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org.biojava.nbio.aaproperties.PeptidePropertiesImpl Maven / Gradle / Ivy
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.aaproperties;
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
import org.biojava.nbio.aaproperties.xml.ElementTable;
import org.biojava.nbio.aaproperties.xml.MyValidationEventHandler;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.util.HashMap;
import java.util.Map;
/**
* This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.
*
* @author kohchuanhock
* @version 2011.08.22
* @since 3.0.2
* @see IPeptideProperties
* @see PeptideProperties
*/
public class PeptidePropertiesImpl implements IPeptideProperties{
private final static Logger logger = LoggerFactory.getLogger(PeptidePropertiesImpl.class);
/**
* @return the molecular weight of water
*/
private double getWaterMoleculeWeight(){
final double hydrogenMW = 1.0079;
final double hydroxideMW = 17.0073;
//H 1.0079 OH 17.0073
return hydrogenMW + hydroxideMW;
}
private char[] getSequence(String sequence, boolean ignoreCase){
if(ignoreCase){
return sequence.toUpperCase().toCharArray();
}else{
return sequence.toCharArray();
}
}
@Override
public double getMolecularWeight(ProteinSequence sequence) {
double value = 0.0;
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
char[] seq = getSequence(sequence.toString(), true);//ignore case
for(char aa:seq){
AminoAcidCompound c = aaSet.getCompoundForString(String.valueOf(aa));
if(Constraints.aa2MolecularWeight.containsKey(c)){
value += Constraints.aa2MolecularWeight.get(c);
}
}
if(value == 0)
return value;
else
return value + getWaterMoleculeWeight();
}
@Override
public double getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException {
File elementMassFile = new File("./src/main/resources/ElementMass.xml");
if(!elementMassFile.exists()){
throw new FileNotFoundException("Cannot locate ElementMass.xml. " +
"Please use getMolecularWeight(ProteinSequence, File, File) to specify ElementMass.xml location.");
}
return getMolecularWeightBasedOnXML(sequence, obtainAminoAcidCompositionTable(elementMassFile, aminoAcidCompositionFile));
}
@Override
public double getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile)
throws JAXBException, FileNotFoundException{
return getMolecularWeightBasedOnXML(sequence, obtainAminoAcidCompositionTable(elementMassFile, aminoAcidCompositionFile));
}
@Override
public double getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable){
double value = 0.0;
char[] seq = sequence.toString().toCharArray();
for(char aa:seq){
Double weight = aminoAcidCompositionTable.getMolecularWeight(aa);
if(weight != null){
value += weight;
}
}
if(value == 0.0)
return value;
else
return value + getWaterMoleculeWeight();
}
@Override
public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
throws JAXBException, FileNotFoundException{
File elementMassFile = new File("./src/main/resources/ElementMass.xml");
if(!elementMassFile.exists()){
throw new FileNotFoundException("Cannot locate ElementMass.xml. " +
"Please use getMolecularWeight(ProteinSequence, File, File) to specify ElementMass.xml location.");
}
return obtainAminoAcidCompositionTable(elementMassFile, aminoAcidCompositionFile);
}
@Override
public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile)
throws JAXBException, FileNotFoundException{
//Parse elementMassFile
ElementTable iTable = new ElementTable();
// Get a JAXB Context for the object we created above
JAXBContext jc = JAXBContext.newInstance(iTable.getClass());
Unmarshaller u = jc.createUnmarshaller();
u.setEventHandler(new MyValidationEventHandler());
iTable = (ElementTable)u.unmarshal(new FileInputStream(elementMassFile));
iTable.populateMaps();
//Parse aminoAcidCompositionFile
AminoAcidCompositionTable aTable = new AminoAcidCompositionTable();
// Get a JAXB Context for the object we created above
JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
Unmarshaller u2 = jc2.createUnmarshaller();
u2.setEventHandler(new MyValidationEventHandler());
aTable = (AminoAcidCompositionTable)u2.unmarshal(new FileInputStream(aminoAcidCompositionFile));
aTable.computeMolecularWeight(iTable);
return aTable;
}
@Override
public double getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced) {
//Tyr => Y
//Trp => W
//Cys => C
//E(Prot) = Numb(Tyr)*Ext(Tyr) + Numb(Trp)*Ext(Trp) + Numb(Cystine)*Ext(Cystine)
//where (for proteins in water measured at 280 nm): Ext(Tyr) = 1490, Ext(Trp) = 5500, Ext(Cystine) = 125;
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
Map extinctAA2Count = this.getExtinctAACount(sequence);
double eProt;
if(!assumeCysReduced){
eProt = extinctAA2Count.get(aaSet.getCompoundForString("Y")) *
Constraints.aa2ExtinctionCoefficient.get(aaSet.getCompoundForString("Y")) +
extinctAA2Count.get(aaSet.getCompoundForString("W")) *
Constraints.aa2ExtinctionCoefficient.get(aaSet.getCompoundForString("W")) +
extinctAA2Count.get(aaSet.getCompoundForString("C")) *
Constraints.aa2ExtinctionCoefficient.get(aaSet.getCompoundForString("C"));
}else
eProt = extinctAA2Count.get(aaSet.getCompoundForString("Y")) *
Constraints.aa2ExtinctionCoefficient.get(aaSet.getCompoundForString("Y")) +
extinctAA2Count.get(aaSet.getCompoundForString("W")) *
Constraints.aa2ExtinctionCoefficient.get(aaSet.getCompoundForString("W"));
return eProt;
}
@Override
public double getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced){
//Absorb(Prot) = E(Prot) / Molecular_weight
double mw = this.getMolecularWeight(sequence);
double eProt = this.getExtinctionCoefficient(sequence, assumeCysReduced);
if (mw == 0.0) {
logger.warn("Molecular weight is 0.0, can't divide by 0: setting absorbance to 0.0");
return 0.0;
}
return eProt / mw;
}
private Map getExtinctAACount(ProteinSequence sequence){
//Cys => C, Tyr => Y, Trp => W
int numW = 0;
int smallW = 0;
double numC = 0;
double smallC = 0;
int numY = 0;
int smallY = 0;
for(char aa:sequence.getSequenceAsString().toCharArray()){
switch(aa){
case 'W': numW++; break;
case 'w': smallW++; break;
case 'C': numC += 0.5; break;
case 'c': smallC += 0.5; break;
case 'Y': numY++; break;
case 'y': smallY++; break;
}
}
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
Map extinctAA2Count = new HashMap();
//Ignore Case is always true
extinctAA2Count.put(aaSet.getCompoundForString("W"), numW + smallW);
extinctAA2Count.put(aaSet.getCompoundForString("C"), (int) (numC + smallC));
extinctAA2Count.put(aaSet.getCompoundForString("Y"), numY + smallY);
return extinctAA2Count;
}
@Override
public double getInstabilityIndex(ProteinSequence sequence) {
double sum = 0.0;
String s = sequence.getSequenceAsString().toUpperCase();
for(int i = 0; i < sequence.getLength() - 1; i++){
String dipeptide = s.substring(i, i+2);
if(Constraints.diAA2Instability.containsKey(dipeptide)){
sum += Constraints.diAA2Instability.get(dipeptide);
}
}
int denominator = s.length() - Utils.getNumberOfInvalidChar(s, null, true);
if (denominator==0) {
logger.warn("Valid length of sequence is 0, can't divide by 0 to calculate instability index: setting instability index value to 0.0");
return 0.0;
}
return sum * 10.0 / denominator;
}
@Override
public double getApliphaticIndex(ProteinSequence sequence) {
// Aliphatic index = X(Ala) + a * X(Val) + b * ( X(Ile) + X(Leu) )
// where X(Ala), X(Val), X(Ile), and X(Leu) are mole percent (100 X mole fraction)
// of alanine, valine, isoleucine, and leucine.
// The coefficients a and b are the relative volume of valine side chain (a = 2.9)
// and of Leu/Ile side chains (b = 3.9) to the side chain of alanine.
// Ala => A, Val => V, Ile => I, Leu => L
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
Map aa2Composition = getAAComposition(sequence);
final double a = 2.9;
final double b = 3.9;
double xAla = aa2Composition.get(aaSet.getCompoundForString("A"));
double xVal = aa2Composition.get(aaSet.getCompoundForString("V"));
double xIle = aa2Composition.get(aaSet.getCompoundForString("I"));
double xLeu = aa2Composition.get(aaSet.getCompoundForString("L"));
return (xAla + (a * xVal) + (b * (xIle + xLeu))) * 100;
}
@Override
public double getAvgHydropathy(ProteinSequence sequence) {
int validLength = 0;
double total = 0.0;
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
char[] seq = this.getSequence(sequence.toString(), true);
for(char aa:seq){
AminoAcidCompound c = aaSet.getCompoundForString(String.valueOf(aa));
if(Constraints.aa2Hydrophathicity.containsKey(c)){
total += Constraints.aa2Hydrophathicity.get(c);
validLength++;
}
}
if (validLength==0) {
logger.warn("Valid length of sequence is 0, can't divide by 0 to calculate average hydropathy: setting average hydropathy to 0");
return 0.0;
}
return total / validLength;
}
@Override
public double getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues) {
if(useExpasyValues){
return this.getIsoelectricPointExpasy(sequence.toString().toUpperCase());
}else{
return this.getIsoelectricPointInnovagen(sequence);
}
}
private double getIsoelectricPointInnovagen(ProteinSequence sequence){
double currentPH = 7.0;
double changeSize = 7.0;
String sequenceString = sequence.toString();
char nTerminalChar = sequenceString.charAt(0);
char cTerminalChar = sequenceString.charAt(sequenceString.length() - 1);
Map chargedAA2Count = this.getChargedAACount(sequence);
double margin;
final double difference = 0.0001;
while(true){
margin = this.getNetChargeInnovagen(chargedAA2Count, currentPH, nTerminalChar, cTerminalChar);
//Within allowed difference
if(margin <= difference && margin >= -difference) break;
changeSize /= 2.0;
if(margin > 0){
currentPH += changeSize;
}else{
currentPH -= changeSize;
}
}
return currentPH;
}
/*
* Pseudo code obtained from email correspondance with ExPASy Helpdesk, Gregoire Rossier
*/
//
// Table of pk values :
// Note: the current algorithm does not use the last two columns.
// Each row corresponds to an amino acid starting with Ala. J, O and U are
// inexistant, but here only in order to have the complete alphabet.
//
// Ct Nt Sm Sc Sn
//
private final double[][] cPk = {
{3.55, 7.59, 0.0}, // A
{3.55, 7.50, 0.0}, // B
{3.55, 7.50, 9.00}, // C
// {4.55, 7.50, 4.05}, // D
// {4.75, 7.70, 4.45}, // E
{3.55, 7.50, 4.05}, // D
{3.55, 7.70, 4.45}, // E
{3.55, 7.50, 0}, // F
{3.55, 7.50, 0}, // G
{3.55, 7.50, 5.98}, // H
{3.55, 7.50, 0.0}, // I
{0.0, 0.0, 0.0}, // J
{3.55, 7.50, 10.00}, // K
{3.55, 7.50, 0.0}, // L
{3.55, 7.00, 0.0},// M
{3.55, 7.50, 0.0},// N
{0.00, 0.00, 0.0},// O
{3.55, 8.36, 0.0},// P
{3.55, 7.50, 0.0}, // Q
{3.55, 7.50, 12.0},// R
{3.55, 6.93, 0.0},// S
{3.55, 6.82, 0.0}, // T
{0.00, 0.00, 0.0}, // U
{3.55, 7.44, 0.0},// V
{3.55, 7.50, 0.0},// W
{3.55, 7.50, 0.0},// X
{3.55, 7.50, 10.00},// Y
{3.55, 7.50, 0.0}}; // Z
private final double PH_MIN = 0.0; /* minimum pH value */
private final double PH_MAX = 14.0; /* maximum pH value */
private final double MAXLOOP = 2000.0; /* maximum number of iterations */
private final double EPSI = 0.0001; /* desired precision */
private double exp10(double pka){
return Math.pow(10, pka);
}
private double getIsoelectricPointExpasy(String sequence){
//
// Compute the amino-acid composition.
//
int[] comp = new int[26];
for(int i = 0; i < sequence.length(); i++){
int index = sequence.charAt(i) - 'A';
if(index < 0 || index >= 26) continue;
comp[index]++;
}
//
// Look up N-terminal and C-terminal residue.
//
int nTermResidue = -1;
int index = 0;
while((nTermResidue < 0 || nTermResidue >= 26) && index < 25){
nTermResidue = sequence.charAt(index++) - 'A';
}
int cTermResidue = -1;
index = 1;
while((cTermResidue < 0 || cTermResidue >= 26) && index < 25){
cTermResidue = sequence.charAt(sequence.length() - index++) - 'A';
}
double phMin = PH_MIN;
double phMax = PH_MAX;
double phMid = 0.0;
double charge = 1.0;
for (int i = 0; i < MAXLOOP && (phMax - phMin) > EPSI; i++){
phMid = phMin + (phMax - phMin) / 2.0;
charge = getNetChargeExpasy(comp, nTermResidue, cTermResidue, phMid);
if (charge > 0.0) phMin = phMid;
else phMax = phMid;
}
return phMid;
}
@Override
public double getIsoelectricPoint(ProteinSequence sequence){
return getIsoelectricPoint(sequence, true);
}
@Override
public double getNetCharge(ProteinSequence sequence) {
return getNetCharge(sequence, true);
}
@Override
public double getNetCharge(ProteinSequence sequence, boolean useExpasyValues){
return getNetCharge(sequence, true, 7.0);
}
@Override
public double getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint){
if(useExpasyValues){
return getNetChargeExpasy(sequence.toString().toUpperCase(), pHPoint);
}else{
return getNetChargeInnovagen(sequence, pHPoint);
}
}
private double getNetChargeExpasy(String sequence, double pHPoint){
//
// Compute the amino-acid composition.
//
int[] comp = new int[26];
for(int i = 0; i < sequence.length(); i++){
int index = sequence.charAt(i) - 'A';
if(index < 0 || index >= 26) continue;
comp[index]++;
}
//
// Look up N-terminal and C-terminal residue.
//
int nTermResidue = sequence.charAt(0) - 'A';
int cTermResidue = sequence.charAt(sequence.length() - 1) - 'A';
return getNetChargeExpasy(comp, nTermResidue, cTermResidue, pHPoint);
}
private double getNetChargeExpasy(int[] comp, int nTermResidue, int cTermResidue, double ph){
double cter = 0.0;
if(cTermResidue >= 0 && cTermResidue < 26) cter = exp10(-cPk[cTermResidue][0]) / (exp10(-cPk[cTermResidue][0]) + exp10(-ph));
double nter = 0.0;
if(nTermResidue >= 0 && nTermResidue < 26) nter = exp10(-ph) / (exp10(-cPk[nTermResidue][1]) + exp10(-ph));
double carg = comp['R' - 'A'] * exp10(-ph) / (exp10(-cPk['R' - 'A'][2]) + exp10(-ph));
double chis = comp['H' - 'A'] * exp10(-ph) / (exp10(-cPk['H' - 'A'][2]) + exp10(-ph));
double clys = comp['K' - 'A'] * exp10(-ph) / (exp10(-cPk['K' - 'A'][2]) + exp10(-ph));
double casp = comp['D' - 'A'] * exp10(-cPk['D' - 'A'][2]) / (exp10(-cPk['D' - 'A'][2]) + exp10(-ph));
double cglu = comp['E' - 'A'] * exp10(-cPk['E' - 'A'][2]) / (exp10(-cPk['E' - 'A'][2]) + exp10(-ph));
double ccys = comp['C' - 'A'] * exp10(-cPk['C' - 'A'][2]) / (exp10(-cPk['C' - 'A'][2]) + exp10(-ph));
double ctyr = comp['Y' - 'A'] * exp10(-cPk['Y' - 'A'][2]) / (exp10(-cPk['Y' - 'A'][2]) + exp10(-ph));
return (carg + clys + chis + nter) - (casp + cglu + ctyr + ccys + cter);
}
private double getNetChargeInnovagen(ProteinSequence sequence, double pHPoint) {
Map chargedAA2Count = this.getChargedAACount(sequence);
String sequenceString = sequence.getSequenceAsString();
return getNetChargeInnovagen(chargedAA2Count, pHPoint, sequenceString.charAt(0), sequenceString.charAt(sequenceString.length() - 1));
}
private double getNetChargeInnovagen(Map chargedAA2Count, double ph, char nTerminalChar, char cTerminalChar){
//Constraints.aa2PKa is aleady reinitialized in getChargedAACount hence no need to do it again
//Lys => K, Arg => R, His => H
//Asp => D, Glu => E, Cys => C, Tyr => Y
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
double nTerminalCharge = 0.0;
AminoAcidCompound nTermCompound = aaSet.getCompoundForString(String.valueOf(nTerminalChar));
if(Constraints.aa2NTerminalPka.containsKey(nTermCompound)){
nTerminalCharge = this.getPosCharge(Constraints.aa2NTerminalPka.get(nTermCompound), ph);
}
double cTerminalCharge = 0.0;
AminoAcidCompound cTermCompound = aaSet.getCompoundForString(String.valueOf(cTerminalChar));
if(Constraints.aa2CTerminalPka.containsKey(cTermCompound)){
cTerminalCharge = this.getNegCharge(Constraints.aa2CTerminalPka.get(cTermCompound), ph);
}
double kCharge = chargedAA2Count.get(aaSet.getCompoundForString("K")) * this.getPosCharge(Constraints.aa2PKa.get(aaSet.getCompoundForString("K")), ph);
double rCharge = chargedAA2Count.get(aaSet.getCompoundForString("R")) * this.getPosCharge(Constraints.aa2PKa.get(aaSet.getCompoundForString("R")), ph);
double hCharge = chargedAA2Count.get(aaSet.getCompoundForString("H")) * this.getPosCharge(Constraints.aa2PKa.get(aaSet.getCompoundForString("H")), ph);
double dCharge = chargedAA2Count.get(aaSet.getCompoundForString("D")) * this.getNegCharge(Constraints.aa2PKa.get(aaSet.getCompoundForString("D")), ph);
double eCharge = chargedAA2Count.get(aaSet.getCompoundForString("E")) * this.getNegCharge(Constraints.aa2PKa.get(aaSet.getCompoundForString("E")), ph);
double cCharge = chargedAA2Count.get(aaSet.getCompoundForString("C")) * this.getNegCharge(Constraints.aa2PKa.get(aaSet.getCompoundForString("C")), ph);
double yCharge = chargedAA2Count.get(aaSet.getCompoundForString("Y")) * this.getNegCharge(Constraints.aa2PKa.get(aaSet.getCompoundForString("Y")), ph);
// if((kCharge + rCharge + hCharge) == 0.0 && (dCharge + eCharge + cCharge + yCharge) == 0.0){
// return 0.0;
// }
return (nTerminalCharge + kCharge + rCharge + hCharge) - (dCharge + eCharge + cCharge + yCharge + cTerminalCharge);
}
private double getPosCharge(double pka, double ph){
return Math.pow(10, pka) / (Math.pow(10, pka) + Math.pow(10, ph));
}
private double getNegCharge(double pka, double ph){
return Math.pow(10, ph) / (Math.pow(10, pka) + Math.pow(10, ph));
}
private Map getChargedAACount(ProteinSequence sequence){
//Lys => K, Arg => R, His => H
//Asp => D, Glu => E, Cys => C, Tyr => Y
int numK = 0;
int numR = 0;
int numH = 0;
int numD = 0;
int numE = 0;
int numC = 0;
int numY = 0;
char[] seq = this.getSequence(sequence.getSequenceAsString(), true);
for(char aa:seq){
switch(aa){
case 'K': numK++; break;
case 'R': numR++; break;
case 'H': numH++; break;
case 'D': numD++; break;
case 'E': numE++; break;
case 'C': numC++; break;
case 'Y': numY++; break;
}
}
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
Map chargedAA2Count = new HashMap();
chargedAA2Count.put(aaSet.getCompoundForString("K"), numK);
chargedAA2Count.put(aaSet.getCompoundForString("R"), numR);
chargedAA2Count.put(aaSet.getCompoundForString("H"), numH);
chargedAA2Count.put(aaSet.getCompoundForString("D"), numD);
chargedAA2Count.put(aaSet.getCompoundForString("E"), numE);
chargedAA2Count.put(aaSet.getCompoundForString("C"), numC);
chargedAA2Count.put(aaSet.getCompoundForString("Y"), numY);
return chargedAA2Count;
}
@Override
public double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode) {
double counter = 0.0;
char[] seq = this.getSequence(sequence.getSequenceAsString(), true);
for(char aa:seq){
if(aminoAcidCode.getShortName().equals(String.valueOf(aa))){
counter++;
}
}
return counter/sequence.getLength();
}
@Override
public Map getAAComposition(ProteinSequence sequence) {
int validLength = 0;
Map aa2Composition = new HashMap();
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
for(AminoAcidCompound aa:aaSet.getAllCompounds()){
aa2Composition.put(aa, 0.0);
}
char[] seq = this.getSequence(sequence.toString(), true);
for(char aa:seq){
if(PeptideProperties.standardAASet.contains(aa)){
AminoAcidCompound compound = aaSet.getCompoundForString(String.valueOf(aa));
aa2Composition.put(compound, aa2Composition.get(compound) + 1.0);
validLength++;
}
}
if(validLength > 0){
for(AminoAcidCompound aa:aaSet.getAllCompounds()){
aa2Composition.put(aa, aa2Composition.get(aa) / validLength);
}
}else{
for(AminoAcidCompound aa:aaSet.getAllCompounds()){
aa2Composition.put(aa, 0.0);
}
}
return aa2Composition;
}
}
