher.singa.structure.parser.plip.MetalComplex
METHIONINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
mmtf() - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser: Structures will be pulled online.
MmtfAminoAcid - Class in de.bioforscher.singa.structure.model.mmtf: The implementation of AminoAcids for mmtf structures.
MmtfAtom - Class in de.bioforscher.singa.structure.model.mmtf: The implementation of Atom for mmtf structures.
MmtfAtom(MmtfAtom) - Constructor for class de.bioforscher.singa.structure.model.mmtf.MmtfAtom
MmtfChain - Class in de.bioforscher.singa.structure.model.mmtf: The implementation of Chain for mmtf structures.
MmtfLeafSubstructure<FamilyType extends StructuralFamily> - Class in de.bioforscher.singa.structure.model.mmtf: The implementation of LeafSubstructure for mmtf structures.
MmtfLeafSubstructure(MmtfLeafSubstructure<?>) - Constructor for class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure: A copy constructor that passes all attributes of the given MmtfLeafSubstructure to a new instance.
MmtfLigand - Class in de.bioforscher.singa.structure.model.mmtf: The implementation of Ligands for mmtf structures.
MmtfModel - Class in de.bioforscher.singa.structure.model.mmtf: The implementation of Model for mmtf structures.
MmtfNucleotide - Class in de.bioforscher.singa.structure.model.mmtf: The implementation of Nucleotides for mmtf structures.
MmtfReducer - Class in de.bioforscher.singa.structure.parser.pdb.structures
MmtfReducer() - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.MmtfReducer
MmtfStructure - Class in de.bioforscher.singa.structure.model.mmtf: The implementation of Structures for mmtf structures.
MmtfStructure(byte[]) - Constructor for class de.bioforscher.singa.structure.model.mmtf.MmtfStructure: Creates a new MmtfStructure
MmtfStructure(byte[], boolean) - Constructor for class de.bioforscher.singa.structure.model.mmtf.MmtfStructure: Creates a new MmtfStructure
Model - Interface in de.bioforscher.singa.structure.model.interfaces: Models represent macro molecular structures.
model(int) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiBranchStep: If only a single model should be parsed, give its pdbIdentifier here.
model(int) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.SingleBranchStep: If only a single model should be parsed, give its pdbIdentifier here.
model(int) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
model(int) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.StructuralModelStep
MODEL_TERMINATOR - Static variable in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.TerminatorTokens
ModelToken - Enum in de.bioforscher.singa.structure.parser.pdb.structures.tokens
MolarMass - Class in de.bioforscher.singa.structure.features.molarmass: In chemistry, the molar mass is a physical property.
MolarMass(Quantity<MolarMass>, FeatureOrigin) - Constructor for class de.bioforscher.singa.structure.features.molarmass.MolarMass
MolarMass(double, FeatureOrigin) - Constructor for class de.bioforscher.singa.structure.features.molarmass.MolarMass
MoleculeAtom - Class in de.bioforscher.singa.structure.model.molecules
MoleculeAtom(int) - Constructor for class de.bioforscher.singa.structure.model.molecules.MoleculeAtom
MoleculeAtom(int, Vector2D) - Constructor for class de.bioforscher.singa.structure.model.molecules.MoleculeAtom
MoleculeAtom(int, Vector2D, Element) - Constructor for class de.bioforscher.singa.structure.model.molecules.MoleculeAtom
MoleculeBond - Class in de.bioforscher.singa.structure.model.molecules
MoleculeBond(int) - Constructor for class de.bioforscher.singa.structure.model.molecules.MoleculeBond
MoleculeBond(int, char) - Constructor for class de.bioforscher.singa.structure.model.molecules.MoleculeBond
MoleculeBond(int, MoleculeAtom, MoleculeAtom, MoleculeBondType) - Constructor for class de.bioforscher.singa.structure.model.molecules.MoleculeBond
MoleculeBondType - Enum in de.bioforscher.singa.structure.model.molecules
MoleculeGraph - Class in de.bioforscher.singa.structure.model.molecules
MoleculeGraph() - Constructor for class de.bioforscher.singa.structure.model.molecules.MoleculeGraph
MoleculeGraphs - Class in de.bioforscher.singa.structure.model.molecules
MoleculeGraphs() - Constructor for class de.bioforscher.singa.structure.model.molecules.MoleculeGraphs
MoleculeIsomorphism - Class in de.bioforscher.singa.structure.algorithms.molecules
MoleculeIsomorphism(RISubgraphFinder<MoleculeAtom, MoleculeBond, Vector2D, Integer, MoleculeGraph>) - Constructor for class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphism
MoleculeIsomorphismFinder - Class in de.bioforscher.singa.structure.algorithms.molecules: A molecule isomorphism finder based on RISubgraphFinder.
MoleculeIsomorphismFinder.AtomConditions - Class in de.bioforscher.singa.structure.algorithms.molecules: Predefined atom conditions for isomorphism testing.
MoleculeIsomorphismFinder.BondConditions - Class in de.bioforscher.singa.structure.algorithms.molecules: Predefined bond conditions for isomorphism testing.
MoleculePathFinder - Class in de.bioforscher.singa.structure.algorithms.molecules
MOLYBDENUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
multiply(Quantity<?>) - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
multiply(Number) - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass

N

NEODYMIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
NEON - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
NEPTUNIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
next() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiParser
nextNodeIdentifier() - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraph
NICKEL - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
NIOBIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
NITROGEN - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
NOBELIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
Nucleotide - Interface in de.bioforscher.singa.structure.model.interfaces: A specific type of LeafSubstructure, representing nucleotides.
nucleotide(int) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.ResidueStep
nucleotide(int) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
NucleotideFamily - Enum in de.bioforscher.singa.structure.model.families

O

OakAminoAcid - Class in de.bioforscher.singa.structure.model.oak
OakAminoAcid(LeafIdentifier, AminoAcidFamily) - Constructor for class de.bioforscher.singa.structure.model.oak.OakAminoAcid
OakAminoAcid(LeafIdentifier, AminoAcidFamily, String) - Constructor for class de.bioforscher.singa.structure.model.oak.OakAminoAcid
OakAminoAcid(OakAminoAcid) - Constructor for class de.bioforscher.singa.structure.model.oak.OakAminoAcid
OakAtom - Class in de.bioforscher.singa.structure.model.oak
OakAtom(int, Element, String, Vector3D) - Constructor for class de.bioforscher.singa.structure.model.oak.OakAtom: Creates a new atom with the given pdbIdentifier, element, name and position.
OakAtom(OakAtom) - Constructor for class de.bioforscher.singa.structure.model.oak.OakAtom: This is a copy constructor.
OakBond - Class in de.bioforscher.singa.structure.model.oak
OakBond(int) - Constructor for class de.bioforscher.singa.structure.model.oak.OakBond
OakBond(int, BondType) - Constructor for class de.bioforscher.singa.structure.model.oak.OakBond
OakBond(OakBond) - Constructor for class de.bioforscher.singa.structure.model.oak.OakBond: This is a copy constructor.
OakChain - Class in de.bioforscher.singa.structure.model.oak
OakChain(String) - Constructor for class de.bioforscher.singa.structure.model.oak.OakChain
OakChain(OakChain) - Constructor for class de.bioforscher.singa.structure.model.oak.OakChain
OakLeafSubstructure<FamilyType extends StructuralFamily> - Class in de.bioforscher.singa.structure.model.oak
OakLeafSubstructure(LeafIdentifier, FamilyType) - Constructor for class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
OakLeafSubstructure(LeafIdentifier, FamilyType, String) - Constructor for class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
OakLeafSubstructure(OakLeafSubstructure<FamilyType>) - Constructor for class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure: This is a copy constructor.
OakLigand - Class in de.bioforscher.singa.structure.model.oak
OakLigand(LeafIdentifier, LigandFamily) - Constructor for class de.bioforscher.singa.structure.model.oak.OakLigand
OakLigand(OakLigand) - Constructor for class de.bioforscher.singa.structure.model.oak.OakLigand
OakModel - Class in de.bioforscher.singa.structure.model.oak
OakModel(int) - Constructor for class de.bioforscher.singa.structure.model.oak.OakModel: Creates a new BranchSubstructure.
OakModel(OakModel) - Constructor for class de.bioforscher.singa.structure.model.oak.OakModel
OakNucleotide - Class in de.bioforscher.singa.structure.model.oak
OakNucleotide(LeafIdentifier, NucleotideFamily) - Constructor for class de.bioforscher.singa.structure.model.oak.OakNucleotide
OakNucleotide(LeafIdentifier, NucleotideFamily, String) - Constructor for class de.bioforscher.singa.structure.model.oak.OakNucleotide
OakNucleotide(OakNucleotide) - Constructor for class de.bioforscher.singa.structure.model.oak.OakNucleotide
OakStructure - Class in de.bioforscher.singa.structure.model.oak
OakStructure() - Constructor for class de.bioforscher.singa.structure.model.oak.OakStructure
OakStructure(OakStructure) - Constructor for class de.bioforscher.singa.structure.model.oak.OakStructure
of(AtomContainer) - Static method in class de.bioforscher.singa.structure.algorithms.gyration.Gyration: Calculates the gyration for the atoms in the container.
of(MoleculeGraph, MoleculeGraph) - Static method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphismFinder
of(MoleculeGraph, MoleculeGraph, BiFunction<MoleculeAtom, MoleculeAtom, Boolean>, BiFunction<MoleculeBond, MoleculeBond, Boolean>) - Static method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphismFinder
of(double) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
of(double, SubstructureSuperimposition) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
of(double, SubstructureSuperimposition, double) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
of(SubstructureSuperimposition, int, int) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.scores.PsScore: Calculates the PsScore for the given SubstructureSuperimposition.
of(SubstitutionMatrix, SubstructureSuperimposition) - Static method in class de.bioforscher.singa.structure.algorithms.superimposition.scores.XieScore
of(String...) - Static method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifiers
of(String, String, PDBSequenceCluster.PDBSequenceClusterIdentity) - Static method in class de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceCluster
omitHydrogens(boolean) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option to true will omit all hydrogen (and eventually deuterium) atoms in amino acids and nucleotides.
OSMIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
OXYGEN - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider

P

PALLADIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
parse() - Method in class de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceCluster
parse() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiChainStep: Returns a list of parsed structures, skipping user contact with parsing.
parse() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiParser: Parses all structures that are queued for this StructureParser.MultiParser.
parse() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.SingleChainStep: Returns the parsed structure, skipping user contact with parsing.
parse() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.SingleParser: Parses the structure as specifies during teh selection process and returns is,
parse(String, String) - Static method in class de.bioforscher.singa.structure.parser.plip.PlipParser
parse(String, InputStream) - Static method in class de.bioforscher.singa.structure.parser.plip.PlipParser
parse() - Method in class de.bioforscher.singa.structure.parser.plip.PlipParser
parse() - Method in class de.bioforscher.singa.structure.parser.sifts.PDBEnzymeMapper
parse() - Method in class de.bioforscher.singa.structure.parser.sifts.PDBPfamMapper
parse() - Method in class de.bioforscher.singa.structure.parser.sifts.PDBUniProtMapper
parse(String) - Static method in class de.bioforscher.singa.structure.parser.sifts.UniProtResidueMapParser
parse(PDBIdentifier) - Static method in class de.bioforscher.singa.structure.parser.sifts.UniProtResidueMapParser
parse() - Method in class de.bioforscher.singa.structure.parser.sifts.UniProtResidueMapParser
parseElectronConfigurationFromString(String) - Static method in class de.bioforscher.singa.structure.elements.ElectronConfiguration
parseLeafSkeleton(List<String>) - Static method in class de.bioforscher.singa.structure.parser.pdb.ligands.CifFileParser
parseLeafSkeleton(String) - Static method in class de.bioforscher.singa.structure.parser.pdb.ligands.LigandParserService
parseLeafSkeleton(InputStream) - Static method in class de.bioforscher.singa.structure.parser.pdb.ligands.LigandParserService
parseLeafSubstructure(List<String>) - Static method in class de.bioforscher.singa.structure.parser.pdb.ligands.CifFileParser
parseLeafSubstructure(InputStream) - Static method in class de.bioforscher.singa.structure.parser.pdb.ligands.LigandParserService
parseLeafSubstructureById(String) - Static method in class de.bioforscher.singa.structure.parser.pdb.ligands.LigandParserService
path(Path) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalSourceStep: The path to parse.
paths(List<Path>) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.LocalSourceStep: The paths to parse.
PATTERN - Static variable in class de.bioforscher.singa.structure.model.identifiers.PDBIdentifier: The pattern to verify the identifier.
pdb() - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser: Structures will be pulled online.
PDBEnzymeMapper - Class in de.bioforscher.singa.structure.parser.sifts
PDBIdentifier - Class in de.bioforscher.singa.structure.model.identifiers: This identifier is used by the Protein Database to identify structures.
PDBIdentifier(String) - Constructor for class de.bioforscher.singa.structure.model.identifiers.PDBIdentifier: Creates a new identifier.
pdbIdentifier(String) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.IdentifierStep: The pdbIdentifier of the PDB structure.
pdbIdentifiers(List<String>) - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.IdentifierStep: The pdbIdentifiers of the PDB structures.
PDBPfamMapper - Class in de.bioforscher.singa.structure.parser.sifts
PDBRestEndpoint<ResultType> - Class in de.bioforscher.singa.structure.parser.pdb.rest
PDBRestEndpoint() - Constructor for class de.bioforscher.singa.structure.parser.pdb.rest.PDBRestEndpoint
PDBSequenceCluster - Class in de.bioforscher.singa.structure.parser.pdb.rest.cluster: A PDBRestEndpoint that uses the PDB REST API to obtain the sequence cluster for a given chain.
PDBSequenceCluster(String, String, PDBSequenceCluster.PDBSequenceClusterIdentity) - Constructor for class de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceCluster
PDBSequenceCluster.PDBSequenceClusterIdentity - Enum in de.bioforscher.singa.structure.parser.pdb.rest.cluster
PDBSequenceClusterMember - Class in de.bioforscher.singa.structure.parser.pdb.rest.cluster
PDBToken - Interface in de.bioforscher.singa.structure.parser.pdb.structures.tokens: Tokens are used to extract information from PDB lines.
PDBUniProtMapper - Class in de.bioforscher.singa.structure.parser.sifts
PFAM_MAPPING_FILE_SEPARATOR - Static variable in interface de.bioforscher.singa.structure.parser.pfam.tokens.PfamToken
pfamIdentifier(String) - Method in class de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder
pfamIdentifier(String) - Method in interface de.bioforscher.singa.structure.parser.pfam.PfamParser.FamilyStep: The Pfam-ID for which data should be fetched.
PfamParser - Class in de.bioforscher.singa.structure.parser.pfam: A parser for the The Pfam protein families database.
PfamParser(PfamParser.Builder) - Constructor for class de.bioforscher.singa.structure.parser.pfam.PfamParser
PfamParser.Builder - Class in de.bioforscher.singa.structure.parser.pfam
PfamParser.ChainStep - Interface in de.bioforscher.singa.structure.parser.pfam
PfamParser.DomainStep - Interface in de.bioforscher.singa.structure.parser.pfam
PfamParser.FamilyStep - Interface in de.bioforscher.singa.structure.parser.pfam
PfamParser.PfamVersion - Enum in de.bioforscher.singa.structure.parser.pfam
PfamParser.VersionStep - Interface in de.bioforscher.singa.structure.parser.pfam
PfamToken - Interface in de.bioforscher.singa.structure.parser.pfam.tokens: A token describing the Pfam mapping file.
PfamToken.IdentifierToken - Enum in de.bioforscher.singa.structure.parser.pfam.tokens
PfamToken.PDBToken - Enum in de.bioforscher.singa.structure.parser.pfam.tokens
PHENYLALANINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
PHOSPHORUS - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
PiCation - Class in de.bioforscher.singa.structure.parser.plip
PiCation(int) - Constructor for class de.bioforscher.singa.structure.parser.plip.PiCation
PiStacking - Class in de.bioforscher.singa.structure.parser.plip
PiStacking(int) - Constructor for class de.bioforscher.singa.structure.parser.plip.PiStacking
PLATINUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
PlipContentHandler - Class in de.bioforscher.singa.structure.parser.plip
PlipContentHandler(String) - Constructor for class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
PlipParser - Class in de.bioforscher.singa.structure.parser.plip
PlipShellGenerator - Class in de.bioforscher.singa.structure.parser.plip: Calculates the shell of residues in indirect contact with the ligand utilizing PLIP interaction data.
PlipShellGenerator.InteractionShell - Enum in de.bioforscher.singa.structure.parser.plip
PLUTONIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
POLONIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
POTASSIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
PRASEODYMIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
processingInstruction(String, String) - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
processingInstruction(String, String) - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
PROLINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
PROMETHIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
PROTACTINIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
PsScore - Class in de.bioforscher.singa.structure.algorithms.superimposition.scores: An implementation of the score to assess the similarity of aligned ligand binding site environments:

Q

query(StructuralMotif) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
query(StructuralMotif) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.QueryStep: Defines the query motif for this Fit3D search.

R

RADIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
RADON - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
RECORD_PATTERN - Static variable in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.AtomToken
RECORD_PATTERN - Static variable in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ChainTerminatorToken: A pattern describing all record names associated with this token structure.
RECORD_PATTERN - Static variable in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.HeaderToken
RECORD_PATTERN - Static variable in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ModelToken: A pattern describing all record names associated with this token structure.
RECORD_PATTERN - Static variable in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.TitleToken
reduceMatches() - Method in class de.bioforscher.singa.structure.algorithms.molecules.MoleculeIsomorphism: This method reduces the found matches to matches were different atoms were hit, i.e.
reference - Variable in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
removeAtom(Integer) - Method in interface de.bioforscher.singa.structure.model.interfaces.AtomContainer: Removes an atom from this container.
removeAtom(Integer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
removeAtom(Integer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
removeAtom(Integer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
removeAtom(Integer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
removeAtom(Integer) - Method in class de.bioforscher.singa.structure.model.oak.OakChain
removeAtom(Integer) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
removeAtom(Integer) - Method in class de.bioforscher.singa.structure.model.oak.OakModel
removeAtom(Integer) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
removeAtom(Integer) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif
removeChain(String) - Method in interface de.bioforscher.singa.structure.model.interfaces.Model: Removes a Chain with the given identifier from the structure.
removeChain(String) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
removeChain(String) - Method in class de.bioforscher.singa.structure.model.oak.OakModel
removeLeafSubstructure(LeafIdentifier) - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Removes a LeafSubstructure from this container.
removeLeafSubstructure(LeafSubstructure) - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer
removeLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
removeLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
removeLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
removeLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.oak.OakChain
removeLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.oak.OakModel
removeLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
removeLeafSubstructure(LeafIdentifier) - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif
removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer) - Method in interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer: Removes all LeafSubstructures from this container that are not referenced in the given LeafSubstructureContainer.
removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain: Removes all LeafSubstructures from this container that are not referenced in the given LeafSubstructureContainer.
removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
removeModel(int) - Method in interface de.bioforscher.singa.structure.model.interfaces.Structure: Removes a Model with the given identifier from the structure.
removeModel(int) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
removeModel(int) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
replaceAromaticsWithDoubleBonds(MoleculeGraph) - Static method in class de.bioforscher.singa.structure.model.molecules.MoleculeGraphs
representationScheme(RepresentationSchemeType) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.AtomStep: Defines a single point RepresentationScheme that should be used to represent single residues.
representationScheme(RepresentationSchemeType) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
RepresentationScheme - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations: This represents a representation scheme of a LeafSubstructure.
RepresentationSchemeFactory - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations: A factory for creating implementations of RepresentationSchemes.
representationSchemeType(RepresentationSchemeType) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.AtomStep: Defines a RepresentationSchemeType to be used for the computed alignments.
representationSchemeType(RepresentationSchemeType) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.Builder
representationSchemeType(RepresentationSchemeType) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.AtomStep: Defines a RepresentationSchemeType to be used during consensus calculation.
representationSchemeType(RepresentationSchemeType) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.Builder
RepresentationSchemeType - Enum in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations: Defines the types for which adequately RepresentationSchemes are defined.
ResidueMapContentHandler - Class in de.bioforscher.singa.structure.parser.sifts
ResidueMapContentHandler(String) - Constructor for class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
restrictToSpecifiedExchanges() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
restrictToSpecifiedExchanges() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.SiteConfigurationStep: Restricts the site alignment to the specified exchanges of the input sites.
retrieveLigandInformation(boolean) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Setting this option to true will retrieve additional information from cif files from the PDB.
RHENIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
RHODIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
rmsdCutoff(double) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
rmsdCutoff(double) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.ParameterStep: Defines the RMSD cutoff up to which matches should be reported.
RUBIDIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
run() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.AtomStep: Creates a new ConsensusAlignment and starts the calculation.
run() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.Builder
run() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment.ParameterStep: Creates a new ConsensusAlignment and starts the calculation.
run() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.AtomStep: Creates a new ConsensusAlignment and starts the calculation.
run() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.Builder
run() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusBuilder.ParameterStep
run() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.AtomStep: Creates a new Fit3D search and starts calculation.
run() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
run() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.ParameterStep: Creates a new Fit3D search and starts calculation.
RUTHENIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
RUTHERFORDIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider

S

SaltBridge - Class in de.bioforscher.singa.structure.parser.plip
SaltBridge(int) - Constructor for class de.bioforscher.singa.structure.parser.plip.SaltBridge
SAMARIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
SCANDIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
SEABORGIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
selectAminoAcid() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.AminoAcidAtomStep
selectAminoAcid() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
selectAtom() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
selectAtom() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.SelectStep
selectAtomContainer() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.AtomContainerAtomStep
selectAtomContainer() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
selectChain() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.ResidueStep
selectChain() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
selectFrom(Structure) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector
selectFrom(Model) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector
selectFrom(Chain) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector
selectFrom(StructuralMotif) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector
selectFrom(AminoAcid) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector
selectFrom(Nucleotide) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector
selectFrom(Ligand) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector
selectModel() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.ChainStep
selectModel() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
selectNucleotide() - Method in interface de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.NucleotideAtomStep
selectNucleotide() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
Selector(Structure) - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
Selector(Model) - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
Selector(Chain) - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
Selector(AminoAcid) - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
Selector(Nucleotide) - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
Selector(Ligand) - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
Selector(StructuralMotif) - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.StructureSelector.Selector
SELENIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
SERINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
setAcceptor(int) - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
setAcceptor(int) - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
setAcceptor(int) - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
setAcceptorAngle(double) - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
setAngle(double) - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
setAngle(double) - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
setAnnotatedAsHetAtom(boolean) - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
setAssignedFamily(LeafSkeleton.AssignedFamily) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton
setAtom1(int) - Method in class de.bioforscher.singa.structure.parser.plip.HydrophobicInteraction
setAtom1(int) - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
setAtom2(int) - Method in class de.bioforscher.singa.structure.parser.plip.HydrophobicInteraction
setAtom2(int) - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
setAtomicMass(Quantity<MolarMass>) - Method in class de.bioforscher.singa.structure.elements.Element: Sets the atomic mass.
setAtoms1(List<Integer>) - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
setAtoms1(List<Integer>) - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
setAtoms1(List<Integer>) - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
setAtoms2(List<Integer>) - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
setAtoms2(List<Integer>) - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
setAtoms2(List<Integer>) - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
setBonds(Map<Pair<String>, BondType>) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton
setBondType(BondType) - Method in class de.bioforscher.singa.structure.model.oak.OakBond
setComplexnum(int) - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
setConsensusTree(BinaryTree<ConsensusContainer>) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
setCoordination(int) - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
setCurrentPdbIdentifier(String) - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
setDistance(double) - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
setDistance(double) - Method in class de.bioforscher.singa.structure.parser.plip.HydrophobicInteraction
setDistance(double) - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
setDistance(double) - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
setDistance(double) - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
setDistance(double) - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
setDistanceAW(double) - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
setDistanceDA(double) - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
setDistanceDW(double) - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
setDistanceHA(double) - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
setDocumentLocator(Locator) - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
setDocumentLocator(Locator) - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
setDonor(int) - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
setDonor(int) - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
setDonor(int) - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
setDonorAngle(double) - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
setDonorAngle(double) - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
setElement(Element) - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeAtom
setGeometry(String) - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
setLastAddedAtomIdentifier(int) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
setLigandCoordinate(double[]) - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
setLigandGroup(String) - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
setLigandGroup(String) - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
setLocation(String) - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
setMetalType(String) - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
setName(String) - Method in class de.bioforscher.singa.structure.model.oak.OakLigand
setOffset(double) - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
setOffset(double) - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
setOptions(StructureParserOptions) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiParser: Sets the StructureParserOptions for this parsing process.
setOptions(StructureParserOptions) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.SingleParser: Sets the StructureParserOptions.
setParent(String) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton
setPdbIdentifier(String) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
setPlipIdentifier(int) - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
setPosition(Vector3D) - Method in interface de.bioforscher.singa.structure.model.interfaces.Atom: Sets the position in three dimensional space.
setPosition(Vector3D) - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfAtom
setPosition(Vector3D) - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
setProtcharged(boolean) - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
setProteinCoordinate(double[]) - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
setProtIsDon(boolean) - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
setProtIsDon(boolean) - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
setProtIsPos(boolean) - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
setPvalue(double) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
setRms(double) - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
setSidechain(boolean) - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
setSource(OakAtom) - Method in class de.bioforscher.singa.structure.model.oak.OakBond
setSource(LeafIdentifier) - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
setSuperimposition(SubstructureSuperimposition) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
setTarget(OakAtom) - Method in class de.bioforscher.singa.structure.model.oak.OakBond
setTarget(LeafIdentifier) - Method in class de.bioforscher.singa.structure.parser.plip.Interaction
setThreeLetterCode(String) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton
setTitle(String) - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
setType(MoleculeBondType) - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeBond
setType(String) - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
setWaterAngle(double) - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
SideChainCentroidRepresentationScheme - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations: An implementation to represent a given LeafSubstructure by its sidechain centroid.
SideChainCentroidRepresentationScheme() - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.SideChainCentroidRepresentationScheme
SILICON - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
SILVER - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
site(StructuralMotif) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
site(StructuralMotif) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.QueryStep: Defines a site that should be aligned against another.
size() - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif: Returns the size of the structural motif (the number of contained LeafSubstructures).
skipAlphaCarbonTargets() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.BatchParameterStep: Sets the option to skip all targets that consist of only alpha carbon atoms to avoid a lot of noise in the results.
skipAlphaCarbonTargets() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
skipBackboneTargets() - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.BatchParameterStep: Sets the option to skip all targets that consist of only backbone atoms to avoid a lot of noise in the results.
skipBackboneTargets() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
skippedEntity(String) - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
skippedEntity(String) - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
SODIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
source - Variable in class de.bioforscher.singa.structure.model.oak.OakBond
SourceLocation - Enum in de.bioforscher.singa.structure.parser.pdb.structures: The location the files should be parsed from.
StarkEstimation - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics
StarkEstimation() - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.StarkEstimation
startDocument() - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
startDocument() - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
startElement(String, String, String, Attributes) - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
startElement(String, String, String, Attributes) - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
startPrefixMapping(String, String) - Method in class de.bioforscher.singa.structure.parser.plip.PlipContentHandler
startPrefixMapping(String, String) - Method in class de.bioforscher.singa.structure.parser.sifts.ResidueMapContentHandler
statisticalModel(StatisticalModel) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
statisticalModel(StatisticalModel) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.ParameterStep: Adds the specified StatisticalModel to the search to calculate significance of matches.
StatisticalModel - Interface in de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics
STRONTIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
StructuralEntityFilter - Class in de.bioforscher.singa.structure.model.oak: This static class bundles filters for LeafSubstructures and Atoms that can be concatenated by using the Predicate interface.
StructuralEntityFilter() - Constructor for class de.bioforscher.singa.structure.model.oak.StructuralEntityFilter
StructuralEntityFilter.AtomFilter - Class in de.bioforscher.singa.structure.model.oak: Filters for Atoms.
StructuralEntityFilter.AtomFilterType - Enum in de.bioforscher.singa.structure.model.oak: Simple StructuralEntityFilter.AtomFilter representation as functional Enum class.
StructuralEntityFilter.ChainFilter - Class in de.bioforscher.singa.structure.model.oak: Filters for Chains.
StructuralEntityFilter.LeafFilter - Class in de.bioforscher.singa.structure.model.oak: Filters for LeafSubstructures.
StructuralEntityFilter.LeafFilterType - Enum in de.bioforscher.singa.structure.model.oak: Simple StructuralEntityFilter.LeafFilter representation as functional Enum class.
StructuralFamily<FamilyType extends Comparable<FamilyType>> - Interface in de.bioforscher.singa.structure.model.families: A StructuralFamily defines a PDB-conform label that can at least be expressed in one-letter and/or three-letter code.
StructuralMotif - Class in de.bioforscher.singa.structure.model.oak
StructuralMotif.Type - Enum in de.bioforscher.singa.structure.model.oak: The type of a StructuralMotif, representing inter (across multiple protein chains) and intra (within one protein chain) StructuralMotifs.
StructuralMotifs - Class in de.bioforscher.singa.structure.model.oak: Utility methods that deal with StructuralMotifs.
Structure - Interface in de.bioforscher.singa.structure.model.interfaces: Structures represent chemical objects in three dimensional space.
StructureCollector - Class in de.bioforscher.singa.structure.parser.pdb.structures: The actual processing of pdb files.
StructureParser - Class in de.bioforscher.singa.structure.parser.pdb.structures: Parses structures in pdb format.
StructureParser() - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser
StructureParser.AdditionalLocalSourceStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures: Using a local pdb installation, additional source steps might be used.
StructureParser.IdentifierStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures: After selecting the source, the identifer(s) to parse can be chosen.
StructureParser.LocalPDB - Class in de.bioforscher.singa.structure.parser.pdb.structures: This class represents a local PDB installation.
StructureParser.LocalSourceStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures: Select a local source to parse from.
StructureParser.MultiBranchStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures: Initiates the structure reduction steps for multiple structures.
StructureParser.MultiChainStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures: Initiates the selection of chains, if multiple structures have been chosen.
StructureParser.MultiParser - Class in de.bioforscher.singa.structure.parser.pdb.structures: The MultiParser performs parsing of multiple structures from a single source.
StructureParser.Reducer - Class in de.bioforscher.singa.structure.parser.pdb.structures: This class remembers what general restrictions are to be applied during the parsing.
StructureParser.SingleBranchStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures: Initiates the structure reduction steps for a single structure.
StructureParser.SingleChainStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures: Initiates the selection of chains, if a single structure has been chosen.
StructureParser.SingleParser - Class in de.bioforscher.singa.structure.parser.pdb.structures: This parser should be used if you require only a single structure.
StructureParserException - Exception in de.bioforscher.singa.structure.parser.pdb.structures: Exceptions encountered during parsing of molecular structures.
StructureParserException(String) - Constructor for exception de.bioforscher.singa.structure.parser.pdb.structures.StructureParserException: Creates a new structure parser exception.
StructureParserOptions - Class in de.bioforscher.singa.structure.parser.pdb.structures: Options for faster or more detailed parsing.
StructureParserOptions() - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions
structureParserOptions - Variable in class de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder
structureParserOptions(StructureParserOptions) - Method in class de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder
structureParserOptions(StructureParserOptions) - Method in interface de.bioforscher.singa.structure.parser.pfam.PfamParser.DomainStep: Specify StructureParserOptions used to parse the structures.
StructureParserOptions.Setting - Enum in de.bioforscher.singa.structure.parser.pdb.structures: Settings that can be passed to the Options.
StructureRepresentation - Class in de.bioforscher.singa.structure.parser.pdb.structures: This class represents any AtomContainer in a pdb format, ready to be written to a file.
Structures - Class in de.bioforscher.singa.structure.model.oak: Methods to use for structures...
StructureSelector - Class in de.bioforscher.singa.structure.parser.pdb.structures
StructureSelector.AminoAcidAtomStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures
StructureSelector.AtomContainerAtomStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures
StructureSelector.AtomStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures
StructureSelector.ChainStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures
StructureSelector.NucleotideAtomStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures
StructureSelector.ResidueStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures
StructureSelector.Selector - Class in de.bioforscher.singa.structure.parser.pdb.structures
StructureSelector.SelectStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures
StructureSelector.StructuralModelStep - Interface in de.bioforscher.singa.structure.parser.pdb.structures
StructureWriter - Class in de.bioforscher.singa.structure.parser.pdb.structures: A class to write Structures objects to PDB format.
substitutionMatrix(SubstitutionMatrix) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
substitutionMatrix(SubstitutionMatrix) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.SiteParameterConfigurationStep: The SubstitutionMatrix to be used to calculate the Xie score.
SubstitutionMatrix - Enum in de.bioforscher.singa.structure.algorithms.superimposition.scores
SubstructureSuperimposer - Class in de.bioforscher.singa.structure.algorithms.superimposition: Calculates the various Superimpositions for structures.
SubstructureSuperimposer(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>) - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer
SubstructureSuperimposition - Class in de.bioforscher.singa.structure.algorithms.superimposition: An implementation of a Superimposition for AtomContainers.
SubstructureSuperimposition(double, Vector, Matrix, List<LeafSubstructure<?>>, List<LeafSubstructure<?>>, List<LeafSubstructure<?>>, List<LeafSubstructure<?>>) - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition
SubstructureSuperimpositionException - Exception in de.bioforscher.singa.structure.algorithms.superimposition
SubstructureSuperimpositionException(String) - Constructor for exception de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimpositionException
subtract(Quantity<MolarMass>) - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
SULFUR - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
SYMBOL - Static variable in class de.bioforscher.singa.structure.features.molarmass.MolarMass

T

TANTALUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
target(LeafSubstructureContainer) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
target(LeafSubstructureContainer) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.TargetStep: Defines the target against which this Fit3D search should be run.
target - Variable in class de.bioforscher.singa.structure.model.oak.OakBond
targets(StructureParser.MultiParser) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
targets(StructureParser.MultiParser) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.TargetStep: Defines the targets against which this Fit3D search should be run in batch mode.
TECHNETIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
TELLURIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
TERBIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
TerminatorTokens - Class in de.bioforscher.singa.structure.parser.pdb.structures.tokens
TerminatorTokens() - Constructor for class de.bioforscher.singa.structure.parser.pdb.structures.tokens.TerminatorTokens
THALLIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
THORIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
THREONINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
THULIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
TIN - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
TITANIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
TitleToken - Enum in de.bioforscher.singa.structure.parser.pdb.structures.tokens
to(Unit<MolarMass>) - Method in class de.bioforscher.singa.structure.features.molarmass.MolarMass
toCostMatrix() - Method in enum de.bioforscher.singa.structure.algorithms.superimposition.scores.SubstitutionMatrix
toCsvLine() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
toRealLeafSubstructure(LeafIdentifier, Map<String, OakAtom>) - Method in class de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton
toSimpleString() - Method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier: Returns a simple version of this LeafIdentifier (e.g.
toString() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusContainer
toString() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DMatch
toString() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.scores.PsScore
toString() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.scores.XieScore
toString() - Method in class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition
toString() - Method in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital
toString() - Method in class de.bioforscher.singa.structure.elements.ElectronConfiguration
toString() - Method in class de.bioforscher.singa.structure.elements.Element
toString() - Method in class de.bioforscher.singa.structure.model.families.LigandFamily
toString() - Method in class de.bioforscher.singa.structure.model.identifiers.LeafIdentifier
toString() - Method in class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
toString() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfAtom
toString() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfChain
toString() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure
toString() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfModel
toString() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfNucleotide
toString() - Method in class de.bioforscher.singa.structure.model.mmtf.MmtfStructure
toString() - Method in class de.bioforscher.singa.structure.model.molecules.MoleculeAtom
toString() - Method in class de.bioforscher.singa.structure.model.oak.OakAtom
toString() - Method in class de.bioforscher.singa.structure.model.oak.OakBond
toString() - Method in class de.bioforscher.singa.structure.model.oak.OakChain
toString() - Method in class de.bioforscher.singa.structure.model.oak.OakLeafSubstructure
toString() - Method in class de.bioforscher.singa.structure.model.oak.OakModel
toString() - Method in class de.bioforscher.singa.structure.model.oak.OakStructure
toString() - Method in class de.bioforscher.singa.structure.model.oak.StructuralMotif
toString() - Method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.Reducer
toString() - Method in class de.bioforscher.singa.structure.parser.plip.HalogenBond
toString() - Method in class de.bioforscher.singa.structure.parser.plip.HydrogenBond
toString() - Method in class de.bioforscher.singa.structure.parser.plip.HydrophobicInteraction
toString() - Method in class de.bioforscher.singa.structure.parser.plip.MetalComplex
toString() - Method in class de.bioforscher.singa.structure.parser.plip.PiCation
toString() - Method in class de.bioforscher.singa.structure.parser.plip.PiStacking
toString() - Method in class de.bioforscher.singa.structure.parser.plip.SaltBridge
toString() - Method in class de.bioforscher.singa.structure.parser.plip.WaterBridge
trimEnd(String) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureCollector: Removes trailing whitespaces.
TRITIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
TRYPTOPHAN_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
TUNGSTEN - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
TYROSINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName

U

UniProtResidueMapParser - Class in de.bioforscher.singa.structure.parser.sifts
UniProtResidueMapParser(PDBIdentifier) - Constructor for class de.bioforscher.singa.structure.parser.sifts.UniProtResidueMapParser
UniqueAtomIdentifer - Class in de.bioforscher.singa.structure.model.identifiers
UniqueAtomIdentifer(String, int, String, int, char, int) - Constructor for class de.bioforscher.singa.structure.model.identifiers.UniqueAtomIdentifer
UNKNOWN_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
UNKOWN - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
URANIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider

V

ValidAlignmentGenerator - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d: This class constructs valid alignments for the Fit3D algorithm.
ValidAlignmentGenerator(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>) - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.ValidAlignmentGenerator
validateWithStructure(OakStructure) - Method in class de.bioforscher.singa.structure.parser.plip.InteractionContainer
ValidCandidateGenerator - Class in de.bioforscher.singa.structure.algorithms.superimposition.fit3d: This class constructs valid candidates for the Fit3D algorithm.
ValidCandidateGenerator(List<LeafSubstructure<?>>, List<LeafSubstructure<?>>) - Constructor for class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.ValidCandidateGenerator
VALINE_ATOM_NAMES - Static variable in enum de.bioforscher.singa.structure.model.oak.AtomName
valueOf(String) - Static method in enum de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.RepresentationSchemeType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.algorithms.superimposition.scores.SubstitutionMatrix: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.model.families.MatcherFamily: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.model.families.NucleotideFamily: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.model.molecules.MoleculeBondType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.model.oak.AtomName: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.model.oak.BondType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilterType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.LeafFilterType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.model.oak.StructuralMotif.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceCluster.PDBSequenceClusterIdentity: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.SourceLocation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions.Setting: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.AtomToken: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ChainTerminatorToken: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.HeaderToken: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.Justification: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton.AssignedFamily: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ModelToken: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.TitleToken: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pfam.PfamParser.PfamVersion: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pfam.tokens.PfamToken.IdentifierToken: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.pfam.tokens.PfamToken.PDBToken: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.plip.InteractionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.structure.parser.plip.PlipShellGenerator.InteractionShell: Returns the enum constant of this type with the specified name.
values() - Static method in enum de.bioforscher.singa.structure.algorithms.superimposition.fit3d.representations.RepresentationSchemeType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.algorithms.superimposition.scores.SubstitutionMatrix: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.elements.ElectronConfiguration.AtomicOrbital: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.model.families.AminoAcidFamily: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.model.families.MatcherFamily: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.model.families.NucleotideFamily: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.model.molecules.MoleculeBondType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.model.oak.AtomName: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.model.oak.BondType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.AtomFilterType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.model.oak.StructuralEntityFilter.LeafFilterType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.model.oak.StructuralMotif.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pdb.rest.cluster.PDBSequenceCluster.PDBSequenceClusterIdentity: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.SourceLocation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions.Setting: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.AtomToken: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ChainTerminatorToken: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.HeaderToken: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.Justification: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.LeafSkeleton.AssignedFamily: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.ModelToken: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pdb.structures.tokens.TitleToken: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pfam.PfamParser.PfamVersion: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pfam.tokens.PfamToken.IdentifierToken: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.pfam.tokens.PfamToken.PDBToken: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.plip.InteractionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.structure.parser.plip.PlipShellGenerator.InteractionShell: Returns an array containing the constants of this enum type, in the order they are declared.
VANADIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
version(PfamParser.PfamVersion) - Method in class de.bioforscher.singa.structure.parser.pfam.PfamParser.Builder
version(PfamParser.PfamVersion) - Method in interface de.bioforscher.singa.structure.parser.pfam.PfamParser.VersionStep: The version of the Pfam database that should be used.
vs(StructuralMotif) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.Builder
vs(StructuralMotif) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.SiteStep: Defines the second site for the pairwise site alignment.

W

WaterBridge - Class in de.bioforscher.singa.structure.parser.plip
WaterBridge(int) - Constructor for class de.bioforscher.singa.structure.parser.plip.WaterBridge
withSettings(StructureParserOptions.Setting...) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions: Create a new Options object using enum constants.
writeClusters(Path) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.affinity.AffinityAlignment: Writes the created clusters to the specified Path.
writeClusters(Path) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusAlignment: Writes the created clusters to the specified Path.
writeLeafSubstructureContainer(LeafSubstructureContainer, Path) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureWriter: Writes a given LeafSubstructureContainer in PDB format.
writeLeafSubstructures(List<LeafSubstructure<?>>, Path) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureWriter: Writes a given list of LeafSubstructures in PDB format.
writeMatches(Path, double) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3D: Writes the matches that were found by this Fit3D search to the specified directory.
writeMatches(Path) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3D: Writes the matches that were found by this Fit3D search to the specified directory.
writeMatches(Path) - Method in class de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DSiteAlignment
writeStructure(OakStructure, Path) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureWriter: Writes a Structure in PDB format.
writeSummaryFile(Path) - Method in interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3D: Writes a CSV summary file of the matches obtained by Fit3Di.
writeToXYZ(AtomContainer, Path) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureWriter
writeWithConsecutiveNumbering(OakStructure, Path) - Static method in class de.bioforscher.singa.structure.parser.pdb.structures.StructureWriter

X

XENON - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
XieScore - Class in de.bioforscher.singa.structure.algorithms.superimposition.scores: An implementation of the score described in:

Y

YTTERBIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
YTTRIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider

Z

ZINC - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider
ZIRCONIUM - Static variable in class de.bioforscher.singa.structure.elements.ElementProvider

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