def make_sf_adduct_optimusfilter(sum_formulae,adducts,output_filename,sigma=0.001,resolution=10000,charge=1):
from pyMS.pyisocalc import pyisocalc
# Extract variables from config dict
# Check if already genrated and load if possible, otherwise calculate fresh
with open(output_filename,'a') as f_out:
for sum_formula in sum_formulae:
#print sum_formula
for adduct in adducts:
try:
sf = pyisocalc.complex_to_simple(sum_formula+adduct)
if sf is None: # not possible to form adduct
continue
isotope_ms = pyisocalc.isodist(sf, plot=False, sigma=sigma, charges=charge,
resolution=resolution)
except KeyError as e:
if str(e).startswith("KeyError:"):
print str(e)
continue
except ValueError as e:
if str(e).startswith("Element not recognised"):
print str(e)
continue
except:
print sf=="", sum_formula, adduct
raise
f_out.write("{} [M{}],-1,{}\n".format(sum_formula,adduct,isotope_ms.get_spectrum(source='centroids')[0][0]))
def calculate_isotope_patterns(sum_formulae,
adduct='',
isocalc_sig=0.01,
isocalc_resolution=200000.,
isocalc_do_centroid=True,
charge=1,
verbose=True):
from pyMS.pyisocalc import pyisocalc
### Generate a mz list of peak centroids for each sum formula with the given adduct
mz_list = {}
for n, sum_formula in enumerate(sum_formulae):
try:
if verbose:
print sum_formula, adduct
sf = pyisocalc.complex_to_simple(sum_formula + adduct)
except KeyError as e:
if str(e).startswith("KeyError: "):
print str(e)
continue
except ValueError as e:
if str(e).startswith("Element not recognised"):
print str(e)
continue
else:
print sum_formula, adduct
raise
if sf == None: #negative atoms as a result of simplification
print 'negative adduct for {} : {}'.format(sum_formula, adduct)
continue
try:
isotope_ms = pyisocalc.isodist(sf,
plot=False,
sigma=isocalc_sig,
charges=charge,
resolution=isocalc_resolution,
do_centroid=isocalc_do_centroid)
except KeyError as e:
if str(e).startswith("KeyError: "):
print str(e)
continue
if not sum_formula in mz_list:
mz_list[sum_formula] = {}
mz_list[sum_formula][adduct] = isotope_ms.get_spectrum(
source='centroids')
return mz_list
def calculate_isotope_patterns(sum_formulae, adduct='', isocalc_sig=0.01, isocalc_resolution=200000.,
isocalc_do_centroid=True, charge=1,verbose=True):
from pyMS.pyisocalc import pyisocalc
### Generate a mz list of peak centroids for each sum formula with the given adduct
mz_list = {}
for n, sum_formula in enumerate(sum_formulae):
try:
if verbose:
print sum_formula, adduct
sf = pyisocalc.complex_to_simple(sum_formula+adduct)
except KeyError as e:
if str(e).startswith("KeyError: "):
print str(e)
continue
except ValueError as e:
if str(e).startswith("Element not recognised"):
print str(e)
continue
else:
print sum_formula, adduct
raise
if sf == None: #negative atoms as a result of simplification
print 'negative adduct for {} : {}'.format(sum_formula,adduct)
continue
try:
isotope_ms = pyisocalc.isodist(sf, plot=False, sigma=isocalc_sig, charges=charge,
resolution=isocalc_resolution, do_centroid=isocalc_do_centroid)
except KeyError as e:
if str(e).startswith("KeyError: "):
print str(e)
continue
if not sum_formula in mz_list:
mz_list[sum_formula] = {}
mz_list[sum_formula][adduct] = isotope_ms.get_spectrum(source='centroids')
return mz_list
