@Transient
@Field(index = Index.UN_TOKENIZED, store = Store.NO)
public String getMass() {
try {
PeptideProperties pp = calculateStats();
if (pp.isHasMass()) {
long mass = Math.round(pp.getMassInDaltons());
return String.format("%09d", mass);
}
return "";
} catch (RuntimeException exp) {
return "";
}
}
/**
* Calculate the predicted properties of this polypeptide.
*
* @return a <code>PeptideProperties</code> object containing the predicted properties of this
* polypeptide.
*/
public PeptideProperties calculateStats() {
if (this.getResidues() == null) {
logger.warn("No residues for '" + this.getUniqueName() + "'");
return null;
}
String residuesString = new String(this.getResidues());
SymbolList residuesSymbolList = null;
PeptideProperties pp = new PeptideProperties();
try {
SymbolTokenization proteinTokenization = ProteinTools.getTAlphabet().getTokenization("token");
residuesSymbolList = new SimpleSymbolList(proteinTokenization, residuesString);
if (residuesSymbolList.length() == 0) {
logger.error(
String.format(
"Polypeptide feature '%s' has zero-length residues", this.getUniqueName()));
return pp;
}
try {
// if the sequence ends with a termination symbol (*), we need to remove it
if (residuesSymbolList.symbolAt(residuesSymbolList.length()) == ProteinTools.ter()) {
if (residuesSymbolList.length() == 1) {
logger.error(
String.format(
"Polypeptide feature '%s' only has termination symbol", this.getUniqueName()));
return pp;
}
residuesSymbolList = residuesSymbolList.subList(1, residuesSymbolList.length() - 1);
}
} catch (IndexOutOfBoundsException exception) {
throw new RuntimeException(exception);
}
} catch (BioException e) {
logger.error("Can't translate into a protein sequence", e);
return pp;
}
pp.setAminoAcids(residuesSymbolList.length());
try {
double isoElectricPoint = new IsoelectricPointCalc().getPI(residuesSymbolList, false, false);
pp.setIsoelectricPoint(isoElectricPoint);
} catch (Exception e) {
logger.error(
String.format("Error computing protein isoelectric point for '%s'", residuesSymbolList),
e);
}
double mass2 = calculateMass(residuesSymbolList);
if (mass2 != -1) {
// mass = mass2;
pp.setMass(mass2);
}
double charge = calculateCharge(residuesString);
pp.setCharge(charge);
return pp;
}
