def Temporary_Immunity(self):
self.hide()
tIFrame = Toplevel()
tIFrame.title("SIR WITH TEMPORARY IMMUNITY")
tIFrame.geometry("700x800")
# self.top.transient(self)
g = Pmw.Blt.Graph(tIFrame)
g.pack(expand=1, fill="both")
E = zeros([2, 1])
A = zeros([2, 2])
C = zeros([2, 1])
A = zeros([2, 2])
B = zeros([2, 2])
E = zeros([2, 1])
C = zeros([2, 1])
# -------------------------------------------------------------------------------------------------------------------------------------------------------
sus = Pmw.EntryField(
tIFrame,
labelpos="w",
value="0.0",
label_text="Initial Susceptibles :",
validate={"validator": "real"},
)
sus.pack(expand=1, padx=5, pady=5)
Infec = Pmw.EntryField(
tIFrame,
labelpos="w",
value="0.0",
label_text="Initial Infectives :",
validate={"validator": "real"},
)
Infec.pack(expand=1, padx=5, pady=5)
contact = Pmw.EntryField(
tIFrame,
labelpos="w",
value="0.0",
label_text="Contact Rate (k) :",
validate={"validator": "real"},
)
contact.pack(expand=1, padx=5, pady=5)
Removal = Pmw.EntryField(
tIFrame,
labelpos="w",
value="0.0",
label_text=" Removal Rate :",
validate={"validator": "real"},
)
Removal.pack(expand=1, padx=10, pady=5)
time_interval = Pmw.EntryField(
tIFrame,
labelpos="w",
value="0",
label_text=" Time Interval :",
validate={"validator": "numeric"},
)
time_interval.pack(expand=1, padx=5, pady=5)
death_rate = Pmw.EntryField(
tIFrame,
labelpos="w",
value="0.0",
label_text=" Death Rate (d) :",
validate={"validator": "real"},
)
death_rate.pack(expand=1, padx=10, pady=5)
immunity = Pmw.EntryField(
tIFrame,
labelpos="w",
value="0.00",
label_text=" Immunity Rate:",
validate={"validator": "real"},
)
immunity.pack(expand=1, padx=10, pady=10)
# --------------------------------------------------------------------------------------------------------------------------------------------------------
# self.top.transient(self)
# self.wButton.config(state='disabled')
def retrive():
k1 = contact.get()
k = float(k1)
ddelta = float(death_rate.get())
aalpha = float(immunity.get())
ggamma = float(Removal.get())
N = int(time_interval.get())
s0 = float(sus.get())
I0 = float(Infec.get())
A[0][0] = 0
A[0][1] = -k
A[1][0] = k
A[1][1] = 0
B[0][0] = 0
B[0][1] = 0
B[1][0] = 0
B[1][1] = 0
E[0][0] = -(ddelta + aalpha)
E[1][0] = -(ggamma + ddelta + +aalpha)
C[0][0] = (ddelta + aalpha) * (1 + aalpha / k)
C[1][0] = 0
def f1(s1, I1):
s_dot = (
s1 * E[0][0]
+ A[0][0] * (s1 ** 2)
+ A[0][1] * s1 * I1
+ B[0][0] * s1
+ B[0][1] * I1
+ C[0][0]
)
return s_dot
def f2(s1, I1):
I_dot = (
I1 * E[1][0]
+ A[1][1] * (I1 ** 2)
+ A[1][0] * s1 * I1
+ B[1][0] * s1
+ B[1][1] * I1
+ C[1][0]
)
return I_dot
# =========RATE OF CHANGE OF THE MODEL WITH RESPECT TO TIME AND DECLARATON OF CONSTANTS================================================================
t = arange(0, N, 0.02455)
s1 = zeros(len(t))
I1 = zeros(len(t))
s1[0] = s0
I1[0] = I0
h = 0.01
# ==========ITERATION FOR A GIVEN TIME INTERVAL=======================================================================================================
for n in range(len(t) - 1):
s1[n + 1] = s1[n] + h * (f1(s1[n], I1[n]))
I1[n + 1] = I1[n] + h * (f2(s1[n], I1[n]))
x_ = tuple(t)
y_ = tuple(s1)
z_ = tuple(I1)
g.configure(
title="Susceptible and Infectives against time for SIR with Temporary Immunity"
)
g.line_create(
"S(t) Vs t", xdata=x_, color="red", ydata=y_, linewidth=2, symbol=""
)
g.line_create(
"I(t) Vs t", xdata=x_, color="orange", ydata=z_, linewidth=2, symbol=""
)
def postscript():
g.postscript_output(fileName="HelloUser1.ps", decorations="no")
def newFile():
for name in g.element_names():
g.element_delete(name)
contact.setentry("")
Removal.setentry("")
time_interval.setentry("")
Infec.setentry("")
sus.setentry("")
immunity.setentry("")
death_rate.setentry("")
# --------------------------------------------------------------------------------------------------------------------------------------------------------
buttons = Pmw.ButtonBox(tIFrame, labelpos="w", label_text="Options")
# buttons = Pmw.ButtonBox(self, labelpos='w', label_text='Options')
buttons.pack(fill="both", expand=1, padx=10, pady=10)
buttons.add("GRID", bg="green", command=g.grid_toggle)
buttons.add("PLOT", bg="green", command=retrive)
buttons.add("CLEAR", bg="green", command=newFile)
buttons.add("SAVE", bg="green", command=postscript)
handler = lambda: self.onCloseOtherFrameT(tIFrame)
buttons.add("QUIT", bg="red", command=handler)
def __init__(self, parent):
# Create the ScrolledCanvas.
self.sc = Pmw.ScrolledCanvas(
parent,
borderframe=1,
labelpos='n',
label_text='ScrolledCanvas',
usehullsize=1,
hull_width=400,
hull_height=300,
)
# Create a group widget to contain the scrollmode options.
w = Pmw.Group(parent, tag_text='Scroll mode')
w.pack(side='bottom', padx=5, pady=5)
hmode = Pmw.OptionMenu(
w.interior(),
labelpos='w',
label_text='Horizontal:',
items=['none', 'static', 'dynamic'],
command=self.sethscrollmode,
menubutton_width=8,
)
hmode.pack(side='left', padx=5, pady=5)
hmode.invoke('dynamic')
vmode = Pmw.OptionMenu(
w.interior(),
labelpos='w',
label_text='Vertical:',
items=['none', 'static', 'dynamic'],
command=self.setvscrollmode,
menubutton_width=8,
)
vmode.pack(side='left', padx=5, pady=5)
vmode.invoke('dynamic')
buttonBox = Pmw.ButtonBox(parent)
buttonBox.pack(side='bottom')
buttonBox.add('yview', text='Show\nyview', command=self.showYView)
buttonBox.add('scroll', text='Page\ndown', command=self.pageDown)
buttonBox.add('center', text='Center', command=self.centerPage)
# Pack this last so that the buttons do not get shrunk when
# the window is resized.
self.sc.pack(padx=5, pady=5, fill='both', expand=1)
self.sc.component('canvas').bind('<1>', self.addcircle)
testEntry = Tkinter.Entry(parent)
self.sc.create_line(20, 20, 100, 100)
self.sc.create_oval(100, 100, 200, 200, fill='green')
self.sc.create_text(100,
20,
anchor='nw',
text='Click in the canvas\nto draw ovals',
font=testEntry.cget('font'))
button = Tkinter.Button(self.sc.interior(),
text='Hello,\nWorld!\nThis\nis\na\nbutton.')
self.sc.create_window(200, 200, anchor='nw', window=button)
# Set the scroll region of the canvas to include all the items
# just created.
self.sc.resizescrollregion()
self.colours = ('red', 'green', 'blue', 'yellow', 'cyan', 'magenta',
'black', 'white')
self.oval_count = 0
self.rand = 12345
def __init__(self, parent):
# Create the toplevel to contain the main menubar.
megaToplevel = Pmw.MegaToplevel(parent, title=title)
toplevel = megaToplevel.interior()
# Create the Balloon for this toplevel.
self.balloon = Pmw.Balloon(toplevel)
# Create and install the MenuBar.
menuBar = Pmw.MainMenuBar(toplevel, balloon=self.balloon)
toplevel.configure(menu=menuBar)
self.menuBar = menuBar
# Add some buttons to the MainMenuBar.
menuBar.addmenu('File', 'Close this window or exit')
menuBar.addmenuitem('File',
'command',
'Close this window',
command=PrintOne('Action: close'),
label='Close')
menuBar.addmenuitem('File', 'separator')
menuBar.addmenuitem('File',
'command',
'Exit the application',
command=PrintOne('Action: exit'),
label='Exit')
menuBar.addmenu('Edit', 'Cut, copy or paste')
menuBar.addmenuitem('Edit',
'command',
'Delete the current selection',
command=PrintOne('Action: delete'),
label='Delete')
menuBar.addmenu('Options', 'Set user preferences')
menuBar.addmenuitem('Options',
'command',
'Set general preferences',
command=PrintOne('Action: general options'),
label='General...')
# Create a checkbutton menu item.
self.toggleVar = Tkinter.IntVar()
# Initialise the checkbutton to 1:
self.toggleVar.set(1)
menuBar.addmenuitem('Options',
'checkbutton',
'Toggle me on/off',
label='Toggle',
command=self._toggleMe,
variable=self.toggleVar)
self._toggleMe()
menuBar.addcascademenu('Options',
'Size',
'Set some other preferences',
traverseSpec='z',
tearoff=1)
for size in ('tiny', 'small', 'average', 'big', 'huge'):
menuBar.addmenuitem('Size',
'command',
'Set size to ' + size,
command=PrintOne('Action: size ' + size),
label=size)
menuBar.addmenu('Help', 'User manuals', name='help')
menuBar.addmenuitem('Help',
'command',
'About this application',
command=PrintOne('Action: about'),
label='About...')
# Create and pack the main part of the window.
self.mainPart = Tkinter.Label(
toplevel,
text='This is the\nmain part of\nthe window',
background='black',
foreground='white',
padx=30,
pady=30)
self.mainPart.pack(fill='both', expand=1)
# Create and pack the MessageBar.
self.messageBar = Pmw.MessageBar(toplevel,
entry_width=40,
entry_relief='groove',
labelpos='w',
label_text='Status:')
self.messageBar.pack(fill='x', padx=10, pady=10)
self.messageBar.message(
'state',
'Balloon/status help not working properly - Tk menubar bug')
buttonBox = Pmw.ButtonBox(toplevel)
buttonBox.pack(fill='x')
buttonBox.add('Disable\nall', command=menuBar.disableall)
buttonBox.add('Enable\nall', command=menuBar.enableall)
buttonBox.add('Create\nmenu', command=self.add)
buttonBox.add('Delete\nmenu', command=self.delete)
buttonBox.add('Create\nitem', command=self.additem)
buttonBox.add('Delete\nitem', command=self.deleteitem)
# Configure the balloon to displays its status messages in the
# message bar.
self.balloon.configure(statuscommand=self.messageBar.helpmessage)
self.testMenuList = []
def __init__(self, parent):
# Create the ScrolledFrame.
self.sf = Pmw.ScrolledFrame(parent,
labelpos = 'n', label_text = 'ScrolledFrame',
usehullsize = 1,
hull_width = 400,
hull_height = 220,
)
# Create a group widget to contain the flex options.
w = Pmw.Group(parent, tag_text='Flex')
w.pack(side = 'bottom', padx = 5, pady = 3)
hflex = Pmw.OptionMenu(w.interior(),
labelpos = 'w',
label_text = 'Horizontal:',
items = ['fixed', 'expand', 'shrink', 'elastic'],
command = self.sethflex,
menubutton_width = 8,
)
hflex.pack(side = 'left', padx = 5, pady = 3)
hflex.invoke('fixed')
vflex = Pmw.OptionMenu(w.interior(),
labelpos = 'w',
label_text = 'Vertical:',
items = ['fixed', 'expand', 'shrink', 'elastic'],
command = self.setvflex,
menubutton_width = 8,
)
vflex.pack(side = 'left', padx = 5, pady = 3)
vflex.invoke('fixed')
# Create a group widget to contain the scrollmode options.
w = Pmw.Group(parent, tag_text='Scroll mode')
w.pack(side = 'bottom', padx = 5, pady = 0)
hmode = Pmw.OptionMenu(w.interior(),
labelpos = 'w',
label_text = 'Horizontal:',
items = ['none', 'static', 'dynamic'],
command = self.sethscrollmode,
menubutton_width = 8,
)
hmode.pack(side = 'left', padx = 5, pady = 3)
hmode.invoke('dynamic')
vmode = Pmw.OptionMenu(w.interior(),
labelpos = 'w',
label_text = 'Vertical:',
items = ['none', 'static', 'dynamic'],
command = self.setvscrollmode,
menubutton_width = 8,
)
vmode.pack(side = 'left', padx = 5, pady = 3)
vmode.invoke('dynamic')
self.radio = Pmw.RadioSelect(parent, selectmode = 'multiple',
command = self.radioSelected)
self.radio.add('center', text = 'Keep centered vertically')
self.radio.pack(side = 'bottom')
buttonBox = Pmw.ButtonBox(parent)
buttonBox.pack(side = 'bottom')
buttonBox.add('add', text = 'Add a button', command = self.addButton)
buttonBox.add('yview', text = 'Show yview', command = self.showYView)
buttonBox.add('scroll', text = 'Page down', command = self.pageDown)
# Pack this last so that the buttons do not get shrunk when
# the window is resized.
self.sf.pack(padx = 5, pady = 3, fill = 'both', expand = 1)
self.frame = self.sf.interior()
self.row = 0
self.col = 0
for count in range(15):
self.addButton()
def __init__(self, parent, filtus, notebook):
Tkinter.Frame.__init__(self, parent)
self.filtus = filtus
self.db = None
self.columnconfigure(0, weight=1)
self.rowconfigure(3, weight=1)
Tkinter.Label(self,
text="Extract subset database",
font=filtus.titlefont,
anchor='c').grid(sticky='news', padx=10, pady=(15, 10))
self.lists = TwoListWidget(self, filtus=filtus, lefttoptext="Samples:")
self.browser = DBbrowser(self,
filtus,
label="Load database:",
updates=self.updateStuff)
self.browser.grid(sticky='news', padx=10, pady=0)
Tkinter.Frame(self, height=2, borderwidth=2,
relief="sunken").grid(padx=10, pady=10, sticky="new")
self.lists.grid(sticky='news', padx=10, pady=0)
### Column filter
colnames = ('', 'CHROM', 'POS', 'OBS', 'HET', 'HOM', 'AFREQ')
operatorNames = [
"equal to", "not equal to", "greater than", "less than"
]
Tkinter.Label(self, text="Variant filter:").grid(sticky='w',
pady=(5, 2),
padx=10)
self.columnFilter = FiltusWidgets.ColumnFilter(
self,
filtus=self.filtus,
colnames=colnames,
operatorNames=operatorNames)
self.columnFilter.component('checkbutton').grid_remove()
self.columnFilter.grid(sticky='nw', padx=10)
####### OUTPUT
Tkinter.Frame(self, height=2, borderwidth=2,
relief="sunken").grid(padx=10, pady=10, sticky="new")
save_interior = Tkinter.Frame(self)
save_interior.columnconfigure(0, weight=1)
self.save_browser = FiltusWidgets.FileBrowser(
save_interior,
filtus=filtus,
label="Output database file name:",
checkbutton=False,
labelpos='nw',
browsesticky='se',
entryfield_entry_width=20,
browsetitle="")
self.save_browser.browsebutton.configure(command=self._browseSave)
self.save_browser.entryfield.configure(command=None)
self.formatSelect = Pmw.RadioSelect(
save_interior,
buttontype="radiobutton",
pady=0,
labelpos="nw",
labelmargin=0,
label_text="Format:"
) #, hull_borderwidth = 2, hull_relief = 'ridge')
self.formatSelect.add("Simple")
self.formatSelect.add("Extended")
self.formatSelect.invoke("Simple")
self.save_browser.grid(sticky='news', padx=(10, 25), pady=(5, 10))
self.formatSelect.grid(row=0, column=1, sticky='e', padx=10, pady=0)
save_interior.grid(sticky='news', padx=10, pady=0)
#######
Tkinter.Frame(self, height=2, borderwidth=3,
relief="raised").grid(sticky='ew', pady=15)
self.lowerButtons = Pmw.ButtonBox(self, padx=50)
self.lowerButtons.add('createButt',
text="Extract subset",
command=self.extractdb)
self.lowerButtons.add('cancelButt',
text="Cancel",
command=notebook.deactivate)
self.lowerButtons.grid(sticky='news', pady=(0, 10))
def __init__(self, master, rateObject=None):
Frame.__init__(self, master)
self.pack(expand=YES, fill=BOTH)
self.frm_tree = Frame(self)
self.frm_tree.pack(side=LEFT, fill=BOTH, expand=1)
self.m_treeBrowser = None
# if rateObject <> None: self.mapObjToGui(rateObject):
self.frm_details = Frame(self)
self.well_icon = PhotoImage(
data=
'R0lGODlhDwAPAPcAAAAAAIAAAACAAICAAAAAgIAAgACAgICAgMDAwP8AAAD/AP//AAAA//8A/wD/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\nBkMuYShQI0s+pvigwInTT86fKIIKHcoz59CjSAMCADs='
)
self.closed_icon = PhotoImage(
data=
'R0lGODlhDwAPAPcAAAAAAIAAAACAAICAAAAAgIAAgACAgICAgMDAwP8AAAD/AP//AAAA//8A/wD/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\nmTZjlkS5sWdHjSAbClUI4AGAo0iTJkXItOnAgAA7'
)
self.open_icon = PhotoImage(
data=
'R0lGODlhDwAPAPcAAAAAAIAAAACAAICAAAAAgIAAgACAgICAgMDAwP8AAAD/AP//AAAA//8A/wD/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\njH4oPtzZkCaAn0CDAn1J9GBAADs='
)
dummy = cRecurrentFile()
self.widgets = []
self.headerLabel = Label(self.frm_details, text="ID")
self.headerLabel.pack(side=TOP, fill=X, expand=0)
#for nm in dummy.aAllowedPerfKeywords:
#w = Pmw.EntryField(self.frm_details,labelpos=W,label_text=nm, validate=None)
#val = w.component('entry')
#val['width']= 10
#w.pack(side=TOP,fill=X,expand=0)
#self.widgets.append(w)
#Pmw.alignlabels(self.widgets)
self.btnSaveWell = Button(
self.frm_details,
text="Save Selected Well") # , command=self.f_savePerf)
self.btnSaveWell.pack(side=TOP, fill=X, expand=0)
self.buttonBox = Pmw.ButtonBox(
self.frm_details, labelpos='n',
label_text='TODO Actions') # , orient='vertical')
self.buttonBox.pack(side=BOTTOM, fill=X, expand=0, padx=0, pady=0)
self.buttonBox.add('ADD DATE', command=lambda s=self: s.m_addDate())
self.buttonBox.add('DEL DATE', command=lambda s=self: s.m_deleteDate())
self.buttonBox.add('ADD WELL', command=lambda s=self: s.m_addWell())
self.buttonBox.add('DEL WELL', command=lambda s=self: s.m_deleteWell())
self.buttonBox.add('ADD PERF', command=lambda s=self: s.m_addWell())
self.buttonBox.add('DEL PERF', command=lambda s=self: s.m_deleteWell())
Litems = []
self.producersList = Pmw.ScrolledListBox(
self.frm_details,
listbox_selectmode=SINGLE,
items=Litems,
labelpos=N,
label_text='Producers Blocks',
listbox_exportselection=0,
#selectioncommand = self.selectCommand, # dblclickcommand = self.selectCommand,
usehullsize=1,
hull_width=180,
hull_height=200)
self.producersList.pack(side=TOP, expand=1, fill=X)
Litems = []
self.injectorsList = Pmw.ScrolledListBox(
self.frm_details,
listbox_selectmode=SINGLE,
items=Litems,
labelpos=N,
label_text='Injectors Blocks',
#selectioncommand = self.selectCommand, # dblclickcommand = self.selectCommand,
usehullsize=1,
hull_width=180,
hull_height=200)
self.injectorsList.pack(side=TOP, expand=1, fill=X)
self.frm_details.pack(side=RIGHT, expand=1, fill=Y, pady=10)
self.lastDate = None
self.lastWell = None
self.lastPerf = None
def main(options, args):
# Create top level logger.
logger = ssdlog.make_logger('EnvMonitor', options)
# Create status object to be shared by all interested parties
if options.statsvc:
# Specified Gen2 status
status_obj = Gen2StatusObject(options.statsvc)
else:
# Specified SOSS status
status_obj = st.cachedStatusObj(options.statint)
# callback for popping up wind monitor
def showWindDirection():
global windWindow
if windWindow:
windWindow.deiconify()
#windWindow.show()
return
# Create the base frame for the widgets
WindMonitor(status_obj, logger)
# Create the base frame for the widgets
root = Tk()
Pmw.initialise(root)
root.title("Environment Monitor")
root.tk.call('tk', 'scaling', 1)
if options.geometry:
root.geometry(options.geometry)
else:
root.geometry("433x742")
def dialogResult(result):
global quitDialog
#print 'You clicked on ', result
quitDialog.deactivate(result)
if result == 'Yes':
root.quit()
def askAboutQuitting():
# Create the dialog.
global quitDialog
quitDialog = Pmw.Dialog(None,
buttons=('No', 'Yes'),
defaultbutton='Yes',
title='Quit Environment Monitor?',
command=dialogResult)
quitDialog.geometry("300x45")
quitDialog.activate(globalMode=1)
quitDialog.withdraw()
def _delete_main_window():
askAboutQuitting()
root.protocol("WM_DELETE_WINDOW", _delete_main_window)
row = 0
widget1 = sg.StatusGraph(root,
title="Wind direction (deg) N:0 E:90",
statusKeys=("TSCL.WINDD", ),
maxDeltas=(300, ),
gconfig=(None, "black", "white", (0, 360, 90), 1,
0, 1),
background="#f5fffc",
statusObj=status_obj)
widget1.grid(row=row, column=0)
widget1.tick()
row += 1
widget2 = sg.StatusGraph(
root,
title="Wind Speed(m/s)",
statusKeys=("TSCL.WINDS_O", "TSCL.WINDS_I"),
alarmValues=(10, 15),
#gconfig = (None, "black", "white", (-1,20,5), 1, 0, 1),
background="#f7fff4",
statusObj=status_obj)
widget2.grid(row=row, column=0)
widget2.tick()
row += 1
widget3 = sg.StatusGraph(root,
title="Temperature(C)",
statusKeys=("TSCL.TEMP_O", "TSCL.TEMP_I"),
statusObj=status_obj)
widget3.grid(row=row, column=0)
widget3.tick()
row += 1
widget4 = sg.StatusGraph(root,
title="Humidity(%)",
statusKeys=("TSCL.HUMI_O", "TSCL.HUMI_I"),
alarmValues=(80, 80),
background="#fffff6",
size=(112, 430),
displayTime=True,
lconfig=THINDEFAULTLINE,
statusObj=status_obj)
widget4.grid(row=row, column=0)
widget4.tick()
row += 1
widget5 = sg.StatusGraph(root,
title="Air Pressure(hPa) :",
size=(97, 430),
statusKeys=("TSCL.ATOM", ),
statusFormats=("%0.1f", ),
lconfig=THINDEFAULTLINE,
statusObj=status_obj)
widget5.grid(row=row, column=0)
widget5.tick()
row += 1
widget6 = sg.StatusGraph(root,
title="Rain Gauge(mm/h) :",
statusKeys=("TSCL.RAIN", ),
statusFormats=("%0.1f", ),
alarmValues=(50, ),
size=(93, 430),
background="#f4f4f4",
statusObj=status_obj)
widget6.grid(row=row, column=0)
widget6.tick()
row += 1
widget7 = sg.StatusGraph(root,
title="Seeing Size(arcsec)",
statusKeys=("TSCL.SEEN", "VGWD.FWHM.AG"),
alarmValues=(1, 1),
statusFormats=("TSC: %0.1f", "VGW: %0.1f"),
displayTime=True,
statusObj=status_obj)
widget7.grid(row=row, column=0)
widget7.tick()
row += 1
# widget8 = sg.StatusGraph(root, title="Sky Transparency(%) :",
# statusKeys=("TSCL.THRU",),
# background="#f4f4f4",
# displayTime=True, statusObj=status_obj)
# widget8.grid(row=row, column=0)
# widget8.tick()
# row +=1
bottomframe = Frame(root, width=440)
buttons = Pmw.ButtonBox(bottomframe)
buttons.add('Quit',
command=askAboutQuitting,
font=('Helvetica', 12, 'bold'))
buttons.grid(row=0, column=0)
resourceframe = ResourceMonitor(bottomframe, status_obj, logger)
resourceframe.grid(row=0, column=1)
resourceframe.tick()
buttons = Pmw.ButtonBox(bottomframe)
buttons.add('Wind Direction',
command=showWindDirection,
font=('Helvetica', 12, 'bold'))
buttons.grid(row=0, column=2)
bottomframe.grid(row=row, column=0)
row += 1
try:
try:
root.mainloop()
except KeyboardInterrupt:
logger.error("Received keyboard interrupt!")
except Exception, e:
logger.error("Top-level exception raised: %s" % str(e))
raise e
hscrollmode='none', #dynamic
vscrollmode='dynamic',
hull_relief='sunken', #vscrollmode=dynamic
hull_background='gray40',
hull_borderwidth=10,
text_background='honeydew4',
text_width=29, #ancho pantalla #29
text_foreground='black',
text_height=9, #alto pantalla
text_padx=10,
text_pady=10,
text_relief='groove',
text_font=('Arial', 12, 'bold'))
display.pack(padx=0, pady=0)
buttons1 = Pmw.ButtonBox(Calculadora, hull_background='gray40')
buttons1.pack(fill='both', expand=1, padx=1, pady=1)
#buttons1.alignbuttons()
buttons1.add('2nd', width=5, bg='steelblue3', fg='white', command=nd)
buttons1.add('Mode', bg='gray30', fg='white')
buttons1.add('Del', bg='gray30', fg='white', command=del_)
buttons1.add('Alpha', bg='gray50', fg='white')
buttons1.add('Stat', bg='gray30', fg='white')
buttons2 = Pmw.ButtonBox(Calculadora, hull_background='gray40')
buttons2.pack(fill='both', expand=1, padx=1, pady=1)
#buttons2.alignbuttons()
buttons2.add('Math',
width=5,
select_mode.grid(row=0, column=0, columnspan=4)
# Add some buttons to the horizontal RadioSelect - mode selection buttons.
for name, symbol, background in (('D', u'\u2609', 'green'), ('W', u'\u2692',
'blue'),
('P', u'\u26DD', 'yellow'), ('R', u'\u29E6',
'red')):
select_mode.add(name, text=symbol, background=background)
select_mode.invoke(3) # select break/rest as default
# ------top left buttons-------
top_left_buttons = Pmw.ButtonBox(
topLeftFrame,
Button_height=1, # Button_width=2,
Button_font="Helvetica 15 bold",
pady=1,
padx=1)
top_left_buttons.grid(row=0, column=0, columnspan=2)
# Add some buttons to the horizontal RadioSelect.
top_left_buttons.add('Delete', command=lambda: current_data.delete_item())
top_left_buttons.add('Edit')
top_left_buttons.add('Save')
top_left_buttons.add('Clear', command=start)
# =====bottom status=============
status = StringVar()
bottom_status_total = Label(bottomFrame,
textvariable=status,
def __init__(self, parent, inactive_channels, selected_channels=[]):
'''
Constructor
'''
self.__inactive_channels = inactive_channels
self.__inactive_channels.sort()
selected_channels.sort()
ch_loader = channel_loader.ChannelLoader.getInstance()
self.__channel_names_list = ch_loader.getNameDict().values()
self.__channel_names_list.sort()
# Update inactive_channels if channels were selected earlier
# Use the fact that empty sequences (lists, etc...) are False (PEP 8)
if not selected_channels:
for c in selected_channels:
try:
self.__inactive_channels.remove(c)
except ValueError:
pass
self.__inactive_channels = inactive_channels
top = Tkinter.Toplevel(parent)
top.title("F Prime Channel Telemetry Filter Selection")
top.focus()
# Constrain size on window so geometry works.
top.maxsize(1000, 400)
top.minsize(600, 400)
top.lift()
self.__top = top
# Container Frame
#
f = Tkinter.Frame(top)
f.pack(side=Tkinter.TOP, anchor=Tkinter.N, fill=Tkinter.BOTH, expand=1)
#
f2 = Tkinter.Frame(top)
f2.pack(side=Tkinter.TOP,
anchor=Tkinter.N,
fill=Tkinter.BOTH,
expand=1)
f3 = Tkinter.Frame(top)
f3.pack(side=Tkinter.TOP,
anchor=Tkinter.N,
fill=Tkinter.BOTH,
expand=1)
#
# Build list boxes for channels
#
ff1 = Tkinter.LabelFrame(f2,
text="Channels Avaliable:",
relief=Tkinter.GROOVE,
borderwidth=2,
padx=5,
pady=5)
ff1.pack(side=Tkinter.LEFT,
anchor=Tkinter.NW,
fill=Tkinter.BOTH,
expand=1,
padx=10,
pady=10)
#
# Scrolled log message list box here...
#
self.__list_box_channels = Pmw.ScrolledListBox(
ff1,
listbox_selectmode=Tkinter.EXTENDED,
listbox_height=15,
selectioncommand=self.__selectionCommandToSelected,
dblclickcommand=self.__selectionCommandToSelected,
items=tuple(self.__inactive_channels))
self.__list_box_channels.pack(side=Tkinter.LEFT,
anchor=Tkinter.NW,
fill=Tkinter.BOTH,
expand=1,
padx=5,
pady=5)
#
bbox = Pmw.ButtonBox(f2, orient=Tkinter.VERTICAL)
bbox.pack(side=Tkinter.LEFT)
bbox.add(">", command=self.__selectChannels)
bbox.add("<", command=self.__deselectChannels)
bbox.add('>>', command=self.__add_all)
bbox.add('<<', command=self.__clear_all)
#
ff2 = Tkinter.LabelFrame(f2,
text="Channels Selected:",
relief=Tkinter.GROOVE,
borderwidth=2,
padx=5,
pady=5)
ff2.pack(side=Tkinter.LEFT,
anchor=Tkinter.NW,
fill=Tkinter.BOTH,
expand=1,
padx=10,
pady=10)
#
# Scrolled log message list box here...
#
self.__list_box_selected = Pmw.ScrolledListBox(
ff2,
listbox_selectmode=Tkinter.EXTENDED,
listbox_height=15,
selectioncommand=self.__selectionCommandToAvaliable,
dblclickcommand=self.__selectionCommandToAvaliable,
items=selected_channels)
self.__list_box_selected.pack(side=Tkinter.LEFT,
anchor=Tkinter.NW,
fill=Tkinter.BOTH,
expand=1,
padx=5,
pady=5)
#
# Buttons to implement all the dialog commands...
#
buttonBox = Pmw.ButtonBox(f3,
labelpos='nw',
label_text='Channel Selection Commands:')
buttonBox.pack(side=Tkinter.BOTTOM,
fill=Tkinter.BOTH,
expand=1,
padx=10,
pady=10)
buttonBox.add('Save', command=self.__save)
buttonBox.add('Load', command=self.__load)
buttonBox.add('Cancel', command=self.__cancel)
buttonBox.add('Ok', command=self.__ok)
#
self.__all_channels_selected = inactive_channels
self.__channels_selected = selected_channels
self.__active_filter_selected = None
# Mouse selection lists for each ScrolledListbox
self.__select_to_selected = []
self.__select_to_avaliable = []
#
self.__top.wait_window(self.__top)
width=300)
t.grid(row=0, column=0, sticky='nsew')
root.grid_rowconfigure(0, weight=1)
root.grid_columnconfigure(0, weight=1)
sb = Scrollbar(root)
sb.grid(row=0, column=1, sticky='ns')
t.configure(yscrollcommand=sb.set)
sb.configure(command=t.yview)
sb = Scrollbar(root, orient=HORIZONTAL)
sb.grid(row=1, column=0, sticky='ew')
t.configure(xscrollcommand=sb.set)
sb.configure(command=t.xview)
t.focus_set()
btnBox = Pmw.ButtonBox(root)
btnBox.grid(row=2, column=0, columnspan=3)
btnBox.add('Quit', command=root.quit)
btnBox.add('Add', command=lambda b='add': buttonPress(b))
btnBox.add('Del', command=lambda b='del': buttonPress(b))
editBox = Pmw.ScrolledText(root,
labelpos=N,
label_text='Contents',
usehullsize=1,
hull_height=400,
hull_width=300,
text_wrap=None)
editBox.grid(row=0, rowspan=2, column=2, sticky='nsew')
# expand out the root
def setup_ui(self,parent, logger):
logger.debug("setting up ana menu gui")
''' buttons for Gen2 application'''
self.buttonBoxView = Pmw.ButtonBox(parent,
labelpos = 'nw',
label_text = 'Viewers:',
frame_borderwidth = 2,
frame_relief = 'groove')
self.buttonBoxView.pack(fill = 'both', expand = 1, padx = 10, pady = 10)
''' buttons for instruments '''
self.buttonBoxIns = Pmw.ButtonBox(parent,
labelpos = 'nw',
label_text = 'Instrument:',
frame_borderwidth = 2,
frame_relief = 'groove')
self.buttonBoxIns.pack(fill = 'both', expand = 1, padx = 10, pady = 10)
''' buttons for more instrument '''
self.buttonBoxProg = Pmw.ButtonBox(parent,
labelpos = 'nw',
label_text = 'Data-sink | Ana-prog:',
frame_borderwidth = 2,
frame_relief = 'groove')
self.buttonBoxProg.pack(fill = 'both', expand = 1, padx = 10, pady = 10)
''' status of a pressed button '''
self.messageBar = Pmw.MessageBar(parent,
entry_width = 40,
entry_relief='groove',
labelpos = 'nw',
label_text = 'Status:')
self.messageBar.pack(fill = 'x', expand = 1, padx = 10, pady = 10)
''' dialog to display the status of datasink server'''
self.ds_dialog = Pmw.TextDialog(parent, scrolledtext_labelpos = 'n',
title = 'Frame Log',
buttons = ('stop data-sink',),
defaultbutton = None,
command=self.stop_datasink)
#label_text = 'incoming frame status')
self.ds_dialog.withdraw()
''' dialog to get proposal id '''
self.prop_dialog = Pmw.PromptDialog(parent,
title = 'Proposal ID',
label_text = 'Prop ID:',
entryfield_labelpos = 'w',
#entry_show = '*',
defaultbutton = 0,
buttons = ('OK','Cancel'),
command = self.get_propid )
self.prop_dialog.withdraw()
''' create the confirmation dialog '''
self.confirm = Pmw.MessageDialog(title = 'Prop ID Confirmation',
message_text = 'Are you really sure?',
defaultbutton = 0,
buttons = ('OK', 'Cancel'))
self.confirm.withdraw()
''' create the confirmation dialog '''
self.pid_format = Pmw.MessageDialog(title = 'PID Format Error',
message_text = 'Pid Format Error\nFormat is oXXXXX',
defaultbutton = 0,
#icon_bitmap='error',
buttons = ('Close',))
self.pid_format.withdraw()
''' Add some buttons to the ButtonBox.'''
self.buttonBoxView.add('FitsViewer', command = self.launch_viewer)
self.buttonBoxView.add('TelStat', command=self.launch_telstat )
#self.buttonBoxGen2.add('DataSink', command = self.init_datasink )
self.buttonBoxView.add('Ds9', command = self.launch_ds9)
self.buttonBoxView.add('Skycat', command = self.launch_skycat)
#self.buttonBoxGen2.add('ANA Prog',command=self.start_ana_prog )
self.buttonBoxIns.add('HDS', command = self.launch_hds)
self.buttonBoxIns.add('SPCAM', command = self.launch_spcam)
self.buttonBoxIns.add('FOCAS', command = self.launch_focas)
self.buttonBoxIns.add('MOIRCS', command = self.launch_moircs)
self.buttonBoxIns.add('IRCS', command = self.launch_ircs)
self.buttonBoxProg.add('DataSink', command = self.init_datasink )
self.buttonBoxProg.add('ANA Prog',command=self.start_ana_prog )
self.buttonBoxProg.add('Avail 1',command='' )
self.buttonBoxProg.add('Avail 2',command='' )
''' Make all the buttons the same width. '''
self.buttonBoxView.alignbuttons()
self.buttonBoxIns.alignbuttons()
self.buttonBoxProg.alignbuttons()
''' disable buttons '''
self.buttonBoxProg.component('DataSink').configure(state='disabled')
#self.buttonBoxView.component('Avail 1').configure(state='disabled')
self.buttonBoxProg.component('Avail 1').configure(state='disabled')
self.buttonBoxProg.component('Avail 2').configure(state='disabled')
#self. exitButton = Tkinter.Button(parent, text = 'Exit', command = parent.destroy)
self. exitButton = Tkinter.Button(parent, text = 'Exit', command = self.close_window)
self.exitButton.pack(side = 'bottom')
logger.debug("ana menu gui done")
def __init__(self, parent, PFMF_client,
set_func = lambda l,f,i : 0,
enable_func=_empty_func,
disable_func=_empty_func):
Tkinter.Frame.__init__(self,parent)
self.pack_propagate(0)
self.params_width = 290
self.PFMF_client = PFMF_client
self.set_func = set_func
self.enable_func = enable_func
self.disable_func = disable_func
self.state = (None, None, None)
self.jobs = {}
self.search_finished = False
self.qseq = None
self.thread_lock = threading.Lock()
self.current_thread = 0
self.matrix_text = None
self.search_type_widgets = []
self.first_search = None
self.plugin_widgets = []
self.plugins = []
self.default_plugin = None
self.current_plugin = None
# ************************************************************
# ******* Search Options on the left *************************
# ************************************************************
self.wOptions = Tkinter.Frame(self, width=self.params_width)
self.wOptions.pack(side='left', anchor='nw', fill='y')
self.wOptions.pack_propagate(0)
# ***** Search Arguments *************************************
self.wCutoffParams = Pmw.Group(self.wOptions,
tag_text='Cutoff Options')
self.wCutoffParams.pack(anchor='nw', fill='x', padx=5, pady=5)
self.vCutoffParams = Tkinter.IntVar()
parent = self.wCutoffParams.interior()
for i, st in enumerate(self._search_types):
rb = Tkinter.Radiobutton(parent,
text=st[1],
variable=self.vCutoffParams,
value=i)
rb.grid(row=i+1,column=0, sticky='w')
ef = Pmw.EntryField(parent,
entry_width=8,
validate=st[4],
value=st[2])
ef.grid(row=i+1, column=1, sticky='w')
self.search_type_widgets.append((rb,ef))
self.vCutoffParams.set(0)
# ***** Plugin input *****************************************
self.wPluginInput = Pmw.Group(self.wOptions,
tag_text='Matrix Options')
self.wPluginInput.pack(fill='x', padx=5, pady=5)
self.wPluginLabel = Tkinter.Label(self.wPluginInput.interior(),
text='Plugin')
self.wPluginLabel.grid(row=0, column=0, sticky='w',
padx=5, pady=5)
self.wPluginChooser = \
OptionMenu(self.wPluginInput.interior(),
items = [],
menubutton_width = 20,
command = self.set_plugin_widgets)
self.wPluginChooser.grid(row=0, column=1, sticky='w')
# ***** Jobs *************************************************
self.wJobs = Pmw.Group(self.wOptions, tag_text='Jobs')
self.wJobs.pack(fill='x', padx=5, pady=5)
self.wJobs1 = Pmw.RadioSelect(self.wJobs.interior(),
buttontype = 'radiobutton',
labelpos = 'w',
command = self._set_l,
orient='vertical',
pady=0)
for text in ['Current', 'All', 'Remaining']:
self.wJobs1.add(text)
self.wJobs1.grid(row=1,column=0)
self.wJobs2 = Pmw.RadioSelect(self.wJobs.interior(),
buttontype = 'radiobutton',
labelpos = 'w',
orient='vertical',
pady=0)
for text in ['Fragments', 'Lengths']:
self.wJobs2.add(text)
self.wJobs2.grid(row=1, column=1, sticky='sw')
self.wJobs1.invoke('Current')
self.wJobs2.invoke('Lengths')
self.wJobsButtons = Pmw.ButtonBox(self.wJobs.interior())
self.wJobsButtons.grid(row=2, column=0, columnspan=2,
pady=2)
self.wJobsButtons.add('Set', command = self._set_jobs)
self.wJobsButtons.add('Unset', command = self._unset_jobs)
self.wJobsButtons.add('Run', command = self._run_searches)
self.wJobsButtons.alignbuttons()
# ************************************************************
# ******* Sequence and Matrix on the right *******************
# ************************************************************
self.wSeqMat = Tkinter.Frame(self)
self.wSeqMat.pack(side='left', anchor='nw',
fill='both', expand = 1)
# ***** Full sequence viewer *********************************
self.wSeqText = ScrolledSeq(self.wSeqMat,
self.PFMF_client.query_sequence,
self.set_func)
self.wSeqText.pack(anchor='nw', fill='x')
self.wSeqText.tag_config('green yellow', background = 'green yellow')
self.wSeqText.tag_config('green', background = 'green')
self.wSeqText.tag_config('red', background = 'red')
self.wSeqText.tag_config('orange', background = 'orange')
self.wSeqText.tag_config('royal blue',
background = 'royal blue')
# ***** Matrix viewer ****************************************
self.wMatrixText = Pmw.ScrolledText(self.wSeqMat,
usehullsize = 1,
text_wrap='none',
text_font = self.ffont,
text_padx = 4,
text_pady = 4,
text_state = 'disabled',
text_cursor = 'left_ptr',
)
self.wMatrixText.pack(anchor='nw', fill='both', expand = 1)
def Host_Vector(self):
self.hide()
hVFrame = Toplevel()
hVFrame.title("SIR WITH HOST VECTORS")
hVFrame.geometry("700x800")
# self.top.transient(self)
g = Pmw.Blt.Graph(hVFrame)
g.pack(expand=1, fill="both")
E = zeros([3, 1])
A = zeros([3, 3])
C = zeros([3, 1])
A = zeros([3, 3])
B = zeros([2, 2])
E = zeros([3, 1])
C = zeros([3, 1])
# --------------------------------------------------------------------------------------------------------------------------------------------------------
# Textfields
# --------------------------------------------------------------------------------------------------------------------------------------------------------
global sus1, sus2, sus3, contact1, contact2, contact3, time_interval, death_rate1, death_rate2
global death_rate3, recovery1, recovery2, recovery3
sus1 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.0",
label_text="Susceptibles1-S1",
validate={"validator": "real"},
)
sus1.pack(expand=1, padx=5, pady=5)
sus2 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.0",
label_text="Susceptibles2-S2",
validate={"validator": "real"},
)
sus2.pack(expand=1, padx=1, pady=2)
sus3 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.0",
label_text="Susceptibles3-S3 ",
validate={"validator": "real"},
)
sus3.pack(expand=1, padx=1, pady=2)
contact1 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.0",
label_text="Contact Rate 1-k12",
validate={"validator": "real"},
)
contact1.pack(expand=1, padx=1, pady=2)
contact2 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.0",
label_text="Contact Rate 2-k21",
validate={"validator": "real"},
)
contact2.pack(expand=1, padx=1, pady=2)
contact3 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.0",
label_text="Contact Rate 3-k23",
validate={"validator": "real"},
)
contact3.pack(expand=1, padx=1, pady=2)
contact4 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.0",
label_text="Contact Rate 4-k32",
validate={"validator": "real"},
)
contact4.pack(expand=1, padx=1, pady=2)
time_interval = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0",
label_text=" Time Interval-t ",
validate={"validator": "numeric"},
)
time_interval.pack(expand=1, padx=1, pady=2)
death_rate1 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.0",
label_text=" Death Rate 1-d1 ",
validate={"validator": "real"},
)
death_rate1.pack(expand=1, padx=1, pady=2)
death_rate2 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.0",
label_text=" Death Rate 2-d2 ",
validate={"validator": "real"},
)
death_rate2.pack(expand=1, padx=1, pady=2)
death_rate3 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.0",
label_text=" Death Rate 3-d3 ",
validate={"validator": "real"},
)
death_rate3.pack(expand=1, padx=1, pady=2)
recovery1 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.00",
label_text="Recovery Rate 1",
validate={"validator": "real"},
)
recovery1.pack(expand=1, padx=1, pady=2)
recovery2 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.00",
label_text="Recovery Rate 2",
validate={"validator": "real"},
)
recovery2.pack(expand=1, padx=1, pady=2)
recovery3 = Pmw.EntryField(
hVFrame,
labelpos="w",
value="0.00",
label_text="Recovery Rate 3",
validate={"validator": "real"},
)
recovery3.pack(expand=1, padx=1, pady=2)
# ------------------------------------------------------------------------------------------------------------------------------------------------------
# self.top.transient(self)
# self.wButton.config(state='disabled')
def retrive():
k12 = float(contact1.get())
k21 = float(contact2.get())
k23 = float(contact3.get())
k32 = float(contact4.get())
ddelta1 = float(death_rate1.get())
ddelta2 = float(death_rate2.get())
ddelta3 = float(death_rate3.get())
ggamma1 = float(recovery1.get())
ggamma2 = float(recovery2.get())
ggamma3 = float(recovery3.get())
N = int(time_interval.get())
s0 = float(sus1.get())
I0 = float(sus2.get())
R0 = float(sus3.get())
A[0][0] = 0
A[0][1] = k12
A[0][2] = 0
A[1][0] = k21
A[1][1] = 0
A[1][2] = k23
A[2][0] = 0
A[2][1] = k32
A[2][2] = 0
B[0][0] = 0
B[0][1] = 0
B[1][0] = 0
B[1][1] = 0
E[0][0] = -k12 - (ggamma1 + ddelta1)
E[1][0] = -k21 - k23 - (ggamma2 + ddelta2)
E[2][0] = -k32 - (ggamma3 + ddelta3)
C[0][0] = ddelta1 + ggamma1
C[1][0] = ddelta2 + ggamma2
C[2][0] = ddelta3 + ggamma3
def f1(s1, I1, R1):
s_dot = s1 * E[0][0] + A[0][1] * s1 * I1 + C[0][0]
return s_dot
def f2(s1, I1, R1):
I_dot = I1 * E[1][0] + A[1][0] * s1 * I1 + A[1][2] * I1 * R1 + C[1][0]
return I_dot
def f3(s1, I1, R1):
R_dot = E[2][0] * R1 + A[2][1] * I1 * R1 + C[2][0]
return R_dot
# =========RATE OF CHANGE OF THE MODEL WITH RESPECT TO TIME AND DECLARATON OF CONSTANTS==============================================================
t = arange(0, N, 0.02455)
s1 = zeros(len(t))
I1 = zeros(len(t))
R1 = zeros(len(t))
s1[0] = s0
I1[0] = I0
R1[0] = R0
h = 0.01
# ==========ITERATION FOR A GIVEN TIME INTERVAL======================================================================================================
for n in range(len(t) - 1):
s1[n + 1] = s1[n] + h * (f1(s1[n], I1[n], R1[n]))
I1[n + 1] = I1[n] + h * (f2(s1[n], I1[n], R1[n]))
R1[n + 1] = R1[n] + h * (f3(s1[n], I1[n], R1[n]))
x_ = tuple(t)
y_ = tuple(s1)
z_ = tuple(I1)
w_ = tuple(R1)
g.configure(
title="A graph of Susceptible and Infective against time for SIR with Host-Vector"
)
g.line_create(
"S1(t) Vs t", xdata=x_, color="blue", ydata=y_, linewidth=2, symbol=""
)
g.line_create(
"S2(t) Vs t", xdata=x_, color="orange", ydata=z_, linewidth=2, symbol=""
)
g.line_create(
"S3(t) Vs t", xdata=x_, color="red", ydata=w_, linewidth=2, symbol=""
)
def postscript():
g.postscript_output(fileName="HelloUser1.ps", decorations="no")
def newFile():
for name in g.element_names():
g.element_delete(name)
contact1.setentry("")
contact2.setentry("")
contact3.setentry("")
contact4.setentry("")
recovery1.setentry("")
recovery2.setentry("")
recovery3.setentry("")
time_interval.setentry("")
sus1.setentry("")
sus2.setentry("")
sus3.setentry("")
death_rate1.setentry("")
death_rate2.setentry("")
death_rate3.setentry("")
# --------------------------------------------------------------------------------------------------------------------------------------------------------
buttons = Pmw.ButtonBox(hVFrame, labelpos="w", label_text="Options")
buttons = Pmw.ButtonBox(hVFrame, labelpos="w", label_text="Options")
buttons.pack(fill="both", expand=1, padx=10, pady=10)
buttons.add("GRID", bg="green", command=g.grid_toggle)
buttons.add("PLOT", bg="green", command=retrive)
buttons.add("CLEAR", bg="green", command=newFile)
buttons.add("SAVE", bg="green", command=postscript)
handler = lambda: self.onCloseOtherFrameV(hVFrame)
buttons.add("QUIT", bg="red", command=handler)
def __init__(self, master, pso_in):
self.win = Toplevel()
self.pso = pso_in
label = Label(self.win, text="MoveFrequency")
label.grid(row=0)
self.moveFrequency = self.pso.optFunction.get_moveFrequency()
self.e1 = Entry(self.win)
self.e1.insert(END, str(self.moveFrequency))
self.e1.grid(row=0, column=1)
label = Label(self.win, text="MoveDistance")
label.grid(row=1)
self.moveDistance = self.pso.optFunction.get_moveDistance()
self.e2 = Entry(self.win)
self.e2.insert(END, str(self.moveDistance))
self.e2.grid(row=1, column=1)
# self.l1 = Listbox(self.win, selectmode=SINGLE, height=2 )
# for item in OPTMOVESTYLE_SELECTION:
# self.l1.insert(END, item)
# self.l1.select_set(self.optFunction.get_optMoveStyle())
# self.l1.activate(self.optFunction.get_optMoveStyle())
# self.l1.grid(row=2, column=1)
self.menu1 = Pmw.OptionMenu(self.win,
labelpos='w',
label_text='OptimumMoveStyle:',
items=OPTMOVESTYLE_SELECTION,
menubutton_width=15)
self.menu1.setvalue(
OPTMOVESTYLE_SELECTION[self.pso.optFunction.get_optMoveStyle()])
self.menu1.grid(row=2, columnspan=2)
self.menu2 = Pmw.OptionMenu(self.win,
labelpos='w',
label_text='UpdateStyle:',
items=UPDATESTYLE_SELECTION,
menubutton_width=15)
self.menu2.setvalue(
UPDATESTYLE_SELECTION[self.pso.optFunction.get_updateStyle()])
self.menu2.grid(row=3, columnspan=2)
self.menu3 = Pmw.OptionMenu(self.win,
labelpos='w',
label_text='DetectionMethod:',
items=DETECTIONMETHOD_SELECTION,
menubutton_width=15)
self.menu3.setvalue(
DETECTIONMETHOD_SELECTION[self.pso.get_detectionMethod()])
self.menu3.grid(row=4, columnspan=2)
self.menu4 = Pmw.OptionMenu(self.win,
labelpos='w',
label_text='ResponseMethod:',
items=RESPONSEMETHOD_SELECTION,
menubutton_width=15)
self.menu4.setvalue(
RESPONSEMETHOD_SELECTION[self.pso.get_responseMethod()])
self.menu4.grid(row=5, columnspan=2)
# make s row of buttons
buttons = Pmw.ButtonBox(self.win)
buttons.grid(row=6, columnspan=2, padx=10, pady=10)
buttons.add('Apply', command=self.apply)
buttons.add('Cancel', command=self.win.destroy)
import Pmw
root = Tk()
root.option_readfile('optionDB')
root.title('ButtonBox')
Pmw.initialise()
def buttonPress(btn):
print 'The "%s" button was pressed' % btn
def defaultKey(event):
buttonBox.invoke()
buttonBox = Pmw.ButtonBox(root, labelpos='nw', label_text='ButtonBox:')
buttonBox.pack(fill=BOTH, expand=1, padx=10, pady=10)
buttonBox.add('OK', command=lambda b='ok': buttonPress(b))
buttonBox.add('Apply', command=lambda b='apply': buttonPress(b))
buttonBox.add('Cancel', command=lambda b='cancel': buttonPress(b))
# Set the default button (the one executed when <Enter> is hit).
buttonBox.setdefault('OK')
root.bind('<Return>', defaultKey)
root.focus_set()
buttonBox.alignbuttons()
root.mainloop()
def fillInUI(self, parent):
global _mp
_mp = self
self.parent = parent
# model table
self.frequentButtons = []
self.infrequentButtons = []
self._getConfig()
import Pmw
# action buttons
self.buttonScroll = Pmw.ScrolledFrame(self.parent, hscrollmode='none')
self.buttonScroll.grid(row=10, column=20, sticky='nsew')
self.freqActionButtons = Pmw.ButtonBox(self.buttonScroll.interior(),
orient='vertical',
pady=0)
self.freqActionButtons.pack()
self._shownActions = self.freqActionButtons
self.infreqActionButtons = Pmw.ButtonBox(self.buttonScroll.interior(),
orient='vertical',
pady=0)
self._freqToggle = Pmw.OptionMenu(
self.parent,
command=self._freqToggleCB,
items=["frequently used", "infrequently used"],
initialitem="frequently used")
self._freqToggle.grid(row=20, column=20)
self._addColumns()
# add buttons from other extensions...
self._addButtons()
# add standard buttons
addButton("add/edit note...",
noteCmd,
balloon="add notation"
" that will be displayed in model table")
addButton("activate",
lambda m, f='active', v=1, smf=setModelField: smf(
m, f, v, openState=1),
moleculesOnly=False,
defaultFrequent=False,
balloon="make selected models active"
"\n(responsive to mouse motions)")
addButton("activate all",
lambda m, f=activateAllCmd: f(),
minModels=0,
moleculesOnly=False,
balloon="activate all models;\n"
"restore previous active states with this same button")
addButton("activate only",
lambda m, f='active', smfo=setModelFieldOnly: smfo(
m, f, openState=1),
moleculesOnly=False,
balloon="make selected models active"
"\n(responsive to mouse motions);\ndeactivate others")
addButton("attributes...",
attributesCmd,
moleculesOnly=False,
balloon="inspect/modify model attributes")
def runClipping(models):
import ModelClip
cd = chimera.dialogs.display(ModelClip.ClipDialog.name)
cd.setModel(models[0])
addButton("clipping...",
runClipping,
moleculesOnly=False,
balloon="adjust per-model clipping plane")
addButton("close",
openModels.close,
moleculesOnly=False,
balloon="close models")
addButton("deactivate",
lambda m, f='active', v=0, smf=setModelField: smf(
m, f, v, openState=1),
moleculesOnly=False,
defaultFrequent=False,
balloon="make selected models inactive"
"\n(insensitive to mouse motions)")
addButton("focus",
focusCmd,
moleculesOnly=False,
balloon="bring selected models fully into view"
"\nin main graphics window")
addButton("hide",
lambda m, f='display', v=0, smf=setModelField: smf(m, f, v),
moleculesOnly=False,
defaultFrequent=False,
balloon="hide selected models; undo with 'show'")
def showRainbowDialog(models):
from chimera import dialogs
from rainbow import RainbowDialog
if len(models) > 1:
target = "models"
else:
target = "residues"
dialogs.display(RainbowDialog.name).configure(models=models,
target=target)
addButton("rainbow...",
showRainbowDialog,
balloon="rainbow-color residues or chains")
addButton("rename...", renameCmd, moleculesOnly=False, maxModels=1)
addButton("select",
selectCmd,
moleculesOnly=False,
balloon="incorporate models into graphics window"
"\nselection using current selection mode"
"\n(see graphics window Selection menu)")
from chainPicker import ChainPicker
addButton("select chain(s)...",
lambda m, cp=ChainPicker: cp(m).enter(),
balloon="select some/all chains\n"
"(using current selection\n"
"mode from Selection menu)")
addButton("sequence...", seqCmd, balloon="inspect molecule sequence")
addButton("show",
lambda m, f='display', v=1, smf=setModelField: smf(m, f, v),
moleculesOnly=False,
defaultFrequent=False,
balloon="unhide selected models")
addButton("show all atoms",
showAllAtomsCmd,
balloon="show all atoms"
" (but use 'show' to undo 'hide')")
addButton("show only",
lambda m, f='display', smfo=setModelFieldOnly: smfo(m, f),
moleculesOnly=False,
balloon="show selected models and hide all others")
addButton("surface main",
lambda m, c="main", sc=surfCmd: sc(m, c),
balloon="surface non-ligand portion of models")
def showTileDialog(models):
from chimera import dialogs
from EnsembleMatch.choose import TileStructuresCB
dialogs.display(TileStructuresCB.name).configure(models=models)
addButton("tile...",
showTileDialog,
minModels=2,
moleculesOnly=False,
balloon="arrange selected models into a"
"\nrectangular grid and focus on them")
addButton(
"toggle active",
lambda m, f='active', tmf=toggleModelField: tmf(m, f, openState=1),
moleculesOnly=False,
balloon="invert active states of selected models")
addButton("trace backbones",
lambda m, bc=backboneCmd: bc(m, resTrace=0),
balloon="show backbone atom trace for protein"
"\nor nucleic acid; undo with 'show all atoms'")
addButton("trace chains",
backboneCmd,
balloon="show residue connectivity trace for protein"
"\nor nucleic acid; undo with 'show all atoms'")
from transformDialog import TransformDialog
addButton("transform as...",
TransformDialog,
moleculesOnly=False,
balloon="rotate/translate models same as another model")
from writePDBdialog import WritePDBdialog
addButton("write PDB",
lambda mols: chimera.dialogs.display(WritePDBdialog.name).
configure(mols, selOnly=False),
balloon="write molecule as PDB file")
from ksdsspDialog import KsdsspDialog
addButton("compute SS",
KsdsspDialog,
balloon="compute secondary structure elements"
"\nusing Kabsch and Sander algorithm")
maxWidth = 0
for actionButtons in [
self.freqActionButtons, self.infreqActionButtons
]:
for i in range(actionButtons.numbuttons()):
w = actionButtons.button(i).winfo_reqwidth()
if w > maxWidth:
maxWidth = w
self.buttonScroll.component('clipper').configure(width=maxWidth + 2,
height='2i')
# add these last, since if they somehow fire before the
# constructor is complete then an exception will occur
chimera.triggers.addHandler('Model', self._fillTable, None)
chimera.triggers.addHandler('OpenState', self._fillTable, None)
def __init__(self):
self.plugin_type = PLUGIN
root = Toplevel()
root.title('MOLE 2.5')
root.resizable(0, 0)
self.parent = root
# region Create Frame and NoteBook
self.mainframe = Frame(self.parent, width=463, height=623)
self.mainframe.pack(fill='both', expand=1)
self.mainframe.bind(
'<<WrongExecutable>>', lambda e: self.when_error(
e, 'Your MOLE 2.0 executable was not found!'))
root.bind(
'<F5>',
(lambda event: self.set_structures(self.input_structure_box)))
balloon = Pmw.Balloon(self.mainframe)
self.points = {}
# Binary file, Working directory, csa file
self.main_parameters = ['', '', '']
self.notebook = Pmw.NoteBook(self.mainframe)
self.notebook.pack(fill='both', expand=1, padx=10, pady=10)
# endregion
# region self.mainPage / settings
self.mainpage = self.notebook.add('Compute Tunnels')
self.mainpage.focus_set()
input_structure_group = Pmw.Group(self.mainpage,
tag_text='Specify Input Structure')
input_structure_group.pack(fill='both')
starting_point_group = Pmw.Group(self.mainpage,
tag_text='Specify Starting Point')
starting_point_group.pack(fill='both')
if self.plugin_type == "PyMOL":
initialized_structs = ('all', ) + plugin.return_tuple_objects()
else:
initialized_structs = ()
self.input_structure_box = Pmw.ScrolledListBox(
input_structure_group.interior(),
items=initialized_structs,
labelpos='nw',
listbox_height=4,
listbox_selectmode=EXTENDED,
)
self.input_structure_box.component('listbox').configure(
exportselection=0, background='white')
self.input_structure_box.pack(fill='both', expand=0, padx=10, pady=5)
balloon.bind(
self.input_structure_box,
'Select one or more structures in which you want to find channels.'
)
if self.plugin_type == "Chimera":
self.input_structure_box.insert('end', 'all')
if plugin.return_object_list() is not None:
for item in plugin.return_object_list():
self.input_structure_box.insert('end', item)
query = Pmw.Group(input_structure_group.interior(),
tag_text="Not Active Residues")
query.pack(fill='both')
self.query_entry = Entry(query.interior(), width=65)
self.query_entry.config(background='white')
self.query_entry.grid(column=0,
row=0,
padx=10,
pady=5,
sticky=W + E + N + S)
self.query_entry.columnconfigure(0, minsize=65)
self.query_entry.bind(
"<KeyRelease>",
lambda event: root.after(2500, self.validate_query))
self.query_entry.bind('<Control-KeyRelease-a>',
lambda event: self.select_all_query_entry())
self.query_entry.focus_set()
balloon.bind(self.query_entry, 'Input not active residues here')
self.query_label = Label(
query.interior(),
text=
'Select atoms/residues not to be included in the calculation using PatternQuery '
'syntax.',
width=68)
self.query_label.grid(column=0,
row=1,
padx=10,
pady=5,
sticky=W + E + N + S,
columnspan=2)
self.query_help = Label(query.interior(),
text='?',
fg="blue",
cursor="hand2")
self.query_help.grid(column=1, row=0, padx=[0, 10], pady=5)
self.query_help.bind(
"<Button-1>", lambda event: webbrowser.open_new(
"https://webchem.ncbr.muni.cz/Wiki"
"/PatternQuery:UserManual"))
balloon.bind(self.query_help, 'PatternQuery Wiki pages.')
self.is_valid = False
self.start_points_box = Pmw.ScrolledListBox(
starting_point_group.interior(),
items=(),
labelpos='nw',
listbox_height=4,
listbox_selectmode=EXTENDED)
self.start_points_box.component('listbox').configure(
exportselection=0, background='white')
self.start_points_box.pack(fill='both', expand=0, padx=10, pady=5)
balloon.bind(
self.start_points_box,
'Starting point list. If no starting point is specified, \nMOLE plugin will try to find suitable '
'starting points automatically.\nOtherwise all selected points will be used.'
)
self.button_box1 = Pmw.ButtonBox(starting_point_group.interior())
self.button_box1.pack(fill='both', expand=0, padx=10, pady=5)
self.button_box1.add(
'AddStartingPoint',
text='Add Starting Point',
command=lambda: self.add_point(self.start_points_box))
self.button_box1.add(
'RemoveStartingPoint',
text='Remove Starting Point',
command=lambda: self.remove_point(self.start_points_box))
self.button_box1.add(
'RefreshStructures',
text='Refresh Structures',
command=lambda: self.set_structures(self.input_structure_box))
self.button_box1.alignbuttons()
property_group = Pmw.Group(self.mainpage, tag_pyclass=None)
property_group.pack(fill='both')
self.overwrite_results = BooleanVar()
self.overwrite_results.set(True)
self.overwrite_results_button = Checkbutton(
property_group.interior(),
text="Overwrite results",
variable=self.overwrite_results,
onvalue=True,
offvalue=False)
self.overwrite_results_button.grid(column=0,
row=0,
padx=10,
pady=5,
sticky=W + E + N + S)
balloon.bind(
self.overwrite_results_button,
'If checked MOLE will overwrite old files in output folder. Otherwise, new folder will be '
'created in output folder.')
self.remove_hydrogens = BooleanVar()
self.remove_hydrogens_button = Checkbutton(
property_group.interior(),
text="Remove hydrogens",
variable=self.remove_hydrogens,
onvalue=True,
offvalue=False)
self.remove_hydrogens_button.grid(column=1,
row=0,
padx=10,
pady=5,
sticky=W + E + N + S)
balloon.bind(
self.remove_hydrogens_button,
'If checked MOLE will remove all hydrogens from the structure prior to the calculation.'
)
self.ignore_het = BooleanVar()
self.ignore_het_button = Checkbutton(property_group.interior(),
text="Ignore HETeroatoms",
variable=self.ignore_het,
onvalue=True,
offvalue=False)
self.ignore_het_button.grid(column=2,
row=0,
padx=10,
pady=5,
sticky=W + E + N + S)
balloon.bind(
self.ignore_het_button,
'If checked MOLE will exclude all HETATM entries prior to the calculation.'
)
self.select_working_directory_button = Button(
property_group.interior(),
text='Save output to:',
command=self.select_working_directory)
self.select_working_directory_button.grid(row=1,
column=0,
sticky=W + E + N + S,
padx=10,
pady=5)
self.select_working_directory_button.columnconfigure(0, weight=1)
balloon.bind(self.select_working_directory_button,
'Where do you wish to save output from MOLE 2.0 plugin.')
self.working_directory = Pmw.EntryField(property_group.interior(),
labelpos='w')
self.working_directory.component('entry').configure(background='white')
self.working_directory.grid(row=1,
column=1,
columnspan=2,
sticky=W + E + N + S,
padx=10,
pady=5)
balloon.bind(self.working_directory,
'Where do you wish to save output from MOLE 2.0 plugin.')
self.generate_csa_selections_button = Button(
property_group.interior(),
text='Generate CSA sites:',
command=self.CSA_button_click)
self.generate_csa_selections_button.grid(column=0,
row=2,
sticky=W + E + N + S,
padx=10,
pady=5)
balloon.bind(
self.generate_csa_selections_button,
'Specify structure by writing its PDB ID and press Generate button.'
)
self.structure_for_CSA = Pmw.EntryField(property_group.interior(),
labelpos='w')
self.structure_for_CSA.component('entry').configure(background='white')
self.structure_for_CSA.component('entry').bind(
'<Return>', lambda event: self.CSA_button_click())
self.structure_for_CSA.grid(column=1,
row=2,
columnspan=2,
sticky=W + E + N + S,
padx=10,
pady=5)
balloon.bind(
self.structure_for_CSA,
'Specify structure by writing its PDB ID and press Generate button.'
)
self.select_CSA_button = Button(property_group.interior(),
text='Select CSA file:',
command=self.select_CSA)
self.select_CSA_button.grid(column=0,
row=3,
sticky=W + E + N + S,
padx=10,
pady=5)
balloon.bind(
self.select_CSA_button,
'Insert location of CSA.dat file containing CSA database for suggesting active sites as a '
'starting points.')
self.CSA = Pmw.EntryField(property_group.interior(), labelpos='w')
self.CSA.component('entry').configure(background='white')
self.CSA.grid(column=1,
columnspan=2,
row=3,
sticky=W + E + N + S,
padx=10,
pady=5)
balloon.bind(
self.CSA,
'Insert location of CSA.dat file containing CSA database for suggesting active sites as a '
'starting points.')
self.select_executable_button = Button(property_group.interior(),
text='MOLE 2.5 location:',
command=self.select_executable)
self.select_executable_button.grid(column=0,
row=4,
sticky=W + E + N + S,
padx=10,
pady=5)
balloon.bind(
self.select_executable_button,
'Select proper path to the MOLE 2.0 command line location')
self.executable = Pmw.EntryField(property_group.interior(),
labelpos='w')
self.executable.component('entry').configure(background='white')
self.executable.grid(column=1,
columnspan=2,
row=4,
sticky=W + E + N + S,
padx=10,
pady=5)
balloon.bind(
self.executable,
'Select proper path to the MOLE 2.5 command line location.')
self.compute_tunnels_button = Button(
self.mainpage,
text='Compute Tunnels',
font=("Helvetica", 12, "bold"),
command=lambda b='tunnels': Manager.Manager(
).construct_params_and_run(self, b))
self.compute_tunnels_button.pack(side=BOTTOM,
fill='both',
expand=0,
padx=10,
pady=5)
# endregion
# region self.paramsPage / params
self.params_page = self.notebook.add('Settings')
cavity_parameters_group = Pmw.Group(self.params_page,
tag_text='Cavity Parameters')
cavity_parameters_group.pack(fill='both', expand=4)
self.probe_radius = Pmw.Counter(cavity_parameters_group.interior(),
labelpos='w',
label_text='Probe Radius',
entryfield_value='3',
increment=0.1,
entryfield_validate={
'validator': 'real',
'separator': '.',
'min': 1.4,
'max': 45
},
datatype={
'counter': 'real',
'separator': '.'
})
self.probe_radius.component('entry').configure(background='white')
balloon.bind(self.probe_radius,
'Radius used for construction of molecular surface.')
self.interior_threshold = Pmw.Counter(
cavity_parameters_group.interior(),
labelpos='w',
label_text='Interior Threshold',
entryfield_value='1.25',
increment=0.1,
entryfield_validate={
'validator': 'real',
'separator': '.',
'min': 0.8,
'max': 45.0
},
datatype={
'counter': 'real',
'separator': '.'
})
self.interior_threshold.component('entry').configure(
background='white')
balloon.bind(self.interior_threshold,
'Lower bound of the tunnel radius.')
self.surface_cover_radius = Pmw.Counter(
cavity_parameters_group.interior(),
labelpos='w',
label_text='Surface Cover Radius',
entryfield_value='10',
increment=0.1,
entryfield_validate={
'validator': 'real',
'separator': '.',
'min': 5.0,
'max': 25.0
},
datatype={
'counter': 'real',
'separator': '.'
})
self.surface_cover_radius.component('entry').configure(
background='white')
balloon.bind(
self.surface_cover_radius,
'Determines the density of tunnel exits on the molecular surface.')
self.origin_radius = Pmw.Counter(cavity_parameters_group.interior(),
labelpos='w',
label_text='Origin Radius',
entryfield_value='5',
increment=0.1,
entryfield_validate={
'validator': 'real',
'separator': '.',
'min': 0.1,
'max': 10.0
},
datatype={
'counter': 'real',
'separator': '.'
})
self.origin_radius.component('entry').configure(background='white')
balloon.bind(
self.origin_radius,
'Better starting points are localized within the defined radius from the original starting point.'
)
filter_settings = Pmw.Group(self.params_page,
tag_text='Tunnel Parameters')
filter_settings.pack(fill='both', expand=4)
self.bottleneck_radius = Pmw.Counter(filter_settings.interior(),
labelpos='w',
label_text='Bottleneck Radius',
entryfield_value='1.25',
increment=0.1,
entryfield_validate={
'validator': 'real',
'separator': '.',
'min': 0.1,
'max': 6.0
},
datatype={
'counter': 'real',
'separator': '.'
})
self.bottleneck_radius.component('entry').configure(background='white')
balloon.bind(self.bottleneck_radius, 'The minimum radius of a tunnel.')
self.bottleneck_length = Pmw.Counter(filter_settings.interior(),
labelpos='w',
label_text='Bottleneck Length',
entryfield_value='3',
increment=0.1,
entryfield_validate={
'validator': 'real',
'separator': '.',
'min': 0.0,
'max': 20.0
},
datatype={
'counter': 'real',
'separator': '.'
})
self.bottleneck_length.component('entry').configure(background='white')
balloon.bind(
self.bottleneck_length,
'Length of a possible profile narrower than the Bottleneck Radius')
self.cutoff_ratio = Pmw.Counter(filter_settings.interior(),
labelpos='w',
label_text='Cutoff Ratio',
entryfield_value='0.7',
increment=0.05,
entryfield_validate={
'validator': 'real',
'separator': '.',
'min': 0.0,
'max': 1.0
},
datatype={
'counter': 'real',
'separator': '.'
})
self.cutoff_ratio.component('entry').configure(background='white')
balloon.bind(
self.cutoff_ratio,
'Determines maximum similarity of tunnels centerline. \nIf two tunnels are more similar than the '
'threshold, the longer is discarded.')
# region load executable location from settingsfile
temp_path = os.path.normcase(
str(os.environ['TEMP']) if 'win32' ==
str.lower(sys.platform) else '/tmp/')
if os.path.exists(CONFIGFILE):
try:
with open(CONFIGFILE, 'r') as f:
self.main_parameters = list(
map(lambda x: os.path.normcase(x), pickle.load(f)))
self.executable.setvalue(self.main_parameters[0])
self.working_directory.setvalue(self.main_parameters[1])
self.CSA.setvalue(self.main_parameters[2])
except:
self.executable.setvalue('')
self.working_directory.setvalue(temp_path)
self.CSA.setvalue('')
else:
self.working_directory.setvalue(temp_path)
self.main_parameters[1] = temp_path
with open(CONFIGFILE, 'w') as f:
pickle.dump(self.main_parameters, f)
# endregion
self.params = (self.probe_radius, self.interior_threshold,
self.surface_cover_radius, self.origin_radius,
self.bottleneck_radius, self.bottleneck_length,
self.cutoff_ratio)
Pmw.alignlabels(self.params)
for counter in self.params:
counter.pack(fill='both', expand=1, padx=10, pady=5)
weight_function_group = Pmw.Group(self.params_page,
tag_text='Weight Function')
weight_function_group.pack(fill='both', expand=0)
self.weight_function = StringVar()
self.voronoi_button = Radiobutton(weight_function_group.interior(),
text='Voronoi Scale',
variable=self.weight_function,
value="VoronoiScale")
self.voronoi_button.grid(column=0,
row=0,
padx=30,
pady=5,
sticky=W + E + N + S)
balloon.bind(
self.voronoi_button,
'Recommended for identification of tunnels leading to the buried active sites'
)
self.length_radius_button = Radiobutton(
weight_function_group.interior(),
text='Length + Radius',
variable=self.weight_function,
value="LengthAndRadius")
self.length_radius_button.grid(column=1,
row=0,
padx=30,
pady=5,
sticky=W + E + N + S)
balloon.bind(self.length_radius_button,
'Old and universal MOLE 2.0 weight function')
self.length_button = Radiobutton(weight_function_group.interior(),
text='Length',
variable=self.weight_function,
value="Length")
self.length_button.grid(column=2,
row=0,
padx=30,
pady=5,
sticky=W + E + N + S)
balloon.bind(self.length_button,
'Recommended for identification of transmembrane pores')
self.voronoi_button.invoke()
# endregion
# region self.pathPage / settings
self.path_page = self.notebook.add('Compute Pores')
input_structure_group = Pmw.Group(
self.path_page, tag_text='Specify pores starting points')
input_structure_group.pack(fill='both')
self.path_starting_points_box = Pmw.ScrolledListBox(
input_structure_group.interior(),
items=(),
labelpos='nw',
label_text='Starting Points',
listbox_height=4,
listbox_selectmode=EXTENDED)
self.path_starting_points_box.component('listbox').configure(
exportselection=0, background='white')
self.path_starting_points_box.pack(fill='both',
expand=0,
padx=10,
pady=5)
self.path_starting_points_box.bind(
'<Delete>',
lambda event: self.remove_point(self.path_starting_points_box))
balloon.bind(
self.path_starting_points_box,
'Starting point list. Every starting point must have coresponding end point.'
)
self.button_box2 = Pmw.ButtonBox(input_structure_group.interior())
self.button_box2.pack(fill='both', expand=0, padx=10, pady=5)
self.button_box2.add(
'AddStartingPoint',
text='Add Starting Points',
command=lambda: self.add_point(self.path_starting_points_box))
self.button_box2.add(
'RemoveStartingPoint',
text='Remove Starting Points',
command=lambda: self.remove_point(self.path_starting_points_box))
self.button_box2.alignbuttons()
input_structure_group = Pmw.Group(self.path_page,
tag_text='Specify pores end points')
input_structure_group.pack(fill='both')
self.path_end_points_box = Pmw.ScrolledListBox(
input_structure_group.interior(),
items=(),
labelpos='nw',
label_text='End Points',
listbox_height=4,
listbox_selectmode=EXTENDED)
self.path_end_points_box.component('listbox').configure(
exportselection=0, background='white')
self.path_end_points_box.bind(
'<Delete>',
lambda event: self.remove_point(self.path_end_points_box))
self.path_end_points_box.pack(fill='both', expand=0, padx=10, pady=5)
balloon.bind(
self.path_end_points_box,
'End points list. Every end point must have coresponding starting point.'
)
self.button_box3 = Pmw.ButtonBox(input_structure_group.interior())
self.button_box3.pack(fill='both', expand=0, padx=10, pady=5)
self.button_box3.add(
'AddEndPoint',
text='Add End Points',
command=lambda: self.add_point(self.path_end_points_box))
self.button_box3.add(
'RemoveEndPoint',
text='Remove end points',
command=lambda: self.remove_point(self.path_end_points_box))
self.button_box3.alignbuttons()
self.compute_pores_button = Button(
self.path_page,
text='Compute Pores',
font=("Helvetica", 12, "bold"),
command=lambda b='pores': Manager.Manager(
).construct_params_and_run(self, b))
self.compute_pores_button.pack(fill='both', expand=0, padx=10, pady=5)
# endregion
# prev set
# region READ
self.read_page = self.notebook.add('Read Channels')
read_group = Pmw.Group(
self.read_page,
tag_text='Select a file with previously computed MOLE tunnels/pores'
)
read_group.pack(fill='both')
self.open_channels_button = Button(read_group.interior(),
text='Open computation results',
command=self.open_channels,
font=("Helvetica", 12, "bold"))
self.open_channels_button.pack(fill='both', expand=0, padx=10, pady=5)
# endregion
# region QuickStartGuide
self.guide_page = self.notebook.add('Quick Guide')
guide = Text(self.guide_page, width=72, wrap=WORD)
guide.config(padx=5, pady=8)
guide.tag_configure('big', font=('Arial', 12, 'bold'))
guide.tag_configure('plain_text', font=('Arial', 10))
guide.tag_configure('smaller', font=('Arial', 9))
guide.insert(END, 'Plugin description:\n\n', 'big')
plugin_description = (
"The plugin is separated into several tabs The crucial for the calculation are: "
"Compute Tunnels, Settings, and Compute Pores. At first, specify location of output "
"folder and MOLE 2.5 command line executable. Afterwards, select a structure in the "
"'input structure listbox' and starting point from the 'starting point listbox'. "
"Additionally, if you provide a path to the CSA database [1], the plugin will suggest "
"you the potential starting points.\n\n")
guide.insert(END, plugin_description, 'plain_text')
guide.insert(END, "Run:\n\n", 'big')
run_description = (
"After selecting one or more structures and one or more starting points by clicking 'Add Starting Point'. Additional "
"search parameters can be adjusted in the Settings tabs. For further info on how to use this "
"please refer the included manual or visit our webpages. Whenever you would feel lost just "
"hover your cursor above any element in order to get tooltip. For more info and news about the "
"MOLE 2.5 visit our webpages.\n")
guide.insert(END, run_description, 'plain_text')
improve_text = (
"\n"
"Also if you would like to make a suggestion on how to "
"improve MOLE or send a bug report, please contact authors at [email protected] "
"or the author of this extension directly - [email protected]\n\n"
)
guide.insert(END, improve_text, 'plain_text')
guide.insert(END, "Happy tunneling! ", 'big')
team_text = (
"Mole development team. http://mole.chemi.muni.cz\n\n"
"[1] Furnham,N., Holliday,G.L., De Beer,T.A.P., Jacobsen,J.O.B., Pearson,W.R. and Thornton,J.M. (2014) "
"The Catalytic Site Atlas 2.0: Cataloging catalytic sites and residues identified in enzymes. Nucleic "
"Acids Res., 42, 1–5.")
guide.insert(END, team_text, 'smaller')
guide.config(state=DISABLED)
guide.pack(side=LEFT, fill='both')
# endregion
# region AuthorsPage
self.authors_page = self.notebook.add('Authors')
authors_text_widget = Text(self.authors_page, width=72, height=17)
authors_text_widget.config(padx=5, bg='#52A300', pady=8)
authors_text_widget.tag_configure('plain_text',
font=('Arial', 10),
foreground='white')
authors_text_widget.insert(
END,
"If you find this tool useful for your work please cite it as:\n\n",
'plain_text')
cite_text = (
"Sehnal D, Svobodova Varekova R, Berka K, Pravda L, Navratilova V,\nBanas P, Ionescu C-M, Otyepka M, "
"Koca J. MOLE2.0: advanced approach for analysis of biomacromolecular channels. Journal of "
"Cheminformatics 2013, 5:39., doi:10.1186/1758-2946-5-39.\n\n"
"If you were using the web server, which is available at http://mole.upol.cz/ please cite it as:\n\n"
"Berka K, Hanak O, Sehnal D, Banas P, Navratilova V, Jaiswal D,Ionescu C-M, Svobodova Varekova R, "
"Koca J, Otyepka M.\nMOLEonline 2.0: interactive web-based analysis of biomacromolecular\nchannels. Nucleic "
"acids research 2012, 40:W222?7., doi:10.1093/nar/gks363")
authors_text_widget.insert(END, cite_text, 'plain_text')
authors_text_widget.config(state=DISABLED)
authors_text_widget.pack(side=LEFT, fill='both')
# endregion
Label(
self.mainframe,
relief='sunken',
anchor=W,
justify=LEFT,
bg='#52A300',
fg='white',
font=("Helvetica", 12),
padx=10,
pady=10,
text=
"(c) 2017 CEITEC & NCBR MU & FCH UPOL\nhttp://mole.chemi.muni.cz v. "
"2.5.17.7.11").pack(fill='both')
self.notebook.setnaturalsize()
self.wd = os.path.realpath(os.path.normcase(self.main_parameters[1]))
self.xml_wd = os.path.realpath(
os.path.normcase(self.main_parameters[1] + "/xml/"))
self.profile_wd = os.path.realpath(
os.path.normcase(self.main_parameters[1] + "/pymol/"))
os.system('xset r off') # for keypress
self.original_view = None
def __init__(self, app):
parent = app.root
self.parent = parent
self.target_data = [None, 0, 0, 0, 30, 30, 30]
self.offtarget_data = [None, 0, 0, 0, 30, 30, 30]
self.build = False
self.read_data()
self.saved = True
# box display settings
self.target_box_is_on_display = True
self.offtarget_box_is_on_display = True
self.box_display_cylinder_size = 0.2
self.target_grid_center_selection_mode = IntVar()
self.offtarget_grid_center_selection_mode = IntVar()
# grid definition
self.grid_spacing = 1.0
self.target_grid_center = [DoubleVar(), DoubleVar(), DoubleVar()]
self.target_grid_center[0].set(self.target_data[1])
self.target_grid_center[1].set(self.target_data[2])
self.target_grid_center[2].set(self.target_data[3])
self.target_grid_size = [IntVar(), IntVar(), IntVar()]
self.target_grid_size[0].set(self.target_data[4])
self.target_grid_size[1].set(self.target_data[5])
self.target_grid_size[2].set(self.target_data[6])
self.offtarget_grid_center = [DoubleVar(), DoubleVar(), DoubleVar()]
self.offtarget_grid_center[0].set(self.offtarget_data[1])
self.offtarget_grid_center[1].set(self.offtarget_data[2])
self.offtarget_grid_center[2].set(self.offtarget_data[3])
self.offtarget_grid_size = [IntVar(), IntVar(), IntVar()]
self.offtarget_grid_size[0].set(self.offtarget_data[4])
self.offtarget_grid_size[1].set(self.offtarget_data[5])
self.offtarget_grid_size[2].set(self.offtarget_data[6])
self.target_grid_center_selection_mode.set(
GRID_CENTER_FROM_COORDINATES)
self.offtarget_grid_center_selection_mode.set(
GRID_CENTER_FROM_COORDINATES_B)
# build main window
self.main_window = Pmw.Dialog(parent,
buttons=('Save Box Info', ),
title='PyMOL AMDock Plugin',
command=self.check_for_exit)
self.main_window.withdraw()
Pmw.setbusycursorattributes(self.main_window.component('hull'))
self.status_bar = Label(self.main_window.interior(),
relief='sunken',
font='times 10',
anchor='w',
fg='green',
bg='black')
self.status_bar.pack(side=BOTTOM, fill='x', expand=1, padx=0, pady=0)
if self.target_data[0] and self.offtarget_data[0]:
self.main_window.geometry('550x640')
else:
self.main_window.geometry('550x400')
# self.main_window.bind('<Return>', self.button_pressed)
# the title
self.title_label = tkinter.Label(
self.main_window.interior(),
text=
'PyMOL AMDock Plugin\n [ Assisted Molecular Docking For AutoDock4 and '
'Autodock Vina ]\nFeel free to write us for any suggestions or errors '
'you find\nhttps://groups.google.com/forum/#!forum/amdock\nThis '
'plugin is based in Daniel Seeliger plugin.',
background='navy',
foreground='white',
font='times 12')
self.title_label.pack(expand=0, fill='both', padx=4, pady=4)
# Target group
self.target_group = Pmw.Group(self.main_window.interior(),
tag_text='Target')
self.target_group.pack(fill='both', expand=0, padx=10, pady=5)
if not self.target_data[0]:
self.target_group.collapse()
# Off-Target group
self.offtarget_group = Pmw.Group(self.main_window.interior(),
tag_text='Off-Target')
self.offtarget_group.pack(fill='both', expand=0, padx=10, pady=5)
if not self.offtarget_data[0]:
self.offtarget_group.collapse()
# Target GRID DEFINITION
self.target_grid_group = Pmw.Group(self.target_group.interior(),
tag_text='Grid Dimensions')
self.target_grid_group.pack(fill='both', expand=0, padx=10, pady=5)
# Off-Target GRID DEFINITION
self.offtarget_grid_group = Pmw.Group(self.offtarget_group.interior(),
tag_text='Grid Dimensions')
self.offtarget_grid_group.pack(fill='both', expand=0, padx=10, pady=5)
# n grid points entries target
self.target_size_x_frame = tkinter.Frame(
self.target_grid_group.interior())
self.target_size_x_label = Label(self.target_size_x_frame, text='X:')
self.target_size_x_location = Entry(
self.target_size_x_frame,
textvariable=self.target_grid_size[0],
bg='black',
fg='yellow',
width=7)
self.target_size_x_scrollbar = Scrollbar(
self.target_size_x_frame,
orient='horizontal',
command=self.target_size_x_changed)
self.target_size_x_scrollbar.set('0.5', '0.51')
self.target_size_y_frame = tkinter.Frame(
self.target_grid_group.interior())
self.target_size_y_label = Label(self.target_size_y_frame, text='Y:')
self.target_size_y_location = Entry(
self.target_size_y_frame,
textvariable=self.target_grid_size[1],
bg='black',
fg='yellow',
width=7)
self.target_size_y_scrollbar = Scrollbar(
self.target_size_y_frame,
orient='horizontal',
command=self.target_size_y_changed)
self.target_size_y_scrollbar.set('0.5', '0.51')
self.target_size_z_frame = tkinter.Frame(
self.target_grid_group.interior())
self.target_size_z_label = Label(self.target_size_z_frame, text='Z:')
self.target_size_z_location = Entry(
self.target_size_z_frame,
textvariable=self.target_grid_size[2],
bg='black',
fg='yellow',
width=7)
self.target_size_z_scrollbar = Scrollbar(
self.target_size_z_frame,
orient='horizontal',
command=self.target_size_z_changed)
self.target_size_z_scrollbar.set('0.5', '0.51')
self.target_size_x_label.pack(side=LEFT)
self.target_size_x_location.pack(side=LEFT)
self.target_size_x_scrollbar.pack(side=LEFT)
self.target_size_x_frame.pack(side=LEFT, padx=4, pady=1)
self.target_size_y_label.pack(side=LEFT)
self.target_size_y_location.pack(side=LEFT)
self.target_size_y_scrollbar.pack(side=LEFT)
self.target_size_y_frame.pack(side=LEFT, padx=4, pady=1)
self.target_size_z_label.pack(side=LEFT)
self.target_size_z_location.pack(side=LEFT)
self.target_size_z_scrollbar.pack(side=LEFT)
self.target_size_z_frame.pack(side=LEFT, padx=4, pady=1)
Pmw.alignlabels([
self.target_size_x_label, self.target_size_y_label,
self.target_size_z_label
])
Pmw.alignlabels([
self.target_size_x_location, self.target_size_y_location,
self.target_size_z_location
])
# n grid points entries off-target
self.offtarget_size_x_frame = tkinter.Frame(
self.offtarget_grid_group.interior())
self.offtarget_size_x_label = Label(self.offtarget_size_x_frame,
text='X:')
self.offtarget_size_x_location = Entry(
self.offtarget_size_x_frame,
textvariable=self.offtarget_grid_size[0],
bg='black',
fg='yellow',
width=7)
self.offtarget_size_x_scrollbar = Scrollbar(
self.offtarget_size_x_frame,
orient='horizontal',
command=self.offtarget_size_x_changed)
self.offtarget_size_x_scrollbar.set('0.5', '0.51')
self.offtarget_size_y_frame = tkinter.Frame(
self.offtarget_grid_group.interior())
self.offtarget_size_y_label = Label(self.offtarget_size_y_frame,
text='Y:')
self.offtarget_size_y_location = Entry(
self.offtarget_size_y_frame,
textvariable=self.offtarget_grid_size[1],
bg='black',
fg='yellow',
width=7)
self.offtarget_size_y_scrollbar = Scrollbar(
self.offtarget_size_y_frame,
orient='horizontal',
command=self.offtarget_size_y_changed)
self.offtarget_size_y_scrollbar.set('0.5', '0.51')
self.offtarget_size_z_frame = tkinter.Frame(
self.offtarget_grid_group.interior())
self.offtarget_size_z_label = Label(self.offtarget_size_z_frame,
text='Z:')
self.offtarget_size_z_location = Entry(
self.offtarget_size_z_frame,
textvariable=self.offtarget_grid_size[2],
bg='black',
fg='yellow',
width=7)
self.offtarget_size_z_scrollbar = Scrollbar(
self.offtarget_size_z_frame,
orient='horizontal',
command=self.offtarget_size_z_changed)
self.offtarget_size_z_scrollbar.set('0.5', '0.51')
self.offtarget_size_x_label.pack(side=LEFT)
self.offtarget_size_x_location.pack(side=LEFT)
self.offtarget_size_x_scrollbar.pack(side=LEFT)
self.offtarget_size_x_frame.pack(side=LEFT, padx=4, pady=1)
self.offtarget_size_y_label.pack(side=LEFT)
self.offtarget_size_y_location.pack(side=LEFT)
self.offtarget_size_y_scrollbar.pack(side=LEFT)
self.offtarget_size_y_frame.pack(side=LEFT, padx=4, pady=1)
self.offtarget_size_z_label.pack(side=LEFT)
self.offtarget_size_z_location.pack(side=LEFT)
self.offtarget_size_z_scrollbar.pack(side=LEFT)
self.offtarget_size_z_frame.pack(side=LEFT, padx=4, pady=1)
Pmw.alignlabels([
self.offtarget_size_x_label, self.offtarget_size_y_label,
self.offtarget_size_z_label
])
Pmw.alignlabels([
self.offtarget_size_x_location, self.offtarget_size_y_location,
self.offtarget_size_z_location
])
# target display option buttons
self.target_display_button_box = Pmw.ButtonBox(
self.target_group.interior(), padx=1, pady=1, orient='horizontal')
self.target_display_button_box.add('Show Box',
command=self.show_target_box)
self.target_display_button_box.add('Hide Box',
command=self.hide_target_box)
self.target_display_button_box.add('Reset', command=self.reset_target)
self.target_display_button_box.pack(side=TOP, expand=1, padx=3, pady=3)
# off-target display option buttons
self.offtarget_display_button_box = Pmw.ButtonBox(
self.offtarget_group.interior(),
padx=1,
pady=1,
orient='horizontal')
self.offtarget_display_button_box.add('Show Box',
command=self.show_offtarget_box)
self.offtarget_display_button_box.add('Hide Box',
command=self.hide_offtarget_box)
self.offtarget_display_button_box.add('Reset',
command=self.reset_offtarget)
self.offtarget_display_button_box.pack(side=TOP,
expand=1,
padx=3,
pady=3)
self.target_grid_center_radiogroups = []
self.offtarget_grid_center_radiogroups = []
self.target_grid_center_radioframe = tkinter.Frame(
self.target_group.interior())
self.target_grid_center_pymol_selection = Pmw.Group(
self.target_grid_center_radioframe,
tag_pyclass=tkinter.Radiobutton,
tag_text='Calculate Grid Center by Selection',
tag_value=GRID_CENTER_FROM_SELECTION,
tag_variable=self.target_grid_center_selection_mode)
self.target_grid_center_pymol_selection.pack(fill='x',
expand=1,
side=TOP)
self.target_grid_center_radiogroups.append(
self.target_grid_center_pymol_selection)
self.target_grid_center_selection_user = Pmw.EntryField(
self.target_grid_center_pymol_selection.interior(),
labelpos='w',
label_text='Selection',
value='(all)',
command=self.target_grid_center_from_selection_changed)
self.target_grid_center_selection_user.pack(fill='x',
padx=4,
pady=1,
expand=0)
self.target_grid_center_coordinates = Pmw.Group(
self.target_grid_center_radioframe,
tag_pyclass=tkinter.Radiobutton,
tag_text='Grid Center Coordinates',
tag_value=GRID_CENTER_FROM_COORDINATES,
tag_variable=self.target_grid_center_selection_mode)
self.target_grid_center_coordinates.pack(fill='x', expand=1, side=TOP)
self.target_grid_center_radiogroups.append(
self.target_grid_center_coordinates)
self.target_grid_center_radioframe.pack(padx=6,
pady=6,
expand='yes',
fill='both')
Pmw.aligngrouptags(self.target_grid_center_radiogroups)
self.offtarget_grid_center_radioframe = tkinter.Frame(
self.offtarget_group.interior())
self.offtarget_grid_center_pymol_selection = Pmw.Group(
self.offtarget_grid_center_radioframe,
tag_pyclass=tkinter.Radiobutton,
tag_text='Calculate Grid Center by Selection',
tag_value=GRID_CENTER_FROM_SELECTION_B,
tag_variable=self.offtarget_grid_center_selection_mode)
self.offtarget_grid_center_pymol_selection.pack(fill='x',
expand=1,
side=TOP)
self.offtarget_grid_center_radiogroups.append(
self.offtarget_grid_center_pymol_selection)
self.offtarget_grid_center_selection_user = Pmw.EntryField(
self.offtarget_grid_center_pymol_selection.interior(),
labelpos='w',
label_text='Selection',
value='(all)',
command=self.offtarget_grid_center_from_selection_changed)
self.offtarget_grid_center_selection_user.pack(fill='x',
padx=4,
pady=1,
expand=0)
self.offtarget_grid_center_coordinates = Pmw.Group(
self.offtarget_grid_center_radioframe,
tag_pyclass=tkinter.Radiobutton,
tag_text='Grid Center Coordinates',
tag_value=GRID_CENTER_FROM_COORDINATES_B,
tag_variable=self.offtarget_grid_center_selection_mode)
self.offtarget_grid_center_coordinates.pack(fill='x',
expand=1,
side=TOP)
self.offtarget_grid_center_radiogroups.append(
self.offtarget_grid_center_coordinates)
self.offtarget_grid_center_radioframe.pack(padx=6,
pady=6,
expand='yes',
fill='both')
Pmw.aligngrouptags(self.offtarget_grid_center_radiogroups)
self.target_center_x_frame = tkinter.Frame(
self.target_grid_center_coordinates.interior())
self.target_center_x_label = Label(self.target_center_x_frame,
text='X:')
self.target_center_x_location = Entry(
self.target_center_x_frame,
textvariable=self.target_grid_center[0],
bg='black',
fg='yellow',
width=10)
self.target_center_x_scrollbar = Scrollbar(
self.target_center_x_frame,
orient='horizontal',
command=self.target_center_x_changed)
self.target_center_x_scrollbar.set('0.5', '0.51')
self.target_center_y_frame = tkinter.Frame(
self.target_grid_center_coordinates.interior())
self.target_center_y_label = Label(self.target_center_y_frame,
text='Y:')
self.target_center_y_location = Entry(
self.target_center_y_frame,
textvariable=self.target_grid_center[1],
bg='black',
fg='yellow',
width=10)
self.target_center_y_scrollbar = Scrollbar(
self.target_center_y_frame,
orient='horizontal',
command=self.target_center_y_changed)
self.target_center_y_scrollbar.set('0.5', '0.51')
self.target_center_z_frame = tkinter.Frame(
self.target_grid_center_coordinates.interior())
self.target_center_z_label = Label(self.target_center_z_frame,
text='Z:')
self.target_center_z_location = Entry(
self.target_center_z_frame,
textvariable=self.target_grid_center[2],
bg='black',
fg='yellow',
width=10)
self.target_center_z_scrollbar = Scrollbar(
self.target_center_z_frame,
orient='horizontal',
command=self.target_center_z_changed)
self.target_center_z_scrollbar.set('0.5', '0.51')
self.target_center_x_label.pack(side=LEFT)
self.target_center_x_location.pack(side=LEFT)
self.target_center_x_scrollbar.pack(side=LEFT)
self.target_center_x_frame.pack(side=LEFT, padx=4, pady=1)
self.target_center_y_label.pack(side=LEFT)
self.target_center_y_location.pack(side=LEFT)
self.target_center_y_scrollbar.pack(side=LEFT)
self.target_center_y_frame.pack(side=LEFT, padx=4, pady=1)
self.target_center_z_label.pack(side=LEFT)
self.target_center_z_location.pack(side=LEFT)
self.target_center_z_scrollbar.pack(side=LEFT)
self.target_center_z_frame.pack(side=LEFT, padx=4, pady=1)
self.offtarget_center_x_frame = tkinter.Frame(
self.offtarget_grid_center_coordinates.interior())
self.offtarget_center_x_label = Label(self.offtarget_center_x_frame,
text='X:')
self.offtarget_center_x_location = Entry(
self.offtarget_center_x_frame,
textvariable=self.offtarget_grid_center[0],
bg='black',
fg='yellow',
width=10)
self.offtarget_center_x_scrollbar = Scrollbar(
self.offtarget_center_x_frame,
orient='horizontal',
command=self.offtarget_center_x_changed)
self.offtarget_center_x_scrollbar.set('0.5', '0.51')
self.offtarget_center_y_frame = tkinter.Frame(
self.offtarget_grid_center_coordinates.interior())
self.offtarget_center_y_label = Label(self.offtarget_center_y_frame,
text='Y:')
self.offtarget_center_y_location = Entry(
self.offtarget_center_y_frame,
textvariable=self.offtarget_grid_center[1],
bg='black',
fg='yellow',
width=10)
self.offtarget_center_y_scrollbar = Scrollbar(
self.offtarget_center_y_frame,
orient='horizontal',
command=self.offtarget_center_y_changed)
self.offtarget_center_y_scrollbar.set('0.5', '0.51')
self.offtarget_center_z_frame = tkinter.Frame(
self.offtarget_grid_center_coordinates.interior())
self.offtarget_center_z_label = Label(self.offtarget_center_z_frame,
text='Z:')
self.offtarget_center_z_location = Entry(
self.offtarget_center_z_frame,
textvariable=self.offtarget_grid_center[2],
bg='black',
fg='yellow',
width=10)
self.offtarget_center_z_scrollbar = Scrollbar(
self.offtarget_center_z_frame,
orient='horizontal',
command=self.offtarget_center_z_changed)
self.offtarget_center_z_scrollbar.set('0.5', '0.51')
self.offtarget_center_x_label.pack(side=LEFT)
self.offtarget_center_x_location.pack(side=LEFT)
self.offtarget_center_x_scrollbar.pack(side=LEFT)
self.offtarget_center_x_frame.pack(side=LEFT, padx=4, pady=1)
self.offtarget_center_y_label.pack(side=LEFT)
self.offtarget_center_y_location.pack(side=LEFT)
self.offtarget_center_y_scrollbar.pack(side=LEFT)
self.offtarget_center_y_frame.pack(side=LEFT, padx=4, pady=1)
self.offtarget_center_z_label.pack(side=LEFT)
self.offtarget_center_z_location.pack(side=LEFT)
self.offtarget_center_z_scrollbar.pack(side=LEFT)
self.offtarget_center_z_frame.pack(side=LEFT, padx=4, pady=1)
self.show_target_box()
self.main_window.show()
self.status_bar.configure(text="Version: %s" % __version__)
def display_arrays(self):
ma = self.main
self.balloon = Pmw.Balloon(ma)
self.menuBar = Pmw.MenuBar(ma, hull_borderwidth=1,
hull_relief = 'raised',
hotkeys=1, balloon = self.balloon)
self.menuBar.pack(fill='x')
self.menuBar.addmenu('File', 'Read, Cancel, Exit')
self.menuBar.addmenuitem('File', 'command',
'Read this file with these arrays',
label='Read',
command= Command(self.btn_press, 'apply'))
self.menuBar.addmenuitem('File', 'command',
'Do not read this file, Look for a new file',
label='Change File',
command= Command(self.btn_press, 'newfile'))
self.menuBar.addmenuitem('File', 'command',
'Close without reading these arrays from this file',
label='Cancel',
command= Command(self.btn_press, 'cancel'))
self.menuBar.addmenuitem('File', 'command',
'Read this file with these arrays, and exit',
label='OK',
command= Command(self.btn_press, 'ok'))
# file buffer display
self.f_win = Pmw.ScrolledText(ma,label_text=self.input_file,
borderframe = 1,usehullsize=0,
text_padx = 10, text_pady = 10,
labelpos=NW,
hull_width=650, hull_height=320)
self.f_win.importfile(self.input_file)
self.f_win.pack(side='top')
# group name
fr_0 = Frame(ma)
fr_0.pack(side='top',anchor='w')
fr_1 = Frame(fr_0)
fr_1.pack(side='left', fill='x',anchor='w')
fr1 = Frame(fr_1)
Label(fr1, text='Group: ').pack(side='left')
self.g_ent = Entry(fr1,width=20)
self.g_ent.selection_clear()
self.g_ent.insert(0,self.group)
self.g_ent.pack(side='left',fill='x')
fr1.pack(side='left',fill='x')
fr_4 = Frame(fr_0)
fr_4.pack(side='left', fill='x',anchor='w')
self.file_type.set('<from column labels>')
self.ftypes = Pmw.OptionMenu(fr_4, labelpos = 'w',
label_text = ' Column File Types: ',
menubutton_textvariable = self.file_type,
menubutton_width = 22,
items = ['<from column labels>',
'xmu','chi','rsp', 'chi.dat', 'feff.dat'],
initialitem = '<from column labels>',
command = Command(self.ftype_choice),
)
# menubutton_width = 18)
self.ftypes.pack(side='left',fill='x')
# arrays name
fr_2 = Frame(ma)
fr_2.pack(side='top',anchor='w')
fr2 = Frame(fr_2)
Label(fr2, text='Arrays: ').pack(side='left')
for i in range(self.array_disp):
self.entr[i] = Entry(fr2, width=10)
self.entr[i].selection_clear()
self.entr[i].insert(0,self.array[i])
self.entr[i].pack(side='left')
fr2.pack(side='top')
#
fr_3 = Frame(ma)
bbox = Pmw.ButtonBox(fr_3)
bbox.pack(side='left',fill='both', expand=1)
b_ok= bbox.add('OK', command = Command(self.btn_press,'ok'))
b_rd= bbox.add('Read', command = Command(self.btn_press,'apply'))
b_ca= bbox.add('Done', command = Command(self.btn_press,'cancel'))
b_nf=bbox.add('Change File', command = Command(self.btn_press,'newfile'))
bbox.setdefault('Read')
bbox.alignbuttons()
self.balloon.bind(b_ok, '',
'Read these arrays from this file and exit')
self.balloon.bind(b_rd, '',
'Read these arrays from this file')
self.balloon.bind(b_ca, '',
'Close without reading these arrays from this file')
self.balloon.bind(b_nf, '',
'Do not read these arrays, Look for a new file')
fr_3.pack()
self.createMsgWin(ma)
def __init__(self, parent=None, **kw):
# Define the megawidget options.
optiondefs = ()
self.defineoptions(kw, optiondefs)
# Initialise the base class (after defining the options).
Pmw.MegaWidget.__init__(self, parent)
# Create the contents.
top = self.interior()
panes = Pmw.PanedWidget(top, orient = 'horizontal')
panes.pack(fill = 'both', expand = 1)
panes.add('widgetlist')
self._widgetlist = Pmw.ScrolledListBox(panes.pane('widgetlist'),
selectioncommand = Pmw.busycallback(self.startDemo),
label_text = 'Select a widget:',
labelpos = 'nw',
vscrollmode = 'dynamic',
hscrollmode = 'none',
listbox_exportselection = 0)
self._widgetlist.pack(fill = 'both', expand = 1, padx = 8)
panes.add('info')
self._status = Tkinter.Label(panes.pane('info'))
self._status.pack(padx = 8, anchor = 'w')
self._example = Tkinter.Frame(panes.pane('info'),
borderwidth = 2,
relief = 'sunken',
background = 'white')
self._example.pack(fill = 'both', expand = 1, padx = 8)
self.buttonBox = Pmw.ButtonBox(top)
self.buttonBox.pack(fill = 'x')
# Add the buttons and make them all the same width.
self._traceText = 'Trace tk calls'
self._stopTraceText = 'Stop trace'
self.buttonBox.add('Trace', text = self._traceText,
command = self.trace)
self.buttonBox.add('Code', text = 'Show code', command = self.showCode)
self.buttonBox.add('Exit', text = 'Exit', command = sys.exit)
self.buttonBox.alignbuttons()
# Create the window to display the python code.
self.codeWindow = Pmw.TextDialog(parent,
title = 'Python source',
buttons = ('Dismiss',),
scrolledtext_labelpos = 'n',
label_text = 'Source')
self.codeWindow.withdraw()
self.codeWindow.insert('end', '')
self.demoName = None
self._loadDemos()
# Check keywords and initialise options.
self.initialiseoptions()
def __init__(self, parent, withTabs=1):
# Repeat random number sequence for each run.
self.rand = 12345
# Default demo is to display a tabbed notebook.
self.withTabs = withTabs
# Create a frame to put everything in
self.mainframe = Tkinter.Frame(parent)
self.mainframe.pack(fill='both', expand=1)
# Find current default colors
button = Tkinter.Button()
defaultbg = button.cget('background')
defaultfg = button.cget('foreground')
button.destroy()
# Create the list of colors to cycle through
self.colorList = []
self.colorList.append((defaultbg, defaultfg))
self.colorIndex = 0
for color in Pmw.Color.spectrum(6, 1.5, 1.0, 1.0, 1):
bg = Pmw.Color.changebrightness(self.mainframe, color, 0.85)
self.colorList.append((bg, 'black'))
bg = Pmw.Color.changebrightness(self.mainframe, color, 0.55)
self.colorList.append((bg, 'white'))
# Set the color to the current default
Pmw.Color.changecolor(self.mainframe, defaultbg, foreground=defaultfg)
defaultPalette = Pmw.Color.getdefaultpalette(self.mainframe)
Pmw.Color.setscheme(self.mainframe, defaultbg, foreground=defaultfg)
# Create the notebook, but don't pack it yet.
if self.withTabs:
tabpos = 'n'
else:
tabpos = None
self.notebook = Pmw.NoteBook(
self.mainframe,
tabpos=tabpos,
createcommand=PrintOne('Create'),
lowercommand=PrintOne('Lower'),
raisecommand=PrintOne('Raise'),
hull_width=300,
hull_height=200,
)
# Create a buttonbox to configure the notebook and pack it first.
buttonbox = Pmw.ButtonBox(self.mainframe)
buttonbox.pack(side='bottom', fill='x')
# Add some buttons to the buttonbox to configure the notebook.
buttonbox.add('Insert\npage', command=self.insertpage)
buttonbox.add('Delete\npage', command=self.deletepage)
buttonbox.add('Add\nbutton', command=self.addbutton)
buttonbox.add('Change\ncolor', command=self.changecolor)
buttonbox.add('Natural\nsize', command=self.notebook.setnaturalsize)
if not self.withTabs:
# Create the selection widget to select the page in the notebook.
self.optionmenu = Pmw.OptionMenu(self.mainframe,
menubutton_width=10,
command=self.notebook.selectpage)
self.optionmenu.pack(side='left', padx=10)
# Pack the notebook last so that the buttonbox does not disappear
# when the window is made smaller.
self.notebook.pack(fill='both', expand=1, padx=5, pady=5)
# Populate some pages of the notebook.
page = self.notebook.add('tmp')
self.notebook.delete('tmp')
page = self.notebook.add('Appearance')
if self.withTabs:
self.notebook.tab('Appearance').focus_set()
button = Tkinter.Button(page,
text='Welcome\nto\nthe\nAppearance\npage')
button.pack(expand=1)
page = self.notebook.add('Fonts')
button = Tkinter.Button(
page, text='This is a very very very very wide Fonts page')
button.pack(expand=1)
page = self.notebook.insert('Applications', before='Fonts')
button = Tkinter.Button(page, text='This is the Applications page')
button.pack(expand=1)
# Initialise the first page and the initial colour.
if not self.withTabs:
self.optionmenu.setitems(self.notebook.pagenames())
apply(Pmw.Color.setscheme, (self.mainframe, ), defaultPalette)
self.pageCounter = 0
def __init__(self, parent, filtus, notebook):
Tkinter.Frame.__init__(self, parent)
self.filtus = filtus
self.db = None
self.columnconfigure(0, weight=1)
self.rowconfigure(3, weight=1)
Tkinter.Label(self,
text="Add samples to database",
font=filtus.titlefont,
anchor='c').grid(sticky='news', padx=10, pady=(15, 10))
self.browser = DBbrowser(self,
filtus,
label="Load database:",
updates=self.updateStuff)
self.browser.grid(sticky='news', padx=10)
Tkinter.Frame(self, height=2, borderwidth=2,
relief="sunken").grid(padx=10, pady=10, sticky="new")
filenames = [VF.shortName for VF in filtus.files]
self.lists = TwoListWidget(self,
filtus=filtus,
lefttoptext="Available samples: %d" %
len(filenames),
items=filenames)
self.lists.grid(sticky='news', padx=10, pady=0)
####### OUTPUT
Tkinter.Frame(self, height=2, borderwidth=2,
relief="sunken").grid(padx=10, pady=10, sticky="new")
save_interior = Tkinter.Frame(self)
save_interior.columnconfigure(0, weight=1)
self.save_browser = FiltusWidgets.FileBrowser(
save_interior,
filtus=filtus,
label="Output database file name:",
checkbutton=False,
labelpos='nw',
browsesticky='se',
entryfield_entry_width=20,
browsetitle="")
self.save_browser.browsebutton.configure(command=self._browseSave)
self.save_browser.entryfield.configure(command=None)
self.formatSelect = Pmw.RadioSelect(
save_interior,
buttontype="radiobutton",
pady=0,
labelpos="nw",
labelmargin=0,
label_text="Format:"
) #, hull_borderwidth = 2, hull_relief = 'ridge')
self.formatSelect.add("Simple")
self.formatSelect.add("Extended")
self.formatSelect.invoke("Simple")
self.save_browser.grid(sticky='news', padx=(10, 25), pady=(5, 10))
self.formatSelect.grid(row=0, column=1, sticky='e', padx=10, pady=0)
save_interior.grid(sticky='news', padx=10, pady=0)
#######
Tkinter.Frame(self, height=2, borderwidth=3,
relief="raised").grid(sticky='ew', pady=15)
self.lowerButtons = Pmw.ButtonBox(self, padx=50)
self.lowerButtons.add('createButt',
text="Add to database",
command=self.addSamples)
self.lowerButtons.add('cancelButt',
text="Cancel",
command=notebook.deactivate)
self.lowerButtons.grid(sticky='news', pady=(0, 10))
def __init__(self, parent, sequences, modification_tags):
self.parent = parent
self.sequences = sequences
self.modification_tags = modification_tags
self.expcond_top = Tkinter.Toplevel(self.parent)
self.expcond_top.title('Experimental Condition Suggestions')
self.expcond_top.wm_transient(self.parent)
self.expcond_top.top_width = 800
self.expcond_top.top_height = 500
geometry_string = "%dx%d%+d%+d" % (
self.expcond_top.top_width, self.expcond_top.top_height, 100, 100
) # width,height,x-offset,y-offset
self.expcond_top.geometry(geometry_string)
# frame1 is on the left
self.frame1 = Tkinter.Frame(self.expcond_top, relief='raised', bd=2)
self.frame1a = Tkinter.Frame(self.frame1, relief='groove', bd=2)
self.frame1b = Tkinter.Frame(self.frame1, relief='groove', bd=2)
self.frame1c = Tkinter.Frame(self.frame1, relief='groove', bd=2)
self.frame2 = Tkinter.Frame(self.expcond_top, relief='raised', bd=2)
# available reagents
self.reactions_dict = {}
filename = './Tools/MassSpectrometry/reactions_dict.pkl'
if os.path.exists(filename):
reactions_file = open(filename, 'rb')
self.reactions_dict = pickle.load(reactions_file)
reactions_file.close()
else:
print 'no reactions file %s found' % (filename)
# put the available reagents into a scrolled frame
self.reagents_sframe = Pmw.ScrolledFrame(self.frame1a,
usehullsize=1,
hull_width=200,
hull_height=200)
rsframe_interior = self.reagents_sframe.interior()
# frame1a has available reagents (radiobutton)
self.reagents_radio = Pmw.RadioSelect(
rsframe_interior,
buttontype='radiobutton',
orient='vertical',
labelpos='nw',
label_text='Available\n Reagents',
selectmode='single')
self.reagents_radio.pack(side='top', expand=0, fill='none')
self.reagents_sframe.pack(side='top', expand=1, fill='both')
keys = self.reactions_dict.keys()
keys.sort()
keys.reverse()
for key in keys:
self.reagents_radio.add(key)
self.reagents_radio.invoke(keys[0])
# available proteases
self.proteases_dict = {}
filename = './Tools/MassSpectrometry/protease_dict.pkl'
if os.path.exists(filename):
protease_file = open(filename, 'rb')
self.proteases_dict = pickle.load(protease_file)
protease_file.close()
else:
print 'no protease file %s found' % (filename)
self.protease_sframe = Pmw.ScrolledFrame(self.frame1b,
usehullsize=1,
hull_width=200,
hull_height=200)
psframe_interior = self.protease_sframe.interior()
self.protease_radio = Pmw.RadioSelect(
psframe_interior,
buttontype='checkbutton',
orient='vertical',
labelpos='nw',
label_text='Available\n Proteases',
selectmode='multiple')
self.protease_radio.pack(side='top', expand=0, fill='none')
self.protease_sframe.pack(side='top', expand=1, fill='both')
keys = self.proteases_dict.keys()
keys.sort()
keys.reverse()
for key in keys:
self.protease_radio.add(key)
self.protease_radio.invoke(keys[0])
# frame1c has the missed cut sites counter
self.missed_cut_sites_counter = FunctionalPmwCounter.functional_pmw_counter(
self.frame1c, 'n', 'Missed cut sites tolerated:', 2, {
'validator': 'integer',
'min': 0,
'max': 99
}, 'integer', 1)
self.missed_cut_sites_counter.pack(side='top', expand=1, fill='both')
# frame2 gets the report and buttonbox
self.report_textbox = Pmw.ScrolledText(self.frame2,
usehullsize=1,
hull_width=400,
hull_height=350)
self.report_textbox.pack(side='top', fill='both', expand=1)
self.report_text = self.report_textbox.component('text')
self.buttonBox = Pmw.ButtonBox(self.frame2)
self.buttonBox.add('Calculate', command=self.calculate_report)
self.buttonBox.add('Cancel', command=self.cancel_calculation)
self.buttonBox.alignbuttons()
self.buttonBox.pack(side='top', fill='x', expand=0)
self.frame1a.pack(side='top', expand=1, fill='both')
self.frame1b.pack(side='top', expand=1, fill='both')
self.frame1c.pack(side='top', expand=1, fill='both')
self.frame1.pack(side='left', expand=0, fill='y')
self.frame2.pack(side='left', expand=1, fill='both')
self.old_stdout = None
def __init__(self, parent, filtus, notebook):
Tkinter.Frame.__init__(self, parent)
self.filtus = filtus
self.db = None
self.results = None
self.columnconfigure(0, weight=1)
self.rowconfigure(3, weight=1)
Tkinter.Label(self,
text="Search database",
font=filtus.titlefont,
anchor='c').grid(sticky='news', padx=10, pady=(15, 10))
self.browser = DBbrowser(self,
filtus,
label="Enter database file name")
self.browser.grid(sticky='news', padx=10, pady=0)
Tkinter.Frame(self, height=2, borderwidth=2,
relief="sunken").grid(padx=10, pady=10, sticky="new")
search_frame = Tkinter.Frame(self)
search_frame.columnconfigure(1, weight=1)
search_frame.rowconfigure(1, weight=1)
sgroup = Pmw.Group(search_frame, tag_text="Query")
search_int = sgroup.interior()
self.chrom = Pmw.EntryField(search_int,
label_text="Chromosome:",
labelpos='w',
entry_width=9,
labelmargin=5)
self.pos = Pmw.EntryField(search_int,
label_text="Position:",
labelpos='w',
entry_width=9,
labelmargin=5)
Pmw.alignlabels([self.chrom, self.pos])
self.chrom.grid(padx=(5, 10), pady=(10, 5))
self.pos.grid(padx=(5, 10), pady=5)
sgroup.grid(sticky='new', padx=(0, 10), pady=12)
self.searchButt = Tkinter.Button(search_frame,
text="Search",
command=self.doSearch)
self.searchButt.grid(row=1, column=0, padx=5, pady=20, sticky='n')
self.resultWindow = Pmw.ScrolledText(search_frame,
borderframe=1,
text_padx=2,
scrollmargin=2,
hscrollmode='dynamic',
label_text="Results",
labelpos="nw",
text_width=10,
text_height=1,
text_wrap='none',
text_font=filtus.monofont)
FiltusWidgets.makeReadOnly(self.resultWindow.component('text'))
self.resultWindow.grid(row=0,
column=1,
sticky='news',
padx=10,
pady=0,
rowspan=2)
search_frame.grid(sticky='news', padx=10, pady=(0, 10))
Tkinter.Frame(self, height=2, borderwidth=3,
relief="raised").grid(sticky='ew', pady=15)
self.lowerButtons = Pmw.ButtonBox(self, padx=50)
self.lowerButtons.add('createButt',
text="Save result",
command=self.save)
self.lowerButtons.add('cancelButt',
text="Cancel",
command=notebook.deactivate)
self.lowerButtons.grid(sticky='news', pady=(0, 10))
def __init__(self, parent):
# Create the ScrolledListBox.
self.box = Pmw.ScrolledListBox(parent,
items=('Sydney', 'Melbourne', 'Brisbane'),
labelpos='nw',
label_text='Cities',
listbox_height = 6,
selectioncommand=self.selectionCommand,
dblclickcommand=self.defCmd,
usehullsize = 1,
hull_width = 200,
hull_height = 200,
)
# Create a group widget to contain the scrollmode options.
w = Pmw.Group(parent, tag_text='Scroll mode')
w.pack(side = 'bottom', padx = 5, pady = 5)
hmode = Pmw.OptionMenu(w.interior(),
labelpos = 'w',
label_text = 'Horizontal:',
items = ['none', 'static', 'dynamic'],
command = self.sethscrollmode,
menubutton_width = 8,
)
hmode.pack(side = 'top', padx = 5, pady = 5)
hmode.invoke('dynamic')
vmode = Pmw.OptionMenu(w.interior(),
labelpos = 'w',
label_text = 'Vertical:',
items = ['none', 'static', 'dynamic'],
command = self.setvscrollmode,
menubutton_width = 8,
)
vmode.pack(side = 'top', padx = 5, pady = 5)
vmode.invoke('dynamic')
buttonBox = Pmw.ButtonBox(parent)
buttonBox.pack(side = 'bottom')
buttonBox.add('yview', text = 'Show\nyview', command = self.showYView)
buttonBox.add('scroll', text = 'Page\ndown', command = self.pageDown)
buttonBox.add('center', text = 'Center', command = self.centerPage)
# Pack this last so that the buttons do not get shrunk when
# the window is resized.
self.box.pack(fill = 'both', expand = 1, padx = 5, pady = 5)
# Do this after packing the scrolled list box, so that the
# window does not resize as soon as it appears (because
# alignlabels has to do an update_idletasks).
Pmw.alignlabels((hmode, vmode))
# Add some more entries to the listbox.
items = ('Andamooka', 'Coober Pedy', 'Innamincka', 'Oodnadatta')
self.box.setlist(items)
self.box.insert(2, 'Wagga Wagga', 'Perth', 'London')
self.box.insert('end', 'Darwin', 'Auckland', 'New York')
index = list(self.box.get(0, 'end')).index('London')
self.box.delete(index)
self.box.delete(7, 8)
self.box.insert('end', 'Bulli', 'Alice Springs', 'Woy Woy')
self.box.insert('end', 'Wallumburrawang', 'Willandra Billabong')
def __init__(self, parent, pCmdArgs=None):
pCmd = '/homes/jschamba/tof/pcan/pcanloop'
if pCmdArgs:
shell = pCmd + ' ' + pCmdArgs
else:
shell = pCmd
args = string.split(shell)
#print "shell", shell, "args", args
self.setDefaultVals()
self.tk = parent
mainFrame = Frame(parent)
run_type = Pmw.OptionMenu(mainFrame,
labelpos=W,
label_text='Run Type:',
menubutton_textvariable=self.runTypeNum,
items=self.runTypeOptions)
user_name = Pmw.OptionMenu(mainFrame,
labelpos=W,
label_text='Operator:',
menubutton_textvariable=self.userNum,
items=self.userOptions)
self.current_time = Pmw.EntryField(mainFrame,
labelpos=W,
label_text="current time:",
entry_state="readonly",
value=time.strftime(
"%a, %d %b %Y %H:%M:%S",
time.localtime()))
self.run_number = Pmw.EntryField(mainFrame,
labelpos=W,
label_text="run number:",
modifiedcommand=self.fileChanged,
entry_textvariable=self.runNum)
self.start_time = Pmw.EntryField(mainFrame,
labelpos=W,
label_text="start time:",
entry_state="readonly",
value=time.strftime(
"%a, %d %b %Y %H:%M:%S",
time.localtime(self.startTime)))
self.run_time = Pmw.EntryField(
mainFrame,
labelpos=W,
label_text="run time:",
entry_state="readonly",
)
if (self.runStatus == 2):
self.run_time.setvalue(int(time.time()) - self.startTime)
else:
self.run_time.setvalue(self.stopTime - self.startTime)
self.data_dir = Pmw.EntryField(mainFrame,
labelpos=W,
label_text="data directory:",
modifiedcommand=self.fileChanged,
entry_textvariable=self.dataDir)
self.data_file = Pmw.EntryField(mainFrame,
labelpos=W,
label_text="data file:",
entry_state="readonly",
value=self.dataFile)
self.log_dir = Pmw.EntryField(mainFrame,
labelpos=W,
label_text="log directory:",
modifiedcommand=self.fileChanged,
entry_textvariable=self.logDir)
self.log_file = Pmw.EntryField(mainFrame,
labelpos=W,
label_text="log file:",
entry_state="readonly",
value=self.logFile)
allwdgs = [
run_type, user_name, self.current_time, self.run_number,
self.start_time, self.run_time, self.data_dir, self.data_file,
self.log_dir, self.log_file
]
for wdg in allwdgs:
wdg.pack(fill=X, expand=1, padx=10, pady=2)
Pmw.alignlabels(allwdgs)
bb = Pmw.ButtonBox(mainFrame,
labelpos=W,
label_text='Run',
frame_borderwidth=2,
frame_relief='groove')
bb.pack(padx=10, pady=10)
bb.add('Start', command=self.runStart)
bb.add('Stop', command=self.runStop)
bb.alignbuttons()
self.cmdEntry = StringVar()
entryBox = Pmw.EntryField(mainFrame,
labelpos=W,
label_text="CAN Command Entry:",
command=self.exeCommand,
entry_textvariable=self.cmdEntry)
entryBox.pack(fill=X, expand=YES)
self.textBox = Pmw.ScrolledText(mainFrame)
self.textBox.pack(fill=BOTH, expand=YES)
mainFrame.pack(fill=BOTH, expand=YES)
self.pid, self.fromchild, self.tochild = spawn(pCmd, args)
tkinter.createfilehandler(self.fromchild, READABLE, self.outputhandler)
parent.after(1000, self.secondElapsed)
def __init__(self, app):
#Initialize the rotamers for the SC rotator
self.setupAAtypes()
#Find Probe and Reduce Executables
findExecutables()
#Start a thread to calculate dots when doing SC rotation
self.dotThread = ThreadDots(self.dotQueue)
self.dotThread.start()
#Get the parent window for our plugin
parent = app.root
self.parent = parent
# Create the dialog.
self.dialog = Pmw.Dialog(parent,
buttons=('Close', 'About'),
title='Protein Interaction Viewer',
command=self.execute)
self.dialog.withdraw()
#self.dialog.protocol('WM_TAKE_FOCUS',self.updateSels)
self.dialog.bind('<FocusIn>', self.updateSels)
#define comboBoxes that will need to be updated when selections are updated
self.cBoxes = []
# Set up the main page
self.notebook = Pmw.NoteBook(self.dialog.interior())
self.notebook.pack(fill='both', expand=1, padx=1, pady=1)
#Add Hydrogen page
########################################
page = self.notebook.add('Edit H')
group = Pmw.Group(page, tag_text='Hydrogen Options')
group.pack(fill='both', expand=1, padx=1, pady=5)
self.h_sel = Pmw.ScrolledListBox(
group.interior(),
label_text='Selection: ',
labelpos='nw',
#scrolledlist_items = self.getSels(),
#dropdown = 0,
listbox_height=10)
#self.cBoxes.append(self.h_sel)
self.h_newSel = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='New Object Name')
self.h_buttons = Pmw.ButtonBox(group.interior())
self.h_buttons.add('Clear H', command=self.clearH)
self.h_buttons.add('Add H', command=self.addH)
self.replVar = IntVar()
self.replaceCheck = Tkinter.Checkbutton(self.h_buttons.interior(),
text='Replace',
variable=self.replVar)
self.replaceCheck.grid(row=0, column=4)
for widget in (self.h_sel, self.h_newSel, self.h_buttons):
widget.pack(fill='x', padx=1, pady=1)
##################################################
#Add Dots page
page = self.notebook.add('Load Dots')
group = Pmw.Group(page, tag_text='Load Dots')
group.pack(fill='both', expand=1, padx=1, pady=5)
frame = Frame(group.interior())
frame.pack(fill='x')
self.d_sel1 = Pmw.ComboBox(
frame,
label_text='Sel1: ',
labelpos='nw',
#scrolledlist_items = self.getSels(),
dropdown=0,
listbox_height=10)
self.cBoxes.append(self.d_sel1)
self.d_sel2 = Pmw.ComboBox(
frame,
label_text='Sel2: ',
labelpos='nw',
#scrolledlist_items = self.getSels(),
dropdown=0,
listbox_height=10)
self.cBoxes.append(self.d_sel2)
self.d_sel1.pack(side=LEFT, padx=10)
self.d_sel2.pack(side=LEFT, padx=10)
self.d_name = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Dots Name',
value='dots')
self.d_params = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Additional Parameters')
self.d_buttons = Pmw.ButtonBox(group.interior())
self.d_buttons.add('Load Dots', command=self.loadDotsButton)
optionFrame = Frame(group.interior())
self.d_selfVar = IntVar()
self.d_selfCheck = Tkinter.Checkbutton(optionFrame,
text="Self",
variable=self.d_selfVar)
self.dotSizeEntry = Pmw.EntryField(optionFrame,
labelpos='w',
label_text="Dot Size: ",
value=0,
validate='real')
self.dotSizeEntry.component("entry").configure(width=5)
self.lineSizeEntry = Pmw.EntryField(optionFrame,
labelpos='w',
label_text="Line Size: ",
value=1,
validate='real')
self.lineSizeEntry.component("entry").configure(width=5)
self.d_name.pack(fill='x')
self.d_params.pack(fill='x')
optionFrame.pack(fill='x')
self.d_selfCheck.pack(side=LEFT, padx=10)
self.dotSizeEntry.pack(side=LEFT, padx=10)
self.lineSizeEntry.pack(side=LEFT, padx=10)
self.d_buttons.pack()
#########################################################
#Add SC rotator page
page = self.notebook.add('Side-chain Rotator')
group = Pmw.Group(page, tag_text='Side-chain Rotator')
group.pack(fill='both', expand=1, padx=1, pady=5)
frame = Frame(group.interior())
frame.pack(fill='x')
self.resLabel = Tkinter.Label(frame, text="")
self.resLabel.grid(row=0, column=2)
self.dihVar = []
self.dihScale = []
for i in range(4):
self.dihVar.append(IntVar())
self.dihScale.append(
Scale(frame,
from_=-180,
to=180,
highlightthickness=0,
sliderlength=20,
resolution=1,
length=130,
variable=self.dihVar[i],
command=lambda x, index=i: self.changeDihedral(index, x),
orient=HORIZONTAL,
label="Chi " + str(i)))
self.dihScale[i].grid(row=i + 1, column=2)
self.dihScale[i].bind("<ButtonRelease-1>", self.rotRelease)
self.dihScale[i].bind('<KeyRelease>', self.rotRelease)
self.dihScale[i].grid_remove()
self.rotBox = Pmw.ScrolledListBox(frame,
label_text='Rotamer: ',
labelpos='nw',
listbox_height=15,
selectioncommand=self.rotBoxCommand)
self.rotBox.grid(rowspan=4, row=1, column=1)
self.showDotsCheckVar = IntVar()
self.showDotsCheck = Tkinter.Checkbutton(
frame,
text="Show Dots",
variable=self.showDotsCheckVar,
command=self.dotCheckCB)
self.showDotsCheck.grid(row=5, column=1)
self.notebook.setnaturalsize()
#get the window to open next to pymol and not on top of it
#first get screen size so we don't go off the screen
swidth = parent.winfo_screenwidth()
pwidth = parent.winfo_width()
rootx = parent.winfo_rootx()
dwidth = self.dialog.winfo_width()
xpos = min(rootx + pwidth + 8, swidth - dwidth)
self.dialog.geometry("+%d+%d" % (xpos, 0))
self.dialog.show()
u.append(x / (2.0 * npoints / 3))
else:
u.append(float(npoints - x) / (npoints / 3))
init()
g = Pmw.Blt.Graph(master)
g.pack(expand=1, fill='both')
curvename = 'string'
g.line_create(curvename,
xdata=tuple(vector_x),
ydata=tuple(u),
pixels=7,
smooth='natural') # smooth the curve by splines
g.element_bind("string", "<ButtonPress>", mouseDown)
g.element_bind("string", "<ButtonRelease>", mouseUp)
g.yaxis_configure(min=-1, max=1)
g.configure(title='Hello world of waves', width=250, height=200)
buttons = Pmw.ButtonBox(master, labelpos='n', label_text='Options')
buttons.pack(fill='x', expand=0, padx=10, pady=10)
buttons.add('Simulate', command=run)
buttons.add('Step', command=step)
buttons.add('Zero', command=zero)
buttons.add('Quit', command=master.quit)
master.mainloop()
def Vertical_Transmission(self):
self.hide()
vTFrame = Toplevel()
vTFrame.title("SIR WITH VERTICAL TRANSMISSION")
vTFrame.geometry("700x800")
# self.top.transient(self)
g = Pmw.Blt.Graph(vTFrame)
g.pack(expand=1, fill="both")
E = zeros([2, 1])
A = zeros([2, 2])
C = zeros([2, 1])
A = zeros([2, 2])
B = zeros([2, 2])
E = zeros([2, 1])
C = zeros([2, 1])
# --------------------------------------------------------------------------------------------------------------------------------------------------------
sus = Pmw.EntryField(
vTFrame,
labelpos="w",
value="0.0",
label_text="Initial Susceptible",
validate={"validator": "real"},
)
sus.pack(expand=1, padx=5, pady=5)
Infec = Pmw.EntryField(
vTFrame,
labelpos="w",
value="0.0",
label_text="Initial Infective Io:",
validate={"validator": "real"},
)
Infec.pack(expand=1, padx=5, pady=5)
contact = Pmw.EntryField(
vTFrame,
labelpos="w",
value="0.0",
label_text="Contact Rate - k ",
validate={"validator": "real"},
)
contact.pack(expand=1, padx=5, pady=5)
Removal = Pmw.EntryField(
vTFrame,
labelpos="w",
value="0.0",
label_text=" Removal Rate ",
validate={"validator": "real"},
)
Removal.pack(expand=1, padx=10, pady=5)
time_interval = Pmw.EntryField(
vTFrame,
labelpos="w",
value="0",
label_text=" Time Interval",
validate={"validator": "numeric"},
)
time_interval.pack(expand=1, padx=5, pady=5)
birth_rate = Pmw.EntryField(
vTFrame,
labelpos="w",
value="0.0",
label_text=" Birth Rate - b :",
validate={"validator": "real"},
)
birth_rate.pack(expand=1, padx=10, pady=5)
immunity1 = Pmw.EntryField(
vTFrame,
labelpos="w",
value="0.00",
label_text=" Immunity Rate ",
validate={"validator": "real"},
)
immunity1.pack(expand=1, padx=10, pady=10)
infected_rate = Pmw.EntryField(
vTFrame,
labelpos="w",
value="0.0",
label_text="Infected Birth - Ib",
validate={"validator": "real"},
)
infected_rate.pack(expand=1, padx=10, pady=5)
vertical = Pmw.EntryField(
vTFrame,
labelpos="w",
value="0.00",
label_text=" Vertical Rate - v",
validate={"validator": "real"},
)
vertical.pack(expand=1, padx=10, pady=10)
probability = Pmw.EntryField(
vTFrame,
labelpos="w",
value="0.00",
label_text="Probability loss -p",
validate={"validator": "real"},
)
probability.pack(expand=1, padx=10, pady=10)
# --------------------------------------------------------------------------------------------------------------------------------------------------------
# self.top.transient(self)
# self.wButton.config(state='disabled')
def retrive():
k1 = contact.get()
k = float(k1)
ggamma = float(Removal.get())
N = int(time_interval.get())
s0 = float(sus.get())
I0 = float(Infec.get())
m = float(immunity1.get())
v = float(vertical.get())
b_prime = float(infected_rate.get())
b = float(birth_rate.get())
p = float(probability.get())
A[0][0] = 0
A[0][1] = -k
A[1][0] = k
A[1][1] = 0
B[0][0] = (m - 1) * b + (p * b_prime + ggamma)
B[0][1] = 0
B[1][0] = 0
B[1][1] = 0
E[0][0] = -b - ggamma
E[1][0] = p * b_prime - v
C[0][0] = b * (1 - m) + (ggamma)
C[1][0] = 0
def f1(s1, I1):
s_dot = (
s1 * E[0][0]
+ A[0][0] * (s1 ** 2)
+ A[0][1] * s1 * I1
+ B[0][0] * s1
+ B[0][1] * I1
+ C[0][0]
)
return s_dot
def f2(s1, I1):
I_dot = (
I1 * E[1][0]
+ A[1][1] * (I1 ** 2)
+ A[1][0] * s1 * I1
+ B[1][0] * s1
+ B[1][1] * I1
+ C[1][0]
)
return I_dot
# =========RATE OF CHANGE OF THE MODEL WITH RESPECT TO TIME AND DECLARATON OF CONSTANTS==================================
t = arange(0, N, 0.02455)
s1 = zeros(len(t))
I1 = zeros(len(t))
s1[0] = s0
I1[0] = I0
h = 0.01
# ==========ITERATION FOR A GIVEN TIME INTERVAL=========================
for n in range(len(t) - 1):
s1[n + 1] = s1[n] + h * (f1(s1[n], I1[n]))
I1[n + 1] = I1[n] + h * (f2(s1[n], I1[n]))
x_ = tuple(t)
y_ = tuple(s1)
z_ = tuple(I1)
g.configure(
title="Susceptible and Infectives against time for SIR with Vertical Transmission"
)
g.line_create(
"S(t) Vs t", xdata=x_, color="red", ydata=y_, linewidth=2, symbol=""
)
g.line_create(
"I(t) Vs t", xdata=x_, color="orange", ydata=z_, linewidth=2, symbol=""
)
def postscript():
g.postscript_output(fileName="HelloUser1.ps", decorations="no")
def newFile():
for name in g.element_names():
g.element_delete(name)
contact.setentry("")
Removal.setentry("")
time_interval.setentry("")
Infec.setentry("")
sus.setentry("")
immunity1.setentry("")
birth_rate.setentry("")
vertical.setentry("")
infected_rate.setentry("")
probability.setentry("")
# --------------------------------------------------------------------------------------------------------------------------------------------------------
buttons = Pmw.ButtonBox(vTFrame, labelpos="w", label_text="Options")
# buttons = Pmw.ButtonBox(self, labelpos='w', label_text='Options')
buttons.pack(fill="both", expand=1, padx=10, pady=10)
buttons.add("GRID", bg="green", command=g.grid_toggle)
buttons.add("PLOT", bg="green", command=retrive)
buttons.add("CLEAR", bg="green", command=newFile)
buttons.add("SAVE", bg="green", command=postscript)
handler = lambda: self.onCloseOtherFrame2(vTFrame)
buttons.add("QUIT", bg="red", command=handler)
