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public interface IPeptideProperties
An interface to generate some basic physico-chemical properties of protein sequences.
The following properties could be generated:
PeptideProperties
Method Summary | |
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Map<AminoAcidCompound,Double> |
getAAComposition(ProteinSequence sequence)
Returns the composition of the 20 standard amino acid in the sequence. |
double |
getAbsorbance(ProteinSequence sequence,
boolean assumeCysReduced)
Returns the absorbance (optical density) of sequence. |
double |
getApliphaticIndex(ProteinSequence sequence)
Returns the apliphatic index of sequence. |
double |
getAvgHydropathy(ProteinSequence sequence)
Returns the average hydropathy value of sequence. |
double |
getEnrichment(ProteinSequence sequence,
AminoAcidCompound aminoAcidCode)
Returns the composition of specified amino acid in the sequence. |
double |
getExtinctionCoefficient(ProteinSequence sequence,
boolean assumeCysReduced)
Returns the extinction coefficient of sequence. |
double |
getInstabilityIndex(ProteinSequence sequence)
Returns the instability index of sequence. |
double |
getIsoelectricPoint(ProteinSequence seuqence)
|
double |
getIsoelectricPoint(ProteinSequence sequence,
boolean useExpasyValues)
Returns the isoelectric point of sequence. |
double |
getMolecularWeight(ProteinSequence sequence)
Returns the molecular weight of sequence. |
double |
getMolecularWeight(ProteinSequence sequence,
File aminoAcidCompositionFile)
Returns the molecular weight of sequence. |
double |
getMolecularWeight(ProteinSequence sequence,
File elementMassFile,
File aminoAcidCompositionFile)
Returns the molecular weight of sequence. |
double |
getMolecularWeightBasedOnXML(ProteinSequence sequence,
AminoAcidCompositionTable aminoAcidCompositionTable)
Returns the molecular weight of sequence. |
double |
getNetCharge(ProteinSequence sequence)
|
double |
getNetCharge(ProteinSequence sequence,
boolean useExpasyValues)
|
double |
getNetCharge(ProteinSequence sequence,
boolean useExpasyValues,
double pHPoint)
Returns the net charge of sequence at pH 7. |
AminoAcidCompositionTable |
obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable). |
AminoAcidCompositionTable |
obtainAminoAcidCompositionTable(File elementMassFile,
File aminoAcidCompositionFile)
This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable). |
Method Detail |
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double getMolecularWeight(ProteinSequence sequence)
sequence
- a protein sequence consisting of non-ambiguous characters only
ProteinSequence
double getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException
sequence
- a protein sequence consisting of non-ambiguous characters only
xml file that details the mass of each elements and isotopesaminoAcidCompositionFile
- xml file that details the composition of amino acids
JAXBException
- thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
FileNotFoundException
- thrown if either elementMassFile or aminoAcidCompositionFile are not founddouble getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException
sequence
- a protein sequence consisting of non-ambiguous characters onlyelementMassFile
- xml file that details the mass of each elements and isotopesaminoAcidCompositionFile
- xml file that details the composition of amino acids
JAXBException
- thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
FileNotFoundException
- thrown if either elementMassFile or aminoAcidCompositionFile are not founddouble getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable)
sequence
- a protein sequence consisting of non-ambiguous characters onlyaminoAcidCompositionTable
- a amino acid composition table obtained by calling IPeptideProperties.obtainAminoAcidCompositionTable
AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException
aminoAcidCompositionFile
- xml file that details the composition of amino acids
JAXBException
- thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
FileNotFoundException
- thrown if either elementMassFile or aminoAcidCompositionFile are not foundAminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException
elementMassFile
- xml file that details the mass of each elements and isotopesaminoAcidCompositionFile
- xml file that details the composition of amino acids
JAXBException
- thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
FileNotFoundException
- thrown if either elementMassFile or aminoAcidCompositionFile are not founddouble getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced)
sequence
- a protein sequence consisting of non-ambiguous characters onlyassumeCysReduced
- true if Cys are assumed to be reduced and false if Cys are
assumed to form cystines
ProteinSequence
double getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced)
sequence
- a protein sequence consisting of non-ambiguous characters onlyassumeCysReduced
- true if Cys are assumed to be reduced and false if Cys are
assumed to form cystines
ProteinSequence
double getInstabilityIndex(ProteinSequence sequence)
sequence
- a protein sequence consisting of non-ambiguous characters only
ProteinSequence
double getApliphaticIndex(ProteinSequence sequence)
sequence
- a protein sequence consisting of non-ambiguous characters only
ProteinSequence
double getAvgHydropathy(ProteinSequence sequence)
sequence
- a protein sequence consisting of non-ambiguous characters only
ProteinSequence
double getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues)
sequence
- a protein sequence consisting of non-ambiguous characters onlyuseExpasyValues
- whether to use Expasy values (Default) or Innovagen values
ProteinSequence
double getIsoelectricPoint(ProteinSequence seuqence)
double getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint)
sequence
- a protein sequence consisting of non-ambiguous characters onlyuseExpasyValues
- whether to use Expasy values (Default) or Innovagen valuespHPoint
- the pH value to use for computation of the net charge. Default at 7.
ProteinSequence
double getNetCharge(ProteinSequence sequence, boolean useExpasyValues)
double getNetCharge(ProteinSequence sequence)
double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode)
sequence
- a protein sequence consisting of non-ambiguous characters onlyaminoAcidCode
- the code of the amino acid to compute
ProteinSequence
,
AminoAcidCompound
Map<AminoAcidCompound,Double> getAAComposition(ProteinSequence sequence)
sequence
- a protein sequence consisting of non-ambiguous characters only
ProteinSequence
,
AminoAcidCompound
|
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