def fillInUI(self, parent):
import Tkinter
import Pmw
self.scale = Pmw.Counter(parent,
labelpos="w",
label_text="Border scale:",
entryfield_value=1.0,
datatype={"counter": "real"},
entryfield_validate={
"validator": "real",
"min": 0.0,
"max": 2.0,
},
increment=0.1)
self.scale.pack(side=Tkinter.BOTTOM,
expand=Tkinter.FALSE,
fill=Tkinter.X)
from chimera.widgets import ModelScrolledListBox
self.modListBox = ModelScrolledListBox(parent,
listbox_selectmode="extended",
labelpos="n",
label_text="Models")
self.modListBox.pack(side=Tkinter.LEFT,
expand=Tkinter.TRUE,
fill=Tkinter.BOTH)
class TileStructuresCB(ModelessDialog):
title = "Tile Structures"
help = "ContributedSoftware/ensembletile/ensembletile.html"
oneshot = True
def configure(self, models=[]):
self.modListBox.setvalue(models)
def fillInUI(self, parent):
import Tkinter
import Pmw
self.scale = Pmw.Counter(parent,
labelpos="w",
label_text="Border scale:",
entryfield_value=1.0,
datatype={"counter": "real"},
entryfield_validate={
"validator": "real",
"min": 0.0,
"max": 2.0,
},
increment=0.1)
self.scale.pack(side=Tkinter.BOTTOM,
expand=Tkinter.FALSE,
fill=Tkinter.X)
from chimera.widgets import ModelScrolledListBox
self.modListBox = ModelScrolledListBox(parent,
listbox_selectmode="extended",
labelpos="n",
label_text="Models")
self.modListBox.pack(side=Tkinter.LEFT,
expand=Tkinter.TRUE,
fill=Tkinter.BOTH)
def Apply(self):
modList = self.modListBox.getvalue()
if len(modList) == 0:
import chimera
raise chimera.UserError("No models selected")
ef = self.scale.component("entryfield")
if not ef.valid():
import chimera
raise chimera.UserError(ScaleErrorText)
s = float(ef.getvalue())
import base
base.tile(modList, s)
class TileStructuresCB(ModelessDialog):
title = "Tile Structures"
help = "ContributedSoftware/ensembletile/ensembletile.html"
oneshot = True
def configure(self, models=[]):
self.modListBox.setvalue(models)
def fillInUI(self, parent):
import Tkinter
import Pmw
self.scale = Pmw.Counter(parent,
labelpos="w",
label_text="Border scale:",
entryfield_value=1.0,
datatype={ "counter":"real" },
entryfield_validate={
"validator":"real",
"min":0.0,
"max":2.0,
},
increment=0.1)
self.scale.pack(side=Tkinter.BOTTOM, expand=Tkinter.FALSE,
fill=Tkinter.X)
from chimera.widgets import ModelScrolledListBox
self.modListBox = ModelScrolledListBox(parent,
listbox_selectmode="extended",
labelpos="n",
label_text="Models")
self.modListBox.pack(side=Tkinter.LEFT, expand=Tkinter.TRUE,
fill=Tkinter.BOTH)
def Apply(self):
modList = self.modListBox.getvalue()
if len(modList) == 0:
import chimera
raise chimera.UserError("No models selected")
ef = self.scale.component("entryfield")
if not ef.valid():
import chimera
raise chimera.UserError(ScaleErrorText)
s = float(ef.getvalue())
import base
base.tile(modList, s)
def fillInUI(self, parent):
import Tkinter
import Pmw
self.scale = Pmw.Counter(parent,
labelpos="w",
label_text="Border scale:",
entryfield_value=1.0,
datatype={ "counter":"real" },
entryfield_validate={
"validator":"real",
"min":0.0,
"max":2.0,
},
increment=0.1)
self.scale.pack(side=Tkinter.BOTTOM, expand=Tkinter.FALSE,
fill=Tkinter.X)
from chimera.widgets import ModelScrolledListBox
self.modListBox = ModelScrolledListBox(parent,
listbox_selectmode="extended",
labelpos="n",
label_text="Models")
self.modListBox.pack(side=Tkinter.LEFT, expand=Tkinter.TRUE,
fill=Tkinter.BOTH)
def fillInUI(self, parent):
import Pmw, Tkinter
self.buttonWidgets['OK']['state'] = 'disabled'
self.buttonWidgets['Apply']['state'] = 'disabled'
from chimera.widgets import ModelScrolledListBox
self.surfListBox = ModelScrolledListBox(
parent,
labelpos='n',
label_text='Surfaces to color by ESP:',
listbox_selectmode="extended",
filtFunc=lambda m: isinstance(m, chimera.MSMSModel),
selectioncommand=self._selSurfCB)
self.surfListBox.grid(row=0, column=0, sticky="nsew", columnspan=2)
Pmw.OptionMenu(parent,
command=self._menuCB,
initialitem="3",
items=[str(x) for x in range(2, 12)],
labelpos='w',
label_text="Number of colors/values:").grid(
row=1, column=0, columnspan=2)
f = self.interpFrame = Tkinter.Frame(parent)
f.grid(row=2, column=0, columnspan=2)
self.wells = []
self.values = []
self._entryOpts = {
'validate': 'real',
'entry_justify': 'center',
'entry_width': 6
}
from CGLtk.color.ColorWell import ColorWell
for color, value in [("red", -10), ("white", 0), ("blue", 10)]:
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value), **self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
from chimera.tkoptions import FloatOption, BooleanOption
self.distDep = BooleanOption(
parent,
3,
"Distance-dependent dielectric",
True,
None,
balloon="If true, charge falls off with distance squared to\n"
"simulate solvent screening effects")
self.dielectric = FloatOption(parent, 4, "Dielectric constant", 4.0,
None)
self.surfDist = FloatOption(parent,
5,
"Distance from surface",
1.4,
None,
balloon="Potential at this distance from\n"
"the surface is used for coloring")
self.hisGroup = Pmw.Group(parent,
hull_padx=2,
tag_text="Implicit Histidine Protonation")
self.hisGroup.grid(row=6, column=0, columnspan=2, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
lab = Tkinter.Label(
interior,
text="Assumed histidine "
"protonation for\nstructures without explicit hydrogens")
from tkFont import Font
font = Font(font=lab.cget('font'))
font.config(size=int(0.75 * float(font.cget('size'))), slant='italic')
lab.config(font=font)
lab.grid(row=0)
Tkinter.Radiobutton(interior,
variable=self.hisProtVar,
value="name",
text="Residue name-based",
command=self._switchHisList).grid(row=1,
sticky='w')
f = Tkinter.Frame(interior)
f.grid(row=2)
Tkinter.Label(f,
text="HID/HIE/HIP = delta/epsilon/both").grid(row=0,
sticky='w')
self.hisDefault = Pmw.OptionMenu(
f,
initialitem=self.HB,
items=[self.HB, "delta", "epsilon", "both"],
labelpos='w',
label_text="HIS = ",
command=lambda a, s=self: setattr(s, 'hisChanged', True))
self.hisDefault.grid(row=1, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(interior,
variable=self.hisProtVar,
value="pick",
textvariable=self._pickText,
command=self._switchHisList).grid(row=3,
sticky='w')
Tkinter.Button(parent,
pady=0,
command=self._colorKeyCB,
text="Create corresponding color key").grid(
row=7, column=0, columnspan=2)
self.hisChanged = False
class EspDialog(ModelessDialog):
title = "Coulombic Surface Coloring"
name = "ESP computation"
help = "ContributedSoftware/coulombic/coulombic.html"
HB = "estimated from H-bonds"
def fillInUI(self, parent):
import Pmw, Tkinter
self.buttonWidgets['OK']['state'] = 'disabled'
self.buttonWidgets['Apply']['state'] = 'disabled'
from chimera.widgets import ModelScrolledListBox
self.surfListBox = ModelScrolledListBox(
parent,
labelpos='n',
label_text='Surfaces to color by ESP:',
listbox_selectmode="extended",
filtFunc=lambda m: isinstance(m, chimera.MSMSModel),
selectioncommand=self._selSurfCB)
self.surfListBox.grid(row=0, column=0, sticky="nsew", columnspan=2)
Pmw.OptionMenu(parent,
command=self._menuCB,
initialitem="3",
items=[str(x) for x in range(2, 12)],
labelpos='w',
label_text="Number of colors/values:").grid(
row=1, column=0, columnspan=2)
f = self.interpFrame = Tkinter.Frame(parent)
f.grid(row=2, column=0, columnspan=2)
self.wells = []
self.values = []
self._entryOpts = {
'validate': 'real',
'entry_justify': 'center',
'entry_width': 6
}
from CGLtk.color.ColorWell import ColorWell
for color, value in [("red", -10), ("white", 0), ("blue", 10)]:
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value), **self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
from chimera.tkoptions import FloatOption, BooleanOption
self.distDep = BooleanOption(
parent,
3,
"Distance-dependent dielectric",
True,
None,
balloon="If true, charge falls off with distance squared to\n"
"simulate solvent screening effects")
self.dielectric = FloatOption(parent, 4, "Dielectric constant", 4.0,
None)
self.surfDist = FloatOption(parent,
5,
"Distance from surface",
1.4,
None,
balloon="Potential at this distance from\n"
"the surface is used for coloring")
self.hisGroup = Pmw.Group(parent,
hull_padx=2,
tag_text="Implicit Histidine Protonation")
self.hisGroup.grid(row=6, column=0, columnspan=2, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
lab = Tkinter.Label(
interior,
text="Assumed histidine "
"protonation for\nstructures without explicit hydrogens")
from tkFont import Font
font = Font(font=lab.cget('font'))
font.config(size=int(0.75 * float(font.cget('size'))), slant='italic')
lab.config(font=font)
lab.grid(row=0)
Tkinter.Radiobutton(interior,
variable=self.hisProtVar,
value="name",
text="Residue name-based",
command=self._switchHisList).grid(row=1,
sticky='w')
f = Tkinter.Frame(interior)
f.grid(row=2)
Tkinter.Label(f,
text="HID/HIE/HIP = delta/epsilon/both").grid(row=0,
sticky='w')
self.hisDefault = Pmw.OptionMenu(
f,
initialitem=self.HB,
items=[self.HB, "delta", "epsilon", "both"],
labelpos='w',
label_text="HIS = ",
command=lambda a, s=self: setattr(s, 'hisChanged', True))
self.hisDefault.grid(row=1, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(interior,
variable=self.hisProtVar,
value="pick",
textvariable=self._pickText,
command=self._switchHisList).grid(row=3,
sticky='w')
Tkinter.Button(parent,
pady=0,
command=self._colorKeyCB,
text="Create corresponding color key").grid(
row=7, column=0, columnspan=2)
self.hisChanged = False
def Apply(self):
for entry in self.values:
entry.invoke()
colors = [w.rgba for w in self.wells]
values = [float(e.getvalue()) for e in self.values]
if self.hisProtVar.get() == "name":
hisScheme = {
self.HB: None,
'delta': 'HID',
'epsilon': 'HIE',
'both': 'HIP'
}[self.hisDefault.getvalue()]
else:
hisScheme = self.hisListingData
from ESP import colorEsp
for surf in self.surfListBox.getvalue():
if self.hisChanged:
# clear out charge values so that histidines
# get new charges
for a in surf.atoms:
a.charge = None
colorEsp(surf,
colors,
values,
dielectric=self.dielectric.get(),
distDep=self.distDep.get(),
surfDist=self.surfDist.get(),
hisScheme=hisScheme)
self.hisChanged = False
def _colorKeyCB(self):
for entry in self.values:
entry.invoke()
from Ilabel.gui import IlabelDialog
from chimera import dialogs
d = dialogs.display(IlabelDialog.name)
d.keyConfigure(
zip([w.rgba for w in self.wells],
[e.getvalue() for e in self.values]))
def _menuCB(self, val):
newNum = int(val)
oldSettings = []
for well, entry in zip(self.wells, self.values):
entry.invoke()
oldSettings.append((well.rgba, float(entry.getvalue())))
well.grid_forget()
well.destroy()
entry.grid_forget()
entry.destroy()
import Pmw
from CGLtk.color.ColorWell import ColorWell
self.wells = []
self.values = []
scale = (len(oldSettings) - 1.0) / (newNum - 1.0)
f = self.interpFrame
for i in range(newNum):
index = i * scale
if index == int(index) \
or int(index) >= len(oldSettings):
color, value = oldSettings[int(index)]
else:
lowc, lowv = oldSettings[int(index)]
highc, highv = oldSettings[int(index) + 1]
frac = index - int(index)
color = []
for lowcomp, highcomp in zip(lowc, highc):
color.append((1.0 - frac) * lowcomp + frac * highcomp)
value = (1.0 - frac) * lowv + frac * highv
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value), **self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
def _selSurfCB(self):
if self.surfListBox.getvalue():
state = 'normal'
else:
state = 'disabled'
self.buttonWidgets['OK']['state'] = state
self.buttonWidgets['Apply']['state'] = state
self._updateHisListing()
def _select(self, hisType):
for r, vars in self._vars.items():
dv, ev = vars
if hisType == "delta":
dv.set(True)
ev.set(False)
self.hisListingData[r] = "HID"
elif hisType == "epsilon":
dv.set(False)
ev.set(True)
self.hisListingData[r] = "HIE"
else:
dv.set(True)
ev.set(True)
self.hisListingData[r] = "HIP"
def _switchHisList(self):
self.hisChanged = True
if not hasattr(self, 'hisListing'):
if self.hisProtVar.get() != "pick":
return
self.hisListingData = {}
import Tix, Tkinter
self.hisFrame = Tkinter.Frame(self.hisGroup.interior())
self.hisListing = Tix.ScrolledHList(self.hisFrame,
width="3i",
options="""hlist.columns 4
hlist.header 1
hlist.indicator 1""")
self.hisListing.hlist.configure(
selectbackground=self.hisListing['background'],
selectborderwidth=0)
self.hisListing.grid(row=0, column=0, columnspan=3, sticky="nsew")
self.hisFrame.rowconfigure(1, weight=1)
self.hisFrame.columnconfigure(0, weight=1)
self.hisFrame.columnconfigure(1, weight=1)
hlist = self.hisListing.hlist
hlist.header_create(0, itemtype="text", text="Model")
hlist.header_create(1, itemtype="text", text="Residue")
hlist.header_create(2, itemtype="text", text="Delta")
hlist.header_create(3, itemtype="text", text="Epsilon")
self._checkButtonStyle = Tix.DisplayStyle(
"window",
background=hlist['background'],
refwindow=self.hisListing,
anchor='center')
self._updateHisListing()
Tkinter.Button(self.hisFrame,
text="All Delta",
pady=0,
highlightthickness=0,
command=lambda p="delta": self._select(p)).grid(
row=1, column=0)
Tkinter.Button(self.hisFrame,
text="All Epsilon",
pady=0,
highlightthickness=0,
command=lambda p="epsilon": self._select(p)).grid(
row=1, column=1)
Tkinter.Button(self.hisFrame,
text="All Both",
pady=0,
highlightthickness=0,
command=lambda p="both": self._select(p)).grid(
row=1, column=2)
if self.hisProtVar.get() == "pick":
self._pickText.set("Specified individually:")
self.hisFrame.grid(row=4, sticky="nsew")
interior = self.hisGroup.interior()
interior.rowconfigure(4, weight=1)
self.uiMaster().rowconfigure(6, weight=4)
else:
self._pickText.set("Specified individually...")
self.hisFrame.grid_forget()
interior = self.hisGroup.interior()
interior.rowconfigure(4, weight=0)
self.uiMaster().rowconfigure(6, weight=0)
def _toggleDelta(self, res):
self.hisChanged = True
old = self.hisListingData[res]
if old == "HIS":
new = "HID"
elif old == "HID":
new = "HIS"
elif old == "HIE":
new = "HIP"
else:
new = "HIE"
self.hisListingData[res] = new
def _toggleEpsilon(self, res):
self.hisChanged = True
old = self.hisListingData[res]
if old == "HIS":
new = "HIE"
elif old == "HID":
new = "HIP"
elif old == "HIE":
new = "HIS"
else:
new = "HID"
self.hisListingData[res] = new
def _updateHisListing(self):
if not hasattr(self, 'hisListing'):
return
self._updateHisListingData()
hlist = self.hisListing.hlist
on = self.hisListing.tk.call('tix', 'getimage', 'ck_on')
off = self.hisListing.tk.call('tix', 'getimage', 'ck_off')
hlist.delete_all()
import Tkinter
row = 0
self._vars = {}
for m in [s.molecule for s in self.surfListBox.getvalue()]:
for r in m.residues:
try:
hisType = self.hisListingData[r]
except KeyError:
continue
hlist.add(row,
itemtype="text",
text="%s (%s)" % (m.name, m.oslIdent()))
hlist.item_create(row,
1,
itemtype="text",
text=r.oslIdent(start=chimera.SelResidue))
var = Tkinter.IntVar(hlist)
var.set(hisType in ["HID", "HIP"])
cmd = lambda r=r: self._toggleDelta(r)
self._vars[r] = [var]
toggle = Tkinter.Checkbutton(hlist,
command=cmd,
variable=var,
image=off,
selectimage=on,
selectcolor="",
indicatoron=False,
borderwidth=0)
hlist.item_create(row,
2,
itemtype="window",
window=toggle,
style=self._checkButtonStyle)
var = Tkinter.IntVar(hlist)
var.set(hisType in ["HIE", "HIP"])
cmd = lambda r=r: self._toggleEpsilon(r)
self._vars[r].append(var)
toggle = Tkinter.Checkbutton(hlist,
command=cmd,
variable=var,
image=off,
selectimage=on,
selectcolor="",
indicatoron=False,
borderwidth=0)
hlist.item_create(row,
3,
itemtype="window",
window=toggle,
style=self._checkButtonStyle)
row += 1
def _updateHisListingData(self):
newData = {}
default = {
'delta': 'HID',
'epsilon': 'HIE',
'both': 'HIP',
self.HB: 'HID'
}[self.hisDefault.getvalue()]
for m in [s.molecule for s in self.surfListBox.getvalue()]:
for r in m.residues:
if r.type not in ["HIS", "HIE", "HIP", "HID"]:
continue
try:
newData[r] = self.hisListingData[r]
except KeyError:
if r.type == 'HIS':
newData[r] = default
else:
newData[r] = r.type
self.hisListingData = newData
def fillInUI(self, parent):
"""fillInUI(parent)
"""
self.status('')
self.track_xform = None
# menu frame
row = 0
from chimera.widgets import ModelOptionMenu
self.menu = ModelOptionMenu(parent, command=self.menu_cb,
labelpos='w', label_text='Model:')
self.menu.grid(row=row, sticky='w', padx=8, pady=8)
# initial transform frame (itf)
row = row + 1
itf = Tkinter.Frame(parent,padx=8,pady=8)
itf.grid(row=row, column=0, sticky='nw')
# record initial
itfg = Hybrid.Button_Row(itf, 'Record transform ',
(('Record',self.record_initial_cb),))
itfg.frame.grid(row=0, column=0, columnspan=3, sticky='w')
# parameters
itfp = Tkinter.Frame(itf, padx=16)
itfp.grid(row=1, column=0, sticky='w')
self.init_trans, self.init_rot, self.init_ang = \
self._make_param_panel(itfp)
# current transform frame (ctf)
row = row + 1
ctf = Tkinter.Frame(parent, padx=8, pady=8)
ctf.grid(row=row, column=0, sticky='nw')
# get current
ctfg = Hybrid.Button_Row(ctf, 'Current transform ',
(('Get',self.record_current_cb),))
ctfg.frame.grid(row=0, column=0, sticky='w')
# parameters
ctfp = Tkinter.Frame(ctf, padx=16)
ctfp.grid(row=1, column=0, sticky='w')
self.curr_trans, self.curr_rot, self.curr_ang = \
self._make_param_panel(ctfp)
# listbox frame
row = row+1
from chimera.widgets import ModelScrolledListBox
self.listbox = ModelScrolledListBox(parent,
labelpos='w',
label_text='Model List:')
self.listbox.component('listbox')['selectmode'] = 'extended'
self.listbox.grid(row=row, sticky='w', padx=8, pady=8)
# apply frame (af)
row = row + 1
af = Tkinter.Frame(parent, padx=8, pady=8)
af.grid(row=row, column=0, sticky='nw')
# apply
afg = Hybrid.Button_Row(af, '',
(('Apply',self.apply_initial_cb),))
afg.frame.grid(row=0, column=0, sticky='w')
text = ' recorded transform to models\n'
text = text + ' selected in above model list '
afgL = Tkinter.Label(af, text = text)
afgL.grid(row=0, column=1, sticky='w')
# reset
afr = Hybrid.Button_Row(af, '',
(('Reset',self.reset_initial_cb),))
afr.frame.grid(row=1, column=0, sticky='w')
text = ' initial transform'
afrL = Tkinter.Label(af, text = text)
afrL.grid(row=1, column=1, sticky='w')
class TrackXformDialog(ModelessDialog):
"""Class TrackXformDialog()
Dialog for tracking transforms in Chimera's camera coordinates.
"""
title= 'Track Model Transfom'
name = 'track model transformation'
buttons = ('Close',)
# @ help = 'ContributedSoftware/SegmentTrack/trackxform.html'
dir_pkg = os.path.dirname(__file__)
help_path = os.path.join(dir_pkg, 'trackxform.html')
help_url = 'file://' + help_path
help = help_url
provideStatus = True
statusPosition = 'above'
statusResizing = False
statusWidth = 40
# ---------------------------------------------------------------------
# Fill in UI
# ---------------------------------------------------------------------
def fillInUI(self, parent):
"""fillInUI(parent)
"""
self.status('')
self.track_xform = None
# menu frame
row = 0
from chimera.widgets import ModelOptionMenu
self.menu = ModelOptionMenu(parent, command=self.menu_cb,
labelpos='w', label_text='Model:')
self.menu.grid(row=row, sticky='w', padx=8, pady=8)
# initial transform frame (itf)
row = row + 1
itf = Tkinter.Frame(parent,padx=8,pady=8)
itf.grid(row=row, column=0, sticky='nw')
# record initial
itfg = Hybrid.Button_Row(itf, 'Record transform ',
(('Record',self.record_initial_cb),))
itfg.frame.grid(row=0, column=0, columnspan=3, sticky='w')
# parameters
itfp = Tkinter.Frame(itf, padx=16)
itfp.grid(row=1, column=0, sticky='w')
self.init_trans, self.init_rot, self.init_ang = \
self._make_param_panel(itfp)
# current transform frame (ctf)
row = row + 1
ctf = Tkinter.Frame(parent, padx=8, pady=8)
ctf.grid(row=row, column=0, sticky='nw')
# get current
ctfg = Hybrid.Button_Row(ctf, 'Current transform ',
(('Get',self.record_current_cb),))
ctfg.frame.grid(row=0, column=0, sticky='w')
# parameters
ctfp = Tkinter.Frame(ctf, padx=16)
ctfp.grid(row=1, column=0, sticky='w')
self.curr_trans, self.curr_rot, self.curr_ang = \
self._make_param_panel(ctfp)
# listbox frame
row = row+1
from chimera.widgets import ModelScrolledListBox
self.listbox = ModelScrolledListBox(parent,
labelpos='w',
label_text='Model List:')
self.listbox.component('listbox')['selectmode'] = 'extended'
self.listbox.grid(row=row, sticky='w', padx=8, pady=8)
# apply frame (af)
row = row + 1
af = Tkinter.Frame(parent, padx=8, pady=8)
af.grid(row=row, column=0, sticky='nw')
# apply
afg = Hybrid.Button_Row(af, '',
(('Apply',self.apply_initial_cb),))
afg.frame.grid(row=0, column=0, sticky='w')
text = ' recorded transform to models\n'
text = text + ' selected in above model list '
afgL = Tkinter.Label(af, text = text)
afgL.grid(row=0, column=1, sticky='w')
# reset
afr = Hybrid.Button_Row(af, '',
(('Reset',self.reset_initial_cb),))
afr.frame.grid(row=1, column=0, sticky='w')
text = ' initial transform'
afrL = Tkinter.Label(af, text = text)
afrL.grid(row=1, column=1, sticky='w')
def Close(self):
"""Close() - close dialog.
"""
ModelessDialog.Close(self)
def menu_cb(self, val):
return
# ---------------------------------------------------------------------
# Paramaters panel
# ---------------------------------------------------------------------
def _make_param_panel(self, frame):
"""_make_param_panel(frame)
Input:
frame
Output:
translation translation text entry
rotation rotation text entry
angle angle text entry
Makes the parameters panel.
"""
row = 0
# translation
transL = Tkinter.Label(frame, text='Translation: ')
transL.grid(row=row, column=0, sticky='w')
trans = Tkinter.Label(frame, text='')
trans.grid(row=row, column=1, sticky='w')
# rotation axis
row = row + 1
rotL = Tkinter.Label(frame, text='Rotation Axes: ')
rotL.grid(row=row, column=0, sticky='w')
rot = Tkinter.Label(frame, text='')
rot.grid(row=row, column=1, sticky='w')
# rotation angle
row = row + 1
angL = Tkinter.Label(frame, text='Rotation Angle: ')
angL.grid(row=row, column=0, sticky='w')
ang = Tkinter.Label(frame, text='')
ang.grid(row=row, column=1, sticky='w')
return trans, rot, ang
# ---------------------------------------------------------------------
# Call back functions
# ---------------------------------------------------------------------
def record_initial_cb(self):
"""record_initial_cb() - callback func for record transform.
"""
model = self.menu.getvalue()
self.record_initial(model)
def record_current_cb(self):
"""record_current_cb() - callback func for current transform.
"""
model = self.menu.getvalue()
self.record_current(model)
def apply_initial_cb(self):
"""apply_initial_cb() - callback function for apply button.
"""
models = self.listbox.getvalue()
for model in models:
self.update_current(model)
model = self.menu.getvalue()
self.record_current(model)
def reset_initial_cb(self):
"""reset_initial_cb() - callback function for reset button.
"""
self.reset_initial()
# ---------------------------------------------------------------------
# Command line (for GUI) functions
# ---------------------------------------------------------------------
def set_model(self, model):
"""set_model(model) - set menu to model.
"""
self.menu.setvalue(model)
def record_initial(self, model):
"""record_initial(model) - record and display model transform.
"""
if not model:
msg = 'No initial model'
self.status(msg, color='blue', blankAfter=5)
self.track_xform = get_xform(model)
self._display_param_initial(self.track_xform)
def record_current(self, model):
"""record_current(model) - display current model transform.
"""
if not model:
msg = 'No current model'
self.status(msg, color='blue', blankAfter=5)
self._display_param_current(model)
def update_current(self, model):
"""update_current(model) - apply recorded transform to model.
"""
if not model:
msg = 'No current model'
self.status(msg, color='blue', blankAfter=5)
if not self.track_xform:
msg = 'No starting transform'
self.status(msg, color='blue', blankAfter=5)
update_xform(model, self.track_xform)
def reset_initial(self):
"""reset_initial() - reset all parameters
"""
self.track_xform = None
self._display_param_initial(None)
self._display_param_current(None)
# ---------------------------------------------------------------------
# GUI functions for parameters
# ---------------------------------------------------------------------
def _display_param_initial(self, xform):
"""_display_param_initial(xform) - display initial transform.
"""
vx, ax, an = self.get_param(xform=xform)
self.init_trans['text'] = vx
self.init_rot['text'] = ax
self.init_ang['text'] = an
def _display_param_current(self, model):
"""_display_param_current(model) - display current transform.
"""
vx, ax, an = self.get_param(model=model)
self.curr_trans['text'] = vx
self.curr_rot['text'] = ax
self.curr_ang['text'] = an
def get_param(self, xform=None, model=None):
"""get_param(xform=None, model=None) - transform parameters.
Input:
xform=None
model=None
Output:
translation
rotation vector
rotation angle
Get transform parameters as text strings, one each for
translation vector, rotation vector, and rotation angle.
Return empty text strings for no model and no xform.
"""
if not xform:
if model:
xform = model.openState.xform
else:
return '','',''
vx = xform.getTranslation()
ax, an = xform.getRotation()
vx_text = '(%7.3f, %7.3f, %7.3f)' % (vx.x, vx.y, vx.z)
ax_text = '(%8.4f, %8.4f, %8.4f)' % (ax.x, ax.y, ax.z)
an_text = '%7.3f' % (an)
return vx_text, ax_text, an_text
def fillInUI(self, parent):
import Pmw, Tkinter
self.buttonWidgets['OK']['state'] = 'disabled'
self.buttonWidgets['Apply']['state'] = 'disabled'
from chimera.widgets import ModelScrolledListBox
self.surfListBox = ModelScrolledListBox(parent, labelpos='n',
label_text='Surfaces to color by ESP:',
listbox_selectmode="extended",
filtFunc=lambda m: isinstance(m, chimera.MSMSModel),
selectioncommand=self._selSurfCB)
self.surfListBox.grid(row=0, column=0, sticky="nsew",
columnspan=2)
Pmw.OptionMenu(parent, command=self._menuCB, initialitem="3",
items=[str(x) for x in range(2, 12)], labelpos='w',
label_text="Number of colors/values:").grid(row=1,
column=0, columnspan=2)
f = self.interpFrame = Tkinter.Frame(parent)
f.grid(row=2, column=0, columnspan=2)
self.wells = []
self.values = []
self._entryOpts = {
'validate': 'real',
'entry_justify': 'center',
'entry_width': 6
}
from CGLtk.color.ColorWell import ColorWell
for color, value in [("red", -10), ("white", 0), ("blue", 10)]:
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value),
**self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
from chimera.tkoptions import FloatOption, BooleanOption
self.distDep = BooleanOption(parent, 3,
"Distance-dependent dielectric", True, None, balloon=
"If true, charge falls off with distance squared to\n"
"simulate solvent screening effects")
self.dielectric = FloatOption(parent, 4, "Dielectric constant",
4.0, None)
self.surfDist = FloatOption(parent, 5, "Distance from surface",
1.4, None, balloon="Potential at this distance from\n"
"the surface is used for coloring")
self.hisGroup = Pmw.Group(parent, hull_padx=2,
tag_text="Implicit Histidine Protonation")
self.hisGroup.grid(row=6, column=0, columnspan=2, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
lab = Tkinter.Label(interior, text="Assumed histidine "
"protonation for\nstructures without explicit hydrogens")
from tkFont import Font
font = Font(font=lab.cget('font'))
font.config(size=int(0.75 * float(font.cget('size'))),
slant='italic')
lab.config(font=font)
lab.grid(row=0)
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="name", text="Residue name-based", command=
self._switchHisList).grid(row=1, sticky='w')
f = Tkinter.Frame(interior)
f.grid(row=2)
Tkinter.Label(f, text="HID/HIE/HIP = delta/epsilon/both").grid(
row=0, sticky='w')
self.hisDefault = Pmw.OptionMenu(f, initialitem=self.HB,
items=[self.HB, "delta", "epsilon", "both"], labelpos='w',
label_text="HIS = ", command=lambda a, s=self:
setattr(s, 'hisChanged', True))
self.hisDefault.grid(row=1, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="pick", textvariable=self._pickText,
command=self._switchHisList).grid(row=3, sticky='w')
Tkinter.Button(parent, pady=0, command=self._colorKeyCB,
text="Create corresponding color key").grid(row=7,
column=0, columnspan=2)
self.hisChanged = False
class EspDialog(ModelessDialog):
title = "Coulombic Surface Coloring"
name = "ESP computation"
help = "ContributedSoftware/coulombic/coulombic.html"
HB = "estimated from H-bonds"
def fillInUI(self, parent):
import Pmw, Tkinter
self.buttonWidgets['OK']['state'] = 'disabled'
self.buttonWidgets['Apply']['state'] = 'disabled'
from chimera.widgets import ModelScrolledListBox
self.surfListBox = ModelScrolledListBox(parent, labelpos='n',
label_text='Surfaces to color by ESP:',
listbox_selectmode="extended",
filtFunc=lambda m: isinstance(m, chimera.MSMSModel),
selectioncommand=self._selSurfCB)
self.surfListBox.grid(row=0, column=0, sticky="nsew",
columnspan=2)
Pmw.OptionMenu(parent, command=self._menuCB, initialitem="3",
items=[str(x) for x in range(2, 12)], labelpos='w',
label_text="Number of colors/values:").grid(row=1,
column=0, columnspan=2)
f = self.interpFrame = Tkinter.Frame(parent)
f.grid(row=2, column=0, columnspan=2)
self.wells = []
self.values = []
self._entryOpts = {
'validate': 'real',
'entry_justify': 'center',
'entry_width': 6
}
from CGLtk.color.ColorWell import ColorWell
for color, value in [("red", -10), ("white", 0), ("blue", 10)]:
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value),
**self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
from chimera.tkoptions import FloatOption, BooleanOption
self.distDep = BooleanOption(parent, 3,
"Distance-dependent dielectric", True, None, balloon=
"If true, charge falls off with distance squared to\n"
"simulate solvent screening effects")
self.dielectric = FloatOption(parent, 4, "Dielectric constant",
4.0, None)
self.surfDist = FloatOption(parent, 5, "Distance from surface",
1.4, None, balloon="Potential at this distance from\n"
"the surface is used for coloring")
self.hisGroup = Pmw.Group(parent, hull_padx=2,
tag_text="Implicit Histidine Protonation")
self.hisGroup.grid(row=6, column=0, columnspan=2, sticky="nsew")
self.hisProtVar = Tkinter.StringVar(parent)
self.hisProtVar.set("name")
interior = self.hisGroup.interior()
interior.columnconfigure(0, weight=1)
lab = Tkinter.Label(interior, text="Assumed histidine "
"protonation for\nstructures without explicit hydrogens")
from tkFont import Font
font = Font(font=lab.cget('font'))
font.config(size=int(0.75 * float(font.cget('size'))),
slant='italic')
lab.config(font=font)
lab.grid(row=0)
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="name", text="Residue name-based", command=
self._switchHisList).grid(row=1, sticky='w')
f = Tkinter.Frame(interior)
f.grid(row=2)
Tkinter.Label(f, text="HID/HIE/HIP = delta/epsilon/both").grid(
row=0, sticky='w')
self.hisDefault = Pmw.OptionMenu(f, initialitem=self.HB,
items=[self.HB, "delta", "epsilon", "both"], labelpos='w',
label_text="HIS = ", command=lambda a, s=self:
setattr(s, 'hisChanged', True))
self.hisDefault.grid(row=1, sticky='w')
self._pickText = Tkinter.StringVar(parent)
self._pickText.set("Specified individually...")
Tkinter.Radiobutton(interior, variable=self.hisProtVar,
value="pick", textvariable=self._pickText,
command=self._switchHisList).grid(row=3, sticky='w')
Tkinter.Button(parent, pady=0, command=self._colorKeyCB,
text="Create corresponding color key").grid(row=7,
column=0, columnspan=2)
self.hisChanged = False
def Apply(self):
for entry in self.values:
entry.invoke()
colors = [w.rgba for w in self.wells]
values = [float(e.getvalue()) for e in self.values]
if self.hisProtVar.get() == "name":
hisScheme = {
self.HB: None,
'delta': 'HID',
'epsilon': 'HIE',
'both': 'HIP'
}[self.hisDefault.getvalue()]
else:
hisScheme = self.hisListingData
from ESP import colorEsp
for surf in self.surfListBox.getvalue():
if self.hisChanged:
# clear out charge values so that histidines
# get new charges
for a in surf.atoms:
a.charge = None
colorEsp(surf, colors, values,
dielectric=self.dielectric.get(),
distDep=self.distDep.get(),
surfDist=self.surfDist.get(),
hisScheme=hisScheme)
self.hisChanged = False
def _colorKeyCB(self):
for entry in self.values:
entry.invoke()
from Ilabel.gui import IlabelDialog
from chimera import dialogs
d = dialogs.display(IlabelDialog.name)
d.keyConfigure(zip([w.rgba for w in self.wells],
[e.getvalue() for e in self.values]))
def _menuCB(self, val):
newNum = int(val)
oldSettings = []
for well, entry in zip(self.wells, self.values):
entry.invoke()
oldSettings.append((well.rgba, float(entry.getvalue())))
well.grid_forget()
well.destroy()
entry.grid_forget()
entry.destroy()
import Pmw
from CGLtk.color.ColorWell import ColorWell
self.wells = []
self.values = []
scale = (len(oldSettings) - 1.0) / (newNum - 1.0)
f = self.interpFrame
for i in range(newNum):
index = i * scale
if index == int(index) \
or int(index) >= len(oldSettings):
color, value = oldSettings[int(index)]
else:
lowc, lowv = oldSettings[int(index)]
highc, highv = oldSettings[int(index)+1]
frac = index - int(index)
color = []
for lowcomp, highcomp in zip(lowc, highc):
color.append((1.0 - frac) * lowcomp
+ frac * highcomp)
value = (1.0 - frac) * lowv + frac * highv
well = ColorWell(f, color=color)
well.grid(row=0, column=len(self.wells))
self.wells.append(well)
entry = Pmw.EntryField(f, value=str(value),
**self._entryOpts)
entry.grid(row=1, column=len(self.values))
self.values.append(entry)
def _selSurfCB(self):
if self.surfListBox.getvalue():
state = 'normal'
else:
state = 'disabled'
self.buttonWidgets['OK']['state'] = state
self.buttonWidgets['Apply']['state'] = state
self._updateHisListing()
def _select(self, hisType):
for r, vars in self._vars.items():
dv, ev = vars
if hisType == "delta":
dv.set(True)
ev.set(False)
self.hisListingData[r] = "HID"
elif hisType == "epsilon":
dv.set(False)
ev.set(True)
self.hisListingData[r] = "HIE"
else:
dv.set(True)
ev.set(True)
self.hisListingData[r] = "HIP"
def _switchHisList(self):
self.hisChanged = True
if not hasattr(self, 'hisListing'):
if self.hisProtVar.get() != "pick":
return
self.hisListingData = {}
import Tix, Tkinter
self.hisFrame = Tkinter.Frame(self.hisGroup.interior())
self.hisListing = Tix.ScrolledHList(self.hisFrame,
width="3i",
options="""hlist.columns 4
hlist.header 1
hlist.indicator 1""")
self.hisListing.hlist.configure(
selectbackground=self.hisListing['background'],
selectborderwidth=0)
self.hisListing.grid(row=0, column=0, columnspan=3,
sticky="nsew")
self.hisFrame.rowconfigure(1, weight=1)
self.hisFrame.columnconfigure(0, weight=1)
self.hisFrame.columnconfigure(1, weight=1)
hlist = self.hisListing.hlist
hlist.header_create(0, itemtype="text", text="Model")
hlist.header_create(1, itemtype="text", text="Residue")
hlist.header_create(2, itemtype="text", text="Delta")
hlist.header_create(3, itemtype="text", text="Epsilon")
self._checkButtonStyle = Tix.DisplayStyle("window",
background=hlist['background'],
refwindow=self.hisListing, anchor='center')
self._updateHisListing()
Tkinter.Button(self.hisFrame, text="All Delta",
pady=0, highlightthickness=0,
command=lambda p="delta": self._select(p)
).grid(row=1, column=0)
Tkinter.Button(self.hisFrame, text="All Epsilon",
pady=0, highlightthickness=0,
command=lambda p="epsilon": self._select(p)
).grid(row=1, column=1)
Tkinter.Button(self.hisFrame, text="All Both",
pady=0, highlightthickness=0,
command=lambda p="both": self._select(p)
).grid(row=1, column=2)
if self.hisProtVar.get() == "pick":
self._pickText.set("Specified individually:")
self.hisFrame.grid(row=4, sticky="nsew")
interior = self.hisGroup.interior()
interior.rowconfigure(4, weight=1)
self.uiMaster().rowconfigure(6, weight=4)
else:
self._pickText.set("Specified individually...")
self.hisFrame.grid_forget()
interior = self.hisGroup.interior()
interior.rowconfigure(4, weight=0)
self.uiMaster().rowconfigure(6, weight=0)
def _toggleDelta(self, res):
self.hisChanged = True
old = self.hisListingData[res]
if old == "HIS":
new = "HID"
elif old == "HID":
new = "HIS"
elif old == "HIE":
new = "HIP"
else:
new = "HIE"
self.hisListingData[res] = new
def _toggleEpsilon(self, res):
self.hisChanged = True
old = self.hisListingData[res]
if old == "HIS":
new = "HIE"
elif old == "HID":
new = "HIP"
elif old == "HIE":
new = "HIS"
else:
new = "HID"
self.hisListingData[res] = new
def _updateHisListing(self):
if not hasattr(self, 'hisListing'):
return
self._updateHisListingData()
hlist = self.hisListing.hlist
on = self.hisListing.tk.call('tix', 'getimage', 'ck_on')
off = self.hisListing.tk.call('tix', 'getimage', 'ck_off')
hlist.delete_all()
import Tkinter
row = 0
self._vars = {}
for m in [s.molecule for s in self.surfListBox.getvalue()]:
for r in m.residues:
try:
hisType = self.hisListingData[r]
except KeyError:
continue
hlist.add(row, itemtype="text", text="%s (%s)"
% (m.name, m.oslIdent()))
hlist.item_create(row, 1, itemtype="text",
text=r.oslIdent(
start=chimera.SelResidue))
var = Tkinter.IntVar(hlist)
var.set(hisType in ["HID", "HIP"])
cmd = lambda r=r: self._toggleDelta(r)
self._vars[r] = [var]
toggle = Tkinter.Checkbutton(hlist, command=cmd,
variable=var, image=off, selectimage=on,
selectcolor="", indicatoron=False,
borderwidth=0)
hlist.item_create(row, 2, itemtype="window",
window=toggle,
style=self._checkButtonStyle)
var = Tkinter.IntVar(hlist)
var.set(hisType in ["HIE", "HIP"])
cmd = lambda r=r: self._toggleEpsilon(r)
self._vars[r].append(var)
toggle = Tkinter.Checkbutton(hlist, command=cmd,
variable=var, image=off, selectimage=on,
selectcolor="", indicatoron=False,
borderwidth=0)
hlist.item_create(row, 3, itemtype="window",
window=toggle,
style=self._checkButtonStyle)
row += 1
def _updateHisListingData(self):
newData = {}
default = {
'delta': 'HID',
'epsilon': 'HIE',
'both': 'HIP',
self.HB: 'HID'
}[self.hisDefault.getvalue()]
for m in [s.molecule for s in self.surfListBox.getvalue()]:
for r in m.residues:
if r.type not in ["HIS", "HIE", "HIP", "HID"]:
continue
try:
newData[r] = self.hisListingData[r]
except KeyError:
if r.type == 'HIS':
newData[r] = default
else:
newData[r] = r.type
self.hisListingData = newData
