cpyMSpec¶

Fast isotope pattern calculator for small molecules.

API Reference¶

class cpyMSpec.spectrum.CentroidedSpectrum[source]¶

Bases: cpyMSpec.spectrum.SpectrumBase

Centroided peaks of a profile/theoretical spectrum

charged(charge)[source]¶

Adds/subtracts electrons and returns a new object.

Parameters:	charge (integer) – number of electrons to add
Returns:	a spectrum with appropriately shifted masses
Return type:	CentroidedSpectrum

copy()[source]¶

Returns:	a (deep) copy of the instance
Return type:	CentroidedSpectrum

removeIntensitiesBelow(min_intensity)[source]¶

trimmed(n_peaks)[source]¶

Parameters:	n_peaks – number of peaks to keep
Returns:	an isotope pattern with removed low-intensity peaks
Return type:	CentroidedSpectrum

class cpyMSpec.spectrum.InstrumentModel(instrument_type, resolving_power, at_mz=200)[source]¶

Bases: object

resolvingPowerAt(mz)[source]¶: Calculates resolving power at a given m/z value

class cpyMSpec.spectrum.ProfileSpectrum(mzs, intensities)[source]¶

Bases: cpyMSpec.spectrum.SpectrumBase

Represents profile spectrum data, which means: * neighbor mass differences are supposed to be locally approximately equal; * occasional gaps might be present, indicating zero-intensity regions

centroids(window_size=5)[source]¶

Detects peaks in raw data.

Parameters:	mzs – sorted array of m/z values intensities – array of corresponding intensities window_size – size of m/z averaging window
Returns:	isotope pattern containing the centroids
Return type:	CentroidedSpectrum

copy()[source]¶

Returns:	a (deep) copy of the instance
Return type:	ProfileSpectrum

class cpyMSpec.spectrum.SpectrumBase[source]¶

Bases: object

addCharge(charge)[source]¶

Adds/subtracts mass of electrons in-place. such that the charge increases by the specified amount.

Parameters:	charge (integer) – number of electrons to add

intensities¶

Returns:	peak intensities
Return type:	list of floats

masses¶

Returns:	peak masses
Return type:	list of floats

size¶

Returns:	number of peaks in the spectrum
Return type:	int

sortByIntensity()[source]¶

sortByMass()[source]¶

sortedByIntensity()[source]¶

sortedByMass()[source]¶

trim(n_peaks)[source]¶

Sorts mass and intensities arrays in descending intensity order, then removes low-intensity peaks from the spectrum.

Parameters:	n_peaks – number of peaks to keep

class cpyMSpec.spectrum.TheoreticalSpectrum[source]¶

Bases: cpyMSpec.spectrum.SpectrumBase

A bag of isotopic peaks computed for a single or multiple sum formulas.

centroids(instrument, min_abundance=0.0001, points_per_fwhm=25)[source]¶

Estimates centroided peaks for a given instrument model.

Parameters:	instrument – instrument model min_abundance – minimum abundance for including a peak points_per_fwhm – grid density used for envelope calculation
Returns:	peaks visible with the instrument used
Return type:	TheoreticalSpectrum

copy()[source]¶

Returns:	a (deep) copy of the instance
Return type:	Spectrum

envelope(instrument)[source]¶

Computes isotopic envelope for a given instrument model

Parameters:	instrument – instrument model to use
Returns:	isotopic envelope as a function of mass
Return type:	function float(mz: float)

cpyMSpec.spectrum.isotopePattern(sum_formula, threshold=0.0001, rel_threshold=True, desired_prob=None)[source]¶

Calculates isotopic peaks for a sum formula.

Parameters:	sum_formula (str) – text representation of an atomic composition threshold (float) – minimum peak abundance rel_threshold (bool) – if True, threshold is relative to the highest peak, otherwise it is a probability desired_prob (float \| None) – total probability covered by the result; if set, threshold parameter is ignored