IsoGen

API reference

All functions below are available directly from import isogen.

Distribution

isodist

isodist(input, type="PEPTIDE", isolen=128, method="FFT", **mass_kwargs)

Generate a two-column (mass, relative intensity) array. input may be a numeric neutral mass, biopolymer sequence, or elemental formula. Select method="FFT", method="BRAIN", or method="NN" for biopolymer inputs. BRAIN is an absolute polynomial-recurrence calculation. Select type="ATOM" for a formula; ATOM supports the FFT method only. mass_kwargs are forwarded to gen_mass_axis, including isotope_spacing, peptide ion_type, and nucleic acid threeend and fiveend.

Elemental formulas

calc_atom_monoisotopic_mass(formula)
calc_atom_mass_axis(formula, isolen=128, isotope_spacing=1.0033)

These functions parse formulas with the native ATOM parser. The mass axis begins at the light-isotope mass used for isotope index zero by the FFT calculation.

Protein masses

calc_pep_mass

calc_pep_mass(
    sequence,
    allow_float=True,
    remove_nan=True,
    all_cyst_ox=False,
    pyroglu=False,
    round_to=2,
    ion_type="H2O",
)

Return the average neutral mass. Numeric input is returned as an existing mass when allow_float is true.

calc_pep_monoisotopic_mass

calc_pep_monoisotopic_mass(
    sequence,
    allow_float=True,
    remove_nan=True,
    all_cyst_ox=False,
    pyroglu=False,
    ion_type="H2O",
)

Return the monoisotopic neutral mass.

calc_pep_mass_axis

calc_pep_mass_axis(
    sequence,
    isolen=128,
    isotope_spacing=1.0033,
    ion_type="H2O",
    **mass_kwargs,
)

Return a peptide mass axis beginning at the monoisotopic mass.

Nucleic-acid masses

RNA

calc_rna_mass(sequence, threeend="OH", fiveend="MP")
calc_rna_monoisotopic_mass(sequence, threeend="OH", fiveend="MP")
calc_rna_mass_axis(
    sequence,
    isolen=128,
    isotope_spacing=1.0027,
    threeend="OH",
    fiveend="MP",
)

DNA

calc_dna_mass(sequence, threeend="OH", fiveend="MP")
calc_dna_monoisotopic_mass(sequence, threeend="OH", fiveend="MP")
calc_dna_mass_axis(
    sequence,
    isolen=128,
    isotope_spacing=1.0027,
    threeend="OH",
    fiveend="MP",
)

Generic mass-axis functions

calc_mass_axis

calc_mass_axis(monoisotopic_mass, isolen=128, isotope_spacing=1.0033)

Return an evenly spaced one-dimensional NumPy array.

gen_mass_axis

gen_mass_axis(
    input,
    type="PEPTIDE",
    isolen=128,
    isotope_spacing=None,
    **mass_kwargs,
)

Dispatch numeric mass, sequence, or ATOM formula input to the appropriate axis calculator.

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