Protein (com.hfg API Documentation)

java.lang.Object
- com.hfg.chem.Molecule
- - com.hfg.bio.seq.BioSequenceImpl
  - - com.hfg.bio.seq.BioSequencePlusImpl
    - - com.hfg.bio.seq.Protein

All Implemented Interfaces:

BioSequence, BioSequencePlus, Matter, HfgXMLSerializable, Cloneable, Comparable

Direct Known Subclasses:

DigestFragment
```
public class Protein
extends BioSequencePlusImpl
```
Biological protein sequence.

Nested Class Summary
- Nested classes/interfaces inherited from class com.hfg.bio.seq.BioSequenceImpl
  BioSequenceImpl.SeqFilterReader

Field Summary
- Fields inherited from class com.hfg.bio.seq.BioSequenceImpl
  GAP_PATTERN
- Fields inherited from class com.hfg.chem.Molecule
  H2O, mLocked, mName, NaCl, NH3

Constructor Summary

Constructors
Constructor and Description

Protein()

Protein(XMLNode inXML)

Constructors
Constructor and Description
`Protein()`
`Protein(XMLNode inXML)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addChain(Protein inChain)` Adds a specified protein chain to this Protein object (with a stoichiometry of one).
`void`	`addChains(Collection<Protein> inChains)` Adds specified protein chains to this Protein object (with a stoichiometry of one).
`void`	`addChains(Protein inChain, int inNumCopies)` Adds a specified number of copies of a specified protein chain to this Protein object.
`Protein`	`addGlycan(Glycan inValue)`
`Protein`	`addGlycans(Glycan inValue, int inCount)`
`void`	`addXLink(ProteinXLink inXLink)`
`AminoAcid`	`aminoAcidAt(int inPosition)`
`void`	`clearCalculatedProperties()`
`void`	`clearElementalCompositionAndCalculatedProperties()`
`Protein`	`clone()` Returns an unlocked copy of the Molecule.
`int`	`compareTo(Object inObj2)`
`protected void`	`countGaps()`
`void`	`createNTerminalPyroGlu()` Convenience method for setting the N-terminal group as pyro-glu based on whether the N-terminal residue is Glu or Gln.
`List<SeqLocation>`	`findNLinkedSites()`
`AminoAcidComposition`	`getAminoAcidComposition()` Returns a Map containing the amino acid composition of the protein including any subchains.
`AminoAcidSet`	`getAminoAcidSet()`
`Double`	`getAverageMass()`
`Double`	`getAverageMass(ProteinAnalysisMode inMode)`
`Protein`	`getChain(String inChainId)` Returns the chain with the specified id.
`Set<String>`	`getChainIds()`
`Collection<Protein>`	`getChains()`
`Collection<Collection<Protein>>`	`getChainStoichiometryGroups()` Returns chains of this Protein object organized into groups that are identical sequences.
`protected Map<String,Integer>`	`getComposition()` Returns a map with AminoAcids as keys and Integers as the values.
`Collection<Protein>`	`getDistinctChains()`
`Map<Element,Float>`	`getElementalComposition(ProteinAnalysisMode inMode)` Returns an unmodifiable copy of the elemental composition Map adjusted (if necessary) for the specified protein analysis mode.
`int`	`getExtinctionCoeff()` Returns the estimated molar extinction coefficient at A₂₈₀.
`List<Glycan>`	`getGlycans()`
`Float`	`getIsoelectricPoint()` Determines the isoelectric point (the pH at which the net charge is zero) for the protein.
`Float`	`getIsoelectricPoint(KaSet inKaSet)` Determines the isoelectric point (the pH at which the net charge is zero) for the protein assuming reducing conditions.
`Float`	`getIsoelectricPoint(KaSet inKaSet, ProteinAnalysisMode inMode)` Determines the isoelectric point (the pH at which the net charge is zero) for the protein.
`byte[]`	`getMD5Checksum()`
`float`	`getMillimolarConcFromAbsorbance280(float inAbsorbance)` Returns the concentration (mM) of the protein solution by using the Beer Lambert Law.
`Double`	`getMonoisotopicMass()`
`Double`	`getMonoisotopicMass(ProteinAnalysisMode inMode)`
`Double`	`getNetCharge(double pH, KaSet inKaSet)` Estimates the protein's net charge at the specified pH assuming reducing conditions.
`Double`	`getNetCharge(double pH, KaSet inKaSet, ProteinAnalysisMode inMode)` Estimates the protein's net charge at the specified pH.
`int`	`getNumChains()` Recursively calculates the number of chains in the protein.
`Double`	`getOrganicAverageMass()` Organic mass values used are from:
`Double`	`getOrganicAverageMass(ProteinAnalysisMode inMode)`
`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.
`float`	`getPercentExtinctionCoeff()` Returns the estimated mass attenuation coefficient (ml mg^-1 cm^-1) at A₂₈₀.
`protected Map<Molecule,Integer>`	`getResidueComposition()`
`byte[]`	`getSHA1Checksum()`
`protected Map<Molecule,Integer>`	`getTerminiComposition()`
`Integer`	`getTotalNumDisulfideBonds()` Returns the total number of specified disulfide bonds or null if the number of disulfides has not been set at any chain level.
`int`	`getTotalNumFreeCysteines()` Returns the total number of free cysteines (or the total number of cysteines if the number of disulfides has not been set at any chain level.
`BioSequenceType`	`getType()`
`protected Map<ProteinXLinkType,Integer>`	`getXLinkComposition()`
`Set<ProteinXLink>`	`getXLinks()`
`protected void`	`getXLinks(Set<ProteinXLink> inXLinkList)`
`boolean`	`hasChains()`
`int`	`hashCode()`
`int`	`length()` If this Protein object contains a sequence, the length of that sequence is returned.
`protected void`	`recalculateElementalComposition()`
`void`	`removeXLink(ProteinXLink inXLink)`
`Set<ProteinXLink>`	`removeXLinks()`
`Set<ProteinXLink>`	`removeXLinks(ProteinXLinkType inXLinkType)`
`void`	`setAminoAcidSet(AminoAcidSet inValue)`
`void`	`setChains(Collection<Protein> inChains)` Specifies the protein's chains.
`Protein`	`setDescription(CharSequence inValue)` Specifies the protein's description.
`Protein`	`setID(String inValue)` Specifies the protein's name / identifier.
`Protein`	`setNCBITaxon(NCBITaxon inValue)`
`Protein`	`setNumDisulfideBonds(int inValue)`
`Protein`	`setSequence(CharSequence inValue)` Specifies the protein's sequence.
`Protein`	`setSequence(Reader inReader)` Specifies the protein's sequence.
`XMLNode`	`toXMLNode()`
`void`	`treatWithPNGaseF()` This method converts the asparagine residue of each putative N-link site into aspartic acid, mimicing enzymatic treatment with PNGase F to remove N-linked carbohydrates.

Methods inherited from class com.hfg.bio.seq.BioSequencePlusImpl
addDbXref, addFeature, addKeyword, addKeywords, addKeywords, addParseException, addReference, clearDbXrefs, clearFeatures, clearKeywords, clearParseExceptions, clearReferences, getClone, getDbXrefs, getFeatures, getFeatures, getKeywords, getMolType, getNCBITaxon, getParseExceptions, getReferences, getRevisionDate, getSeqRepositoryDivision, getSeqTopology, setClone, setMolType, setReferences, setRevisionDate, setSeqRepositoryDivision, setSeqTopology

Methods inherited from class com.hfg.bio.seq.BioSequenceImpl
containsGaps, equals, getChemicalFormula, getChemicalFormulaWithSubscripts, getDescription, getElementalComposition, getID, getNumGaps, getReverseSequenceStream, getSequence, getSequenceReader, getSequenceStream, getSubSequence, getSubSequenceReader, getTotalGapLength, residueAt, setCompressionThreshold, setNumGaps, setResidueAt, setTotalGapLength, toString

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface com.hfg.bio.seq.BioSequencePlus
hadParseExceptions

Methods inherited from interface com.hfg.bio.seq.BioSequence
getAttribute, getAttributeNames, getDescription, getID, getSequence, getSequenceReader, getSequenceStream, getSubSequence, getSubSequenceReader, hasAttribute, instantiate, removeAttribute, residueAt, setAttribute

Methods inherited from interface com.hfg.chem.Matter
getChemicalFormula, getElementalComposition

- Constructor Detail
  - Protein
```
public Protein()
```
  - Protein
```
public Protein(XMLNode inXML)
```
- Method Detail
  - getType
```
public BioSequenceType getType()
```
    Specified by:
    
    getType in interface BioSequence
    
    Overrides:
    
    getType in class BioSequenceImpl
  - clone
```
public Protein clone()
```
    Description copied from class: Molecule
    
    Returns an unlocked copy of the Molecule.
    
    Specified by:
    
    clone in interface BioSequence
    
    Overrides:
    
    clone in class BioSequencePlusImpl
    
    Returns:
    
    an unlocked copy of the Molecule
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Molecule
  - compareTo
```
public int compareTo(Object inObj2)
```
    Specified by:
    
    compareTo in interface Comparable
    
    Overrides:
    
    compareTo in class Molecule
  - getMD5Checksum
```
public byte[] getMD5Checksum()
```
    Specified by:
    
    getMD5Checksum in interface BioSequence
    
    Overrides:
    
    getMD5Checksum in class BioSequenceImpl
  - getSHA1Checksum
```
public byte[] getSHA1Checksum()
```
    Specified by:
    
    getSHA1Checksum in interface BioSequence
    
    Overrides:
    
    getSHA1Checksum in class BioSequenceImpl
  - getNumChains
```
public int getNumChains()
```
    Recursively calculates the number of chains in the protein.
    
    Returns:
    
    the number of chains in the protein.
  - setID
```
public Protein setID(String inValue)
```
    Specifies the protein's name / identifier.
    
    Specified by:
    
    setID in interface BioSequence
    
    Overrides:
    
    setID in class BioSequenceImpl
    
    Parameters:
    
    inValue - the name / identifier for the protein
    
    Returns:
    
    this Protein object to enable method chaining
  - setDescription
```
public Protein setDescription(CharSequence inValue)
```
    Specifies the protein's description.
    
    Specified by:
    
    setDescription in interface BioSequence
    
    Overrides:
    
    setDescription in class BioSequenceImpl
    
    Parameters:
    
    inValue - the description of the protein
    
    Returns:
    
    this Protein object to enable method chaining
  - setSequence
```
public Protein setSequence(CharSequence inValue)
```
    Specifies the protein's sequence. A Protein can contain either a sequence or other Protein objects as chains but not both.
    
    Specified by:
    
    setSequence in interface BioSequence
    
    Overrides:
    
    setSequence in class BioSequenceImpl
    
    Parameters:
    
    inValue - the sequence of the protein
    
    Returns:
    
    this Protein object to enable method chaining
  - setNCBITaxon
```
public Protein setNCBITaxon(NCBITaxon inValue)
```
    Specified by:
    
    setNCBITaxon in interface BioSequencePlus
    
    Overrides:
    
    setNCBITaxon in class BioSequencePlusImpl
  - setSequence
```
public Protein setSequence(Reader inReader)
```
    Specifies the protein's sequence. A Protein can contain either a sequence or other Protein objects as chains but not both.
    
    Specified by:
    
    setSequence in interface BioSequence
    
    Overrides:
    
    setSequence in class BioSequenceImpl
    
    Parameters:
    
    inReader - the sequence of the protein specified via a Reader
    
    Returns:
    
    this Protein object to enable method chaining
  - setChains
```
public void setChains(Collection<Protein> inChains)
```
    Specifies the protein's chains. A Protein can contain either a sequence or other Protein objects as chains but not both.
    
    Parameters:
    
    inChains - Protein objects that are chains of this Protein object
  - addChain
```
public void addChain(Protein inChain)
```
    Adds a specified protein chain to this Protein object (with a stoichiometry of one). A Protein can contain either a sequence or other Protein objects as chains but not both.
    
    Parameters:
    
    inChain - Protein object that is a chain of this Protein object
  - addChains
```
public void addChains(Collection<Protein> inChains)
```
    Adds specified protein chains to this Protein object (with a stoichiometry of one). A Protein can contain either a sequence or other Protein objects as chains but not both.
    
    Parameters:
    
    inChains - Protein objects that are chains of this Protein object
  - addChains
```
public void addChains(Protein inChain,
                      int inNumCopies)
```
    Adds a specified number of copies of a specified protein chain to this Protein object. (Ex. 2 heavy or light chains in an antibody.) A Protein can contain either a sequence or other Protein objects as chains but not both.
    
    Parameters:
    
    inChain - Protein object that is a chain of this Protein object
    
    inNumCopies - the number of copies of the specified chain that should be added
  - hasChains
```
public boolean hasChains()
```
  - getChains
```
public Collection<Protein> getChains()
```
  - getChain
```
public Protein getChain(String inChainId)
```
    Returns the chain with the specified id.
    
    Parameters:
    
    inChainId - the id of the chain to return
    
    Returns:
    
    the requested chain
  - getDistinctChains
```
public Collection<Protein> getDistinctChains()
```
  - getChainStoichiometryGroups
```
public Collection<Collection<Protein>> getChainStoichiometryGroups()
```
    Returns chains of this Protein object organized into groups that are identical sequences.
    
    Returns:
    
    the protein's chains grouped by sequence
  - getChainIds
```
public Set<String> getChainIds()
```
  - length
```
public int length()
```
    If this Protein object contains a sequence, the length of that sequence is returned. If this Protein object contains other Protein chains, the sum of their lengths is returned.
    
    Specified by:
    
    length in interface BioSequence
    
    Overrides:
    
    length in class BioSequenceImpl
    
    Returns:
    
    the total sequence length
  - clearElementalCompositionAndCalculatedProperties
```
public void clearElementalCompositionAndCalculatedProperties()
```
    Overrides:
    
    clearElementalCompositionAndCalculatedProperties in class BioSequenceImpl
  - setAminoAcidSet
```
public void setAminoAcidSet(AminoAcidSet inValue)
```
  - getAminoAcidSet
```
public AminoAcidSet getAminoAcidSet()
```
  - getParent
```
public 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.
    
    Returns:
    
    the Protein object that contains this Protein object as a chain / subunit or null if this Protein object is the top object.
  - countGaps
```
protected void countGaps()
```
    Overrides:
    
    countGaps in class BioSequenceImpl
  - getAminoAcidComposition
```
public AminoAcidComposition getAminoAcidComposition()
```
    Returns a Map containing the amino acid composition of the protein including any subchains.
    
    Returns:
    
    a Map with AminoAcids as keys and Integers as the values
  - getElementalComposition
```
public Map<Element,Float> getElementalComposition(ProteinAnalysisMode inMode)
```
    Returns an unmodifiable copy of the elemental composition Map adjusted (if necessary) for the specified protein analysis mode. The keys are Element objects and the values are Floats. Why Floats instead of Integers you ask? Because some amino acid codes such as B and Z are ambiguous averages.
    
    Returns:
    
    the elemental composition map
  - getMonoisotopicMass
```
public Double getMonoisotopicMass()
```
    Specified by:
    
    getMonoisotopicMass in interface Matter
    
    Overrides:
    
    getMonoisotopicMass in class BioSequenceImpl
  - getMonoisotopicMass
```
public Double getMonoisotopicMass(ProteinAnalysisMode inMode)
```
  - getAverageMass
```
public Double getAverageMass()
```
    Specified by:
    
    getAverageMass in interface Matter
    
    Overrides:
    
    getAverageMass in class BioSequenceImpl
  - getAverageMass
```
public Double getAverageMass(ProteinAnalysisMode inMode)
```
  - getOrganicAverageMass
```
public Double getOrganicAverageMass()
```
    Description copied from class: BioSequenceImpl
    Organic mass values used are from:
```
      Zhang Z, Pan H, Chen X. 2009. Mass spectrometry for structural characterization
      of therapeutic antibodies. Mass Spectrom Rev 28:147-176.
    
```
    Specified by:
    
    getOrganicAverageMass in interface Matter
    
    Overrides:
    
    getOrganicAverageMass in class BioSequenceImpl
    
    Returns:
    
    the organic average mass for the sequence
  - getOrganicAverageMass
```
public Double getOrganicAverageMass(ProteinAnalysisMode inMode)
```
  - getIsoelectricPoint
```
public Float getIsoelectricPoint()
```
    Determines the isoelectric point (the pH at which the net charge is zero) for the protein. Uses KaSet.BJELLQVIST by default.
    
    Returns:
    
    the isoelectric point for the protein
  - getIsoelectricPoint
```
public Float getIsoelectricPoint(KaSet inKaSet)
```
    Determines the isoelectric point (the pH at which the net charge is zero) for the protein assuming reducing conditions.
    
    Parameters:
    
    inKaSet - the specific set of pKa values to use in calculating the isoelectric point
    
    Returns:
    
    the isoelectric point for the protein
  - getIsoelectricPoint
```
public Float getIsoelectricPoint(KaSet inKaSet,
                                 ProteinAnalysisMode inMode)
```
    Determines the isoelectric point (the pH at which the net charge is zero) for the protein.
    
    Parameters:
    
    inKaSet - the specific set of pKa values to use in calculating the isoelectric point
    
    inMode - the anlysis mode conditions to apply to the calculation
    
    Returns:
    
    the isoelectric point for the protein
  - getNetCharge
```
public Double getNetCharge(double pH,
                           KaSet inKaSet)
```
    Estimates the protein's net charge at the specified pH assuming reducing conditions.
    
    Parameters:
    
    pH - the specific pH value at which to calculate the protein's net charge
    
    inKaSet - the specific set of pKa values to use in calculating the isoelectric point
    
    Returns:
    
    the net charge of the protein at the specified pH
  - getNetCharge
```
public Double getNetCharge(double pH,
                           KaSet inKaSet,
                           ProteinAnalysisMode inMode)
```
    Estimates the protein's net charge at the specified pH.
    
    Parameters:
    
    pH - the specific pH value at which to calculate the protein's net charge
    
    inKaSet - the specific set of pKa values to use in calculating the isoelectric point
    
    inMode - the anlysis mode conditions to apply to the calculation
    
    Returns:
    
    the net charge of the protein at the specified pH
  - getTotalNumDisulfideBonds
```
public Integer getTotalNumDisulfideBonds()
```
    Returns the total number of specified disulfide bonds or null if the number of disulfides has not been set at any chain level.
    
    Returns:
    
    the total number of specified disulfide bonds
  - setNumDisulfideBonds
```
public Protein setNumDisulfideBonds(int inValue)
```
  - getTotalNumFreeCysteines
```
public int getTotalNumFreeCysteines()
```
    Returns the total number of free cysteines (or the total number of cysteines if the number of disulfides has not been set at any chain level.
    
    Returns:
    
    the total number of free cysteines
  - getExtinctionCoeff
```
public int getExtinctionCoeff()
```
    Returns the estimated molar extinction coefficient at A₂₈₀. If the number of disulfide bonds has not been specified, it assumes that all cysteines are disulfide-linked.
    This method utilizes the coefficients derived by Pace et al. (1995) Protein Science 4:2411-2423.
    
    Returns:
    
    the estimated molar extinction coefficient for the protein
  - getPercentExtinctionCoeff
```
public float getPercentExtinctionCoeff()
```
    Returns the estimated mass attenuation coefficient (ml mg^-1 cm^-1) at A₂₈₀. If the number of disulfide bonds has not been specified, it assumes that all cysteines are disulfide-linked.
    This method utilizes the coefficients derived by Pace et al. (1995) Protein Science 4:2411-2423.
    
    Returns:
    
    the estimated percent molar extinction coefficient for the protein
  - getMillimolarConcFromAbsorbance280
```
public float getMillimolarConcFromAbsorbance280(float inAbsorbance)
```
    Returns the concentration (mM) of the protein solution by using the Beer Lambert Law.
```
     Abs = PCE

     Where: Abs = Absorbance at a specific wavelength
     P = path length of the cell (assumed to be 1 cm)
     C = concentration in moles / liter
     E = Molar extinction coeff at a specific wavelength

     
```
    Parameters:
    
    inAbsorbance - the observed absorbance at 280nm
    
    Returns:
    
    the estimated protein concentration in mM
  - aminoAcidAt
```
public AminoAcid aminoAcidAt(int inPosition)
```
  - createNTerminalPyroGlu
```
public void createNTerminalPyroGlu()
```
    Convenience method for setting the N-terminal group as pyro-glu based on whether the N-terminal residue is Glu or Gln.
  - treatWithPNGaseF
```
public void treatWithPNGaseF()
```
    This method converts the asparagine residue of each putative N-link site into aspartic acid, mimicing enzymatic treatment with PNGase F to remove N-linked carbohydrates. This method is not reversible and assumes that all putative N-link sites have attached carbohydrate structures.
  - findNLinkedSites
```
public List<SeqLocation> findNLinkedSites()
```
  - toXMLNode
```
public XMLNode toXMLNode()
```
    Specified by:
    
    toXMLNode in interface BioSequence
    
    Specified by:
    
    toXMLNode in interface HfgXMLSerializable
    
    Overrides:
    
    toXMLNode in class BioSequencePlusImpl
  - addGlycans
```
public Protein addGlycans(Glycan inValue,
                          int inCount)
```
  - addGlycan
```
public Protein addGlycan(Glycan inValue)
```
  - getGlycans
```
public List<Glycan> getGlycans()
```
  - addXLink
```
public void addXLink(ProteinXLink inXLink)
```
  - getXLinks
```
public Set<ProteinXLink> getXLinks()
```
  - removeXLink
```
public void removeXLink(ProteinXLink inXLink)
```
  - removeXLinks
```
public Set<ProteinXLink> removeXLinks()
```
  - removeXLinks
```
public Set<ProteinXLink> removeXLinks(ProteinXLinkType inXLinkType)
```
  - clearCalculatedProperties
```
public void clearCalculatedProperties()
```
    Overrides:
    
    clearCalculatedProperties in class BioSequenceImpl
  - getXLinks
```
protected void getXLinks(Set<ProteinXLink> inXLinkList)
```
  - getComposition
```
protected Map<String,Integer> getComposition()
```
    Returns a map with AminoAcids as keys and Integers as the values.
    
    Overrides:
    
    getComposition in class BioSequenceImpl
    
    Returns:
    
    Map with 1-letter code Strings as keys and Integers as the values
  - getResidueComposition
```
protected Map<Molecule,Integer> getResidueComposition()
```
    Overrides:
    
    getResidueComposition in class BioSequenceImpl
  - getTerminiComposition
```
protected Map<Molecule,Integer> getTerminiComposition()
```
    Overrides:
    
    getTerminiComposition in class BioSequenceImpl
  - getXLinkComposition
```
protected Map<ProteinXLinkType,Integer> getXLinkComposition()
```
    Overrides:
    
    getXLinkComposition in class BioSequenceImpl
  - recalculateElementalComposition
```
protected void recalculateElementalComposition()
```
    Overrides:
    
    recalculateElementalComposition in class BioSequenceImpl

Class Protein

Nested Class Summary

Nested classes/interfaces inherited from class com.hfg.bio.seq.BioSequenceImpl

Field Summary

Fields inherited from class com.hfg.bio.seq.BioSequenceImpl

Fields inherited from class com.hfg.chem.Molecule

Constructor Summary

Method Summary

Methods inherited from class com.hfg.bio.seq.BioSequencePlusImpl

Methods inherited from class com.hfg.bio.seq.BioSequenceImpl

Methods inherited from class com.hfg.chem.Molecule

Methods inherited from class java.lang.Object

Methods inherited from interface com.hfg.bio.seq.BioSequencePlus

Methods inherited from interface com.hfg.bio.seq.BioSequence

Methods inherited from interface com.hfg.chem.Matter

Constructor Detail

Protein

Protein

Method Detail

getType

clone

hashCode

compareTo

getMD5Checksum

getSHA1Checksum

getNumChains

setID

setDescription

setSequence

setNCBITaxon

setSequence

setChains

addChain

addChains

addChains

hasChains

getChains

getChain

getDistinctChains

getChainStoichiometryGroups

getChainIds

length

clearElementalCompositionAndCalculatedProperties

setAminoAcidSet

getAminoAcidSet

getParent

countGaps

getAminoAcidComposition

getElementalComposition

getMonoisotopicMass

getMonoisotopicMass

getAverageMass

getAverageMass

getOrganicAverageMass

getOrganicAverageMass

getIsoelectricPoint

getIsoelectricPoint

getIsoelectricPoint

getNetCharge

getNetCharge

getTotalNumDisulfideBonds

setNumDisulfideBonds

getTotalNumFreeCysteines

getExtinctionCoeff

getPercentExtinctionCoeff

getMillimolarConcFromAbsorbance280

aminoAcidAt

createNTerminalPyroGlu

treatWithPNGaseF

findNLinkedSites

toXMLNode

addGlycans

addGlycan

getGlycans

addXLink

getXLinks

removeXLink

removeXLinks

removeXLinks

clearCalculatedProperties