Source code for emzed.utils.isotope_calculator

#encoding: utf-8

def _setupIsotopeDistributionGenerator(formula, R, fullC13, minp, **kw):
    from emzed.core.chemistry import IsotopeDistributionGenerator
    if fullC13:
        kw.update(dict(C=dict(C12=0.0, C13=1.0)))
    return IsotopeDistributionGenerator(formula, R, minp, **kw)

[docs]def plotIsotopeDistribution(formula, R=None, fullC13=False, minp=0.01, plotGauss=None, **kw): """ plots isotope distribution for given molecular formula *formula*. for all parameters, despite *plotGauss*: see isotopeDistributionTable() If *R* is provided, gaussian peaks are plotted, else centroids. This behavior can be overrun by setting *plotGauss* to *True* or *False*. If *plotGauss* is *True*, bell shaped curves are plotted, else the centroids according to the used resolution are shown. For low *minp* the choice *plotGauss=False* the plot is drawn faster. .. pycon:: emzed.utils.plotIsotopeDistribution("C3H7NO2", C=dict(C13=0.5, C12=0.5), R=5000) !noexec .. image:: isopattern_alanin.png """ gen = _setupIsotopeDistributionGenerator(formula, R, fullC13, minp, **kw)
[docs]def isotopeDistributionTable(formula, R=None, fullC13=False, minp=0.01, **kw): """ generates Table for most common isotopes of molecule with given mass *formula*. If the resolution *R* is given, the measurement device is simulated, and overlapping peaks may merge. *fullC13=True* assumes that only C13 carbon is present in formula. Further you can give a threshold *minp* for considering only isotope peaks with an abundance above the value. Standard is *minp=0.01*. If you have special elementary isotope abundances which differ from the natural abundances, you can tell that like ``emzed.utils.isotopeDistributionTable("S4C4", C=dict(C13=0.5, C12=0.5))`` Examples: .. pycon:: import emzed # natural abundances: tab = emzed.utils.isotopeDistributionTable("C3H7NO2") tab.abundance /= tab.abundance.sum() print tab # artifical abundances: tab = emzed.utils.isotopeDistributionTable("C3H7NO2", C=dict(C13=0.5, C12=0.5)) tab.abundance /= tab.abundance.sum() print tab \ """ from ..core.data_types import Table gen = _setupIsotopeDistributionGenerator(formula, R, fullC13, minp, **kw) t = Table(["mf", "mass", "abundance"], [str, float, float], ["%s", "%.6f", "%.3f"], []) for mass, formula, abundance in gen.getCentroids(): t.addRow([formula, mass, abundance], False) t.resetInternals() t.replaceColumn("abundance", t.abundance / t.abundance.sum, format_ = "%.4f", type_=float) return t