/usr/share/mmass/gui/dlg_notation.py is in mmass 5.1.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Copyright (C) 2005-2012 Martin Strohalm <www.mmass.org>
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# Complete text of GNU GPL can be found in the file LICENSE.TXT in the
# main directory of the program.
# -------------------------------------------------------------------------
# load libs
import wx
# load modules
import mwx
import config
import mspy
# NOTATION LABEL
# --------------
class dlgNotation(wx.Dialog):
"""Set notation label."""
def __init__(self, parent, notation, button='Add'):
# initialize document frame
wx.Dialog.__init__(self, parent, -1, 'Notation', style=wx.DEFAULT_DIALOG_STYLE)
self.notation = notation
self.button = button
# set dlg title
format = 'Notation for m/z: %0.' + `config.main['mzDigits']` + 'f'
title = format % (self.notation.mz)
self.SetTitle(title)
# make GUI
sizer = self.makeGUI()
self.setData()
# fit layout
self.Layout()
sizer.Fit(self)
self.SetSizer(sizer)
self.Centre()
# ----
def makeGUI(self):
"""Make GUI elements."""
labelBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, ""), wx.HORIZONTAL)
formulaBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, ""), wx.HORIZONTAL)
# make elements
label_label = wx.StaticText(self, -1, "Label:", style=wx.ALIGN_RIGHT)
self.label_value = wx.TextCtrl(self, -1, '', size=(300,-1), style=wx.TE_PROCESS_ENTER)
self.label_value.Bind(wx.EVT_TEXT_ENTER, self.onOK)
formula_label = wx.StaticText(self, -1, "Formula:", style=wx.ALIGN_RIGHT)
self.formula_value = mwx.formulaCtrl(self, -1, '', size=(300,-1), style=wx.TE_PROCESS_ENTER)
self.formula_value.Bind(wx.EVT_TEXT, self.onFormula)
self.formula_value.Bind(wx.EVT_TEXT_ENTER, self.onOK)
theoreticalMZ_label = wx.StaticText(self, -1, "Theoretical m/z:", style=wx.ALIGN_RIGHT)
self.theoreticalMZ_value = wx.TextCtrl(self, -1, '', size=(120,-1), style=wx.TE_PROCESS_ENTER, validator=mwx.validator('float'))
self.theoreticalMZ_value.Bind(wx.EVT_TEXT_ENTER, self.onOK)
charge_label = wx.StaticText(self, -1, " z:")
self.charge_value = wx.TextCtrl(self, -1, '', size=(30,-1), style=wx.TE_PROCESS_ENTER, validator=mwx.validator('int'))
self.charge_value.Bind(wx.EVT_TEXT, self.onFormula)
self.charge_value.Bind(wx.EVT_TEXT_ENTER, self.onOK)
self.radical_check = wx.CheckBox(self, -1, "M*", size=(50,-1))
self.radical_check.Bind(wx.EVT_CHECKBOX, self.onMassType)
self.mzByUser_radio = wx.RadioButton(self, -1, "Manual", style=wx.RB_GROUP)
self.mzByUser_radio.SetFont(wx.SMALL_FONT)
self.mzByUser_radio.Bind(wx.EVT_RADIOBUTTON, self.onMassType)
self.mzByUser_radio.SetValue(True)
self.mzByFormulaMo_radio = wx.RadioButton(self, -1, "Mo")
self.mzByFormulaMo_radio.SetFont(wx.SMALL_FONT)
self.mzByFormulaMo_radio.Bind(wx.EVT_RADIOBUTTON, self.onMassType)
self.mzByFormulaAv_radio = wx.RadioButton(self, -1, "Av")
self.mzByFormulaAv_radio.SetFont(wx.SMALL_FONT)
self.mzByFormulaAv_radio.Bind(wx.EVT_RADIOBUTTON, self.onMassType)
buttons = self.makeButtons()
# pack elements
labelBox.Add(label_label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
labelBox.Add(self.label_value, 1, wx.TOP|wx.RIGHT|wx.BOTTOM|wx.ALIGN_CENTER_VERTICAL, 10)
formulaGrid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
formulaGrid.Add(formula_label, (0,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
formulaGrid.Add(self.formula_value, (0,1), (1,7), flag=wx.EXPAND)
formulaGrid.Add(theoreticalMZ_label, (1,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
formulaGrid.Add(self.theoreticalMZ_value, (1,1))
formulaGrid.Add(charge_label, (1,2), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
formulaGrid.Add(self.charge_value, (1,3))
formulaGrid.Add(self.radical_check, (1,4), flag=wx.ALIGN_CENTER_VERTICAL)
formulaGrid.Add(self.mzByUser_radio, (1,5), flag=wx.ALIGN_CENTER_VERTICAL)
formulaGrid.Add(self.mzByFormulaMo_radio, (1,6), flag=wx.ALIGN_CENTER_VERTICAL)
formulaGrid.Add(self.mzByFormulaAv_radio, (1,7), flag=wx.ALIGN_CENTER_VERTICAL)
formulaGrid.AddGrowableCol(1)
formulaBox.Add(formulaGrid, 1, wx.EXPAND|wx.ALL, 10)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(labelBox, 0, wx.EXPAND|wx.CENTER|wx.ALL, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(formulaBox, 0, wx.EXPAND|wx.CENTER|wx.LEFT|wx.RIGHT|wx.BOTTOM, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(buttons, 0, wx.CENTER|wx.LEFT|wx.RIGHT|wx.BOTTOM, mwx.PANEL_SPACE_MAIN)
return mainSizer
# ----
def makeButtons(self):
"""Make buttons."""
# make items
cancel_butt = wx.Button(self, wx.ID_CANCEL, "Cancel")
ok_butt = wx.Button(self, wx.ID_OK, self.button)
ok_butt.Bind(wx.EVT_BUTTON, self.onOK)
ok_butt.SetDefault()
# pack items
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(cancel_butt, 0, wx.RIGHT, 15)
sizer.Add(ok_butt, 0)
return sizer
# ----
def setData(self):
"""Set data to elements."""
# set label
self.label_value.SetValue(self.notation.label)
# set formula
if self.notation.formula:
self.formula_value.SetValue(self.notation.formula)
# set calc. m/z
self.mzByUser_radio.SetValue(True)
if self.notation.theoretical:
self.theoreticalMZ_value.SetValue(str(self.notation.theoretical))
# set charge
if self.notation.charge != None:
self.charge_value.SetValue(str(self.notation.charge))
# set radical
self.radical_check.SetValue(bool(self.notation.radical))
# ----
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 onMassType(self, evt=None):
"""Mass type changed."""
if self.mzByUser_radio.GetValue():
self.theoreticalMZ_value.Enable(True)
else:
self.theoreticalMZ_value.Enable(False)
self.onFormula()
# ----
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)
# ----
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