Uses of Class
com.hfg.bio.seq.Protein

Packages that use Protein

Package	Description
com.hfg.bio
com.hfg.bio.proteinproperty	Classes for calculating physical properties of proteins.
com.hfg.bio.seq
com.hfg.bio.seq.alignment
com.hfg.bio.seq.pattern
com.hfg.bio.seq.translation

Uses of Protein in com.hfg.bio

Subclasses of Protein in com.hfg.bio

Modifier and Type	Class and Description
class	DigestFragment Product of a proteolytic digest.

Methods in com.hfg.bio with parameters of type Protein

Modifier and Type	Method and Description
List<DigestFragment>	Protease.digest(Protein inProtein, DigestSettings inSettings)

Uses of Protein in com.hfg.bio.proteinproperty

Methods in com.hfg.bio.proteinproperty with parameters of type Protein

Modifier and Type	Method and Description
String	ChemicalFormula.calculate(Protein inProtein)
Integer	ExtinctionCoeff.calculate(Protein inProtein)
Float	Hydrophobicity.calculate(Protein inProtein)
Float	PctExtinctionCoeff.calculate(Protein inProtein)
Integer	SeqLength.calculate(Protein inProtein)
Float	IsoelectricPoint.calculate(Protein inProtein, S inSettings) Determines the isoelectric point (the pH at which the net charge is zero) for the protein.
T	SingleValueProteinProperty.calculate(Protein inProtein, S inSettings)
String	ChemicalFormula.calculate(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings)
Integer	ExtinctionCoeff.calculate(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings)
Float	Hydrophobicity.calculate(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings)
Double	Mass.calculate(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings) Determines the mass of the specified protein.
Float	PctExtinctionCoeff.calculate(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings)
Integer	SeqLength.calculate(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings)
protected Map<IonizableGroup,Integer>	IsoelectricPoint.constructIonizableGroupMap(Protein inProtein, S inSettings)
double	IsoelectricPoint.getNetCharge(double pH, Protein inProtein, S inSettings) Estimates the protein's net charge at the specified pH.
protected int	ExtinctionCoeff.getRawValue(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings)

Uses of Protein in com.hfg.bio.seq

Methods in com.hfg.bio.seq that return Protein

Modifier and Type	Method and Description
Protein	Protein.addGlycan(Glycan inValue)
Protein	Protein.addGlycans(Glycan inValue, int inCount)
Protein	Protein.clone()
Protein	ProteinFactory.createSeqObj()
Protein	Protein.getChain(String inChainId) Returns the chain with the specified id.
Protein	Protein.getParent() Protein objects can be recursively composed of other Protein objects that represent chains or subunits and this method returns the Protein object that contains this Protein object or null if this Protein object is the top object.
Protein	ProteinDigest.getProtein()
Protein	Protein.setDescription(CharSequence inValue) Specifies the protein's description.
Protein	Protein.setID(String inValue) Specifies the protein's name / identifier.
Protein	Protein.setNCBITaxon(NCBITaxon inValue)
Protein	Protein.setNumDisulfideBonds(int inValue)
Protein	Protein.setSequence(CharSequence inValue) Specifies the protein's sequence.
Protein	Protein.setSequence(Reader inReader) Specifies the protein's sequence.

Methods in com.hfg.bio.seq that return types with arguments of type Protein

Modifier and Type	Method and Description
Collection<Protein>	Protein.getChains()
Collection<Collection<Protein>>	Protein.getChainStoichiometryGroups() Returns chains of this Protein object organized into groups that are identical sequences.
Collection<Protein>	Protein.getDistinctChains()

Methods in com.hfg.bio.seq with parameters of type Protein

Modifier and Type	Method and Description
void	Protein.addChain(Protein inChain) Adds a specified protein chain to this Protein object (with a stoichiometry of one).
void	Protein.addChains(Protein inChain, int inNumCopies) Adds a specified number of copies of a specified protein chain to this Protein object.
protected void	ProteinXLink.setParentProtein(Protein inParentProtein) Sets the protein container to which this x-link belongs.

Method parameters in com.hfg.bio.seq with type arguments of type Protein

Modifier and Type	Method and Description
void	Protein.addChains(Collection<Protein> inChains) Adds specified protein chains to this Protein object (with a stoichiometry of one).
void	Protein.setChains(Collection<Protein> inChains) Specifies the protein's chains.

Constructors in com.hfg.bio.seq with parameters of type Protein

Constructor and Description
ProteinDigest(Protein inProtein, DigestSettings inSettings)
ProteinXLink(ProteinXLinkType inType, Protein inDonorChain, int inDonorPosition, Protein inAcceptorChain, int inAcceptorPosition)

Uses of Protein in com.hfg.bio.seq.alignment

Methods in com.hfg.bio.seq.alignment with parameters of type Protein

Modifier and Type	Method and Description
List<PairwiseSeqAlignment>	PairwiseSeqAligner.align(Protein inQuery, Protein inSubject)
String	PairwiseSeqAligner.showScoring(Collection<Protein> inQueries, Protein inSubject)

Method parameters in com.hfg.bio.seq.alignment with type arguments of type Protein

Modifier and Type	Method and Description
MultipleSequenceAlignment<T>	MultipleSequenceAligner.align(List<Protein> inSequences)
String	PairwiseSeqAligner.showScoring(Collection<Protein> inQueries, Protein inSubject)

Uses of Protein in com.hfg.bio.seq.pattern

Methods in com.hfg.bio.seq.pattern with parameters of type Protein

Modifier and Type	Method and Description
List<ProteinPatternMatch>	ProteinPatternMatcher.match(Protein inQuery)

Uses of Protein in com.hfg.bio.seq.translation

Methods in com.hfg.bio.seq.translation that return Protein

Modifier and Type	Method and Description
Protein	NucleicAcidTranslator.translate(NucleicAcid inSeq, TranslationFrame inFrame)