def get_mass(self):
logging.info(self.sum_formula)
logging.info(pyisocalc.parseSumFormula(self.sum_formula))
spec = pyisocalc.perfect_pattern(pyisocalc.parseSumFormula(self.sum_formula), charge=0)
logging.info(spec)
mass = spec.get_spectrum(source='centroids')[0][np.argmax(spec.get_spectrum(source='centroids')[1])]
logging.info(mass)
return mass
def get_isotope_pattern(self, formula_adduct_string, charge):
perfect_pattern = pyisocalc.perfect_pattern(pyisocalc.parseSumFormula(formula_adduct_string), charge=charge)
sigma = self.sigma_at_mz(perfect_pattern.get_spectrum(source='centroids')[0][0])
pts_per_mz = self.points_per_mz(sigma)
spec = pyisocalc.apply_gaussian(perfect_pattern, sigma, pts_per_mz)
centroided_mzs, centroided_ints, _ = gradient(*spec.get_spectrum())
spec.add_centroids(centroided_mzs, centroided_ints)
return spec
def get_isotope_pattern(self, formula_adduct_string, charge):
perfect_pattern = pyisocalc.perfect_pattern(
pyisocalc.parseSumFormula(formula_adduct_string), charge=charge)
sigma = self.sigma_at_mz(
perfect_pattern.get_spectrum(source='centroids')[0][0])
pts_per_mz = self.points_per_mz(sigma)
spec = pyisocalc.apply_gaussian(perfect_pattern, sigma, pts_per_mz)
centroided_mzs, centroided_ints, _ = gradient(*spec.get_spectrum())
spec.add_centroids(centroided_mzs, centroided_ints)
return spec
def get_mass(self):
logging.info(self.sum_formula)
logging.info(pyisocalc.parseSumFormula(self.sum_formula))
spec = pyisocalc.perfect_pattern(pyisocalc.parseSumFormula(
self.sum_formula),
charge=0)
logging.info(spec)
mass = spec.get_spectrum(source='centroids')[0][np.argmax(
spec.get_spectrum(source='centroids')[1])]
logging.info(mass)
return mass
def get_mz(self, adduct):
"""
Calculate the precursor mass for this molecule with a given adduct
:param adduct: object of class Adduct
:return: float
"""
try:
formula = self.make_ion_formula(adduct)
spec = pyisocalc.perfect_pattern(pyisocalc.parseSumFormula(formula), charge=adduct.charge)
mass = spec.get_spectrum(source='centroids')[0][np.argmax(spec.get_spectrum(source='centroids')[1])]
return mass
except:
logging.debug(self.name, adduct)
return -1.
def get_mz(self, adduct):
"""
Calculate the precursor mass for this molecule with a given adduct
:param adduct: object of class Adduct
:return: float
"""
try:
formula = self.make_ion_formula(adduct)
spec = pyisocalc.perfect_pattern(
pyisocalc.parseSumFormula(formula), charge=adduct.charge)
mass = spec.get_spectrum(source='centroids')[0][np.argmax(
spec.get_spectrum(source='centroids')[1])]
return mass
except:
logging.debug(self.name, adduct)
return -1.
def get_principal_peak(self, formula_adduct_string, charge):
perfect_pattern = pyisocalc.perfect_pattern(
pyisocalc.parseSumFormula(formula_adduct_string),
charge=charge).get_spectrum(source='centroids')
return perfect_pattern[0][np.argmax(perfect_pattern[1])]