BioJava:CookBook:AAPROP:main

From BioJava

Contents 1 How can I compute physico-chemical properties via APIs? 2 Short Example 1: Computing molecular weight using default values 3 Short Example 2: Computing molecular weight using user-defined values 4 Short Example 3: Computing molecular weight for multiple sequences 5 Short Example 4: Computing composition of protein sequence 6 Short Example 5: Computing of all other physico-chemical properties

How can I compute physico-chemical properties via APIs?

BioJava provides a set of APIs to generate some commonly used physiochemical properties. They are

• Molecular Weight (See also: How to define the XML files to customize mass of Amino Acids in the computation of Molecular Weight?)
• Absorbance
• Extinction Coefficient
• Instability Index
• Apliphatic Index
• Average Hydropathy Value
• Isoelectric Point
• Net Charge at pH 7
• Composition of specified amino acid
• Composition of the 20 standard amino acid

The class providing the core functionality for this is the IPeptideProperties class.

Short Example 1: Computing molecular weight using default values

String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
boolean ignoreCase = true;
System.out.println("Molecular Weight: " + PeptideProperties.getMolecularWeight(sequence, ignoreCase));

Short Example 2: Computing molecular weight using user-defined values

String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
File elementMassFile = new File("./src/main/resources/ElementMass.xml");
File aminoAcidCompositionFile = new File("./src/main/resources/AminoAcidComposition.xml");
boolean ignoreCase = true;
System.out.println("Molecular Weight: " + PeptideProperties.getMolecularWeight(sequence, elementMassFile, aminoAcidCompositionFile, ignoreCase));

(See also: How to define the XML files to customize mass of Amino Acids in the computation of Molecular Weight?)

Short Example 3: Computing molecular weight for multiple sequences

String[] sequences = new String[3];
sequences[0] = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
sequences[1] = "KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS";
sequences[2] = "VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP";
 
File elementMassFile = new File("./src/main/resources/ElementMass.xml");
File aminoAcidCompositionFile = new File("./src/main/resources/AminoAcidComposition.xml");
boolean ignoreCase = true;
AminoAcidCompositionTable table = PeptideProperties.obtainAminoAcidCompositionTable(elementMassFile, aminoAcidCompositionFile, ignoreCase);
 
//The difference between this example and short example 2 is that the elementMassFile and aminoAcidCompositionFile will be only parsed once 
//and stored in AminoAcidCompositionTable for quick and easy reuse in the computation of multiple sequences.
for(String sequence:sequences){
    System.out.println("Molecular Weight: " + PeptideProperties.getMolecularWeightBasedOnXML(sequence, table, ignoreCase));
}

Short Example 4: Computing composition of protein sequence

String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
boolean ignoreCase = true;
 
//Enrichment of a specific amino acid type
System.out.println("Composition of A: " + PeptideProperties.getEnrichment(sequence, "A", ignoreCase));
 
//Enrichment of a list of amino acid types
Map<String, Double> composition = PeptideProperties.getAACompositionString(sequence, ignoreCase);
for(String aa:composition.keySet()){
	System.out.println("Composition of " + aa + ": " + composition.get(aa));
}

Short Example 5: Computing of all other physico-chemical properties

String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTRECMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
boolean ignoreCase = true;
 
//Absorbance
System.out.println("Absorbance (Cys Reduced): " + PeptideProperties.getAbsorbance(sequence, true, ignoreCase));
System.out.println("Absorbance (Cys Not Reduced): " + PeptideProperties.getAbsorbance(sequence, false, ignoreCase));
 
//Extinction Coefficient
System.out.println("Extinction Coefficient (Cys Reduced): " + PeptideProperties.getExtinctionCoefficient(sequence, true, ignoreCase));
System.out.println("Extinction Coefficient (Cys Not Reduced): " + PeptideProperties.getExtinctionCoefficient(sequence, false, ignoreCase));
 
//Instability Index
System.out.println("Instability Index: " + PeptideProperties.getInstabilityIndex(sequence, ignoreCase));
 
//Apliphatic Index
System.out.println("Apliphatic Index: " + PeptideProperties.getApliphaticIndex(sequence, ignoreCase));
 
//Average Hydropathy Value
System.out.println("Average Hydropathy Value: " + PeptideProperties.getAvgHydropathy(sequence, ignoreCase));
 
//Isoelectric Point
System.out.println("Isoelectric Point: " + PeptideProperties.getIsoelectricPoint(sequence, ignoreCase));
 
//Net Charge
System.out.println("Net Charge at pH 7: " + PeptideProperties.getNetCharge(sequence, ignoreCase));