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 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.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):
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.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):
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.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()
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
rs = Hybrid.Scale(parent, ' Radius ', 0, 1000, .1, '')
rs.frame.grid(row=row, column=0, sticky='ew')
row = row + 1
# rs.callback(self.flatten_cb)
rs.entry.bind('<KeyPress-Return>', self.flatten_cb)
self.radius = rs.variable
# Mesh
mf = Tkinter.Frame(parent)
mf.grid(row=row, column=0, sticky='w')
row = row + 1
sm = Hybrid.Checkbutton(mf, 'Show triangle mesh,', True)
sm.button.grid(row=0, column=0, sticky='w')
self.show_mesh = sm.variable
self.show_mesh.add_callback(self.show_mesh_cb)
cl = Tkinter.Label(mf, text='color')
cl.grid(row=0, column=1, sticky='w')
initial_color = (.5, .5, .5, 1)
from CGLtk.color import ColorWell
mc = ColorWell.ColorWell(mf, callback=self.mesh_color_changed_cb)
mc.grid(row=0, column=2, sticky='w')
self.mesh_color = mc
mc.showColor(initial_color)
mo = Hybrid.Entry(mf, ' z offset ', 5, '0')
mo.frame.grid(row=0, column=3, sticky='w')
self.mesh_offset = mo.variable
mo.entry.bind('<KeyPress-Return>', self.mesh_offset_changed_cb)
# Orthographic camera mode.
import chimera
c = chimera.viewer.camera
oc = Hybrid.Checkbutton(parent, 'Use orthographic camera mode.',
c.ortho)
oc.button.grid(row=row, column=0, sticky='w')
row = row + 1
self.orthographic = oc.variable
self.orthographic.add_callback(self.orthographic_cb)
#
# 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.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.model = None
self.position_handler = None
self.screen_position = (-.6, -.6)
self.last_xyz_position = None
self.frozen_model_list = []
self.toplevel_widget = parent.winfo_toplevel()
self.toplevel_widget.withdraw()
row = 0
import Tkinter
from CGLtk import Hybrid
sb = Hybrid.Checkbutton(parent, 'Show scale bar', 0)
sb.button.grid(row=row, column=0, sticky='w')
row = row + 1
self.show_scalebar = sb.variable
self.show_scalebar.add_callback(self.settings_changed_cb)
bf = Tkinter.Frame(parent)
bf.grid(row=row, column=0, sticky='w')
row = row + 1
le = Hybrid.Entry(bf, 'Length ', 5, '10')
le.frame.grid(row=0, column=0, sticky='w')
le.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.bar_length = le.variable
te = Hybrid.Entry(bf, ' Thickness', 3, '1')
te.frame.grid(row=0, column=1, sticky='w')
te.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.bar_thickness = te.variable
cl = Tkinter.Label(bf, text=' Color ')
cl.grid(row=0, column=2, sticky='w')
from CGLtk.color import ColorWell
bc = ColorWell.ColorWell(bf, callback=self.settings_changed_cb)
self.bar_color = bc
bc.showColor((1, 1, 1), doCallback=0)
bc.grid(row=0, column=3, sticky='w')
lf = Tkinter.Frame(parent)
lf.grid(row=row, column=0, sticky='w')
row = row + 1
# \u00C5 is the Angstrom symbol
lb = Hybrid.Entry(lf, 'Label ', 5, u'# \u00C5')
lb.frame.grid(row=0, column=0, sticky='w')
lb.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.label_text = lb.variable
xo = Hybrid.Entry(lf, ' Offset ', 3, '')
xo.frame.grid(row=0, column=1, sticky='w')
xo.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.label_x_offset = xo.variable
yo = Hybrid.Entry(lf, '', 3, '')
yo.frame.grid(row=0, column=2, sticky='w')
yo.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.label_y_offset = yo.variable
ct = Tkinter.Label(lf, text=' Color ')
ct.grid(row=0, column=3, sticky='w')
from CGLtk.color import ColorWell
lc = ColorWell.ColorWell(lf, callback=self.settings_changed_cb)
self.label_color = lc
lc.showColor((1, 1, 1), doCallback=0)
lc.grid(row=0, column=4, sticky='w')
ore = Hybrid.Radiobutton_Row(parent, 'Orientation ',
('horizontal', 'vertical'),
self.orientation_cb)
ore.frame.grid(row=row, column=0, sticky='w')
row = row + 1
self.orientation = ore.variable
self.orientation.set('horizontal', invoke_callbacks=0)
pf = Tkinter.Frame(parent)
pf.grid(row=row, column=0, sticky='w')
row = row + 1
pp = Hybrid.Checkbutton(pf, 'Preserve screen position', 1)
pp.button.grid(row=0, column=0, sticky='w')
self.preserve_position = pp.variable
self.preserve_position.add_callback(self.settings_changed_cb)
xp = Hybrid.Entry(pf, '', 5, '')
xp.frame.grid(row=0, column=1, sticky='w')
xp.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.screen_x_position = xp.variable
yp = Hybrid.Entry(pf, '', 5, '')
yp.frame.grid(row=0, column=2, sticky='w')
yp.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
self.screen_y_position = yp.variable
self.set_screen_position_entries()
mb = Hybrid.Checkbutton(parent,
'Move scale bar with data models locked', 0)
mb.button.grid(row=row, column=0, sticky='w')
row = row + 1
self.move_scalebar = mb.variable
self.move_scalebar.add_callback(self.move_scalebar_cb)
import SimpleSession
chimera.triggers.addHandler(SimpleSession.SAVE_SESSION,
self.save_session_cb, None)
chimera.triggers.addHandler(chimera.CLOSE_SESSION,
self.close_session_cb, None)
def fillInUI(self, parent):
self.sel_handler = None
self.last_selected = set()
import Tkinter
from CGLtk import Hybrid
top = parent.winfo_toplevel()
menubar = Tkinter.Menu(top, type="menubar", tearoff=False)
top.config(menu=menubar)
file_menu_entries = (('Export...', self.export_cb), )
fmenu = Hybrid.cascade_menu(menubar, 'File', file_menu_entries)
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
columns = (
('region', lambda r: r.rid),
('grid points', lambda r: r.point_count()),
('grouped', lambda r: len(r.children())),
('has surface', lambda r: 1 if r.has_surface() else 0),
('contacts', lambda r: len(r.contacting_regions())),
('edge distance', lambda r: r.edge_distance()),
('bounds', lambda r: tuple(r.bounds()[0]) + tuple(r.bounds()[1]),
'%d,%d,%d,%d,%d,%d', False),
)
self.computed_attributes = dict([c[:2] for c in columns])
self.keys = set([c[0] for c in columns])
defaults = dict([(c[0], True) for c in columns])
prefs = {}
mi = (self.columnMenu, prefs, defaults, True)
from CGLtk.Table import SortableTable
self.attribute_table = t = SortableTable(parent, menuInfo=mi)
for cspec in columns:
name, func = cspec[:2]
format = cspec[2] if len(cspec) >= 3 else format_item
display = cspec[3] if len(cspec) >= 4 else True
t.addColumn(name,
func,
format=format,
display=display,
font='TkFixedFont',
refresh=False)
self.add_columns() # Additional region attributes.
t.setData([])
t.launch(browseCmd=self.table_line_selected)
t.grid(row=row, column=0, sticky="nsew")
parent.rowconfigure(row, weight=1)
parent.columnconfigure(0, weight=1)
row += 1
naf = Tkinter.Frame(parent)
naf.grid(row=row, column=0, sticky='new')
naf.columnconfigure(1, weight=1)
row += 1
ke = Hybrid.Entry(naf, 'Set attribute ', 15)
ke.frame.grid(row=0, column=0, sticky='w')
self.key_name = ke.variable
ke.entry.bind('<KeyPress-Return>', self.new_value_cb)
ve = Hybrid.Entry(naf, ' to value ', 15)
ve.frame.grid(row=0, column=1, sticky='ew')
self.value = ve.variable
ve.entry.bind('<KeyPress-Return>', self.new_value_cb)
ol = Tkinter.Label(naf, text=' or ')
ol.grid(row=0, column=2, sticky='e')
sb = Tkinter.Button(naf, text='snapshot', command=self.snapshot_cb)
sb.grid(row=0, column=3, sticky='e')
fl = Hybrid.Checkbutton_Entries(parent, False, 'Filter list ',
(50, 'grid_points > 1000'))
fl.frame.grid(row=row, column=0, sticky='new')
row += 1
self.use_filter, self.filter_text = fl.variables
self.use_filter.add_callback(self.filter_cb)
e = fl.entries[0]
fl.frame.columnconfigure(1, weight=1)
e.grid(sticky='ew')
e.bind('<KeyPress-Return>', self.filter_cb)
op = Hybrid.Popup_Panel(parent, resize_dialog=False)
opf = op.frame
opf.grid(row=row, column=0, sticky='news')
opf.grid_remove()
opf.columnconfigure(0, weight=1)
self.optionsPanel = op.panel_shown_variable
row += 1
orow = 0
cb = op.make_close_button(opf)
cb.grid(row=orow, column=0, sticky='e')
l = Tkinter.Label(opf, text='Options', font='TkCaptionFont')
l.grid(column=0, row=orow, sticky='w', pady=5)
orow += 1
ss = Hybrid.Checkbutton(opf, 'Show selected region surface', False)
ss.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.show_selected = ss.variable
msg = Tkinter.Label(parent, width=60, anchor='w', justify='left')
msg.grid(column=0, row=row, sticky='ew')
self.msg = msg
self.Update()
def fillInUI(self, parent):
self.molecules = []
self.add_model_handler = None
self.remove_model_handler = None
import Tkinter
from CGLtk import Hybrid
row = 0
mm = Hybrid.Option_Menu(parent, 'Molecule: ')
mm.frame.grid(row=row, column=0, sticky='w')
row = row + 1
mm.add_callback(self.molecule_menu_cb)
self.molecule_menu = mm
labels = []
for text in (
'Space group: ',
'Cell size: ',
'Cell angles: ',
'Number of SMTRY matrices: ',
'Number of space group symmetries: ',
'Number of MTRIX matrices: ',
):
lbl = Tkinter.Label(parent, text=text)
lbl.grid(row=row, column=0, sticky='w')
row = row + 1
labels.append(lbl)
(
self.space_group,
self.cell_size,
self.cell_angles,
self.smtry_count,
self.sg_smtry_count,
self.mtrix_count,
) = labels
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')
usr = Hybrid.Checkbutton(opf, 'Use SMTRY records in PDB header', True)
usr.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.use_smtry_records = usr.variable
ucr = Hybrid.Checkbutton(
opf, 'Use CRYST1 record if SMTRY records are missing', True)
ucr.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.use_cryst1_smtry = ucr.variable
umr = Hybrid.Checkbutton(
opf, 'Use MTRIX records for non-crystallographic symmetry', True)
umr.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.use_mtrix_records = umr.variable
co = Hybrid.Entry(opf, 'Cell origin ', 12, '0 0 0')
co.frame.grid(row=orow, column=0, sticky='w')
orow += 1
self.grid_orig = co.variable
co.entry.bind('<KeyPress-Return>', self.origin_change_cb)
nc = Hybrid.Entry(opf, 'Number of cells ', 12, '1 1 1')
nc.frame.grid(row=orow, column=0, sticky='w')
orow += 1
self.ncells = nc.variable
nc.entry.bind('<KeyPress-Return>', self.make_unit_cell_cb)
br = Hybrid.Button_Row(parent, '', (
('Make copies', self.make_unit_cell_cb),
('Outline', self.show_outline_cb),
('Delete copies', self.close_unit_cell_cb),
))
br.frame.grid(row=row, column=0, sticky='e')
row = row + 1
def fillInUI(self, parent):
self.filter_widgets = fw = []
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
self.gaussian = 'Gaussian'
self.median = 'Median 3x3x3'
self.bin = 'Bin'
self.laplacian = 'Laplacian'
self.fourier = 'Fourier Transform'
self.scale = 'Scale'
ft = Hybrid.Option_Menu(parent, 'Filter type:',
self.gaussian, self.median, self.bin,
self.laplacian, self.fourier, self.scale)
ft.button.configure(indicatoron = False)
ft.frame.grid(row = row, column = 0, sticky = 'w')
row += 1
self.filter_type = ft.variable
ft.add_callback(self.filter_type_changed_cb)
ws = Hybrid.Scale(parent, 'Width ', 1.0, 10.0, 0.0, 1.0)
ws.frame.grid(row = row, column = 0, sticky = 'ew')
row += 1
ws.callback(self.filter_parameter_changed_cb)
ws.entry.bind('<KeyPress-Return>', self.filter_cb)
self.sdev = ws
Hybrid.Balloon_Help(ws.label, 'Width is one standard deviation.',
delay = 0.5)
fw.append((self.gaussian, ws.frame))
mi = Hybrid.Scale(parent, 'Iterations ', 0, 5, 1, 1, 2)
mi.frame.grid(row = row, column = 0, sticky = 'ew')
row += 1
mi.callback(self.filter_parameter_changed_cb)
mi.entry.bind('<KeyPress-Return>', self.filter_cb)
self.median_iterations = mi
fw.append((self.median, mi.frame))
bs = Hybrid.Entry(parent, 'Bin size', 5, '2')
bs.frame.grid(row = row, column = 0, sticky = 'w')
row += 1
self.binsize = bs.variable
bs.entry.bind('<KeyPress-Return>', self.filter_cb)
fw.append((self.bin, bs.frame))
sf = Tkinter.Frame(parent)
sf.grid(row = row, column = 0, sticky = 'w')
row += 1
fw.append((self.scale, sf))
sh = Hybrid.Entry(sf, 'Shift', 5, '0')
sh.frame.grid(row = 0, column = 0, sticky = 'w')
self.shift = sh.variable
sh.entry.bind('<KeyPress-Return>', self.filter_cb)
sc = Hybrid.Entry(sf, 'Scale', 5, '1')
sc.frame.grid(row = 0, column = 1, sticky = 'w')
self.scale_factor = sc.variable
sc.entry.bind('<KeyPress-Return>', self.filter_cb)
vt = Hybrid.Option_Menu(sf, 'Value type', 'same', 'int8', 'uint8', 'int16', 'uint16', 'int32', 'uint32', 'float32', 'float64')
vt.frame.grid(row = 0, column = 2, sticky = 'w')
self.value_type = vt.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')
sr = Hybrid.Checkbutton(opf, 'Displayed subregion only', True)
sr.button.grid(row = orow, column = 0, sticky = 'w')
orow += 1
self.use_subregion = sr.variable
ss = Hybrid.Checkbutton(opf, 'Displayed subsampling only', False)
ss.button.grid(row = orow, column = 0, sticky = 'w')
orow += 1
self.use_step = ss.variable
ta = Hybrid.Checkbutton(opf, 'Adjust threshold for constant volume', True)
ta.button.grid(row = orow, column = 0, sticky = 'w')
orow += 1
self.adjust_thresholds = ta.variable
iu = Hybrid.Checkbutton(opf, 'Immediate update', False)
iu.button.grid(row = orow, column = 0, sticky = 'w')
orow += 1
self.immediate_update = iu.variable
self.filter_type_changed_cb()
self.set_scale_range(initial = True)
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 import widgets
from SurfaceColor import colorable_surface_models
sm = widgets.ModelOptionMenu(parent,
labelpos='w',
label_text='Color surface ',
listFunc=colorable_surface_models,
command=self.surface_menu_cb)
sm.grid(row=row, column=0, sticky='w')
self.surface_menu = sm
row = row + 1
from SurfaceColor import coloring_methods
methods = [cm.menu_name for cm in coloring_methods]
csm = Hybrid.Option_Menu(parent, 'by ', *methods)
csm.frame.grid(row=row, column=0, sticky='w')
self.color_source_menu = csm.variable
csm.add_callback(self.color_source_changed_cb)
row = row + 1
from VolumeViewer import Volume_Menu
vm = Volume_Menu(parent, 'file', open_button='browse...')
vm.frame.grid(row=row, column=0, sticky='w')
self.volume_menu = vm
row += 1
oaf = Tkinter.Frame(parent)
oaf.grid(row=row, column=0, sticky='w')
row = row + 1
self.origin_axis_frame = oaf
oe = Hybrid.Entry(oaf, 'origin ', 8, '0 0 0')
oe.frame.grid(row=0, column=0, sticky='w')
self.origin_variable = oe.variable
oe.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
cb = Tkinter.Button(oaf, text='center', command=self.set_center_cb)
cb.grid(row=0, column=1, sticky='w')
ae = Hybrid.Entry(oaf, 'axis ', 8, '0 0 1')
ae.frame.grid(row=0, column=2, sticky='w')
self.axis_frame = ae.frame
self.axis_variable = ae.variable
ae.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
cg = Colorwell_GUI(parent, 5, self.settings_changed_cb)
cg.set_color_palette('rainbow')
self.colormap_gui = cg
self.colormap_gui.frame.grid(row=row, column=0, sticky='w')
row = 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='ne')
cf = Tkinter.Frame(opf)
cf.grid(row=orow, column=0, sticky='w')
orow += 1
color_counts = ('2', '3', '5', '10', '15', '20')
cc = Hybrid.Option_Menu(cf, 'Colors ', *color_counts)
cc.frame.grid(row=0, column=0, sticky='w')
self.color_count = cc.variable
self.color_count.set('5')
cc.add_callback(self.change_color_count_cb)
cpat = ('Rainbow', 'Gray', 'Red-Blue', 'Cyan-Maroon')
cp = Hybrid.Option_Menu(cf, 'Palette', *cpat)
cp.frame.grid(row=0, column=1, sticky='w')
self.palette = cp.variable
cp.add_callback(self.change_color_palette_cb)
rc = Tkinter.Button(cf, text='Reverse', command=self.reverse_colors_cb)
rc.grid(row=0, column=2, sticky='w')
ckb = Tkinter.Button(opf,
text="Create color key",
command=self.colormap_gui.color_key_cb)
ckb.grid(row=orow, column=0, sticky='w')
orow += 1
dcf = Tkinter.Frame(opf)
dcf.grid(row=orow, column=0, sticky='w')
orow += 1
db = Tkinter.Button(dcf,
text='Set',
command=self.show_default_colormap_values)
db.grid(row=0, column=0, sticky='w')
dt = Tkinter.Label(dcf, text=' full range of surface values')
dt.grid(row=0, column=1, sticky='w')
so = Hybrid.Entry(opf, 'Surface offset ', 5, '1.4')
so.frame.grid(row=orow, column=0, sticky='w')
self.surface_offset = so.variable
self.surface_offset_frame = so.frame
orow += 1
so.entry.bind('<KeyPress-Return>', self.settings_changed_cb)
ocf = Tkinter.Frame(opf)
ocf.grid(row=orow, column=0, sticky='w')
orow += 1
self.outside_color_frame = ocf
ocl = Tkinter.Label(ocf, text='Color outside volume')
ocl.grid(row=0, column=0, sticky='w')
outside_color = (.5, .5, .5, 1)
from CGLtk.color import ColorWell
cw = ColorWell.ColorWell(ocf)
cw.showColor(outside_color)
cw.grid(row=0, column=1, sticky='w')
self.outside_color = cw
co = Hybrid.Checkbutton(opf, 'Only color sliced surface face', 0)
co.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.color_caps_only = co.variable
ppc = Hybrid.Checkbutton(opf, 'Per-pixel coloring', False)
ppc.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.per_pixel_color = ppc.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
# Show current coloring if one already exists from session restore.
self.surface_menu_cb()
# Show axix, origin, volume widgets if appropriate.
self.color_source_changed_cb()
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):
self.default_radius = 1
self.default_color = (1,0.6,0.8,.5) # Pink eraser
t = parent.winfo_toplevel()
self.toplevel_widget = t
t.withdraw()
parent.columnconfigure(0, weight = 1)
row = 0
import Tkinter
from CGLtk import Hybrid
sh = Hybrid.Checkbutton(parent, 'Show volume-erasing sphere ', True)
sh.button.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.show_sphere_var = sh.variable
sh.callback(self.show_sphere_cb)
crf = Tkinter.Frame(parent)
crf.grid(row = row, column = 0, sticky = 'ew')
crf.columnconfigure(2, weight = 1)
row = row + 1
cl = Tkinter.Label(crf, text = 'Color')
cl.grid(row = 0, column = 0, sticky = 'w')
from CGLtk.color import ColorWell
sc = ColorWell.ColorWell(crf, color = self.default_color,
callback = self.change_sphere_color_cb)
sc.grid(row = 0, column = 1, sticky = 'w')
self.sphere_color = sc
rs = Hybrid.Scale(crf, ' Radius ', 0, 30, .1, 2)
rs.frame.grid(row = 0, column = 2, sticky = 'ew')
row = row + 1
rs.callback(self.change_radius_cb)
rs.entry.bind('<KeyPress-Return>', self.change_radius_cb)
self.sphere_radius_scale = rs
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('button 2')
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 move sphere')
mbl.grid(row = 0, column = 1, sticky = 'w')
ka = Tkinter.Label(parent, text = 'Erase using keyboard accelerator "es".')
ka.grid(row = row, column = 0, sticky = 'w')
row = row + 1
from Accelerators import add_accelerator
add_accelerator('es', 'Erase volume data inside sphere', self.Erase)
add_accelerator('eo', 'Erase volume data outside sphere',
self.erase_outside_sphere)
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):
from chimera.widgets import MoleculeScrolledListBox
self.molList = MoleculeScrolledListBox(parent,
labelpos='w',
listbox_selectmode="extended",
label_text="Solvate: ")
self.molList.grid(row=0, column=0, sticky="nsew")
self.solvateMethod = Pmw.RadioSelect(parent,
buttontype='radiobutton',
command=self.changeMethod,
labelpos='w',
label_text="Solvate method:")
self.solvateMethod.add("Box")
self.solvateMethod.add("Cap")
self.solvateMethod.add("Oct")
self.solvateMethod.add("Shell")
self.solvateMethod.setvalue("Box")
self.solvateMethod.grid(row=1, column=0, sticky="nsew")
self.method = "Box"
rcf1 = Tkinter.Frame(parent)
rcf1.grid(row=2, column=0, sticky="nsew")
self.solvent = prefs[SOLVENT_MODEL]
from Solvate import ValidSolventModels
self.solventModel = Pmw.OptionMenu(rcf1,
label_text="Solvent Model:",
labelpos='w',
items=ValidSolventModels,
initialitem=self.solvent,
command=self.changeSolvent)
self.solventModel.grid(row=0, column=0)
rcf2 = Tkinter.Frame(rcf1)
rcf2.grid(row=0, column=1)
rcf1.columnconfigure(1, weight=1)
self.extentLabel = Tkinter.Label(rcf2, text="Box size:")
self.extentLabel.grid(row=0, column=0)
self.extentValue = Hybrid.StringVariable(rcf2)
ev = Tkinter.Entry(rcf2,
width=5,
textvariable=self.extentValue.tk_variable)
ev.grid(row=0, column=1)
rcf3 = Tkinter.Frame(parent)
rcf3.grid(row=3, column=0)
self.centerLabel = Tkinter.Label(rcf3,
text="Cap center (in ambmask):",
state='disabled')
self.centerLabel.grid(row=0, column=0)
self.centerValue = Hybrid.StringVariable(rcf3)
self.centerEntry = Tkinter.Entry(
rcf3,
width=5,
textvariable=self.centerValue.tk_variable,
state='disabled')
self.centerEntry.grid(row=0, column=1)
self.removeExisting = Hybrid.Checkbutton(
parent, "Remove existing ions/solvent", True)
self.removeExisting.button.grid(row=4, column=0)
parent.rowconfigure(0, weight=1)
parent.columnconfigure(0, weight=1)