def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
import Tkinter
from CGLtk import Hybrid
from chimera.widgets import MoleculeOptionMenu
mm = MoleculeOptionMenu(parent, labelpos = 'w', label_text = 'Molecule ')
mm.grid(row = row, column = 0, sticky = 'w')
self.molecule_menu = mm
row = row + 1
cd = Hybrid.Entry(parent, 'Contact distance', 5, '1.0')
cd.frame.grid(row = row, column = 0, sticky = 'w')
self.contact_distance = cd.variable
cd.entry.bind('<KeyPress-Return>', self.show_contacts)
row = row + 1
mc = Hybrid.Checkbutton(parent, 'Create copies of contacting molecules.', False)
mc.button.grid(row = row, column = 0, sticky = 'w')
row += 1
self.copy_molecule = mc.variable
msg = Tkinter.Label(parent, anchor = 'w', justify = 'left')
msg.grid(row = row, column = 0, sticky = 'ew')
row = row + 1
self.message_label = msg
def set_color_count(self, n):
if n == self.n:
return
if n > len(self.colorwells):
# Add more color buttons
for c in range(len(self.colorwells), n):
from CGLtk.color import ColorWell
cw = ColorWell.ColorWell(self.frame)
cw.grid(row=2 * (c / 5), column=c % 5)
self.colorwells.append(cw)
from CGLtk import Hybrid
e = Hybrid.Entry(self.frame, '', 5, '')
e.frame.grid(row=2 * (c / 5) + 1, column=c % 5)
e.entry.bind('<KeyPress-Return>', self.colormap_changed_cb)
self.entry_fields.append(e)
# Map additional colorwells
for c in range(self.n, n):
self.colorwells[c].grid()
self.entry_fields[c].frame.grid()
# Unmap extra colorwells
for c in range(n, self.n):
self.colorwells[c].grid_remove()
self.entry_fields[c].frame.grid_remove()
self.n = n
def color_source(self):
csname = self.color_source_menu.get()
from SurfaceColor import coloring_methods
csclass = [cm for cm in coloring_methods if cm.menu_name == csname][0]
cs = csclass()
cmap = self.colormap()
if cmap:
cs.set_colormap(cmap)
if cs.uses_volume_data:
cs.set_volume(self.volume_menu.volume())
if cs.uses_origin:
o = parse_vector(self.origin_variable.get(), default=(0, 0, 0))
cs.set_origin(o)
if cs.uses_axis:
a = parse_vector(self.axis_variable.get(), default=(0, 0, 1))
cs.set_axis(a)
cs.per_pixel_coloring = self.per_pixel_color.get()
from SurfaceColor import Electrostatic_Color
if isinstance(cs, Electrostatic_Color):
from CGLtk import Hybrid
cs.offset = Hybrid.float_variable_value(self.surface_offset, 0)
return cs
def __init__(self, parent, title, values_cb):
self.values_cb = values_cb
self.name_to_value = {}
import Tkinter
f = Tkinter.Frame(parent)
self.frame = f
if title:
label = Tkinter.Label(f, text=title)
label.grid(row=0, column=0, sticky='w')
self.label = label
from CGLtk import Hybrid
v = Hybrid.StringVariable(parent)
self.variable = v
mb = Tkinter.Menubutton(f,
textvariable=v.tk_variable,
indicatoron=1,
borderwidth=2,
relief='raised',
highlightthickness=2,
anchor='c')
mb.grid(row=0, column=1, sticky='w')
m = Tkinter.Menu(mb, tearoff=0, postcommand=self.update_menu)
self.menu = m
mb['menu'] = m
self.update_menu()
def color_source(self):
csname = self.color_source_menu.get()
from SurfaceColor import coloring_methods
csclass = [cm for cm in coloring_methods if cm.menu_name == csname][0]
cs = csclass()
cmap = self.colormap()
if cmap:
cs.set_colormap(cmap)
if cs.uses_volume_data:
cs.set_volume(self.volume_menu.volume())
if cs.uses_origin:
o = parse_vector(self.origin_variable.get(), default = (0,0,0))
cs.set_origin(o)
if cs.uses_axis:
a = parse_vector(self.axis_variable.get(), default = (0,0,1))
cs.set_axis(a)
cs.per_pixel_coloring = self.per_pixel_color.get()
from SurfaceColor import Electrostatic_Color
if isinstance(cs, Electrostatic_Color):
from CGLtk import Hybrid
cs.offset = Hybrid.float_variable_value(self.surface_offset, 0)
return cs
def fillInUI(self, parent):
self.surface_change_handler = None
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
import Tkinter
from CGLtk import Hybrid
from chimera import widgets
from MeasureVolume import surface_models
sm = widgets.ModelOptionMenu(parent, labelpos = 'w',
label_text = 'Surface ',
listFunc = surface_models,
command = self.surface_menu_cb)
sm.grid(row = row, column = 0, sticky = 'w')
self.surface_menu = sm
row = row + 1
ve = Hybrid.Entry(parent, 'Volume = ', 20)
ve.entry.configure(relief = Tkinter.FLAT, state = 'readonly',
highlightthickness = 0)
ve.frame.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.volume = ve.variable
ae = Hybrid.Entry(parent, 'Area = ', 20)
ae.entry.configure(relief = Tkinter.FLAT, state = 'readonly',
highlightthickness = 0)
ae.frame.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.area = ae.variable
au = Hybrid.Checkbutton(parent, 'Update automatically', True)
au.button.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.autoupdate = au.variable
au.callback(self.update_switch_cb)
# Set menu to a displayed surface.
surfs = filter(lambda sm: sm.display, surface_models())
if surfs:
self.surface_menu.setvalue(surfs[0])
def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
parent.columnconfigure(0, weight=1) # Allow scalebar to expand.
row = 0
import Tkinter
from CGLtk import Hybrid
from chimera.widgets import MoleculeOptionMenu
mm = MoleculeOptionMenu(parent,
labelpos='w',
label_text='Molecule ',
command=self.show_cumulative_transform)
mm.grid(row=row, column=0, sticky='w')
self.molecule_menu = mm
row = row + 1
ea = Hybrid.Entry(parent, 'Euler angles ', 25, '0 0 0')
ea.frame.grid(row=row, column=0, sticky='e')
row = row + 1
self.euler_angles = ea.variable
tr = Hybrid.Entry(parent, 'Shift ', 25, '0 0 0')
tr.frame.grid(row=row, column=0, sticky='e')
row = row + 1
self.translation = tr.variable
cas = Tkinter.Label(parent, text='', justify='left')
cas.grid(row=row, column=0, sticky='w')
self.cumulative = cas
row = row + 1
el = Tkinter.Label(
parent,
text=
'Apply rotation and translation to atom coordinates\n using the molecule coordinate system.',
justify='left')
el.grid(row=row, column=0, sticky='w')
row = row + 1
self.show_cumulative_transform(None)
def mesh_offset_changed_cb(self, event = None):
p = self.mesh_surface_piece()
if p:
varray, tarray = p.geometry
from CGLtk import Hybrid
mesh_offset = Hybrid.float_variable_value(self.mesh_offset, 0)
varray[:,2] = mesh_offset
p.geometry = varray, tarray
def fillInUI(self, parent):
SaveModeless.fillInUI(self, parent)
from CGLtk import Hybrid
br = Hybrid.Entry(self.clientArea, 'Bit rate (Kb/sec):', 6,
self.default_bit_rate)
br.frame.grid(row=0, column=0, sticky='w')
self.bit_rate = br.variable
def mesh_offset_changed_cb(self, event=None):
p = self.mesh_surface_piece()
if p:
varray, tarray = p.geometry
from CGLtk import Hybrid
mesh_offset = Hybrid.float_variable_value(self.mesh_offset, 0)
varray[:, 2] = mesh_offset
p.geometry = varray, tarray
def fillInUI(self, parent):
self.default_color = (0, 0, 0.8, 1)
t = parent.winfo_toplevel()
self.toplevel_widget = t
t.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
import Tkinter
from CGLtk import Hybrid
mmf = Tkinter.Frame(parent)
mmf.grid(row=row, column=0, sticky='w')
row = row + 1
mb = Hybrid.Option_Menu(mmf, 'Use mouse ', 'button 1', 'button 2',
'button 3', 'ctrl button 1', 'ctrl button 2',
'ctrl button 3')
mb.variable.set('ctrl button 3')
mb.frame.grid(row=0, column=0, sticky='w')
mb.add_callback(self.bind_mouse_button_cb)
self.mouse_button = mb
mbl = Tkinter.Label(mmf, text=' to choose blobs')
mbl.grid(row=0, column=1, sticky='w')
crf = Tkinter.Frame(parent)
crf.grid(row=row, column=0, sticky='ew')
crf.columnconfigure(1, weight=1)
row = row + 1
cl = Tkinter.Label(crf, text='Color blob ')
cl.grid(row=0, column=0, sticky='w')
from CGLtk.color import ColorWell
sc = ColorWell.ColorWell(crf, color=self.default_color)
sc.grid(row=0, column=1, sticky='w')
self.blob_color = sc
msg = Tkinter.Label(parent, anchor='w', justify='left')
msg.grid(row=row, column=0, sticky='ew')
row = row + 1
self.message_label = msg
callbacks = (self.mouse_down_cb, self.mouse_drag_cb, self.mouse_up_cb)
icon = self.mouse_mode_icon('pickblob.gif')
from chimera import mousemodes
mousemodes.addFunction('pick blobs', callbacks, icon)
self.bind_mouse_button_cb()
def settings_changed_cb(self, event=None):
cap = self.show_caps.get()
from surfcaps import capper
c = capper()
if cap:
if self.use_cap_color.get():
color = self.cap_color.rgba
else:
color = None
c.set_cap_color(color)
c.set_style(self.cap_style.get() == 'mesh')
from CGLtk import Hybrid
sf = Hybrid.float_variable_value(self.subdivision_factor, 1.0)
c.set_subdivision_factor(sf)
cap_offset = Hybrid.float_variable_value(self.cap_offset,
c.default_cap_offset)
c.set_cap_offset(cap_offset)
c.show_caps()
else:
c.unshow_caps()
def settings_changed_cb(self, event = None):
cap = self.show_caps.get()
from surfcaps import capper
c = capper()
if cap:
if self.use_cap_color.get():
color = self.cap_color.rgba
else:
color = None
c.set_cap_color(color)
c.set_style(self.cap_style.get() == 'mesh')
from CGLtk import Hybrid
sf = Hybrid.float_variable_value(self.subdivision_factor, 1.0)
c.set_subdivision_factor(sf)
cap_offset = Hybrid.float_variable_value(self.cap_offset,
c.default_cap_offset)
c.set_cap_offset(cap_offset)
c.show_caps()
else:
c.unshow_caps()
def flatten_cb(self, event = None):
self.Unflatten()
self.message('')
import FlattenIcosahedron
mlist = FlattenIcosahedron.multiscale_models()
from CGLtk import Hybrid
r = Hybrid.float_variable_value(self.radius)
if r == None:
r = FlattenIcosahedron.model_radius(mlist)
if r != None:
self.radius.set(r)
elif r <= 0:
self.message('Radius must be greater than 0.')
return
if r != None:
FlattenIcosahedron.flatten_icosahedron(mlist, r)
if self.show_mesh.get() and mlist:
rgba = self.mesh_color.rgba
zoffset = Hybrid.float_variable_value(self.mesh_offset, 0)
self.show_triangle_mesh(mlist[0].surface_model(), r, rgba, zoffset)
def flatten_cb(self, event=None):
self.Unflatten()
self.message('')
import FlattenIcosahedron
mlist = FlattenIcosahedron.multiscale_models()
from CGLtk import Hybrid
r = Hybrid.float_variable_value(self.radius)
if r == None:
r = FlattenIcosahedron.model_radius(mlist)
if r != None:
self.radius.set(r)
elif r <= 0:
self.message('Radius must be greater than 0.')
return
if r != None:
FlattenIcosahedron.flatten_icosahedron(mlist, r)
if self.show_mesh.get() and mlist:
rgba = self.mesh_color.rgba
zoffset = Hybrid.float_variable_value(self.mesh_offset, 0)
self.show_triangle_mesh(mlist[0].surface_model(), r, rgba,
zoffset)
def colormap(self, message_cb):
cmap = []
for c in range(self.n):
v = self.entry_fields[c].variable
if v.get().strip() == '':
continue # unused color
from CGLtk import Hybrid
dv = Hybrid.float_variable_value(v)
if dv == None:
message_cb('Data value "%s" is not a number' % v.get())
continue
cw = self.colorwells[c]
cmap.append((dv, cw.rgba))
cmap.sort()
return cmap
def colormap(self, message_cb):
cmap = []
for c in range(self.n):
v = self.entry_fields[c].variable
if v.get().strip() == '':
continue # unused color
from CGLtk import Hybrid
dv = Hybrid.float_variable_value(v)
if dv == None:
message_cb('Data value "%s" is not a number' % v.get())
continue
cw = self.colorwells[c]
cmap.append((dv, cw.rgba))
cmap.sort()
return cmap
def fillInUI(self, parent):
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent,
labelpos='w',
listbox_selectmode="extended",
label_text="Add ions : ")
self.molList.grid(row=0, column=0, sticky="nsew")
rcf1 = Tkinter.Frame(parent)
rcf1.grid(row=2, column=0, sticky="nsew")
from Addions import ValidIontypes
self.iontype = "Cl-"
self.iontypeOption = Pmw.OptionMenu(rcf1,
label_text="Ion types:",
labelpos='w',
items=ValidIontypes,
initialitem=self.iontype,
command=self.changeIontype)
self.iontypeOption.grid(row=0, column=0)
rcf2 = Tkinter.Frame(parent)
rcf2.grid(row=3, column=0)
rcf2.columnconfigure(2, weight=1)
self.numionOption = Pmw.RadioSelect(rcf2,
buttontype='radiobutton',
command=self.changeNumion,
labelpos='w',
label_text="# of ions:")
self.numionOption.add("neutralize")
self.numionOption.add("specific number:")
self.numionOption.setvalue("neutralize")
self.numionOption.grid(row=0, column=0)
self.numion = "neutralize"
self.numionValue = Hybrid.StringVariable(rcf2)
self.numionEntry = Tkinter.Entry(
rcf2,
width=5,
textvariable=self.numionValue.tk_variable,
state='disabled')
self.numionEntry.grid(row=0, column=1)
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)
def fillInUI(self, parent):
from CGLtk import Hybrid
parent.columnconfigure(0, weight=1)
row = 0
vl = Hybrid.Scrollable_List(parent, 'Memory use', 5)
vl.listbox['font'] = 'Courier' # fixed width font so columns line up
vl.heading['font'] = 'Courier'
self.object_listbox = vl.listbox
self.object_list_heading = vl.heading
vl.frame.grid(row=row, column=0, sticky='news')
parent.rowconfigure(row, weight=1)
row = row + 1
self.update_use()
def subdivision_levels(self, radius, update_subdivision_spacing = True):
from CGLtk import Hybrid
subdivision_factor = Hybrid.float_variable_value(self.subdivision_factor,
1)
if subdivision_factor <= 0:
subdivision_factor = 1
from math import log, pow
subdivision_levels = max(0, int(round(log(subdivision_factor)/log(2))))
if update_subdivision_spacing:
import Icosahedron
edge = radius * Icosahedron.icosahedron_edge_length()
subdivision_spacing = edge / pow(2.0, subdivision_levels)
self.subdivision_spacing['text'] = ' spacing %.3g' % subdivision_spacing
return subdivision_levels
def _componentsCB(self, opt, update=True):
cf = self.componentsFrame
if hasattr(self, 'wells'):
for well in self.wells:
well.grid_forget()
well.destroy()
for label in self.labels:
label.frame.grid_forget()
self.reverseButton.grid_forget()
self.reverseButton.destroy()
else:
Tkinter.Label(cf, text="Colors").grid(row=0)
Tkinter.Label(cf, text="Labels").grid(row=0, column=1)
if isinstance(opt, int):
numComponents = opt
self.numComponents.set(opt)
else:
numComponents = opt.get()
wellSize = min(38, int((7 * 38) / numComponents))
from CGLtk.color.ColorWell import ColorWell
self.wells = []
self.labels = []
from CGLtk import Hybrid
for i in range(numComponents):
well = ColorWell(cf,
width=wellSize,
height=wellSize,
callback=self._keyChangeCB,
color='white')
well.grid(row=i + 1)
self.wells.append(well)
label = Hybrid.Entry(cf, "", 10)
label.variable.add_callback(self._keyTypingCB)
label.frame.grid(row=i + 1, column=1, sticky='ew')
self.labels.append(label)
self.reverseButton = Tkinter.Button(cf,
command=self.reverseKey,
text="Reverse ordering of above",
pady=0)
self.reverseButton.grid(row=numComponents + 1, column=0, columnspan=2)
self.notebook.setnaturalsize()
if update:
self._keyChangeCB()
def subdivision_levels(self, radius, update_subdivision_spacing=True):
from CGLtk import Hybrid
subdivision_factor = Hybrid.float_variable_value(
self.subdivision_factor, 1)
if subdivision_factor <= 0:
subdivision_factor = 1
from math import log, pow
subdivision_levels = max(0,
int(round(log(subdivision_factor) / log(2))))
if update_subdivision_spacing:
import Icosahedron
edge = radius * Icosahedron.icosahedron_edge_length()
subdivision_spacing = edge / pow(2.0, subdivision_levels)
self.subdivision_spacing[
'text'] = ' spacing %.3g' % subdivision_spacing
return subdivision_levels
def fillInUI(self, parent):
subsample_size_text = '(%d,%d,%d)' % self.subsample_size
size_text = '(%d,%d,%d)' % self.full_data_size
step_ranges = map(lambda r: '%d-%d' % r, self.allowed_step_ranges)
allowed_steps = '%s %s %s' % tuple(step_ranges)
msg = ('There are multiple possible subsample cell sizes for\n' +
'%s %s as subsamples of %s %s.\n' %
(self.subsample_name, subsample_size_text, self.full_data_name,
size_text) + 'Possibile cell sizes are %s.' % allowed_steps)
import Tkinter
lbl = Tkinter.Label(parent, text=msg, justify='left')
lbl.grid(row=0, column=0, sticky='w')
csize = '%d %d %d' % tuple(
map(lambda r: r[1], self.allowed_step_ranges))
from CGLtk import Hybrid
cs = Hybrid.Entry(parent, 'Cell size ', 15, csize)
cs.frame.grid(row=1, column=0, sticky='w')
self.cell_size_var = cs.variable
def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
row = 0
import Tkinter
from CGLtk import Hybrid
from chimera import widgets
from SurfaceZone import zonable_surface_models
sm = widgets.ModelOptionMenu(parent,
labelpos='w',
label_text='Surface ',
listFunc=zonable_surface_models,
command=self.surface_menu_cb)
sm.grid(row=row, column=0, sticky='w')
self.surface_menu = sm
row = row + 1
rs = Hybrid.Scale(parent, 'Radius ', 0, 30, .1, 2)
rs.frame.grid(row=row, column=0, sticky='ew')
row = row + 1
rs.callback(self.radius_changed_cb)
rs.entry.bind('<KeyPress-Return>', self.radius_changed_cb)
self.radius = rs
#
# Specify a label width so dialog is not resized for long messages.
#
msg = Tkinter.Label(parent, width=40, anchor='w', justify='left')
msg.grid(row=row, column=0, sticky='ew')
row = row + 1
self.message_label = msg
self.surface_menu_cb() # Set slider for current surface
def state_from_dialog(self, icosahedron_dialog):
d = icosahedron_dialog
self.is_visible = d.isVisible()
t = d.uiMaster().winfo_toplevel()
self.geometry = t.wm_geometry()
self.radius = d.radius.value(d.default_radius)
self.sphere_factor = d.sphere_factor.value(0)
self.orientation = d.orientation.get()
from CGLtk import Hybrid
self.subdivision_factor = Hybrid.float_variable_value(
d.subdivision_factor, 1)
self.style = d.surface_style.get()
self.color = d.color.rgba
if d.surface_model is None:
self.surface_model = None
else:
from SessionUtil.stateclasses import Model_State
self.surface_model = Model_State()
self.surface_model.state_from_model(d.surface_model)
def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
from CGLtk import Hybrid
self.NORMAL_MOVEMENT = 'Normal'
self.MOVE_SELECTION = 'Move selection'
self.MOVE_MOLECULE = 'Move molecule'
self.MOVE_CHAIN = 'Move chain'
self.MOVE_SECONDARY_STRUCTURE = 'Move helix, strand, or turn'
modes = (self.NORMAL_MOVEMENT, self.MOVE_SELECTION, self.MOVE_MOLECULE,
self.MOVE_CHAIN, self.MOVE_SECONDARY_STRUCTURE)
mm = Hybrid.Option_Menu(parent, 'Movement mouse mode ', *modes)
mm.frame.grid(row=row, column=0, sticky='w')
self.mode = mm.variable
mm.add_callback(self.mode_changed_cb)
def state_from_dialog(self, icosahedron_dialog):
d = icosahedron_dialog
self.is_visible = d.isVisible()
t = d.uiMaster().winfo_toplevel()
self.geometry = t.wm_geometry()
self.radius = d.radius.value(d.default_radius)
self.sphere_factor = d.sphere_factor.value(0)
self.orientation = d.orientation.get()
from CGLtk import Hybrid
self.subdivision_factor = Hybrid.float_variable_value(d.subdivision_factor,
1)
self.style = d.surface_style.get()
self.color = d.color.rgba
if d.surface_model is None:
self.surface_model = None
else:
from SessionUtil.stateclasses import Model_State
self.surface_model = Model_State()
self.surface_model.state_from_model(d.surface_model)
def fillInUI(self, parent):
self.requested_halt = False
self.xform_handler = None
self.last_relative_xform = None
t = parent.winfo_toplevel()
self.toplevel_widget = t
t.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
import Tkinter
from CGLtk import Hybrid
from VolumeViewer import Volume_Menu
ff = Tkinter.Frame(parent)
ff.grid(row=row, column=0, sticky='w')
row = row + 1
from chimera.widgets import ModelOptionMenu
om = ModelOptionMenu(ff,
labelpos='w',
label_text='Fit ',
listFunc=fit_object_models,
sortFunc=compare_fit_objects,
command=self.object_chosen_cb)
om.grid(row=0, column=0, sticky='w')
self.object_menu = om
fm = Volume_Menu(ff, ' in map ')
fm.frame.grid(row=0, column=1, sticky='w')
self.map_menu = fm
gf = Tkinter.Frame(parent)
gf.grid(row=row, column=0, sticky='w')
row += 1
cl = Tkinter.Label(gf, text='Correlation')
cl.grid(row=0, column=0, sticky='w')
cv = Tkinter.Label(gf,
width=6,
anchor='w',
relief=Tkinter.SUNKEN,
borderwidth=2)
cv.grid(row=0, column=1, padx=5, sticky='w')
self.corr_label = cv
al = Tkinter.Label(gf, text='Average map value')
al.grid(row=0, column=2, sticky='w')
av = Tkinter.Label(gf,
width=6,
anchor='w',
relief=Tkinter.SUNKEN,
borderwidth=2)
av.grid(row=0, column=3, padx=5, sticky='w')
self.ave_label = av
ub = Tkinter.Button(gf, text='Update', command=self.update_metric_cb)
ub.grid(row=0, column=4, sticky='w')
op = Hybrid.Popup_Panel(parent)
opf = op.frame
opf.grid(row=row, column=0, sticky='news')
opf.grid_remove()
opf.columnconfigure(0, weight=1)
self.options_panel = op.panel_shown_variable
row += 1
orow = 0
cb = op.make_close_button(opf)
cb.grid(row=orow, column=1, sticky='e')
ru = Hybrid.Checkbutton(opf, 'Real-time correlation / average update',
False)
ru.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.realtime_update = ru.variable
ru.callback(self.realtime_cb)
sm = Hybrid.Checkbutton_Entries(
opf, False, 'Use map simulated from atoms, resolution ', (4, ''))
sm.frame.grid(row=orow, column=0, sticky='nw')
orow += 1
self.simulate_map, self.map_resolution = sm.variables
self.simulate_map.add_callback(self.simulate_map_cb)
sm.entries[0].bind('<KeyPress-Return>', self.simulate_resolution_cb)
dt = Hybrid.Checkbutton(
opf, 'Use only data above contour level from first map', True)
dt.button.grid(row=orow, column=0, sticky='w')
orow += 1
dt.button['state'] = 'disabled'
self.limit_data = dt
self.above_threshold = dt.variable
opt = Hybrid.Radiobutton_Row(opf, 'Optimize ',
('overlap', 'correlation'))
opt.frame.grid(row=orow, column=0, sticky='w')
orow += 1
self.optimize = opt.variable
self.opt_widget = opt
cam = Hybrid.Checkbutton(
opf, 'Correlation calculated about mean data value', False)
cam.button.grid(row=orow, column=0, sticky='w')
orow += 1
cam.button['state'] = 'disabled'
self.cam_widget = cam
self.corr_about_mean = cam.variable
al = Hybrid.Checkbutton_Row(opf, 'Allow ', ('rotation', 'shift'))
al.frame.grid(row=orow, column=0, sticky='w')
orow += 1
ar, ash = [c.variable for c in al.checkbuttons]
ar.set(True)
ash.set(True)
self.allow_rotation = ar
self.allow_shift = ash
mm = Hybrid.Checkbutton(opf, 'Move whole molecules', True)
mm.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.move_whole_molecules = mm.variable
self.mwm_button = mm.button
#
# Specify a label width so dialog is not resized for long messages.
#
msg = Tkinter.Label(parent, width=40, anchor='w', justify='left')
msg.grid(row=row, column=0, sticky='ew')
row = row + 1
self.message_label = msg
self.halt_button = self.buttonWidgets['Halt']
self.allow_halt(False)
self.update_gray_out()
self.activate_undo_redo()
def fillInUI(self, parent):
t = parent.winfo_toplevel()
self.toplevel_widget = t
t.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
import Tkinter
from CGLtk import Hybrid
from VolumeViewer import Volume_Menu
ff = Tkinter.Frame(parent)
ff.grid(row=row, column=0, sticky='w')
row = row + 1
# Map selection (only Volumes)
fm = Volume_Menu(ff, 'Map: ')
fm.frame.grid(row=0, column=0, sticky='w')
self.map_menu = fm
# Resolution
rs = Hybrid.Entry(ff, 'Resolution ', 5)
rs.frame.grid(row=0, column=1, sticky='w')
self.resolution = rs.variable
# Cut-off
co = Hybrid.Entry(ff, 'Cut-off level ', 10)
co.frame.grid(row=0, column=2, sticky='w')
self.cutoff = co.variable
self.save_button = Tkinter.Button(ff,
text="From Volume Viewer",
font=self.arialBondF,
height=1,
command=self.get_cutoff)
self.save_button.grid(row=0, column=3, sticky='w')
hf = Tkinter.Frame(parent)
hf.grid(row=row, column=0, sticky='w')
row += 1
# Space
msg = Tkinter.Label(hf, anchor='w', justify='left')
msg.grid(row=2, column=0, sticky='ew')
row = row + 1
self.message_label = msg
# PDB's panel
self.pdbs = Tkinter.Frame(parent)
self.pdbs.grid(row=3, column=0, sticky='ew')
self.pdbs.columnconfigure(1, weight=1)
from chimera.widgets import MoleculeScrolledListBox, \
ModelOptionMenu
self.modelList = MoleculeScrolledListBox(
self.pdbs,
labelpos='nw',
label_text="Target PDBs to be fitted:",
listbox_selectmode='extended',
listbox_height=11)
self.modelList.grid(row=row, column=0, sticky='nsew')
self.pdbs.rowconfigure(row, weight=1)
self.pdbs.columnconfigure(0, weight=1)
self.modelList1 = MoleculeScrolledListBox(
self.pdbs,
labelpos='nw',
label_text="Target PDBs to be fixed:",
listbox_selectmode='extended',
listbox_height=11)
self.modelList1.grid(row=row, column=1, sticky='nsew')
self.pdbs.rowconfigure(row, weight=1)
self.pdbs.columnconfigure(0, weight=1)
row += 1
# Disable Results panel at first
self.results_button = self.buttonWidgets['Results']
self.results_button['state'] = 'disabled'
def fillInUI(self, parent):
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
row = 0
import Tkinter
from CGLtk import Hybrid
from surfcaps import capper
c = capper()
cp = Hybrid.Checkbutton(parent, 'Cap surfaces at clip planes',
c.caps_shown())
cp.button.grid(row=row, column=0, sticky='w')
row = row + 1
self.show_caps = cp.variable
self.show_caps.add_callback(self.settings_changed_cb)
ccf = Tkinter.Frame(parent)
ccf.grid(row=row, column=0, sticky='w')
row = row + 1
ucc = Hybrid.Checkbutton(ccf, 'Use cap color ',
not c.cap_color is None)
ucc.button.grid(row=0, column=0, sticky='w')
self.use_cap_color = ucc.variable
self.use_cap_color.add_callback(self.settings_changed_cb)
from CGLtk.color import ColorWell
cc = ColorWell.ColorWell(ccf, callback=self.settings_changed_cb)
self.cap_color = cc
rgba = c.cap_color
if rgba is None:
rgba = (1, 1, 1, 1)
cc.showColor(rgba, doCallback=0)
cc.grid(row=0, column=1, sticky='w')
cs = Hybrid.Radiobutton_Row(parent, 'Cap style: ', ('solid', 'mesh'),
self.settings_changed_cb)
cs.frame.grid(row=row, column=0, sticky='w')
if c.mesh_style: style = 'mesh'
else: style = 'solid'
cs.variable.set(style, invoke_callbacks=False)
row = row + 1
self.cap_style = cs.variable
sf = Hybrid.Entry(parent, 'Mesh subdivision factor', 4,
'%g' % c.subdivision_factor)
sf.frame.grid(row=row, column=0, sticky='w')
row = row + 1
self.subdivision_factor = sf.variable
sf.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
cd = Hybrid.Entry(parent, 'Cap to clip plane distance', 5,
'%.3g' % c.cap_offset)
cd.frame.grid(row=row, column=0, sticky='w')
row = row + 1
self.cap_offset = cd.variable
cd.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
import SimpleSession
chimera.triggers.addHandler(SimpleSession.SAVE_SESSION,
self.save_session_cb, None)
chimera.replyobj.status("Capping surfaces might reduce responsiveness",
color="orange red")
def fillInUI(self, parent):
self.morph_maps = {} # Writable maps for pairs of end-point maps.
self.default_f_range = (0.0, 1.0, 0.1)
self.play_stop_button = self.buttonWidgets['Play']
import Tkinter
from CGLtk import Hybrid
frame = parent
frame.columnconfigure(0, weight=1)
row = 0
h = Tkinter.Label(parent, text='Interpolate between two maps')
h.grid(row=row, column=0, sticky='w')
row += 1
from VolumeViewer import volume_list, Volume_Menu
vlist = volume_list()
vm1 = Volume_Menu(parent,
'First map',
open_button=True,
show_on_open=True)
vm1.frame.grid(row=row, column=0, sticky='w')
if len(vlist) >= 1:
vm1.set_volume(vlist[0])
row += 1
self.map_menu_1 = vm1
vm2 = Volume_Menu(parent,
'Second map',
open_button=True,
show_on_open=True)
vm2.frame.grid(row=row, column=0, sticky='w')
if len(vlist) >= 2:
vm2.set_volume(vlist[1])
row += 1
self.map_menu_2 = vm2
self.scale = Hybrid.Scale(parent, 'Fraction ', 0.0, 1.0, 0.01, 0)
self.scale.frame.grid(row=row, column=0, sticky='ew')
self.scale.callback(self.scale_changed_cb)
self.scale.entry.bind('<KeyPress-Return>', self.scale_changed_cb)
row += 1
op = Hybrid.Popup_Panel(parent)
opf = op.frame
opf.grid(row=row, column=0, sticky='news')
opf.grid_remove()
opf.columnconfigure(0, weight=1)
self.options_panel = op.panel_shown_variable
row += 1
orow = 0
cb = op.make_close_button(opf)
cb.grid(row=orow, column=1, sticky='e')
fr = Tkinter.Frame(opf)
fr.grid(row=orow, column=0, sticky='w')
orow += 1
fmin, fmax, fstep = self.default_f_range
fn = Hybrid.Entry(fr, 'Movie start ', 5, fmin)
fn.frame.grid(row=0, column=0, sticky='w')
fx = Hybrid.Entry(fr, ' end ', 5, fmax)
fx.frame.grid(row=0, column=1, sticky='w')
fs = Hybrid.Entry(fr, ' step ', 5, fstep)
fs.frame.grid(row=0, column=2, sticky='w')
self.f_range_variables = (fn.variable, fx.variable, fs.variable)
um = Hybrid.Checkbutton(opf, 'Undisplay original maps', True)
um.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.undisplay_maps = um.variable
mu = Hybrid.Checkbutton_Entries(opf, False,
'Multiplier for second map',
(4, '1.0'))
mu.frame.grid(row=orow, column=0, sticky='w')
orow += 1
self.use_multiplier, self.map_2_multiplier = mu.variables
ta = Hybrid.Checkbutton(opf, 'Adjust threshold for constant volume',
False)
ta.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.adjust_thresholds = ta.variable
am = Hybrid.Checkbutton(opf,
'Add to first map instead of interpolating',
False)
am.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.add_maps = am.variable
am.callback(self.add_mode_cb)
rt = Hybrid.Checkbutton(opf, 'Round trip when recording movie', True)
rt.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.roundtrip = rt.variable
#
# Specify a label width so dialog is not resized for long messages.
#
msg = Tkinter.Label(parent, width=40, anchor='w', justify='left')
msg.grid(row=row, column=0, sticky='ew')
row = row + 1
self.message_label = msg
def fillInUI(self, parent):
self.plot = None
t = parent.winfo_toplevel()
self.toplevel_widget = t
t.withdraw()
parent.columnconfigure(0, weight=1)
row = 0
from chimera.preferences import addCategory, HiddenCategory
prefs = addCategory("SAXS",
HiddenCategory,
optDict={'saxs executable': ''})
self.preferences = prefs
import Tkinter
from CGLtk import Hybrid
from chimera import widgets as w
mm = w.ExtendedMoleculeOptionMenu(
parent,
label_text='Molecule ',
labelpos='w',
labels=['selected atoms', 'all molecules'])
mm.grid(row=row, column=0, sticky='w')
row += 1
self.molecule_menu = mm
ep = Hybrid.Entry(parent, 'Experimental profile ', 25, browse=True)
ep.frame.grid(row=row, column=0, sticky='ew')
row += 1
self.experimental_profile = ep.variable
op = Hybrid.Popup_Panel(parent)
opf = op.frame
opf.grid(row=row, column=0, sticky='news')
opf.grid_remove()
opf.columnconfigure(0, weight=1)
self.options_panel = op.panel_shown_variable
row += 1
orow = 0
cb = op.make_close_button(opf)
cb.grid(row=orow, column=1, sticky='e')
np = Hybrid.Checkbutton(opf, 'Use new plot window', False)
np.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.new_plot = np.variable
ex = Hybrid.Entry(opf,
'Executable ',
25,
initial=prefs['saxs executable'],
browse=True)
ex.frame.grid(row=orow, column=0, sticky='ew')
orow += 1
ex.entry.xview('end')
self.executable = ex.variable
def fillInUI(self, parent):
from sys import getrefcount
import Tkinter, Pmw
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
self.columnMenu = Tkinter.Menu(menubar)
menubar.add_cascade(label="Columns", menu=self.columnMenu)
from chimera.tkgui import aquaMenuBar
aquaMenuBar(menubar, parent, row = 0)
row = 1
from CGLtk.Table import SortableTable
self.cavityTable = SortableTable(parent, menuInfo=
(self.columnMenu, prefs, dict.fromkeys(
defaults[SHOWN_COLS], True), False))
if not self.tableData:
from CASTp import mouthFieldNames, pocketFieldNames
# add preferred columns first
shownCols = prefs[SHOWN_COLS]
for fn in ("ID", "MS volume", "SA volume",
"pocket MS area", "pocket SA area",
"# openings"):
if fn[0] == '#' or fn == "ID":
kw = {'format': "%d"}
else:
kw = {'format': "%6.1f", 'font': "TkFixedFont"}
self.cavityTable.addColumn(fn, "lambda c: "
"c.pocketInfo['%s']" % fn, **kw)
for fn in ("mouth MS area", "mouth SA area",
"MS circumference sum",
"SA circumference sum"):
self.cavityTable.addColumn(fn, "lambda c: "
"c.mouthInfo['%s']" % fn,
format="%6.1f", font='TkFixedFont')
for fieldNames, attrName in [
(pocketFieldNames, "pocketInfo"),
(mouthFieldNames, "mouthInfo")]:
for fn in fieldNames:
if fn[0] == '#' or fn == "ID":
kw = {'format': "%d"}
else:
kw = {'format': "%6.1f", 'font': "TkFixedFont"}
c = self.cavityTable.addColumn(fn,
"lambda c: "
"getattr(c, '%s')['%s']" %
(attrName, fn), **kw)
if fn == "ID":
self.cavityTable.sortBy(c)
self.cavityTable.sortBy(c)
self.cavityTable.setData(self.cavities)
self.cavityTable.launch(browseCmd=self._selCavityCB,
restoreInfo=self.tableData)
self.cavityTable.grid(row=row, column=0, sticky="nsew")
parent.rowconfigure(row, weight=1)
parent.columnconfigure(0, weight=1)
row += 1
grp = Pmw.Group(parent,
tag_text="Treatment of Chosen Pocket Atoms")
grp.grid(row=row)
checkFrame = grp.interior()
from CGLtk import Hybrid
def buttonCB(s=self):
self._selCavityCB(self.cavityTable.selected())
self.doSelect = Hybrid.Checkbutton(checkFrame, "Select",
prefs[DO_SELECT])
self.doSelect.variable.add_callback(buttonCB)
self.doSelect.button.grid(row=0, sticky='w')
f = Tkinter.Frame(checkFrame)
f.grid(row=1, sticky='w')
self.doColor = Hybrid.Checkbutton(f, "Color",
prefs[DO_COLOR])
self.doColor.variable.add_callback(buttonCB)
self.doColor.button.grid(row=0, column=0)
from CGLtk.color.ColorWell import ColorWell
self.pocketColor = ColorWell(f, color=prefs[POCKET_COLOR],
noneOkay=True)
self.pocketColor.grid(row=0, column=1)
Tkinter.Label(f, text=" (and color all other atoms ").grid(
row=0, column=2)
self.nonpocketColor = ColorWell(f, color=prefs[NONPOCKET_COLOR],
noneOkay=True)
self.nonpocketColor.grid(row=0, column=3)
Tkinter.Label(f, text=")").grid(row=0, column=4)
self.doSurface = Hybrid.Checkbutton(checkFrame, "Surface",
prefs[DO_SURFACE])
self.doSurface.variable.add_callback(buttonCB)
self.doSurface.button.grid(row=2, sticky='w')
self.doZoom = Hybrid.Checkbutton(checkFrame, "Zoom in on",
prefs[DO_ZOOM])
self.doZoom.variable.add_callback(buttonCB)
self.doZoom.button.grid(row=3, sticky='w')
self.excludeMouth = Hybrid.Checkbutton(checkFrame,
"Exclude mouth atoms", prefs[EXCLUDE_MOUTH])
self.excludeMouth.variable.add_callback(buttonCB)
self.excludeMouth.button.grid(row=4, sticky='w')
row += 1
def fillInUI(self, parent):
self.key_buffer = ''
self.key_callback_registered = None
self.time_out_id = None
import Accelerators
self.preferences = Accelerators.accelerator_preferences_category()
self.top = parent.winfo_toplevel()
self.top.wm_withdraw() # Do not show automatically when dialog created
parent.columnconfigure(0, weight = 1)
row = 0
import Tkinter
from CGLtk import Hybrid
al = Hybrid.Scrollable_List(parent, 'Available shortcuts', 10,
self.accelerator_selection_cb)
self.accelerator_listbox = al.listbox
al.frame.grid(row = row, column = 0, sticky = 'news')
parent.rowconfigure(row, weight = 1)
row = row + 1
fi = Hybrid.Entry(parent, 'Filter list ', 20)
fi.entry.bind('<KeyRelease>', self.filter_cb)
fi.frame.grid(row = row, column = 0, sticky = 'ew')
self.filter_text = fi.variable
row = row + 1
ao = Hybrid.Checkbutton(parent, 'Enable keyboard shortcuts', False)
ao.button.grid(row = row, column = 0, sticky = 'w')
row = row + 1
ao.callback(self.activate_accelerators_cb)
self.active_var = ao.variable
from chimera import statusline
sl = Hybrid.Checkbutton(parent, 'Show main window status line',
statusline.status_line_shown())
sl.button.grid(row = row, column = 0, sticky = 'w')
row = row + 1
sl.callback(self.status_line_cb)
self.status_line_var = sl.variable
from chimera import triggers
triggers.addHandler('status line', self.status_line_visibility_cb, None)
rf = Tkinter.Frame(parent)
rf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
rb = Tkinter.Button(rf, text = 'Load', command = self.load_cb)
rb.grid(row = 0, column = 0, sticky = 'w')
afl = Tkinter.Label(rf, text = ' shortcuts file')
afl.grid(row = 0, column = 1, sticky = 'w')
path = self.preferences['path'] # Path might be None
af = Hybrid.Entry(parent, '', 20, path)
af.entry.xview_moveto(1) # show right most part of path
af.entry.bind('<KeyPress-Return>', self.load_cb)
af.frame.grid(row = row, column = 0, sticky = 'ew')
row = row + 1
self.accelerator_file = af.variable
tot = self.preferences['time out']
tm = Hybrid.Entry(parent, 'Key press time-out (seconds) ', 3, tot)
tm.frame.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.time_out = tm.variable
self.time_out.add_callback(self.time_out_changed_cb)
#
# Specify a label width so dialog is not resized for long messages.
#
msg = Tkinter.Label(parent, width = 30, anchor = 'w', justify = 'left')
msg.grid(row = row, column = 0, sticky = 'ew')
row = row + 1
self.message_label = msg
self.load_accelerators()
def fillInUI(self, parent):
self.phantom_device = None
self.cursor_model = None
self.phantom_handler = None
self.gradient_force = None
self.phantom_button_down = 0
self.last_phantom_transform = None
self.last_roll = None
self.key_callback_registered = None
self.mode = 'cursor' # 'cursor', 'move models', 'zoom',
# 'contour level', 'move marker'
self.command_list_shown = False
import Tkinter
from CGLtk import Hybrid
row = 0
po = Hybrid.Checkbutton_Row(parent, 'Enable',
('cursor', 'forces', 'key commands'))
po.frame.grid(row=row, column=0, sticky='w')
row = row + 1
self.phantom_on, self.force_field, self.commands = \
[c.variable for c in po.checkbuttons]
self.phantom_on.add_callback(self.settings_changed_cb)
self.force_field.add_callback(self.settings_changed_cb)
self.commands.add_callback(self.toggle_commands_cb)
cf = Tkinter.Frame(parent)
cf.grid(row=row, column=0, sticky='w')
row = row + 1
cs = Hybrid.Option_Menu(cf, 'Cursor shape ', 'cross', 'jack', 'sphere',
'volume crosshair')
cs.frame.grid(row=0, column=0, sticky='nw')
row = row + 1
cs.variable.set('jack')
cs.add_callback(self.settings_changed_cb)
self.cursor_shape = cs.variable
from VolumeViewer import active_volume
v = active_volume()
if v:
csize = '%.3g' % (10 * max(v.data.step))
else:
csize = '1'
cs = Hybrid.Entry(cf, ' size ', 5, csize)
cs.frame.grid(row=0, column=1, sticky='w')
cs.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.cursor_size = cs.variable
cl = Tkinter.Label(cf, text=' color ')
cl.grid(row=0, column=2, sticky='w')
from CGLtk.color import ColorWell
cc = ColorWell.ColorWell(cf, callback=self.settings_changed_cb)
self.cursor_color = cc
cc.showColor((0, 0.5, 1), doCallback=0)
cc.grid(row=0, column=3, sticky='w')
sp = Hybrid.Popup_Panel(parent)
spf = sp.frame
spf.grid(row=row, column=0, sticky='news')
spf.grid_remove()
spf.columnconfigure(0, weight=1)
self.settings_panel = sp.panel_shown_variable
row += 1
srow = 0
cb = sp.make_close_button(spf)
cb.grid(row=srow, column=1, sticky='e')
pr = Hybrid.Entry(spf, 'Phantom physical range (mm) ', 5, '200')
pr.frame.grid(row=srow, column=0, sticky='w')
srow += 1
pr.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.phantom_range = pr.variable
mf = Hybrid.Entry(spf, 'Maximum force (lbs) ', 5, '.4')
mf.frame.grid(row=srow, column=0, sticky='w')
srow += 1
mf.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.maximum_force = mf.variable
af = Hybrid.Checkbutton(spf, 'Auto-adjust force constant', 1)
af.button.grid(row=srow, column=0, sticky='w')
srow += 1
self.auto_adjust_force_constant = af.variable
self.force_field.add_callback(self.settings_changed_cb)
fc = Hybrid.Logarithmic_Scale(spf, 'Force constant ', .0001, 100, 1,
'%.2g')
fc.frame.grid(row=srow, column=0, sticky='ew')
srow += 1
fc.set_value(1)
fc.callback(self.force_constant_changed_cb)
fc.entry.bind('<KeyPress-Return>', self.force_constant_changed_cb)
self.force_constant = fc
vf = Tkinter.Frame(spf)
vf.grid(row=srow, column=0, sticky='ew')
srow += 1
self.label_row(vf, 0, ('', 'x', 'y', 'z'))
pl = self.label_row(vf, 1, ('Phantom position', '', '', ''))
self.phantom_position_labels = pl[1:]
cpl = self.label_row(vf, 2, ('Chimera position', '', '', ''))
self.chimera_position_labels = cpl[1:]
vpl = self.label_row(vf, 3, ('Volume position', '', '', ''))
self.volume_position_labels = vpl[1:]
vil = self.label_row(vf, 4, ('Volume index', '', '', ''))
self.volume_index_labels = vil[1:]
gl = self.label_row(vf, 5, ('Gradient', '', '', ''))
self.gradient_labels = gl[1:]
fl = self.label_row(vf, 6, ('Force', '', '', ''))
self.force_labels = fl[1:]
dvl = self.label_row(vf, 7, ('Data value', ''))
self.data_value_label = dvl[1]
def fillInUI(self, parent):
self.averaging_interval = 1 # seconds
self.target_fps = 10.0 # frames per second
self.standard_window_size = (512, 512)
self.initial_size = 32
self.frame_rate_timer = Frame_Rate_Timer(self.report_actual_frame_rate,
self.averaging_interval)
hb = self.buttonWidgets['Halt']
self.halt_button = hb
hb['state'] = 'disabled'
rs = self.buttonWidgets['Report Scores']
self.report_button = rs
rs['state'] = 'disabled'
import Tkinter
from CGLtk import Hybrid
row = 0
parent.columnconfigure(0, weight=1)
rt = Hybrid.Scrollable_Text(parent, None, 15, horizontal_scroll=False)
rt.text['width'] = 50
rt.text['wrap'] = 'word'
self.results_box = rt.text
rt.frame.grid(row=row, column=0, sticky='news')
parent.rowconfigure(row, weight=1)
row = row + 1
descrip = (
'Running benchmarks takes 5-10 minutes to complete.\n\n' +
'Measure graphics card and CPU performance ' +
'for volume data rendering. The scores ' +
'give the edge size of a cubic volume data ' +
'array such that rendering or contouring or recoloring ' +
'can be performed %.0f ' % self.target_fps +
'times per second.\n\n' +
'The surface and mesh benchmarks measure the ' +
'rendering rates for triangles and lines respectively. ' +
'The contour benchmark measures ' +
'CPU and memory performance. ' +
'The solid benchmark measures 2 dimensional texture ' +
'mapping performance. The recolor benchmark measures ' +
'bandwidth to the graphics card.\n\n' +
'The frame rate buttons give the redraw ' +
'rate for your currently displayed view ' +
'reported at one second intervals.\n\n' +
'The molecule benchmark measures and reports frames per '
'second when displaying different representations of molecules, '
'and operations per second for the Ops call.\n\n'
'For an accurate benchmark, please do not use the CPU for other '
'tasks while benchmarks are running, and leave the entire Chimera '
'graphics window visible.\n\n')
self.show_result(descrip)
self.results_box.see('1.0')
frf = Tkinter.Frame(parent)
frf.grid(row=row, column=0, sticky='w')
row = row + 1
mr = Hybrid.Checkbutton(frf, 'Measure frame rate continuously or ',
False)
mr.button.grid(row=0, column=0, sticky='w')
self.monitor_frame_rate = mr.variable
self.monitor_frame_rate.add_callback(self.monitor_cb)
frb = Tkinter.Button(frf,
text='one time',
command=self.actual_frame_rate)
frb.grid(row=0, column=1, sticky='w')
it = Hybrid.Checkbutton(parent, 'Show individual test controls', False)
it.button.grid(row=row, column=0, sticky='w')
row = row + 1
itf = Tkinter.Frame(parent)
itf.grid(row=row, column=0, sticky='w')
row = row + 1
trow = 0
it.popup_frame(itf)
it.popup_frame_cb() # Hide panel
bmb = Hybrid.Button_Row(itf, 'Run',
(('molecule', self.molSphere_benchmark),
('surface', self.surface_benchmark),
('mesh', self.mesh_benchmark),
('contour', self.contour_benchmark),
('solid', self.solid_benchmark),
('recolor', self.recolor_benchmark)))
bmb.frame.grid(row=trow, column=0, sticky='w')
trow += 1
smf = Tkinter.Frame(itf)
smf.grid(row=trow, column=0, sticky='w')
trow += 1
sml = Hybrid.Entry(smf, 'Show standard model, size ', 4,
repr(self.initial_size))
sml.frame.grid(row=0, column=0, sticky='w')
self.standard_model_size_var = sml.variable
smb = Hybrid.Button_Row(smf, ', ', (
('surface', self.standard_surface),
('mesh', self.standard_mesh),
('solid', self.standard_solid),
))
smb.frame.grid(row=0, column=1, sticky='w')
sv = Hybrid.Button_Row(itf, 'Set standard view', (
('camera', self.set_standard_camera_parameters),
('window size', self.set_standard_window_size),
))
sv.frame.grid(row=trow, column=0, sticky='w')
trow += 1
sf = Tkinter.Frame(parent)
sf.grid(row=row, column=0, sticky='w')
row += 1
sb = Tkinter.Button(sf, text='Show', command=self.show_scores_web_page)
sb.grid(row=0, column=0, sticky='w')
sl = Tkinter.Label(sf, text=' scores reported by others')
sl.grid(row=0, column=1, sticky='w')
def fillInUI(self, parent):
self.last_xy = None
import Tkinter
from CGLtk import Hybrid
parent.columnconfigure(0, weight = 1)
row = 0
cr = Hybrid.Checkbutton(parent, 'Constrain mouse rotations', 0)
cr.button.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.constrain_rotations = cr.variable
cr.callback(self.constrain_rotation_cb)
raf = Tkinter.Frame(parent)
raf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
ra = Hybrid.Entry(raf, 'Axis ', 8, '0 0 1')
ra.frame.grid(row = 0, column = 0, sticky = 'w')
self.rot_axis = ra.variable
rotx_cb = lambda v=self.rot_axis: v.set('1 0 0')
roty_cb = lambda v=self.rot_axis: v.set('0 1 0')
rotz_cb = lambda v=self.rot_axis: v.set('0 0 1')
rab = Hybrid.Button_Row(raf, ' ',
(('x', rotx_cb),
('y', roty_cb),
('z', rotz_cb)))
rab.frame.grid(row = 0, column = 1, sticky = 'w')
rof = Tkinter.Frame(parent)
rof.grid(row = row, column = 0, sticky = 'w')
row = row + 1
ro = Hybrid.Entry(rof, 'Origin ', 8, '0 0 0')
ro.frame.grid(row = 0, column = 0, sticky = 'w')
self.rot_origin = ro.variable
zorigin_cb = lambda v=self.rot_origin: v.set('0 0 0')
rob = Hybrid.Button_Row(rof, ' ',
(('zero', zorigin_cb),
('center', self.set_rotation_origin_at_center),))
rob.frame.grid(row = 0, column = 1, sticky = 'w')
sep = Tkinter.Frame(parent, relief = Tkinter.GROOVE,
borderwidth=1, height=2)
sep.grid(row = row, column = 0, sticky = 'ew', pady = 10)
row = row + 1
tr = Hybrid.Checkbutton(parent, 'Constrain mouse translations', 0)
tr.button.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.constrain_translations = tr.variable
tr.callback(self.constrain_translation_cb)
taf = Tkinter.Frame(parent)
taf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
ta = Hybrid.Entry(taf, 'Axis ', 8, '0 0 1')
ta.frame.grid(row = 0, column = 0, sticky = 'w')
self.trans_axis = ta.variable
tx_cb = lambda v=self.trans_axis: v.set('1 0 0')
ty_cb = lambda v=self.trans_axis: v.set('0 1 0')
tz_cb = lambda v=self.trans_axis: v.set('0 0 1')
tab = Hybrid.Button_Row(taf, ' ',
(('x', tx_cb),
('y', ty_cb),
('z', tz_cb)))
tab.frame.grid(row = 0, column = 1, sticky = 'w')
ttf = Tkinter.Frame(parent)
ttf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
tt = Hybrid.Option_Menu(ttf, 'Allow only ',
'parallel', 'perpendicular')
tt.variable.set('parallel')
tt.frame.grid(row = 0, column = 0, sticky = 'w')
self.translation_type = tt.variable
tl = Tkinter.Label(ttf, text = ' motion')
tl.grid(row = 0, column = 1, sticky = 'w')
sep = Tkinter.Frame(parent, relief = Tkinter.GROOVE,
borderwidth=1, height=2)
sep.grid(row = row, column = 0, sticky = 'ew', pady = 10)
row = row + 1
rl = Tkinter.Label(parent, text = 'Axis and origin relative to')
rl.grid(row = row, column = 0, sticky = 'w')
row = row + 1
mmf = Tkinter.Frame(parent)
mmf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
mm = Hybrid.Option_Menu(mmf, 'model ')
mm.frame.grid(row = 0, column = 0, sticky = 'w')
self.model_menu = mm
self.model_name = mm.variable
from chimera import openModels
openModels.addAddHandler(self.model_list_changed_cb, None)
openModels.addRemoveHandler(self.model_list_changed_cb, None)
ml = Tkinter.Label(mmf, text = ' coordinates.')
ml.grid(row = 0, column = 1, sticky = 'w')
self.update_model_menu()
self.register_mouse_modes()