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kohchuanhockkohchuanhock
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Add one more method to enable the creation of aminoacidtable without explicit specification of elementmass.xml
improved the cookbook tester to use the newly added method and combined shortexample 4 with 5 git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9027 7c6358e6-4a41-0410-a743-a5b2a554c398
1 parent 124967e commit 3310e09

5 files changed

Lines changed: 96 additions & 14 deletions

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‎biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/IPeptideProperties.java‎

Lines changed: 28 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -34,16 +34,25 @@
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/**
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* TODO
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* 4) Write tutorials for BioJava - Cookbook BioJava Wiki -> ProteinStructure
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* 5) Make the xml file more restrictive.
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* 6) Simplify the MW.xml and give a isotope example.
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* 7) combine 4 and 5 and change into ".. Composition of Peptides.. "
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* 9) Check spellings especially physico-chemical properties
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* 13) Definition of the xml in the cook book
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* 2) How to write the formulae for Net Charge where there are summation and power. Likewise for Instability index - Use images if not possible
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* 12) Write an email to in bio-javalist after solving all the above
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*
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* Meetings
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* Wednesday 6 July
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* Tuesday 12 July
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* Thursday 21 July
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*
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* DONE
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* 9) Next week to be on wednesday
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* 10) Add one more method to improve the reading of amino acid table
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* 11) Improve the CookbookTester
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*
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* Question
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* 1) Where should the method auto locate the elementMass file
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* 2) How to write the formulae for Net Charge where there are summation and power. Likewise for Instability index
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*
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*
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*
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*
@@ -131,6 +140,21 @@ public interface IPeptideProperties{
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*/
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public double getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable) throws Exception;
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/**
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* This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to
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* IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
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* Note that ElementMass.xml is assumed to be able to be seen in default location.
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*
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* @param aminoAcidCompositionFile
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* xml file that details the composition of amino acids
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* @return the initialized amino acid composition table
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* @throws JAXBException
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* thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
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* @throws FileNotFoundException
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* thrown if either elementMassFile or aminoAcidCompositionFile are not found
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*/
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public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException;
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/**
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* This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to
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* IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).

‎biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/PeptideProperties.java‎

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Original file line numberDiff line numberDiff line change
@@ -99,6 +99,24 @@ public static final double getMolecularWeight(String sequence, File aminoAcidCom
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return pp.getMolecularWeight(pSequence, aminoAcidCompositionFile);
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}
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/**
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* An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to
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* IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
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* Note that ElementMass.xml is assumed to be able to be seen in default location.
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*
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* @param aminoAcidCompositionFile
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* xml file that details the composition of amino acids
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* @return the initialized amino acid composition table
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* @throws JAXBException
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* thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
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* @throws FileNotFoundException
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* thrown if either elementMassFile or aminoAcidCompositionFile are not found
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*/
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public static final AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException{
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IPeptideProperties pp = new PeptidePropertiesImpl();
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return pp.obtainAminoAcidCompositionTable(aminoAcidCompositionFile);
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}
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/**
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* An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to
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* IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).

‎biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/PeptidePropertiesImpl.java‎

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Original file line numberDiff line numberDiff line change
@@ -132,6 +132,33 @@ public double getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCo
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return value;
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}
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@Override
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public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException{
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File elementMassFile = new File("./src/main/resources/ElementMass.xml");
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if(elementMassFile.exists() == false){
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throw new FileNotFoundException("Cannot locate ElementMass.xml. " +
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"Please use getMolecularWeight(ProteinSequence, File, File) to specify ElementMass.xml location.");
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}
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//Parse elementMassFile
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ElementTable iTable = new ElementTable();
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// Get a JAXB Context for the object we created above
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JAXBContext jc = JAXBContext.newInstance(iTable.getClass());
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Unmarshaller u = jc.createUnmarshaller();
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u.setEventHandler(new MyValidationEventHandler());
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iTable = (ElementTable)u.unmarshal(new FileInputStream(elementMassFile));
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iTable.populateMaps();
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//Parse aminoAcidCompositionFile
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AminoAcidCompositionTable aTable = new AminoAcidCompositionTable();
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// Get a JAXB Context for the object we created above
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JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
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Unmarshaller u2 = jc2.createUnmarshaller();
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u2.setEventHandler(new MyValidationEventHandler());
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aTable = (AminoAcidCompositionTable)u2.unmarshal(new FileInputStream(aminoAcidCompositionFile));
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aTable.computeMolecularWeight(iTable);
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return aTable;
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}
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@Override
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public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException{
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//Parse elementMassFile

‎biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/AminoAcidComposition.java‎

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Original file line numberDiff line numberDiff line change
@@ -35,6 +35,7 @@ public class AminoAcidComposition {
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/**
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* Stores the name of the element and the amount this amino acid contains
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*/
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private Map<String, Integer> elementName2Count;
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/**
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* Stores the name of the isotope and the amount this amino acid contains

‎biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/xml/CookBookTester.java‎

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Original file line numberDiff line numberDiff line change
@@ -19,9 +19,8 @@ public void shortExample1(){
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@Test
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public void shortExample2() throws FileNotFoundException, JAXBException{
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String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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File elementMassFile = new File("./src/main/resources/ElementMass.xml");
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File aminoAcidCompositionFile = new File("./src/main/resources/AminoAcidComposition.xml");
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System.out.println("Molecular Weight: " + PeptideProperties.getMolecularWeight(sequence, elementMassFile, aminoAcidCompositionFile));
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System.out.println("Molecular Weight: " + PeptideProperties.getMolecularWeight(sequence, aminoAcidCompositionFile));
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}
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@Test
@@ -31,9 +30,8 @@ public void shortExample3() throws Exception{
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sequences[1] = "KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS";
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sequences[2] = "VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP";
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34-
File elementMassFile = new File("./src/main/resources/ElementMass.xml");
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File aminoAcidCompositionFile = new File("./src/main/resources/AminoAcidComposition.xml");
36-
AminoAcidCompositionTable table = PeptideProperties.obtainAminoAcidCompositionTable(elementMassFile, aminoAcidCompositionFile);
34+
AminoAcidCompositionTable table = PeptideProperties.obtainAminoAcidCompositionTable(aminoAcidCompositionFile);
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3836
for(String sequence:sequences){
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System.out.println("Molecular Weight: " + PeptideProperties.getMolecularWeightBasedOnXML(sequence, table));
@@ -43,29 +41,43 @@ public void shortExample3() throws Exception{
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@Test
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public void shortExample4(){
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String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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//Enrichment of a specific amino acid type
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System.out.println("Composition of A: " + PeptideProperties.getEnrichment(sequence, "A"));
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}
48-
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@Test
50-
public void shortExample5(){
51-
String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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48+
//Enrichment of a list of amino acid types
5249
Map<String, Double> composition = PeptideProperties.getAACompositionString(sequence);
5350
for(String aa:composition.keySet()){
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System.out.println("Composition of " + aa + ": " + composition.get(aa));
5552
}
5653
}
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@Test
59-
public void shortExample6(){
57+
public void shortExample5(){
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String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTRECMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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//Absorbance
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System.out.println("Absorbance (Cys Reduced): " + PeptideProperties.getAbsorbance(sequence, true));
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System.out.println("Absorbance (Cys Not Reduced): " + PeptideProperties.getAbsorbance(sequence, false));
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//Extinction Coefficient
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System.out.println("Extinction Coefficient (Cys Reduced): " + PeptideProperties.getExtinctionCoefficient(sequence, true));
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System.out.println("Extinction Coefficient (Cys Not Reduced): " + PeptideProperties.getExtinctionCoefficient(sequence, false));
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//Instability Index
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System.out.println("Instability Index: " + PeptideProperties.getInstabilityIndex(sequence));
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//Apliphatic Index
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System.out.println("Apliphatic Index: " + PeptideProperties.getApliphaticIndex(sequence));
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//Average Hydropathy Value
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System.out.println("Average Hydropathy Value: " + PeptideProperties.getAvgHydropathy(sequence));
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//Isoelectric Point
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System.out.println("Isoelectric Point: " + PeptideProperties.getIsoelectricPoint(sequence));
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//Net Charge
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System.out.println("Net Charge at pH 7: " + PeptideProperties.getNetCharge(sequence));
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}
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}

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