def parse_color(fields, name):
if len(fields) == 0:
raise syn, 'Missing %s value' % name
# Color from color dialog
if fields[0] in ('colorpanel', 'fromeditor', 'editor'):
from CGLtk.color import ColorWell
if not ColorWell._colorPanel:
from chimera import dialogs
dialogs.display("color editor")
raise syn, 'Choose color in panel first'
return ColorWell.colorPanel().rgba
# Chimera color defined with colordef
from chimera import Color
c = Color.lookup(fields[0])
if c:
return c.rgba()
try:
# Tk color name.
from chimera.tkgui import app
color = [c / 65535.0 for c in app.winfo_rgb(fields[0])]
except:
# Comma separated list of rgb or rgba float values.
color = parse_values(fields, 'color', float, (3, 4))
return color
def show_side_view():
'Show side view dialog'
from chimera import dialogs
from chimera import viewing
dialogs.display(viewing.ViewerDialog.name)
d = dialogs.find(viewing.ViewerDialog.name, create=1)
d.nb.raise_page('pSideView')
def parse_color(fields, name):
if len(fields) == 0:
raise syn, 'Missing %s value' % name
# Color from color dialog
if fields[0] in ('colorpanel', 'fromeditor', 'editor'):
from CGLtk.color import ColorWell
if not ColorWell._colorPanel:
from chimera import dialogs
dialogs.display("color editor")
raise syn, 'Choose color in panel first'
return ColorWell.colorPanel().rgba
# Chimera color defined with colordef
from chimera import Color
c = Color.lookup(fields[0])
if c:
return c.rgba()
try:
# Tk color name.
from chimera.tkgui import app
color = [c/65535.0 for c in app.winfo_rgb(fields[0])]
except:
# Comma separated list of rgb or rgba float values.
color = parse_values(fields, 'color', float, (3,4))
return color
def initiateAddHyd(models, cancelCB=None, okCB=None, hisScheme=None, addFunc=AddH.hbondAddHydrogens): """Request the addition of hydrogens to the given models. If all atoms in the models have known hydrogen-adding geometries, the hydrogens are added immediately. Otherwise, a dialog is started to request the missing information from the user. Once the user 'Ok's the information-gathering dialog, the hydrogens are added. The dialog can instead be cancelled, in which case no hydrogens are added. This function may be called from the user interface or from other functions. If the latter, then typically the cancelCB and okCB callback functions are provided so that the calling function can ascertain whether hydrogens were in fact added to the models. """ unks = AddH.gatherUnknowns(models) if unks: dialogs.display(addHinfoDialog.name) dialog = dialogs.find(addHinfoDialog.name) dialog.setAtoms(unks) dialog.models = models dialog.cancelCB = cancelCB dialog.okCB = okCB dialog.hisScheme = hisScheme dialog.addFunc = addFunc else: addFunc(models, hisScheme=hisScheme) if okCB: okCB()
def Apply(self):
val = self.seqMenu1.get()
if val == self.ALL:
seqs1 = self.mav.seqs
else:
seqs1 = [s for s in self.mav.seqs if s.name == val]
val = self.seqMenu2.get()
if val == self.ALL:
seqs2 = self.mav.seqs
else:
seqs2 = [s for s in self.mav.seqs if s.name == val]
denom = self.denominator.get()
for s1 in seqs1:
for s2 in seqs2:
pi = percentIdentity(s1, s2, denominator=denom)
self.mav.status("%s vs. %s:\n"
" %.2f%% identity\n" % (s1.name,
s2.name, pi))
# since once OK is clicked, the mouse may be
# over a part of the alignment that causes a
# status message, also send to regular status
# line
replyobj.status("%s vs. %s: %.2f%% identity\n"
% (s1.name, s2.name, pi), log=True)
if len(seqs1) > 1 or len(seqs2) > 1:
self.mav.status("Percent identity info in Reply Log")
from chimera import dialogs, tkgui
dialogs.display(tkgui._ReplyDialog.name)
def Apply(self):
val = self.seqMenu1.get()
if val == self.ALL:
seqs1 = self.mav.seqs
else:
seqs1 = [s for s in self.mav.seqs if s.name == val]
val = self.seqMenu2.get()
if val == self.ALL:
seqs2 = self.mav.seqs
else:
seqs2 = [s for s in self.mav.seqs if s.name == val]
denom = self.denominator.get()
for s1 in seqs1:
for s2 in seqs2:
pi = percentIdentity(s1, s2, denominator=denom)
self.mav.status("%s vs. %s:\n"
" %.2f%% identity\n" %
(s1.name, s2.name, pi))
# since once OK is clicked, the mouse may be
# over a part of the alignment that causes a
# status message, also send to regular status
# line
replyobj.status("%s vs. %s: %.2f%% identity\n" %
(s1.name, s2.name, pi),
log=True)
if len(seqs1) > 1 or len(seqs2) > 1:
self.mav.status("Percent identity info in Reply Log")
from chimera import dialogs, tkgui
dialogs.display(tkgui._ReplyDialog.name)
def showRainbowDialog(models):
from chimera import dialogs
from rainbow import RainbowDialog
if len(models) > 1:
target = "models"
else:
target = "residues"
dialogs.display(RainbowDialog.name).configure(models=models,
target=target)
def showRainbowDialog(models): from chimera import dialogs from rainbow import RainbowDialog if len(models) > 1: target = "models" else: target = "residues" dialogs.display(RainbowDialog.name).configure( models=models, target=target)
def _showBondRotUI(trigger, myData, br): if chimera.nogui: return if trigger == bondRotMgr.CREATED: # some window managers are slow to raise windows # only auto-raise the dialog if a new rotation is created dialogs.display(StructMeasure.name) d = dialogs.find(StructMeasure.name) d.setCategoryMenu(BONDROTS) d.rotChange(trigger, br)
def _reportStatus(msg, assigned, propList, modelList, rba):
if len(assigned) == 1:
phrase = "one atom"
else:
phrase = "%d atoms" % len(assigned)
pList = [ repr(p) for p in propList ]
if len(pList) == 1:
s = pList[0]
plural = ""
verb = "was"
else:
s = ", ".join(pList[:-1]) + " and " + pList[-1]
plural = "s"
verb = "were"
msg += ("Attribute%s %s %s created for %s.\n"
% (plural, s, verb, phrase))
chimera.replyobj.status(msg)
chimera.replyobj.message(msg)
if rba and assigned:
try:
from ShowAttr import ShowAttrDialog
except ImportError:
# No "render by attribute", just ignore
pass
else:
from chimera import dialogs
d = dialogs.display(ShowAttrDialog.name)
d.configure(models=modelList, attrsOf="atoms",
attrName=None)
d.refreshAttrs()
d.configure(models=modelList, attrsOf="atoms",
attrName=propList[0])
def _selectModelCB(self, tableSel):
if self.treatmentSelAtom.get():
from chimera import selection
selection.clearCurrent()
selection.addCurrent(tableSel)
selection.addImpliedCurrent()
if self.treatmentSelModel.get():
from ModelPanel import ModelPanel
from chimera import dialogs
d = dialogs.display(ModelPanel.name)
d.selectionChange(tableSel)
shown = {}
if self.treatmentHideOthers.get():
for m in self.molList:
key = (m.id, m.subid)
shown[key] = m in tableSel or not tableSel
else:
for m in tableSel:
key = (m.id, m.subid)
shown[key] = True
for m in chimera.openModels.list():
key = (m.id, m.subid)
try:
m.display = shown[key]
except KeyError:
pass
def _getParameters(self, mols, nogui, addhyd):
timestamp("_getParameters")
import DockPrep
import chimera
self.originalAtoms = set([])
for m in mols:
self.originalAtoms.update(m.atoms)
from AddCharge import AMBER99SB
kw = {
"doneCB": self._finishDockPrep,
"gaffType": True,
"chargeModel": AMBER99SB
}
if nogui or chimera.nogui:
if not addhyd:
kw["addHFunc"] = None
DockPrep.prep(mols, nogui=nogui, **kw)
else:
from DockPrep.gui import DockPrepDialog
from chimera import dialogs
d = dialogs.display(DockPrepDialog.name, wait=True)
d.addHydVar.set(addhyd)
d.applyKeywords = kw
d.molListBox.setvalue(mols)
d.writeMol2Var.set(False)
"""
def Apply(self):
minimize = self.minimizeVar.get()
steps = 60
ef = self.stepsCounter.component("entryfield")
if ef.valid():
value = int(ef.getvalue())
if value > 0:
steps = value
self.state.makeMovie(minimize=minimize, steps=steps)
action = self.createActionMenu.getvalue()
if action == ActionShowModelPanel:
from ModelPanel import ModelPanel
from chimera import dialogs
dialogs.display(ModelPanel.name)
elif action == ActionHideConformations:
self.state.hideConformations()
def Apply(self):
from chimera import UserError
attrName = self.attrNameOption.get()
from chimera.misc import stringToAttr
fixedAttrName = stringToAttr(attrName, collapse=False)
if fixedAttrName != attrName:
self.enter()
raise UserError("Attribute name must be composed only"
" of letters, digits, and underscores and must"
" not start with a digit.")
refName = self.refMenu.getvalue()
sels = self.alignList.getcurselection()
if len(sels) == 0:
self.enter()
raise UserError('Select at least one evaluation '
'structure to assess')
refMol = self.mols[refName]
evalMols = []
for sel in sels:
evalMols.append(self.mols[sel])
self.mav.assessMatch(refMol, evalMols, attrName)
from chimera import dialogs
from ShowAttr import ShowAttrDialog
d = dialogs.display(ShowAttrDialog.name)
d.configure(models=evalMols,
attrsOf="residues",
attrName=attrName,
mode="Select")
def Apply(self):
minimize = self.minimizeVar.get()
steps = 60
ef = self.stepsCounter.component("entryfield")
if ef.valid():
value = int(ef.getvalue())
if value > 0:
steps = value
self.state.makeMovie(minimize=minimize, steps=steps)
action = self.createActionMenu.getvalue()
if action == ActionShowModelPanel:
from ModelPanel import ModelPanel
from chimera import dialogs
dialogs.display(ModelPanel.name)
elif action == ActionHideConformations:
self.state.hideConformations()
def Apply(self):
from chimera import UserError
attrName = self.attrNameOption.get()
from chimera.misc import stringToAttr
fixedAttrName = stringToAttr(attrName, collapse=False)
if fixedAttrName != attrName:
self.enter()
raise UserError("Attribute name must be composed only"
" of letters, digits, and underscores and must"
" not start with a digit.")
refName = self.refMenu.getvalue()
sels = self.alignList.getcurselection()
if len(sels) == 0:
self.enter()
raise UserError('Select at least one evaluation '
'structure to assess')
refMol = self.mols[refName]
evalMols = []
for sel in sels:
evalMols.append(self.mols[sel])
self.mav.assessMatch(refMol, evalMols, attrName)
from chimera import dialogs
from ShowAttr import ShowAttrDialog
d = dialogs.display(ShowAttrDialog.name)
d.configure(models=evalMols, attrsOf="residues",
attrName=attrName, mode="Select")
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 show_seg_marker_dialog():
"""Shows the Segment Marker dialog.
show_seg_marker_dialog()
"""
from chimera import dialogs
return dialogs.display(Segment_Marker.name)
def color_key_cb(self, *args):
if self.n < 2:
raise chimera.UserError("At least two colors needed to create key")
from Ilabel.gui import IlabelDialog
from chimera import dialogs
d = dialogs.display(IlabelDialog.name)
d.keyConfigure([(w.rgba, h.variable.get()) for w, h in zip(self.colorwells,
self.entry_fields)[:self.n]])
def show_vol_morph_dialog():
"""Shows the Volume Morph dialog.
show_vol_morph_dialog()
"""
from chimera import dialogs
return dialogs.display(Volume_Morph.name)
def show_simple_distance_dialog():
"""Shows the Measure Stick dialog.
show_simple_distance_dialog()
"""
from chimera import dialogs
return dialogs.display(Measure_Stick.name)
def displayDialog(wait=False):
if dialogs.find(BugReportGUI.name):
replyobj.status("Bug report already in progress!",
color="red", blankAfter=15)
return None
else:
br_gui = dialogs.display(BugReportGUI.name, wait)
return br_gui
def activate(self, molecules=None):
from chimera import dialogs
d = dialogs.display(self.module('gui').MatchMaker.name)
if molecules:
d.refMolList.setvalue(molecules[0])
d.matchMolList.setvalue(molecules[1:])
d.showSeqVar.set(False)
return None
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 displayDialog(wait=False):
if dialogs.find(BugReportGUI.name):
replyobj.status("Bug report already in progress!",
color="red",
blankAfter=15)
return None
else:
br_gui = dialogs.display(BugReportGUI.name, wait)
return br_gui
def color_secondary_structure():
'Color secondary structure using ColorSS extension'
import ColorSS
from chimera import dialogs
d = dialogs.find(ColorSS.ColorSSDialog.name, create=False)
if d == None:
d = dialogs.display(ColorSS.ColorSSDialog.name)
d.Close()
d.Apply()
def color_key_cb(self, *args):
if self.n < 2:
raise chimera.UserError("At least two colors needed to create key")
from Ilabel.gui import IlabelDialog
from chimera import dialogs
d = dialogs.display(IlabelDialog.name)
d.keyConfigure([
(w.rgba, h.variable.get())
for w, h in zip(self.colorwells, self.entry_fields)[:self.n]
])
def show_attribute_histogram(molecule, attribute_name):
import ShowAttr
from chimera import dialogs
d = dialogs.display(ShowAttr.ShowAttrDialog.name)
d.configure(models=[molecule],
mode='Render',
attrsOf=ShowAttr.ATTRS_ATOMS,
attrName=attribute_name)
d.renderNotebook.selectpage('Colors')
def _prepDialog(nogui, mols, **kw):
if nogui or chimera.nogui:
prep(mols, **kw)
return None
from gui import DockPrepDialog
from chimera import dialogs
d = dialogs.display(DockPrepDialog.name, wait=True)
d.applyKeywords = kw
d.molListBox.setvalue(mols)
return d
def _prepDialog(nogui, mols, **kw): if nogui or chimera.nogui: prep(mols, **kw) return None from gui import DockPrepDialog from chimera import dialogs d = dialogs.display(DockPrepDialog.name, wait=True) d.applyKeywords = kw d.molListBox.setvalue(mols) return d
def show_attribute_histogram(molecule, attribute_name):
import ShowAttr
from chimera import dialogs
d = dialogs.display(ShowAttr.ShowAttrDialog.name)
d.configure(models = [molecule],
mode = 'Render',
attrsOf = ShowAttr.ATTRS_ATOMS,
attrName = attribute_name)
d.renderNotebook.selectpage('Colors')
def seqCmd(items):
global _seqInspectors
todo = []
for item in items:
if not _seqInspectors.has_key(item):
from chimera.Sequence import StructureSequence
if isinstance(item, StructureSequence):
from MultAlignViewer.MAViewer import MAViewer
copySeq = StructureSequence.__copy__(item)
copySeq.name = item.fullName()
_addSeqInspector(item, mavSeq=copySeq)
else:
todo.extend(item.sequences())
continue
_seqInspectors[item].enter()
if todo:
if len(todo) > 1:
from seqPanel import SeqPickerDialog
from chimera import dialogs
d = dialogs.display(SeqPickerDialog.name)
d.molListBox.setvalue(todo)
else:
seqCmd(todo)
def _getParameters(self, mols, nogui, addhyd):
timestamp("_getParameters")
import DockPrep
import chimera
self.originalAtoms = set([])
for m in mols:
self.originalAtoms.update(m.atoms)
from AddCharge import AMBER99SB
kw = { "doneCB": self._finishDockPrep, "gaffType": True,
"chargeModel": AMBER99SB }
if nogui or chimera.nogui:
if not addhyd:
kw["addHFunc"] = None
DockPrep.prep(mols, nogui=nogui, **kw)
else:
from DockPrep.gui import DockPrepDialog
from chimera import dialogs
d = dialogs.display(DockPrepDialog.name, wait=True)
d.addHydVar.set(addhyd)
d.applyKeywords = kw
d.molListBox.setvalue(mols)
d.writeMol2Var.set(False)
"""
def seqCmd(items): global _seqInspectors todo = [] for item in items: if not _seqInspectors.has_key(item): from chimera.Sequence import StructureSequence if isinstance(item, StructureSequence): from MultAlignViewer.MAViewer import MAViewer copySeq = StructureSequence.__copy__(item) copySeq.name = item.fullName() _addSeqInspector(item, mavSeq=copySeq) else: todo.extend(item.sequences()) continue _seqInspectors[item].enter() if todo: if len(todo) > 1: from seqPanel import SeqPickerDialog from chimera import dialogs d = dialogs.display(SeqPickerDialog.name) d.molListBox.setvalue(todo) else: seqCmd(todo)
def showTileDialog(models): from chimera import dialogs from EnsembleMatch.choose import TileStructuresCB dialogs.display(TileStructuresCB.name).configure( models=models)
def show_memory_use_dialog():
from chimera import dialogs
return dialogs.display(Memory_Use_Dialog.name)
def show_seg_mask_dialog():
"""show_seg_mask_dialog() - shows the Segment Mask dialog.
"""
from chimera import dialogs
return dialogs.display(Segment_Mask.name)
def show_crystal_contacts_dialog(): from chimera import dialogs return dialogs.display(Crystal_Contacts_Dialog.name)
def activate(self):
from chimera.dialogs import display
display(self.module('gui').WritePrmtopDialog.name)
return None
def show_fit_map_dialog():
from chimera import dialogs
return dialogs.display(Fit_Map_Dialog.name)
def show_track_xform_dialog():
"""show_track_xform_dialog() - shows the Track Transform dialog.
"""
from chimera import dialogs
return dialogs.display(TrackXformDialog.name)
def activate(self):
from chimera import dialogs
gui = self.module('gui')
dlg = dialogs.display(gui.BuildStructureDialog.name)
dlg.notebook.selectpage(gui.ADD_ATOMS)
return None
def Results(self):
from chimera import dialogs, tkgui
dialogs.display(tkgui._ReplyDialog.name)
def showDialog(models, mode): import ShowAttr from chimera import dialogs d = dialogs.display(ShowAttr.ShowAttrDialog.name) d.configure(models=models, mode=mode)
def activate(self): from chimera import dialogs dialogs.display(self.module().ShowAttrDialog.name).configure( mode="Render") return None
def show_unit_cell_dialog(): from chimera import dialogs return dialogs.display(Unit_Cell_Dialog.name)
def raiseViewingTab(tab):
from chimera import dialogs, viewing
d = dialogs.display(viewing.ViewerDialog.name)
d.nb.raise_page('p' + tab)
def activate(self):
from chimera.dialogs import display
display(self.module('gui').WriteMol2Dialog.name)
return None
def raiseStructMeasureTab(tab): from chimera import dialogs from StructMeasure.gui import StructMeasure d = dialogs.display(StructMeasure.name) d.notebook.selectpage(tab)
def showPreferences(self):
from chimera import dialogs
d = dialogs.display('preferences')
d.menu.invoke(index = FETCH_PREFERENCES)
def activate(self):
from chimera.dialogs import display
display(self.module("gui").StructureDiagramDialog.name)
return None
def show_morph_map_dialog():
from chimera import dialogs
return dialogs.display(Morph_Map_Dialog.name)
def showPreferences(self):
from chimera import dialogs
d = dialogs.display('preferences')
d.menu.invoke(index=FETCH_PREFERENCES)
def activate(self):
from chimera import dialogs
dialogs.display(
self.module().ShowAttrDialog.name).configure(mode="Render")
return None
def show_benchmark_dialog():
from chimera import dialogs
return dialogs.display(Benchmark_Dialog.name)
def showDialog(models, mode):
import ShowAttr
from chimera import dialogs
d = dialogs.display(ShowAttr.ShowAttrDialog.name)
d.configure(models=models, mode=mode)
