class AveragineCache(object):
def __init__(self, averagine, backend=None, cache_truncation=1.0):
if backend is None:
backend = {}
self.backend = backend
self.averagine = Averagine(averagine)
self.cache_truncation = cache_truncation
def has_mz_charge_pair(self, mz, charge=1, charge_carrier=PROTON, truncate_after=0.95, ignore_below=0.0):
if self.cache_truncation == 0.0:
key_mz = mz
else:
key_mz = round(mz / self.cache_truncation) * self.cache_truncation
if (key_mz, charge, charge_carrier) in self.backend:
# return shift_isotopic_pattern(
# mz, [p.clone() for p in self.backend[key_mz, charge, charge_carrier]])
return self.backend[key_mz, charge, charge_carrier].clone().shift(mz)
else:
tid = self.averagine.isotopic_cluster(
mz, charge, charge_carrier, truncate_after, ignore_below)
self.backend[key_mz, charge, charge_carrier] = tid.clone()
return tid
isotopic_cluster = has_mz_charge_pair
def __repr__(self):
return "AveragineCache(%r)" % self.averagine
def clear(self):
self.backend.clear()
class AveragineCache(object):
def __init__(self, averagine, backend=None, cache_truncation=1.0):
if backend is None:
backend = {}
self.backend = backend
self.averagine = Averagine(averagine)
self.cache_truncation = cache_truncation
def has_mz_charge_pair(self,
mz,
charge=1,
charge_carrier=PROTON,
truncate_after=0.95,
ignore_below=0.0):
if self.cache_truncation == 0.0:
key_mz = mz
else:
key_mz = round(mz / self.cache_truncation) * self.cache_truncation
if (key_mz, charge, charge_carrier) in self.backend:
# return shift_isotopic_pattern(
# mz, [p.clone() for p in self.backend[key_mz, charge, charge_carrier]])
return self.backend[key_mz, charge,
charge_carrier].clone().shift(mz)
else:
tid = self.averagine.isotopic_cluster(mz, charge, charge_carrier,
truncate_after, ignore_below)
self.backend[key_mz, charge, charge_carrier] = tid.clone()
return tid
isotopic_cluster = has_mz_charge_pair
def __repr__(self):
return "AveragineCache(%r)" % self.averagine
def clear(self):
self.backend.clear()
def __init__(self, averagine, backend=None, cache_truncation=1.0):
if backend is None:
backend = {}
self.backend = backend
self.averagine = Averagine(averagine)
self.cache_truncation = cache_truncation
def __init__(self, averagine, backend=None, cache_truncation=1.0):
if backend is None:
backend = {}
self.backend = backend
self.averagine = Averagine(averagine)
self.cache_truncation = cache_truncation
class AveragineCache(object):
"""A wrapper around a :class:`Averagine` instance which will cache isotopic patterns
produced for new (m/z, charge) pairs and reuses it for nearby m/z values
Attributes
----------
averagine : :class:`~Averagine`
The averagine to use to generate new isotopic patterns
cache_truncation : float
Number of decimal places to round off the m/z for caching purposes
"""
def __init__(self, averagine, backend=None, cache_truncation=1.0):
if backend is None:
backend = {}
self.backend = backend
self.averagine = Averagine(averagine)
self.cache_truncation = cache_truncation
def has_mz_charge_pair(self,
mz,
charge=1,
charge_carrier=PROTON,
truncate_after=0.95,
ignore_below=0.0):
if self.cache_truncation == 0.0:
key_mz = mz
else:
key_mz = round(mz / self.cache_truncation) * self.cache_truncation
if (key_mz, charge, charge_carrier) in self.backend:
return self.backend[key_mz, charge,
charge_carrier].clone().shift(mz)
else:
tid = self.averagine.isotopic_cluster(mz, charge, charge_carrier,
truncate_after, ignore_below)
self.backend[key_mz, charge, charge_carrier] = tid.clone()
return tid
def isotopic_cluster(self,
mz,
charge=1,
charge_carrier=PROTON,
truncate_after=0.95,
ignore_below=0.0):
"""Generate a theoretical isotopic pattern for the given m/z and charge state, thresholded
by theoretical peak height and density.
Mimics :meth:`.Averagine.isotopic_cluster` but uses the object's cache through
:meth:`has_mz_charge_pair`.
Parameters
----------
mz : float
The reference m/z to calculate the neutral mass to interpolate from
charge : int, optional
The reference charge state to calculate the neutral mass. Defaults to 1
charge_carrier : float, optional
The mass of the charge carrier. Defaults to the mass of a proton.
truncate_after : float, optional
The percentage of the signal in the theoretical isotopic pattern to include.
Defaults to 0.95, including the first 95% of the signal in the generated pattern
ignore_below : float, optional
Omit theoretical peaks whose intensity is below this number.
Defaults to 0.0
Returns
-------
:class:`.TheoreticalIsotopicPattern`
The generated and thresholded pattern
"""
return self.has_mz_charge_pair(mz, charge, charge_carrier,
truncate_after, ignore_below)
def __repr__(self):
return "AveragineCache(%r)" % self.averagine
def clear(self):
self.backend.clear()
for k, v in b.items():
a[k] += v
return dict(a)
try:
_Averagine = Averagine
_TheoreticalIsotopicPattern = TheoreticalIsotopicPattern
from ms_deisotope._c.averagine import Averagine, TheoreticalIsotopicPattern
except ImportError as e:
print(e, "averagine")
peptide = Averagine({
"C": 4.9384,
"H": 7.7583,
"N": 1.3577,
"O": 1.4773,
"S": 0.0417
})
glycopeptide = Averagine({
"C": 10.93,
"H": 15.75,
"N": 1.6577,
"O": 6.4773,
"S": 0.02054
})
glycan = Averagine({'C': 7.0, 'H': 11.8333, 'N': 0.5, 'O': 5.16666})
permethylated_glycan = Averagine({
'C': 12.0,
'H': 21.8333,
'N': 0.5,
class AveragineCache(object):
"""A wrapper around a :class:`Averagine` instance which will cache isotopic patterns
produced for new (m/z, charge) pairs and reuses it for nearby m/z values
Attributes
----------
averagine : :class:`~Averagine`
The averagine to use to generate new isotopic patterns
cache_truncation : float
Number of decimal places to round off the m/z for caching purposes
"""
def __init__(self, averagine, backend=None, cache_truncation=1.0):
if backend is None:
backend = {}
self.backend = backend
self.averagine = Averagine(averagine)
self.cache_truncation = cache_truncation
def __call__(self, mz, charge=1, charge_carrier=PROTON, truncate_after=TRUNCATE_AFTER, ignore_below=IGNORE_BELOW):
return self.isotopic_cluster(mz, charge, charge_carrier, truncate_after, ignore_below)
def has_mz_charge_pair(self, mz, charge=1, charge_carrier=PROTON, truncate_after=TRUNCATE_AFTER,
ignore_below=IGNORE_BELOW):
if self.cache_truncation == 0.0:
key_mz = mz
else:
key_mz = round(mz / self.cache_truncation) * self.cache_truncation
if (key_mz, charge, charge_carrier) in self.backend:
return self.backend[key_mz, charge, charge_carrier].clone().shift(mz)
else:
tid = self.averagine.isotopic_cluster(
mz, charge, charge_carrier, truncate_after, ignore_below)
self.backend[key_mz, charge, charge_carrier] = tid.clone()
return tid
def isotopic_cluster(self, mz, charge=1, charge_carrier=PROTON, truncate_after=TRUNCATE_AFTER,
ignore_below=IGNORE_BELOW):
"""Generate a theoretical isotopic pattern for the given m/z and charge state, thresholded
by theoretical peak height and density.
Mimics :meth:`.Averagine.isotopic_cluster` but uses the object's cache through
:meth:`has_mz_charge_pair`.
Parameters
----------
mz : float
The reference m/z to calculate the neutral mass to interpolate from
charge : int, optional
The reference charge state to calculate the neutral mass. Defaults to 1
charge_carrier : float, optional
The mass of the charge carrier. Defaults to the mass of a proton.
truncate_after : float, optional
The percentage of the signal in the theoretical isotopic pattern to include.
Defaults to TRUNCATE_AFTER, including the first 95% of the signal in the generated pattern
ignore_below : float, optional
Omit theoretical peaks whose intensity is below this number.
Defaults to 0.0
Returns
-------
:class:`.TheoreticalIsotopicPattern`
The generated and thresholded pattern
"""
return self.has_mz_charge_pair(mz, charge, charge_carrier, truncate_after, ignore_below)
def __repr__(self):
return "AveragineCache(%r)" % self.averagine
def clear(self):
self.backend.clear()
def populate(self, min_mz=10, max_mz=3000, min_charge=1, max_charge=8, charge_carrier=PROTON,
truncate_after=TRUNCATE_AFTER, ignore_below=IGNORE_BELOW):
for i in range(int(min_mz), int(max_mz)):
for j in range(min(max_charge, min_charge), max(min_charge, max_charge)):
self.isotopic_cluster(i, j, PROTON, TRUNCATE_AFTER, IGNORE_BELOW)
return self