def _activation(self, scan):
filter_string = self._filter_string(scan)
tandem_sequence = filter_string.get("tandem_sequence")
# If the tandem sequence exists, the last entry is the most recent tandem acquisition.
# It will list contain one or more activation types. Alternatively, multiple activations
# of the same precursor may exist in the list as separate events in the tandem sequence.
if tandem_sequence is not None:
activation_event = tandem_sequence[-1]
activation_type = list(activation_event.get("activation_type"))
has_supplemental_activation = filter_string.get("supplemental_activation")
if activation_type is not None:
energy = list(activation_event.get("activation_energy"))
if len(tandem_sequence) > 1:
prev_event = tandem_sequence[-2]
# Merge previous tandem sequences of the same precursor
if abs(prev_event['isolation_mz'] - activation_event['isolation_mz']) < 1e-3:
activation_type = list(prev_event.get("activation_type")) + activation_type
energy = list(prev_event.get("activation_energy")) + energy
has_supplemental_activation = True
if has_supplemental_activation and len(activation_type) > 1:
activation_type.append(supplemental_term_map[
dissociation_methods_map[activation_type[-1]]])
if len(activation_type) == 1:
return ActivationInformation(activation_type[0], energy[0])
else:
return MultipleActivationInformation(activation_type, energy)
return None
def _activation(self, scan):
energy_str = self.info_reader.GetScanItem(
scan.function, scan.block if scan.block >= 0 else scan.scan,
MassLynxRawDefs.MassLynxScanItem.COLLISION_ENERGY)
if energy_str:
energy = float(energy_str)
return ActivationInformation(HCD, energy)
def _activation(self, scan):
filter_line = self._filter_line(scan)
activation_type = filter_line.get("activation_type")
if activation_type is not None:
energy = filter_line.get("activation_energy")
return ActivationInformation(activation_type, energy)
return None
def __init__(self,
scan_time=None,
neutral_mass=None,
mz=None,
intensity=None,
charge=None,
precursor_scan_id=None,
product_scan_id=None,
defaulted=None,
orphan=None,
drift_time=None,
coisolation=None,
activation=None,
**kwargs):
super(MSnRecord, self).__init__(scan_time, drift_time, **kwargs)
self.neutral_mass = neutral_mass
self.mz = mz
self.intensity = intensity
self.charge = charge
self.precursor_scan_id = precursor_scan_id
self.product_scan_id = product_scan_id
self.defaulted = defaulted
self.orphan = orphan
self.coisolation = [
CoIsolation(*c) if c else c for c in (coisolation or [])
]
self.activation = ActivationInformation.from_dict(
activation) if isinstance(activation, dict) else activation
def __init__(self, scan_time=None, neutral_mass=None, mz=None, intensity=None, charge=None,
precursor_scan_id=None, product_scan_id=None, defaulted=None, orphan=None,
drift_time=None, coisolation=None, activation=None, **kwargs):
super(MSnRecord, self).__init__(scan_time, drift_time, **kwargs)
self.neutral_mass = neutral_mass
self.mz = mz
self.intensity = intensity
self.charge = charge
self.precursor_scan_id = precursor_scan_id
self.product_scan_id = product_scan_id
self.defaulted = defaulted
self.orphan = orphan
self.coisolation = [CoIsolation(*c) if c else c for c in (coisolation or [])]
self.activation = ActivationInformation.from_dict(
activation) if isinstance(activation, dict) else activation
def _activation(self, scan):
record = self._get_scan_record(scan)
return ActivationInformation('cid', record.CollisionEnergy)