def onOK(self, evt=None):
"""Get label."""
# get data
label = self.label_value.GetValue()
formula = self.formula_value.GetValue()
theoretical = self.theoreticalMZ_value.GetValue()
charge = self.charge_value.GetValue()
radical = self.radical_check.GetValue()
# check label
if label:
self.notation.label = label
else:
wx.Bell()
return
# get formula
if formula:
try:
mspy.compound(formula)
self.notation.formula = formula
except:
wx.Bell()
return
else:
self.notation.formula = None
# get m/z
if theoretical:
try:
self.notation.theoretical = float(theoretical)
except:
wx.Bell()
return
else:
self.notation.theoretical = None
# get charge
if charge:
try:
self.notation.charge = int(charge)
except:
wx.Bell()
return
else:
self.notation.charge = None
# get radical
if radical:
self.notation.radical = 1
else:
self.notation.radical = 0
# close dialog
self.EndModal(wx.ID_OK)
def onOK(self, evt=None):
"""Get label."""
# get data
label = self.label_value.GetValue()
formula = self.formula_value.GetValue()
theoretical = self.theoreticalMZ_value.GetValue()
charge = self.charge_value.GetValue()
radical = self.radical_check.GetValue()
# check label
if label:
self.notation.label = label
else:
wx.Bell()
return
# get formula
if formula:
try:
mspy.compound(formula)
self.notation.formula = formula
except:
wx.Bell()
return
else:
self.notation.formula = None
# get m/z
if theoretical:
try:
self.notation.theoretical = float(theoretical)
except:
wx.Bell()
return
else:
self.notation.theoretical = None
# get charge
if charge:
try:
self.notation.charge = int(charge)
except:
wx.Bell()
return
else:
self.notation.charge = None
# get radical
if radical:
self.notation.radical = 1
else:
self.notation.radical = 0
# close dialog
self.EndModal(wx.ID_OK)
def loadCompounds(path=os.path.join(config.confdir, 'compounds.xml'), clear=True):
"""Parse compounds XML and get data."""
container = {}
# parse XML
document = xml.dom.minidom.parse(path)
# get references
groupTags = document.getElementsByTagName('group')
if groupTags:
for groupTag in groupTags:
groupName = groupTag.getAttribute('name')
container[groupName] = {}
compoundTags = groupTag.getElementsByTagName('compound')
if compoundTags:
for compoundTag in compoundTags:
try:
name = compoundTag.getAttribute('name')
compound = mspy.compound(compoundTag.getAttribute('formula'))
compound.description = _getNodeText(compoundTag)
container[groupName][name] = compound
except:
pass
# update current lib
if container and clear:
compounds.clear()
for group in container:
compounds[group] = container[group]
def readLibraryXML(self, path):
"""Read xml library."""
compounds = {}
# parse XML file
try:
document = xml.dom.minidom.parse(path)
except:
return False
if not document.getElementsByTagName("mMassCompounds"):
return False
# read data
groupTags = document.getElementsByTagName("group")
if groupTags:
for groupTag in groupTags:
groupName = groupTag.getAttribute("name")
compounds[groupName] = {}
compoundTags = groupTag.getElementsByTagName("compound")
if compoundTags:
for compoundTag in compoundTags:
try:
name = compoundTag.getAttribute("name")
compound = mspy.compound(compoundTag.getAttribute("formula"))
compound.description = self._getNodeText(compoundTag)
compounds[groupName][name] = compound
except:
pass
return compounds
def readLibraryXML(self, path):
"""Read xml library."""
compounds = {}
# parse XML file
try:
document = xml.dom.minidom.parse(path)
except:
return False
if not document.getElementsByTagName('mMassCompounds'):
return False
# read data
groupTags = document.getElementsByTagName('group')
if groupTags:
for groupTag in groupTags:
groupName = groupTag.getAttribute('name')
compounds[groupName] = {}
compoundTags = groupTag.getElementsByTagName('compound')
if compoundTags:
for compoundTag in compoundTags:
try:
name = compoundTag.getAttribute('name')
compound = mspy.compound(
compoundTag.getAttribute('formula'))
compound.description = self._getNodeText(
compoundTag)
compounds[groupName][name] = compound
except:
pass
return compounds
def loadCompounds(path=os.path.join(config.confdir, "compounds.xml"), clear=True):
"""Parse compounds XML and get data."""
container = {}
# parse XML
document = xml.dom.minidom.parse(path)
# get references
groupTags = document.getElementsByTagName("group")
if groupTags:
for groupTag in groupTags:
groupName = groupTag.getAttribute("name")
container[groupName] = {}
compoundTags = groupTag.getElementsByTagName("compound")
if compoundTags:
for compoundTag in compoundTags:
try:
name = compoundTag.getAttribute("name")
compound = mspy.compound(compoundTag.getAttribute("formula"))
compound.description = _getNodeText(compoundTag)
container[groupName][name] = compound
except:
pass
# update current lib
if container and clear:
compounds.clear()
for group in container:
compounds[group] = container[group]
def updateFormulaMass(self):
"""Update formula mass."""
# get formula
gain = self.itemGainFormula_value.GetValue()
loss = self.itemLossFormula_value.GetValue()
# show formula masses
try:
gain = mspy.compound(gain)
loss = mspy.compound(loss)
gainMass = gain.mass()
lossMass = loss.mass()
self.itemMoMass_value.SetValue(str(gainMass[0] - lossMass[0]))
self.itemAvMass_value.SetValue(str(gainMass[1] - lossMass[1]))
except:
wx.Bell()
self.itemMoMass_value.SetValue('')
self.itemAvMass_value.SetValue('')
def _checkFormula(self):
"""Check current formula."""
try:
formula = mspy.compound(self.GetValue())
self.SetBackgroundColour(wx.NullColour)
except:
self.SetBackgroundColour((250,100,100))
self.Refresh()
def updateFormulaMass(self):
"""Update formula mass."""
# get formula
gain = self.itemGainFormula_value.GetValue()
loss = self.itemLossFormula_value.GetValue()
# show formula masses
try:
gain = mspy.compound(gain)
loss = mspy.compound(loss)
gainMass = gain.mass()
lossMass = loss.mass()
self.itemMoMass_value.SetValue(str(gainMass[0] - lossMass[0]))
self.itemAvMass_value.SetValue(str(gainMass[1] - lossMass[1]))
except:
wx.Bell()
self.itemMoMass_value.SetValue('')
self.itemAvMass_value.SetValue('')
def getParams(self):
"""Get all params from dialog."""
# try to get values
try:
formula = self.formula_value.GetValue()
loss = self.exchangeLoss_value.GetValue()
gain = self.exchangeGain_value.GetValue()
if not formula or not loss or not gain:
raise ValueError
self.currentCompound = mspy.compound(formula)
lossCmpd = mspy.compound(loss)
gainCmpd = mspy.compound(gain)
config.envelopeFit["loss"] = str(loss)
config.envelopeFit["gain"] = str(gain)
config.envelopeFit["fit"] = "peaklist"
if self.fitToSpectrum_radio.GetValue():
config.envelopeFit["fit"] = "spectrum"
config.envelopeFit["charge"] = int(self.charge_value.GetValue())
config.envelopeFit["scaleMin"] = int(
self.scaleMin_value.GetValue())
config.envelopeFit["scaleMax"] = int(
self.scaleMax_value.GetValue())
config.envelopeFit["fwhm"] = float(self.fwhm_value.GetValue())
config.envelopeFit["forceFwhm"] = self.forceFwhm_check.GetValue()
config.envelopeFit["autoAlign"] = self.autoAlign_check.GetValue()
config.envelopeFit["relThreshold"] = (
float(self.relThreshold_value.GetValue()) / 100.0)
return True
except:
wx.Bell()
return False
def getParams(self):
"""Get all params from dialog."""
# try to get values
try:
formula = self.formula_value.GetValue()
loss = self.exchangeLoss_value.GetValue()
gain = self.exchangeGain_value.GetValue()
if not formula or not loss or not gain:
raise ValueError
self.currentCompound = mspy.compound(formula)
lossCmpd = mspy.compound(loss)
gainCmpd = mspy.compound(gain)
config.envelopeFit["loss"] = str(loss)
config.envelopeFit["gain"] = str(gain)
config.envelopeFit["fit"] = "peaklist"
if self.fitToSpectrum_radio.GetValue():
config.envelopeFit["fit"] = "spectrum"
config.envelopeFit["charge"] = int(self.charge_value.GetValue())
config.envelopeFit["scaleMin"] = int(self.scaleMin_value.GetValue())
config.envelopeFit["scaleMax"] = int(self.scaleMax_value.GetValue())
config.envelopeFit["fwhm"] = float(self.fwhm_value.GetValue())
config.envelopeFit["forceFwhm"] = self.forceFwhm_check.GetValue()
config.envelopeFit["autoAlign"] = self.autoAlign_check.GetValue()
config.envelopeFit["relThreshold"] = float(self.relThreshold_value.GetValue()) / 100.0
return True
except:
wx.Bell()
return False
def getParams(self):
"""Get all params from dialog."""
# try to get values
try:
formula = self.formula_value.GetValue()
loss = self.exchangeLoss_value.GetValue()
gain = self.exchangeGain_value.GetValue()
if not formula or not loss or not gain:
raise ValueError
self.currentCompound = mspy.compound(formula)
lossCmpd = mspy.compound(loss)
gainCmpd = mspy.compound(gain)
config.envelopeFit['loss'] = str(loss)
config.envelopeFit['gain'] = str(gain)
config.envelopeFit['fit'] = 'peaklist'
if self.fitToSpectrum_radio.GetValue():
config.envelopeFit['fit'] = 'spectrum'
config.envelopeFit['charge'] = int(self.charge_value.GetValue())
config.envelopeFit['scaleMin'] = int(self.scaleMin_value.GetValue())
config.envelopeFit['scaleMax'] = int(self.scaleMax_value.GetValue())
config.envelopeFit['fwhm'] = float(self.fwhm_value.GetValue())
config.envelopeFit['forceFwhm'] = self.forceFwhm_check.GetValue()
config.envelopeFit['autoAlign'] = self.autoAlign_check.GetValue()
config.envelopeFit['relThreshold'] = float(self.relThreshold_value.GetValue())/100.
return True
except:
wx.Bell()
return False
def updateFormulaMass(self):
"""Update formula mass."""
# get formula
formula = self.itemFormula_value.GetValue()
# show formula masses
try:
formula = mspy.compound(formula)
mass = formula.mass()
self.itemMoMass_value.SetValue(str(mass[0]))
self.itemAvMass_value.SetValue(str(mass[1]))
except:
self.itemMoMass_value.SetValue('')
self.itemAvMass_value.SetValue('')
def updateFormulaMass(self):
"""Update formula mass."""
# get formula
formula = self.itemFormula_value.GetValue()
# show formula masses
try:
formula = mspy.compound(formula)
mass = formula.mass()
self.itemMoMass_value.SetValue(str(mass[0]))
self.itemAvMass_value.SetValue(str(mass[1]))
except:
self.itemMoMass_value.SetValue("")
self.itemAvMass_value.SetValue("")
def calcDataPoints(self, peaks, polarity=1):
"""Calculate requested mass and mass defect."""
buff = []
# init Kendrick formula
kendrickFormula = mspy.compound(
config.massDefectPlot["kendrickFormula"])
# calculate data points
for peak in peaks:
mass = peak[0]
if not config.massDefectPlot["ignoreCharge"] and peak[1]:
mass = mspy.mz(peak[0],
1 * polarity,
peak[1],
agentFormula="H",
agentCharge=1)
# calc mass defect
md = mspy.md(
mass=mass,
mdType=config.massDefectPlot["yAxis"],
kendrickFormula=kendrickFormula,
rounding=config.massDefectPlot["nominalMass"],
)
# re-calculate selected mass
if config.massDefectPlot["xAxis"] == "mz":
mass = peak[0]
elif config.massDefectPlot["xAxis"] == "nominal":
mass = mspy.nominalmass(peak[0],
config.massDefectPlot["nominalMass"])
elif config.massDefectPlot["xAxis"] == "kendrick":
mass = mspy.nominalmass(peak[0] *
kendrickFormula.nominalmass() /
kendrickFormula.mass(0))
else:
mass = peak[0]
# append point
buff.append((mass, md))
return buff
def updateLossFormulaMass(self):
"""Update loss formula mass."""
# erase old value
self.itemLossMoMass_value.SetValue("")
# get current item
focus = self.FindFocus()
for x in range(4):
item = self.itemLosses_values[x]
# found focused item
if item is focus:
try:
formula = item.GetValue()
formula = mspy.compound(formula)
mass = formula.mass()
self.itemLossMoMass_value.SetValue(str(mass[0]))
except:
pass
def updateLossFormulaMass(self):
"""Update loss formula mass."""
# erase old value
self.itemLossMoMass_value.SetValue('')
# get current item
focus = self.FindFocus()
for x in range(4):
item = self.itemLosses_values[x]
# found focused item
if item is focus:
try:
formula = item.GetValue()
formula = mspy.compound(formula)
mass = formula.mass()
self.itemLossMoMass_value.SetValue(str(mass[0]))
except:
pass
def getItemData(self):
"""Get formated item data."""
# get data
name = self.itemName_value.GetValue()
description = self.itemDescription_value.GetValue()
formula = self.itemFormula_value.GetValue()
# check values
if not name or not formula:
wx.Bell()
return False
# make compound
try:
compound = mspy.compound(formula)
compound.name = name
compound.description = description
except:
wx.Bell()
return False
return compound
def getItemData(self):
"""Get formated item data."""
# get data
name = self.itemName_value.GetValue()
description = self.itemDescription_value.GetValue()
formula = self.itemFormula_value.GetValue()
# check values
if not name or not formula:
wx.Bell()
return False
# make compound
try:
compound = mspy.compound(formula)
compound.name = name
compound.description = description
except:
wx.Bell()
return False
return compound
def onFormula(self, evt=None):
"""Check formula and calculate m/z."""
if evt != None:
evt.Skip()
# user-defined m/z
if self.mzByUser_radio.GetValue():
return
# get data
formula = self.formula_value.GetValue()
charge = self.charge_value.GetValue()
radical = self.radical_check.GetValue()
if not formula or not charge:
self.theoreticalMZ_value.SetValue('')
return
# get m/z from formula
try:
compound = mspy.compound(formula)
charge = int(charge)
if radical:
mz = compound.mz(charge=charge, agentFormula='e', agentCharge=-1)
else:
mz = compound.mz(charge=charge, agentFormula='H', agentCharge=1)
except:
self.theoreticalMZ_value.SetValue('')
return
# set formula
if self.mzByFormulaMo_radio.GetValue():
theoretical = '%0.6f' % mz[0]
self.theoreticalMZ_value.SetValue(theoretical)
elif self.mzByFormulaAv_radio.GetValue():
theoretical = '%0.6f' % mz[1]
self.theoreticalMZ_value.SetValue(theoretical)
def onFormula(self, evt=None):
"""Check formula and calculate m/z."""
if evt is not None:
evt.Skip()
# user-defined m/z
if self.mzByUser_radio.GetValue():
return
# get data
formula = self.formula_value.GetValue()
charge = self.charge_value.GetValue()
radical = self.radical_check.GetValue()
if not formula or not charge:
self.theoreticalMZ_value.SetValue("")
return
# get m/z from formula
try:
compound = mspy.compound(formula)
charge = int(charge)
if radical:
mz = compound.mz(charge=charge, agentFormula="e", agentCharge=-1)
else:
mz = compound.mz(charge=charge, agentFormula="H", agentCharge=1)
except:
self.theoreticalMZ_value.SetValue("")
return
# set formula
if self.mzByFormulaMo_radio.GetValue():
theoretical = "%0.6f" % mz[0]
self.theoreticalMZ_value.SetValue(theoretical)
elif self.mzByFormulaAv_radio.GetValue():
theoretical = "%0.6f" % mz[1]
self.theoreticalMZ_value.SetValue(theoretical)
def getParams(self):
"""Get all params from dialog."""
# try to get values
try:
choices = ["fraction", "standard", "relative", "kendrick"]
config.massDefectPlot["yAxis"] = choices[
self.yAxis_choice.GetSelection()]
config.massDefectPlot[
"nominalMass"] = self.nominalMass_choice.GetStringSelection(
).lower()
config.massDefectPlot["relIntCutoff"] = (
float(self.relIntCutoff_value.GetValue()) / 100.0)
config.massDefectPlot[
"removeIsotopes"] = self.removeIsotopes_check.GetValue()
config.massDefectPlot[
"ignoreCharge"] = self.ignoreCharge_check.GetValue()
config.massDefectPlot[
"showNotations"] = self.showNotations_check.GetValue()
config.massDefectPlot[
"showAllDocuments"] = self.showAllDocuments_check.GetValue()
formula = self.kendrickFormula_value.GetValue()
cmpd = mspy.compound(formula)
config.massDefectPlot["kendrickFormula"] = str(formula)
if config.massDefectPlot["yAxis"] == "kendrick" and cmpd.mass(
0) == 0:
raise ValueError
return True
except:
wx.Bell()
return False
def getParams(self):
"""Get all params from dialog."""
# try to get values
try:
choices = ['fraction', 'standard', 'relative', 'kendrick']
config.massDefectPlot['yAxis'] = choices[
self.yAxis_choice.GetSelection()]
config.massDefectPlot[
'nominalMass'] = self.nominalMass_choice.GetStringSelection(
).lower()
config.massDefectPlot['relIntCutoff'] = float(
self.relIntCutoff_value.GetValue()) / 100.
config.massDefectPlot[
'removeIsotopes'] = self.removeIsotopes_check.GetValue()
config.massDefectPlot[
'ignoreCharge'] = self.ignoreCharge_check.GetValue()
config.massDefectPlot[
'showNotations'] = self.showNotations_check.GetValue()
config.massDefectPlot[
'showAllDocuments'] = self.showAllDocuments_check.GetValue()
formula = self.kendrickFormula_value.GetValue()
cmpd = mspy.compound(formula)
config.massDefectPlot['kendrickFormula'] = str(formula)
if config.massDefectPlot['yAxis'] == 'kendrick' and cmpd.mass(
0) == 0:
raise ValueError
return True
except:
wx.Bell()
return False
def runGenerateIons(self, compounds):
"""Calculate compounds ions."""
# run task
try:
# set adducts
adducts = {
"Na": "Na",
"K": "K",
"Li": "Li",
"NH4": "NH4",
"-H2O": "H-2O-1",
"ACN": "CH3CN",
"MeOH": "CH3OH",
}
# get max charge and polarity
polarity = 1
if config.compoundsSearch["maxCharge"] < 0:
polarity = -1
maxCharge = abs(config.compoundsSearch["maxCharge"]) + 1
# generate compounds ions
self.currentCompounds = []
for name, compound in sorted(compounds.items()):
# check compound
if not compound.isvalid():
continue
# walk in charges
for z in range(1, maxCharge):
# 0 name, 1 m/z, 2 z, 3 adduct, 4 formula, 5 error, 6 matches
# main ion
mz = compound.mz(
z * polarity)[config.compoundsSearch["massType"]]
self.currentCompounds.append([
name, mz, z * polarity, None, compound.expression,
None, []
])
# radicals
if config.compoundsSearch["radicals"]:
mz = compound.mz(
z * polarity, agentFormula="e",
agentCharge=-1)[config.compoundsSearch["massType"]]
self.currentCompounds.append([
name,
mz,
z * polarity,
"radical",
compound.expression,
None,
[],
])
mspy.CHECK_FORCE_QUIT()
# add adducts
for item in config.compoundsSearch["adducts"]:
if item in ("Na", "K", "Li", "NH4", "ACN", "MeOH"):
formula = "%s(%s)(H-1)" % (
compound.expression,
adducts[item],
)
elif item in ("-H2O"):
formula = "%s(%s)" % (compound.expression,
adducts[item])
formula = mspy.compound(formula)
if formula.isvalid():
mz = formula.mz(
z *
polarity)[config.compoundsSearch["massType"]]
self.currentCompounds.append([
name,
mz,
z * polarity,
item,
formula.expression,
None,
[],
])
mspy.CHECK_FORCE_QUIT()
# add combinations
for item1 in ("Na", "K", "Li", "NH4"):
if item1 in config.compoundsSearch["adducts"]:
for item2 in ("ACN", "MeOH", "-H2O"):
if item2 in config.compoundsSearch["adducts"]:
if item2 in ("ACN", "MeOH"):
adduct = "%s+%s" % (item1, item2)
formula = "%s(%s)(%s)(H-2)" % (
compound.expression,
adducts[item1],
adducts[item2],
)
elif item2 in ("-H2O"):
adduct = "%s%s" % (item1, item2)
formula = "%s(%s)(%s)(H-1)" % (
compound.expression,
adducts[item1],
adducts[item2],
)
formula = mspy.compound(formula)
if formula.isvalid():
mz = formula.mz(z * polarity)[
config.compoundsSearch["massType"]]
self.currentCompounds.append([
name,
mz,
z * polarity,
adduct,
formula.expression,
None,
[],
])
# task canceled
except mspy.ForceQuit:
self.currentCompounds = []
return
def runGenerateIons(self, compounds):
"""Calculate compounds ions."""
# run task
try:
# set adducts
adducts = {
'Na': 'Na',
'K': 'K',
'Li': 'Li',
'NH4': 'NH4',
'-H2O': 'H-2O-1',
'ACN': 'CH3CN',
'MeOH': 'CH3OH'
}
# get max charge and polarity
polarity = 1
if config.compoundsSearch['maxCharge'] < 0:
polarity = -1
maxCharge = abs(config.compoundsSearch['maxCharge']) + 1
# generate compounds ions
self.currentCompounds = []
for name, compound in sorted(compounds.items()):
# check compound
if not compound.isvalid():
continue
# walk in charges
for z in range(1, maxCharge):
# 0 name, 1 m/z, 2 z, 3 adduct, 4 formula, 5 error, 6 matches
# main ion
mz = compound.mz(
z * polarity)[config.compoundsSearch['massType']]
self.currentCompounds.append([
name, mz, z * polarity, None, compound.expression,
None, []
])
# radicals
if config.compoundsSearch['radicals']:
mz = compound.mz(
z * polarity, agentFormula='e',
agentCharge=-1)[config.compoundsSearch['massType']]
self.currentCompounds.append([
name, mz, z * polarity, 'radical',
compound.expression, None, []
])
mspy.CHECK_FORCE_QUIT()
# add adducts
for item in config.compoundsSearch['adducts']:
if item in ('Na', 'K', 'Li', 'NH4', 'ACN', 'MeOH'):
formula = '%s(%s)(H-1)' % (compound.expression,
adducts[item])
elif item in ('-H2O'):
formula = '%s(%s)' % (compound.expression,
adducts[item])
formula = mspy.compound(formula)
if formula.isvalid():
mz = formula.mz(
z *
polarity)[config.compoundsSearch['massType']]
self.currentCompounds.append([
name, mz, z * polarity, item,
formula.expression, None, []
])
mspy.CHECK_FORCE_QUIT()
# add combinations
for item1 in ('Na', 'K', 'Li', 'NH4'):
if item1 in config.compoundsSearch['adducts']:
for item2 in ('ACN', 'MeOH', '-H2O'):
if item2 in config.compoundsSearch['adducts']:
if item2 in ('ACN', 'MeOH'):
adduct = '%s+%s' % (item1, item2)
formula = '%s(%s)(%s)(H-2)' % (
compound.expression,
adducts[item1], adducts[item2])
elif item2 in ('-H2O'):
adduct = '%s%s' % (item1, item2)
formula = '%s(%s)(%s)(H-1)' % (
compound.expression,
adducts[item1], adducts[item2])
formula = mspy.compound(formula)
if formula.isvalid():
mz = formula.mz(z * polarity)[
config.compoundsSearch['massType']]
self.currentCompounds.append([
name, mz, z * polarity, adduct,
formula.expression, None, []
])
# task canceled
except mspy.ForceQuit:
self.currentCompounds = []
return
def onGenerate(self, evt=None):
"""Generate compounds ions."""
# check processing
if self.processing:
return
# clear recent
self.currentCompounds = None
compounds = {}
# clear match panel
if self.matchPanel:
self.matchPanel.clear()
# get params
if not self.getParams():
self.updateCompoundsList()
return
# get compounds from selected group or formula
if self.currentTool == 'compounds':
group = self.compounds_choice.GetStringSelection()
if group and group in libs.compounds:
compounds = libs.compounds[group]
else:
formula = self.formula_value.GetValue()
if formula:
try:
compounds[formula] = mspy.compound(formula)
except:
wx.Bell()
# check compounds
if not compounds:
self.updateCompoundsList()
return
# show processing gauge
self.onProcessing(True)
self.generate_butt.Enable(False)
self.match_butt.Enable(False)
self.annotate_butt.Enable(False)
# do processing
self.processing = threading.Thread(target=self.runGenerateIons,
kwargs={'compounds': compounds})
self.processing.start()
# pulse gauge while working
while self.processing and self.processing.isAlive():
self.gauge.pulse()
# update compounds list
self._compoundsFilter = 0
self.updateCompoundsList()
# hide processing gauge
self.onProcessing(False)
self.generate_butt.Enable(True)
self.match_butt.Enable(True)
self.annotate_butt.Enable(True)
# send data to match panel
if self.matchPanel:
self.matchPanel.setData(self.currentCompounds)
def getParams(self):
"""Get all params from dialog."""
# try to get values
try:
# compound
compound = self.compound_value.GetValue()
if not compound:
return False
# charging agent
ionseriesAgent = self.ionseriesAgentFormula_value.GetValue()
if not ionseriesAgent:
return False
# ionseries
config.massCalculator['ionseriesAgentCharge'] = int(self.ionseriesAgentCharge_value.GetValue())
if self.ionseriesNegative_radio.GetValue():
config.massCalculator['ionseriesPolarity'] = -1
else:
config.massCalculator['ionseriesPolarity'] = 1
# pattern
patternFwhm = float(self.patternFwhm_value.GetValue())
patternIntensity = float(self.patternIntensity_value.GetValue())
patternBaseline = float(self.patternBaseline_value.GetValue())
patternShift = float(self.patternShift_value.GetValue())
config.massCalculator['patternShowPeaks'] = self.showPeaks_check.GetValue()
config.massCalculator['patternPeakShape'] = 'gaussian'
if self.patternPeakShape_choice.GetStringSelection() == 'Asymmetrical':
config.massCalculator['patternPeakShape'] = 'gausslorentzian'
except:
wx.Bell()
return False
# check compound
try:
self.currentCompound = mspy.compound(compound)
except:
return False
if not self.currentCompound.isvalid():
wx.Bell()
return False
# check charging agent
try:
if ionseriesAgent != 'e':
agent = mspy.compound(ionseriesAgent)
config.massCalculator['ionseriesAgent'] = ionseriesAgent
except:
return False
if ionseriesAgent == 'e':
config.massCalculator['ionseriesAgentCharge'] = -1
self.ionseriesAgentCharge_value.ChangeValue('-1')
# check pattern values
if patternFwhm < 0.001 \
or patternIntensity < 1 \
or patternBaseline >= patternIntensity:
wx.Bell()
return False
else:
config.massCalculator['patternFwhm'] = patternFwhm
config.massCalculator['patternIntensity'] = patternIntensity
config.massCalculator['patternBaseline'] = patternBaseline
config.massCalculator['patternShift'] = patternShift
return True
def runGenerator(self):
"""Generate formula for given mass."""
# run task
try:
self.currentFormulae = []
# get agent charge
agentCharge = 1
if config.massToFormula["ionization"] == "e":
agentCharge = -1
# approximate CHNO composition from neutral mass
mass = mspy.mz(
mass=self.currentMass,
charge=0,
currentCharge=config.massToFormula["charge"],
agentFormula=config.massToFormula["ionization"],
agentCharge=agentCharge,
)
composition = {}
if config.massToFormula["autoCHNO"]:
if mass < 500:
composition = {
"C": [0, 40],
"H": [0, 80],
"N": [0, 20],
"O": [0, 20],
}
elif mass < 1000:
composition = {
"C": [0, 80],
"H": [0, 130],
"N": [0, 30],
"O": [0, 30],
}
elif mass < 2000:
composition = {
"C": [0, 160],
"H": [0, 250],
"N": [0, 40],
"O": [0, 70],
}
else:
composition = {
"C": [0, 180],
"H": [0, 300],
"N": [0, 60],
"O": [0, 90],
}
# add user-specified compositions
minComposition = mspy.compound(
config.massToFormula["formulaMin"]).composition()
for el in minComposition:
if el in composition:
composition[el][0] = minComposition[el]
else:
composition[el] = [minComposition[el], minComposition[el]]
maxComposition = mspy.compound(
config.massToFormula["formulaMax"]).composition()
for el in maxComposition:
if el in composition:
composition[el][1] = maxComposition[el]
else:
composition[el] = [0, maxComposition[el]]
# calculate formulae
formulae = mspy.formulator(
mz=self.currentMass,
charge=config.massToFormula["charge"],
tolerance=config.massToFormula["tolerance"],
units=config.massToFormula["units"],
composition=composition,
agentFormula=config.massToFormula["ionization"],
agentCharge=agentCharge,
limit=config.massToFormula["countLimit"],
)
# make compounds
buff = []
for formula in formulae:
# make compound
cmpd = mspy.compound(formula)
mass = cmpd.mass(0)
mz = cmpd.mz(
config.massToFormula["charge"],
config.massToFormula["ionization"],
1,
)[0]
error = mspy.delta(self.currentMass, mz,
config.massToFormula["units"])
errorDa = mspy.delta(self.currentMass, mz, "Da")
# compare isotopic pattern
similarity = None
if config.massToFormula["checkPattern"] and cmpd.isvalid(
charge=config.massToFormula["charge"],
agentFormula=config.massToFormula["ionization"],
):
similarity = self.compareIsotopicPattern(
cmpd,
config.massToFormula["charge"],
config.massToFormula["ionization"],
errorDa,
)
# count ratios
countC = float(cmpd.count("C", groupIsotopes=True))
countH = float(cmpd.count("H", groupIsotopes=True))
hc = None
if countC:
hc = countH / countC
# count rdbe
rdbe = cmpd.rdbe()
# add item
buff.append([
cmpd.formula(), mass, mz, error, hc, rdbe, similarity, cmpd
])
self.currentFormulae = buff
# task canceled
except mspy.ForceQuit:
return
def getParams(self):
"""Get all params from dialog."""
# try to get values
try:
# compound
compound = self.compound_value.GetValue()
if not compound:
return False
# charging agent
ionseriesAgent = self.ionseriesAgentFormula_value.GetValue()
if not ionseriesAgent:
return False
# ionseries
config.massCalculator['ionseriesAgentCharge'] = int(
self.ionseriesAgentCharge_value.GetValue())
if self.ionseriesNegative_radio.GetValue():
config.massCalculator['ionseriesPolarity'] = -1
else:
config.massCalculator['ionseriesPolarity'] = 1
# pattern
patternFwhm = float(self.patternFwhm_value.GetValue())
patternIntensity = float(self.patternIntensity_value.GetValue())
patternBaseline = float(self.patternBaseline_value.GetValue())
patternShift = float(self.patternShift_value.GetValue())
config.massCalculator[
'patternShowPeaks'] = self.showPeaks_check.GetValue()
config.massCalculator['patternPeakShape'] = 'gaussian'
if self.patternPeakShape_choice.GetStringSelection(
) == 'Asymmetrical':
config.massCalculator['patternPeakShape'] = 'gausslorentzian'
except:
wx.Bell()
return False
# check compound
try:
self.currentCompound = mspy.compound(compound)
except:
return False
if not self.currentCompound.isvalid():
wx.Bell()
return False
# check charging agent
try:
if ionseriesAgent != 'e':
agent = mspy.compound(ionseriesAgent)
config.massCalculator['ionseriesAgent'] = ionseriesAgent
except:
return False
if ionseriesAgent == 'e':
config.massCalculator['ionseriesAgentCharge'] = -1
self.ionseriesAgentCharge_value.ChangeValue('-1')
# check pattern values
if patternFwhm < 0.001 \
or patternIntensity < 1 \
or patternBaseline >= patternIntensity:
wx.Bell()
return False
else:
config.massCalculator['patternFwhm'] = patternFwhm
config.massCalculator['patternIntensity'] = patternIntensity
config.massCalculator['patternBaseline'] = patternBaseline
config.massCalculator['patternShift'] = patternShift
return True
def onGenerate(self, evt=None):
"""Generate compounds ions."""
# check processing
if self.processing:
return
# clear recent
self.currentCompounds = None
compounds = {}
# clear match panel
if self.matchPanel:
self.matchPanel.clear()
# get params
if not self.getParams():
self.updateCompoundsList()
return
# get compounds from selected group or formula
if self.currentTool == 'compounds':
group = self.compounds_choice.GetStringSelection()
if group and group in libs.compounds:
compounds = libs.compounds[group]
else:
formula = self.formula_value.GetValue()
if formula:
try:
compounds[formula] = mspy.compound(formula)
except:
wx.Bell()
# check compounds
if not compounds:
self.updateCompoundsList()
return
# show processing gauge
self.onProcessing(True)
self.generate_butt.Enable(False)
self.match_butt.Enable(False)
self.annotate_butt.Enable(False)
# do processing
self.processing = threading.Thread(target=self.runGenerateIons, kwargs={'compounds':compounds})
self.processing.start()
# pulse gauge while working
while self.processing and self.processing.isAlive():
self.gauge.pulse()
# update compounds list
self._compoundsFilter = 0
self.updateCompoundsList()
# hide processing gauge
self.onProcessing(False)
self.generate_butt.Enable(True)
self.match_butt.Enable(True)
self.annotate_butt.Enable(True)
# send data to match panel
if self.matchPanel:
self.matchPanel.setData(self.currentCompounds)
def runGenerateIons(self, compounds):
"""Calculate compounds ions."""
# run task
try:
# set adducts
adducts = {'Na':'Na', 'K':'K', 'Li':'Li', 'NH4':'NH4', '-H2O':'H-2O-1', 'ACN':'CH3CN', 'MeOH':'CH3OH'}
# get max charge and polarity
polarity = 1
if config.compoundsSearch['maxCharge'] < 0:
polarity = -1
maxCharge = abs(config.compoundsSearch['maxCharge'])+1
# generate compounds ions
self.currentCompounds = []
for name, compound in sorted(compounds.items()):
# check compound
if not compound.isvalid():
continue
# walk in charges
for z in range(1, maxCharge):
# 0 name, 1 m/z, 2 z, 3 adduct, 4 formula, 5 error, 6 matches
# main ion
mz = compound.mz(z*polarity)[config.compoundsSearch['massType']]
self.currentCompounds.append([name, mz, z*polarity, None, compound.expression, None, []])
# radicals
if config.compoundsSearch['radicals']:
mz = compound.mz(z*polarity, agentFormula='e', agentCharge=-1)[config.compoundsSearch['massType']]
self.currentCompounds.append([name, mz, z*polarity, 'radical', compound.expression, None, []])
mspy.CHECK_FORCE_QUIT()
# add adducts
for item in config.compoundsSearch['adducts']:
if item in ('Na', 'K', 'Li', 'NH4', 'ACN', 'MeOH'):
formula = '%s(%s)(H-1)' % (compound.expression, adducts[item])
elif item in ('-H2O'):
formula = '%s(%s)' % (compound.expression, adducts[item])
formula = mspy.compound(formula)
if formula.isvalid():
mz = formula.mz(z*polarity)[config.compoundsSearch['massType']]
self.currentCompounds.append([name, mz, z*polarity, item, formula.expression, None, []])
mspy.CHECK_FORCE_QUIT()
# add combinations
for item1 in ('Na', 'K', 'Li', 'NH4'):
if item1 in config.compoundsSearch['adducts']:
for item2 in ('ACN', 'MeOH', '-H2O'):
if item2 in config.compoundsSearch['adducts']:
if item2 in ('ACN', 'MeOH'):
adduct = '%s+%s' % (item1, item2)
formula = '%s(%s)(%s)(H-2)' % (compound.expression, adducts[item1], adducts[item2])
elif item2 in ('-H2O'):
adduct = '%s%s' % (item1, item2)
formula = '%s(%s)(%s)(H-1)' % (compound.expression, adducts[item1], adducts[item2])
formula = mspy.compound(formula)
if formula.isvalid():
mz = formula.mz(z*polarity)[config.compoundsSearch['massType']]
self.currentCompounds.append([name, mz, z*polarity, adduct, formula.expression, None, []])
# task canceled
except mspy.ForceQuit:
self.currentCompounds = []
return