CoarseIsotopePatternGenerator
- class pyopenms.CoarseIsotopePatternGenerator
Bases:
objectCython implementation of _CoarseIsotopePatternGenerator
Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1CoarseIsotopePatternGenerator.html
- __init__()
Cython signature: void CoarseIsotopePatternGenerator()
Cython signature: void CoarseIsotopePatternGenerator(size_t max_isotope)
Cython signature: void CoarseIsotopePatternGenerator(size_t max_isotope, bool round_masses)
Methods
Cython signature: void CoarseIsotopePatternGenerator()
Cython signature: IsotopeDistribution approximateFromPeptideWeight(double mass, unsigned int num_peaks, unsigned int charge)
Cython signature: libcpp_vector[double] approximateIntensities(double mass, unsigned int num_peaks)
Cython signature: IsotopeDistribution calcFragmentIsotopeDist(IsotopeDistribution & fragment_isotope_dist, IsotopeDistribution & comp_fragment_isotope_dist, libcpp_set[unsigned int] & precursor_isotopes, double fragment_mono_mass) Calculate isotopic distribution for a fragment molecule
Cython signature: IsotopeDistribution estimateForFragmentFromDNAWeight(double average_weight_precursor, double average_weight_fragment, libcpp_set[unsigned int] & precursor_isotopes)
Cython signature: IsotopeDistribution estimateForFragmentFromPeptideWeight(double average_weight_precursor, double average_weight_fragment, libcpp_set[unsigned int] & precursor_isotopes) Estimate peptide fragment IsotopeDistribution from the precursor's average weight, fragment's average weight, and a set of isolated precursor isotopes
Cython signature: IsotopeDistribution estimateForFragmentFromPeptideWeightAndS(double average_weight_precursor, unsigned int S_precursor, double average_weight_fragment, unsigned int S_fragment, libcpp_set[unsigned int] & precursor_isotopes)
Cython signature: IsotopeDistribution estimateForFragmentFromRNAWeight(double average_weight_precursor, double average_weight_fragment, libcpp_set[unsigned int] & precursor_isotopes)
Cython signature: IsotopeDistribution estimateForFragmentFromWeightAndComp(double average_weight_precursor, double average_weight_fragment, libcpp_set[unsigned int] & precursor_isotopes, double C, double H, double N, double O, double S, double P)
Cython signature: IsotopeDistribution estimateFromDNAWeight(double average_weight) Estimate Nucleotide Isotopedistribution from weight
Cython signature: IsotopeDistribution estimateFromPeptideWeight(double average_weight) Estimate Peptide Isotopedistribution from weight and number of isotopes that should be reported
Cython signature: IsotopeDistribution estimateFromPeptideWeightAndS(double average_weight, unsigned int S) Estimate peptide IsotopeDistribution from average weight and exact number of sulfurs
Cython signature: IsotopeDistribution estimateFromRNAWeight(double average_weight) Estimate Nucleotide Isotopedistribution from weight
Cython signature: IsotopeDistribution estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P)
Cython signature: IsotopeDistribution estimateFromWeightAndCompAndS(double average_weight, unsigned int S, double C, double H, double N, double O, double P) Estimate IsotopeDistribution from weight, exact number of sulfurs, and average remaining composition
Cython signature: size_t getMaxIsotope() Returns the currently set maximum isotope
Cython signature: bool getRoundMasses() Returns the current value of the flag to round masses to integer values (true) or return accurate masses (false)
Cython signature: IsotopeDistribution run(EmpiricalFormula)
Cython signature: void setMaxIsotope(size_t max_isotope) Sets the maximal isotope with 'max_isotope'
Cython signature: void setRoundMasses(bool round_masses_) Sets the round_masses_ flag to round masses to integer values (true) or return accurate masses (false)
- approximateFromPeptideWeight()
Cython signature: IsotopeDistribution approximateFromPeptideWeight(double mass, unsigned int num_peaks, unsigned int charge)
Roughly approximate peptide IsotopeDistribution from monoisotopic weight using Poisson distribution. m/z values approximated by adding one neutron mass (divided by charge) for every peak, starting at the given monoisotopic weight. Foundation from: Bellew et al, https://dx.doi.org/10.1093/bioinformatics/btl276 This method is around 50 times faster than estimateFromPeptideWeight, but only an approximation. The following are the intensities of the first 6 peaks generated for a monoisotopic mass of 1000: estimateFromPeptideWeight: 0.571133000;0.306181000;0.095811100;0.022036900;0.004092170;0.000644568 approximateFromPeptideWeight: 0.573753000;0.318752000;0.088542200;0.016396700;0.002277320;0.000253036 KL divergences of the first 20 intensities of estimateFromPeptideWeight and this approximation range from 4.97E-5 for a monoisotopic mass of 20 to 0.0144 for a mass of 2500. For comparison, when comparing an observed pattern with a theoretical ground truth, the observed pattern is said to be an isotopic pattern if the KL between the two is below 0.05 for 2 peaks and below 0.6 for >=6 peaks by Guo Ci Teo et al.
- approximateIntensities()
Cython signature: libcpp_vector[double] approximateIntensities(double mass, unsigned int num_peaks)
Roughly approximate peptidic isotope pattern intensities from monoisotopic weight using Poisson distribution. Foundation from: Bellew et al, https://dx.doi.org/10.1093/bioinformatics/btl276 This method is around 100 times faster than estimateFromPeptideWeight, but only an approximation, see approximateFromPeptideWeight.
- calcFragmentIsotopeDist()
Cython signature: IsotopeDistribution calcFragmentIsotopeDist(IsotopeDistribution & fragment_isotope_dist, IsotopeDistribution & comp_fragment_isotope_dist, libcpp_set[unsigned int] & precursor_isotopes, double fragment_mono_mass) Calculate isotopic distribution for a fragment molecule
- estimateForFragmentFromDNAWeight()
Cython signature: IsotopeDistribution estimateForFragmentFromDNAWeight(double average_weight_precursor, double average_weight_fragment, libcpp_set[unsigned int] & precursor_isotopes)
Estimate DNA fragment IsotopeDistribution from the precursor’s average weight, fragment’s average weight, and a set of isolated precursor isotopes.
- estimateForFragmentFromPeptideWeight()
Cython signature: IsotopeDistribution estimateForFragmentFromPeptideWeight(double average_weight_precursor, double average_weight_fragment, libcpp_set[unsigned int] & precursor_isotopes) Estimate peptide fragment IsotopeDistribution from the precursor’s average weight, fragment’s average weight, and a set of isolated precursor isotopes
- estimateForFragmentFromPeptideWeightAndS()
Cython signature: IsotopeDistribution estimateForFragmentFromPeptideWeightAndS(double average_weight_precursor, unsigned int S_precursor, double average_weight_fragment, unsigned int S_fragment, libcpp_set[unsigned int] & precursor_isotopes)
Estimate peptide fragment IsotopeDistribution from the precursor’s average weight, number of sulfurs in the precursor, fragment’s average weight, number of sulfurs in the fragment, and a set of isolated precursor isotopes.
- estimateForFragmentFromRNAWeight()
Cython signature: IsotopeDistribution estimateForFragmentFromRNAWeight(double average_weight_precursor, double average_weight_fragment, libcpp_set[unsigned int] & precursor_isotopes)
Estimate RNA fragment IsotopeDistribution from the precursor’s average weight, fragment’s average weight, and a set of isolated precursor isotopes
- estimateForFragmentFromWeightAndComp()
Cython signature: IsotopeDistribution estimateForFragmentFromWeightAndComp(double average_weight_precursor, double average_weight_fragment, libcpp_set[unsigned int] & precursor_isotopes, double C, double H, double N, double O, double S, double P)
Estimate fragment IsotopeDistribution from the precursor’s average weight, fragment’s average weight, a set of isolated precursor isotopes, and average composition
- estimateFromDNAWeight()
Cython signature: IsotopeDistribution estimateFromDNAWeight(double average_weight) Estimate Nucleotide Isotopedistribution from weight
- estimateFromPeptideWeight()
Cython signature: IsotopeDistribution estimateFromPeptideWeight(double average_weight) Estimate Peptide Isotopedistribution from weight and number of isotopes that should be reported
- estimateFromPeptideWeightAndS()
Cython signature: IsotopeDistribution estimateFromPeptideWeightAndS(double average_weight, unsigned int S) Estimate peptide IsotopeDistribution from average weight and exact number of sulfurs
- estimateFromRNAWeight()
Cython signature: IsotopeDistribution estimateFromRNAWeight(double average_weight) Estimate Nucleotide Isotopedistribution from weight
- estimateFromWeightAndComp()
Cython signature: IsotopeDistribution estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P)
- estimateFromWeightAndCompAndS()
Cython signature: IsotopeDistribution estimateFromWeightAndCompAndS(double average_weight, unsigned int S, double C, double H, double N, double O, double P) Estimate IsotopeDistribution from weight, exact number of sulfurs, and average remaining composition
- getMaxIsotope()
Cython signature: size_t getMaxIsotope() Returns the currently set maximum isotope
- getRoundMasses()
Cython signature: bool getRoundMasses() Returns the current value of the flag to round masses to integer values (true) or return accurate masses (false)
- run()
Cython signature: IsotopeDistribution run(EmpiricalFormula)
- setMaxIsotope()
Cython signature: void setMaxIsotope(size_t max_isotope) Sets the maximal isotope with ‘max_isotope’
- setRoundMasses()
Cython signature: void setRoundMasses(bool round_masses_) Sets the round_masses_ flag to round masses to integer values (true) or return accurate masses (false)