Examples with TopDownBitArrayPrecursor de.ipbhalle.metfraglib.precursor.TopDownBitArrayPrecursor used on opensource projects

Example 1 with TopDownBitArrayPrecursor

use of de.ipbhalle.metfraglib.precursor.TopDownBitArrayPrecursor in project MetFragRelaunched by ipb-halle.

the class SimulateSpectrumHDX method generateDeuteratedSpectrumNegative.

/**
 * @param candidate
 * @return
 * @throws AtomTypeNotKnownFromInputListException
 * @throws Exception
 */
public static double[][] generateDeuteratedSpectrumNegative(ICandidate candidate, int method) throws AtomTypeNotKnownFromInputListException, Exception {
    int numberPositions = searchForDeuteriumExchangeablePositions((TopDownBitArrayPrecursor) candidate.getPrecursorMolecule()).length;
    HDTopDownBitArrayPrecursor preHDX = new HDTopDownBitArrayPrecursor(candidate.getImplicitHydrogenAtomContainer(), (byte) numberPositions);
    preHDX.preprocessPrecursor();
    MatchList matchList = candidate.getMatchList();
    double[][] spectrumHDX = null;
    if (method == 3)
        spectrumHDX = new double[matchList.getNumberElements() * 2][2];
    else
        spectrumHDX = new double[matchList.getNumberElements()][2];
    for (int i = 0; i < matchList.getNumberElements(); i++) {
        IFragment frag = matchList.getElement(i).getBestMatchedFragment();
        IPeak peak = matchList.getElement(i).getMatchedPeak();
        int[] setAtoms = ((DefaultBitArrayFragment) frag).getAtomsFastBitArray().getSetIndeces();
        int numberDeuteriums = 0;
        for (int k = 0; k < setAtoms.length; k++) {
            numberDeuteriums += preHDX.getNumberDeuteriumsConnectedToAtomIndex(0, setAtoms[k]);
        }
        spectrumHDX[i][1] = peak.getAbsoluteIntensity();
        // [M-D]-
        if (method == 1) {
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            spectrumHDX[i][0] += Constants.HYDROGEN_MASS - Constants.getMonoisotopicMassOfAtom("D");
        } else // [M]-
        if (method == 2) {
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
        // nothing to do
        } else // [M]- [M-D]-
        if (method == 3) {
            spectrumHDX[i * 2][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            spectrumHDX[(i * 2) + 1][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            spectrumHDX[(i * 2) + 1][0] += Constants.HYDROGEN_MASS - Constants.getMonoisotopicMassOfAtom("D");
        } else // predict based on deuteriums
        if (method == 4) {
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            if (numberDeuteriums != 0)
                spectrumHDX[i][0] += Constants.HYDROGEN_MASS - Constants.getMonoisotopicMassOfAtom("D");
        } else // predict based on adduct
        if (method == 5) {
            byte adductTypeIndex = ((DefaultFragmentToPeakMatch) matchList.getElement(i)).getBestMatchedFragmentAdductTypeIndex();
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            if (adductTypeIndex == 1)
                spectrumHDX[i][0] += Constants.getMonoisotopicMassOfAtom("D") - Constants.HYDROGEN_MASS;
        }
    }
    return spectrumHDX;
}

Example 2 with TopDownBitArrayPrecursor

use of de.ipbhalle.metfraglib.precursor.TopDownBitArrayPrecursor in project MetFragRelaunched by ipb-halle.

the class TopDownPrecursorCandidate method initialisePrecursorCandidate.

@Override
public void initialisePrecursorCandidate() throws AtomTypeNotKnownFromInputListException, Exception {
    this.precursorStructure = new TopDownBitArrayPrecursor(this.getImplicitHydrogenAtomContainer());
    this.precursorStructure.preprocessPrecursor();
}

Example 3 with TopDownBitArrayPrecursor

use of de.ipbhalle.metfraglib.precursor.TopDownBitArrayPrecursor in project MetFragRelaunched by ipb-halle.

the class SimulateSpectrumHDX method generateDeuteratedSpectrumPositive.

/**
 * @param candidate
 * @return
 * @throws AtomTypeNotKnownFromInputListException
 * @throws Exception
 */
public static double[][] generateDeuteratedSpectrumPositive(ICandidate candidate, int method) throws AtomTypeNotKnownFromInputListException, Exception {
    int numberPositions = searchForDeuteriumExchangeablePositions((TopDownBitArrayPrecursor) candidate.getPrecursorMolecule()).length;
    HDTopDownBitArrayPrecursor preHDX = new HDTopDownBitArrayPrecursor(candidate.getImplicitHydrogenAtomContainer(), (byte) numberPositions);
    preHDX.preprocessPrecursor();
    MatchList matchList = candidate.getMatchList();
    double[][] spectrumHDX = null;
    if (method == 3)
        spectrumHDX = new double[matchList.getNumberElements() * 2][2];
    else
        spectrumHDX = new double[matchList.getNumberElements()][2];
    for (int i = 0; i < matchList.getNumberElements(); i++) {
        IFragment frag = matchList.getElement(i).getBestMatchedFragment();
        IPeak peak = matchList.getElement(i).getMatchedPeak();
        int[] setAtoms = ((DefaultBitArrayFragment) frag).getAtomsFastBitArray().getSetIndeces();
        int numberDeuteriums = 0;
        for (int k = 0; k < setAtoms.length; k++) {
            numberDeuteriums += preHDX.getNumberDeuteriumsConnectedToAtomIndex(0, setAtoms[k]);
        }
        if (method != 3) {
            spectrumHDX[i][1] = peak.getAbsoluteIntensity();
        } else {
            spectrumHDX[i * 2][1] = peak.getAbsoluteIntensity();
            spectrumHDX[(i * 2) + 1][1] = peak.getAbsoluteIntensity();
        }
        // [M+D]+
        if (method == 1) {
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            spectrumHDX[i][0] += Constants.getMonoisotopicMassOfAtom("D") - Constants.HYDROGEN_MASS;
        } else // [M]+
        if (method == 2) {
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
        // nothing to do
        } else // [M]+ [M+D]+
        if (method == 3) {
            spectrumHDX[i * 2][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            spectrumHDX[(i * 2) + 1][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            spectrumHDX[(i * 2) + 1][0] += Constants.getMonoisotopicMassOfAtom("D") - Constants.HYDROGEN_MASS;
        } else // predict based on in silico added deuteriums
        if (method == 4) {
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            if (numberDeuteriums != 0)
                spectrumHDX[i][0] += Constants.getMonoisotopicMassOfAtom("D") - Constants.HYDROGEN_MASS;
        } else // predict based on adduct
        if (method == 5) {
            byte adductTypeIndex = ((DefaultFragmentToPeakMatch) matchList.getElement(i)).getBestMatchedFragmentAdductTypeIndex();
            spectrumHDX[i][0] = peak.getMass() - (numberDeuteriums) * Constants.HYDROGEN_MASS + (numberDeuteriums) * Constants.getMonoisotopicMassOfAtom("D");
            if (adductTypeIndex == 2)
                spectrumHDX[i][0] += Constants.getMonoisotopicMassOfAtom("D") - Constants.HYDROGEN_MASS;
        }
        if (method != 3) {
            spectrumHDX[i][0] = MathTools.round(spectrumHDX[i][0]);
        } else {
            spectrumHDX[i * 2][0] = MathTools.round(spectrumHDX[i * 2][0]);
            spectrumHDX[(i * 2) + 1][0] = MathTools.round(spectrumHDX[(i * 2) + 1][0]);
        }
    }
    return spectrumHDX;
}