def __init__(self, src_path=None):
self.currentPanelId = -1
self.panels = []
self.unique_id = 0
ModelessDialog.__init__(self)
self.NULL_PANEL = Panel(-1, self, name="")
self.NULL_PANEL.cmdStack.delB.configure(state="disabled")
self.NULL_PANEL.cmdStack.addB.configure(state="disabled")
self.NULL_PANEL.undoStack.delB.configure(state="disabled")
self.NULL_PANEL.undoStack.addB.configure(state="disabled")
self.refreshPanelInfo(-1)
self.save_path = None
self.updateWindowTitle()
self.gTitleOption.set("Chimera Demo")
if src_path:
self.loadDemo(src_path)
self.setSavePath(src_path)
self.updateWindowTitle()
self._toplevel.bind('<KeyRelease>', self.keyReleaseCB)
self._DIRTY = False
self._cached_save = None
def __init__(self, residue, resType, lib, sessionData=None):
self._sesHandlerID = chimera.triggers.addHandler(
SAVE_SESSION, self._sessionCB, None)
self.residue = residue
self.lib = lib
self.resType = resType
self.title = "%s Side-Chain Rotamers" % residue
if sessionData:
self.bbdep, self.rotamers, self.tableData = sessionData
else:
from Rotamers import getRotamers
self.bbdep, self.rotamers = getRotamers(residue,
log=True,
lib=lib,
resType=resType)
from Midas import linewidth, color
linewidth(2, self.rotamers)
color('byhet', self.rotamers)
chimera.openModels.add(self.rotamers,
sameAs=residue.molecule,
hidden=True,
noprefs=True)
registerAttribute(chimera.Molecule, "chis")
registerAttribute(chimera.Molecule, "rotamerProb")
self.tableData = None
self.resHandlerID = chimera.triggers.addHandler(
'Residue', self._resChangeCB, None)
self.dependentDialogInfo = [('Clashes', 'clash'), ('H-Bonds', 'hbond'),
('Density', 'volume')]
for label, ddn in self.dependentDialogInfo:
setattr(self, ddn + "Dialog", None)
ModelessDialog.__init__(self)
def __init__(self, models):
self.models = models
if len(models) > 1:
self.title = "Add Note to %d Models" % (len(models))
else:
self.title = "Add Note to %s" % models[0].name
ModelessDialog.__init__(self)
def __init__(self, residue, resType, lib, sessionData=None):
self._sesHandlerID = chimera.triggers.addHandler(SAVE_SESSION,
self._sessionCB, None)
self.residue = residue
self.lib = lib
self.resType = resType
self.title = "%s Side-Chain Rotamers" % residue
if sessionData:
self.bbdep, self.rotamers, self.tableData = sessionData
else:
from Rotamers import getRotamers
self.bbdep, self.rotamers = getRotamers(residue,
log=True, lib=lib, resType=resType)
from Midas import linewidth, color
linewidth(2, self.rotamers)
color('byhet', self.rotamers)
chimera.openModels.add(self.rotamers,
sameAs=residue.molecule, hidden=True, noprefs=True)
registerAttribute(chimera.Molecule, "chis")
registerAttribute(chimera.Molecule, "rotamerProb")
self.tableData = None
self.resHandlerID = chimera.triggers.addHandler(
'Residue', self._resChangeCB, None)
self.dependentDialogInfo = [('Clashes', 'clash'),
('H-Bonds', 'hbond'), ('Density', 'volume')]
for label, ddn in self.dependentDialogInfo:
setattr(self, ddn + "Dialog", None)
ModelessDialog.__init__(self)
def __init__(self):
self.director = None
self.this_dir = os.path.split(os.path.abspath(__file__))[0]
ModelessDialog.__init__(self)
self.cache_width = None
self.cache_height = None
## get the width and height when the frame options are expanded
self.frmOptionsFrame.grid(row=FRM_OPTS_ROW ,column=0, columnspan=3, sticky='nsew')
chimera.tkgui.app.update_idletasks()
self.frm_width, self.frm_height = \
(self.frmOptionsFrame.winfo_width(), self.frmOptionsFrame.winfo_height())
self.frmOptionsFrame.grid_forget()
chimera.tkgui.app.update_idletasks()
## get the width and height when the movie options are expanded
self.movOptionsFrame.grid(row=MOV_OPTS_ROW,column=0, columnspan=3, sticky='nsew')
chimera.tkgui.app.update_idletasks()
self.mov_width, self.mov_height = \
(self.movOptionsFrame.winfo_width(), self.movOptionsFrame.winfo_height())
self.movOptionsFrame.grid_forget()
chimera.tkgui.app.update_idletasks()
w,h = map(int,self.getCurrentDimensions())
self._toplevel.wm_geometry('%sx%s' % (w+30,h+20))
#self.director.adjustGfxSize()
chimera.tkgui.app.after(1000, self.showStatus, "Click the record button to start capturing frames")
def destroy(self):
self.mainDialog = None
if self.readScriptDialog:
self.readScriptDialog.destroy()
if self.saveDialog:
self.saveDialog.destroy()
ModelessDialog.destroy(self)
def destroy(self): self.mainDialog = None if self.readScriptDialog: self.readScriptDialog.destroy() if self.saveDialog: self.saveDialog.destroy() ModelessDialog.destroy(self)
def __init__(self, mol=None, seq=None, blastData=None, sessionData=None):
self.loaded = {}
self.reference = mol
if isinstance(self.reference, StructureSequence):
self.molecule = self.reference.molecule
elif isinstance(self.reference, Molecule):
self.molecule = self.reference
self.sequence = seq # for session data only
if seq is None:
self.seq, self.refResList = self._makeSeq(mol)
else:
self.seq = seq
if self.reference:
seq, resList = self._makeSeq(mol)
self.refResList = self._getResidues(self.seq,
seq, resList)
if blastData:
self.initBlast(*blastData)
else:
self.initSession(*sessionData)
self.title = "Blast: %s" % self.basename
ModelessDialog.__init__(self)
if not blastData:
self._updateLoadButton()
if self.molecule:
self.closeHandler = chimera.openModels.addRemoveHandler(
self._modelClosedCB, None)
else:
self.closeHandler = None
self.sesHandler = chimera.triggers.addHandler(
SAVE_SESSION,
self._sessionCB, None)
chimera.extension.manager.registerInstance(self)
def __init__(self, src_path = None):
self.currentPanelId = -1
self.panels = []
self.unique_id = 0
ModelessDialog.__init__(self)
self.NULL_PANEL = Panel(-1, self, name="")
self.NULL_PANEL.cmdStack.delB.configure(state="disabled")
self.NULL_PANEL.cmdStack.addB.configure(state="disabled")
self.NULL_PANEL.undoStack.delB.configure(state="disabled")
self.NULL_PANEL.undoStack.addB.configure(state="disabled")
self.refreshPanelInfo(-1)
self.save_path = None
self.updateWindowTitle()
self.gTitleOption.set("Chimera Demo")
if src_path:
self.loadDemo(src_path)
self.setSavePath(src_path)
self.updateWindowTitle()
self._toplevel.bind('<KeyRelease>', self.keyReleaseCB)
self._DIRTY = False
self._cached_save = None
def __init__(self, models): self.models = models if len(models) > 1: self.title = "Add Note to %d Models" % (len(models)) else: self.title = "Add Note to %s" % models[0].name ModelessDialog.__init__(self)
def __init__(self, sessionData=None, *args, **kw):
self.pausetime = 0.5 #time to wait between submitting a command and checking for output/refreshing the text (seconds)
self.starttime = time.time()
self.latvectime = time.time()
dir, file = os.path.split(__file__)
icon = os.path.join(dir, 'Lev00Logo.tiff')
chimera.tkgui.app.toolbar.add(
icon,
lambda d=chimera.dialogs.display, n=Lev00Dialog.name: d(n),
'Run Lev00',
None)
self.App = "Lev00"
self.fulltext = ""
self.toption = 0
ModelessDialog.__init__(self, *args, **kw)
print "In init"
self.home = os.path.expanduser("~")
self.appdir = self.home + "/." + self.App
#check for ~/.Lev00. If it doesn't exist, create it
if not (os.path.isdir(self.appdir)):
print "Making ", self.appdir
os.mkdir(self.appdir)
self.getShell()
#Look for the Lev00 root directory. Prompt user if necessary
self.getappdir()
#self.rootdir="/Users/ggibb2/Projects/CP2k/lev00_3.49"
#Ask user to select the working directory
self.getWorkingDir()
# Create lev00 process
self.ChimeraInterface = tetr_lev00_Chimera_plugin.Lev00(
self.rootdir, self.wkdir, self.myshell)
self.wdirlabel.config(text="wkdir= '" + self.wkdir + "'")
# Create variable to store Lev00 output
self.ChimeraInterfaceOutput = Tk.StringVar()
time.sleep(self.pausetime)
#Update the Lev00 text on screen
self.updateText(self.ChimeraInterface.getOutput())
#load 'geom.xyz'
self.ChimeraInterface.refreshGeom()
#set view options to those selected in the GUI
self.SetViewOption()
self.timer()
def __init__(self, model):
self.title = 'PDB Headers for %s' % model.name
self.model = model
from chimera import preferences
self.prefs = preferences.addCategory("PDB headers dialog",
preferences.HiddenCategory,
optDict={"ordering": "Alphabetical"})
ModelessDialog.__init__(self)
def __init__(self, models): self.models = models if len(models) > 1: name = "Multiple Models" else: name = models[0].name self.title = "Compute Secondary Structure for %s" % name ModelessDialog.__init__(self)
def __init__(self, models): self.models = models if len(models) > 1: name = "Multiple Models" else: name = models[0].name self.title = "Set Transformation of %s" % name ModelessDialog.__init__(self)
def __init__(self, models):
self.models = models
if len(models) > 1:
name = "Multiple Models"
else:
name = models[0].name
self.title = "Compute Secondary Structure for %s" % name
ModelessDialog.__init__(self)
def destroy(self): self.mav.triggers.deleteHandler(ADD_ASSOC, self.addAssocHandlerID) self.mav.triggers.deleteHandler(DEL_ASSOC, self.delAssocHandlerID) self.mav = None chimera.openModels.deleteAddHandler(self.addHandlerID) chimera.openModels.deleteRemoveHandler(self.removeHandlerID) ModelessDialog.destroy(self)
def destroy(self, *args):
self.mouseLabelingVar.set(True)
self.mouseModeButton.invoke()
chimera.triggers.deleteHandler(SAVE_SESSION, self._sessionHandlerID)
chimera.triggers.deleteHandler(CLOSE_SESSION, self._closeHandlerID)
chimera.triggers.deleteHandler(BEGIN_RESTORE_SESSION,
self._beginRestoreHandlerID)
chimera.openModels.close([self.model, self.keyModel])
ModelessDialog.destroy(self)
def destroy(self):
chimera.triggers.deleteHandler('Residue', self.resHandlerID)
chimera.triggers.deleteHandler(SAVE_SESSION, self._sesHandlerID)
chimera.openModels.close(self.rotamers)
for label, ddn in self.dependentDialogInfo:
dd = getattr(self, ddn + 'Dialog', None)
if dd:
dd.destroy()
ModelessDialog.destroy(self)
def destroy(self):
chimera.triggers.deleteHandler('Residue', self.resHandlerID)
chimera.triggers.deleteHandler(SAVE_SESSION, self._sesHandlerID)
chimera.openModels.close(self.rotamers)
for label, ddn in self.dependentDialogInfo:
dd = getattr(self, ddn + 'Dialog', None)
if dd:
dd.destroy()
ModelessDialog.destroy(self)
def __init__(self, model):
self.title = 'PDB Headers for %s' % model.name
self.model = model
from chimera import preferences
self.prefs = preferences.addCategory(
"PDB headers dialog",
preferences.HiddenCategory,
optDict={"ordering": "Alphabetical"})
ModelessDialog.__init__(self)
def __init__(self, title="Add Hydrogens", models=None, useHBonds=None, cb=None, **kw): self.title = title self.cb = cb self.startModels = models if useHBonds is None: self.startUseHBonds = prefs[HBOND_GUIDED] else: self.startUseHBonds = useHBonds ModelessDialog.__init__(self, **kw)
def __init__(self, cb, unchargedResidues, unchargedAtoms, method, status, gaffType, showCharges=False): self.cb = cb self.unchargedResidues = unchargedResidues self.unchargedAtoms = unchargedAtoms self.status = status self.method = method self.gaffType = gaffType self.showCharges = showCharges ModelessDialog.__init__(self)
def __init__(self, modelList, subSelection, *args, **kw): from chimera import preferences self._removeHandler = None for m in modelList: m.preclusterColor = m.color self.subSelection = subSelection self._cluster(modelList) ModelessDialog.__init__(self, *args, **kw) chimera.extension.manager.registerInstance(self) self._removeHandler = chimera.openModels.addRemoveHandler( self._modelsChanged, None)
def __init__(self, movie, startFrame, stride, endFrame, useSel, ignoreBulk,
ignoreHyds):
self.movie = movie
self.movie.subdialogs.append(self)
self.startFrame = startFrame
self.stride = stride
self.endFrame = endFrame
self.useSel = useSel
self.ignoreBulk = ignoreBulk
self.ignoreHyds = ignoreHyds
ModelessDialog.__init__(self)
def __init__(self, movie, startFrame, stride, endFrame, useSel, ignoreBulk, ignoreHyds): self.movie = movie self.movie.subdialogs.append(self) self.startFrame = startFrame self.stride = stride self.endFrame = endFrame self.useSel = useSel self.ignoreBulk = ignoreBulk self.ignoreHyds = ignoreHyds ModelessDialog.__init__(self)
def __init__(self, groupPanel):
self.groupPanel = groupPanel
options = {
"shownButs": {},
"executionList": ['attributes...'],
"shownColumns": {}
}
self.prefs = preferences.addCategory("Pseudobond Group Panel",
preferences.HiddenCategory,
optDict=options)
ModelessDialog.__init__(self)
def __init__(self, modelList, subSelection, *args, **kw):
from chimera import preferences
self._removeHandler = None
for m in modelList:
m.preclusterColor = m.color
self.subSelection = subSelection
self._cluster(modelList)
ModelessDialog.__init__(self, *args, **kw)
chimera.extension.manager.registerInstance(self)
self._removeHandler = chimera.openModels.addRemoveHandler(
self._modelsChanged, None)
def __init__(self, groupPanel):
self.groupPanel = groupPanel
options = {
"shownButs": {},
"executionList": ['attributes...'],
"shownColumns": {}
}
self.prefs = preferences.addCategory("Pseudobond Group Panel",
preferences.HiddenCategory,
optDict=options)
ModelessDialog.__init__(self)
def destroy(self, *args): self.mouseLabelingVar.set(True) self.mouseModeButton.invoke() chimera.triggers.deleteHandler(SAVE_SESSION, self._sessionHandlerID) chimera.triggers.deleteHandler(CLOSE_SESSION, self._closeHandlerID) chimera.triggers.deleteHandler(BEGIN_RESTORE_SESSION, self._beginRestoreHandlerID) chimera.openModels.close([self.model, self.keyModel]) ModelessDialog.destroy(self)
def __init__(self, modelPanel):
self.modelPanel = modelPanel
options = {
"freqButs": {},
"executionList": ['attributes...'],
"shownColumns": {},
"showColor": False,
"lastUse": None
}
self.prefs = preferences.addCategory("Model Panel",
preferences.HiddenCategory,
optDict=options)
ModelessDialog.__init__(self)
def __init__(self, modelPanel):
self.modelPanel = modelPanel
options = {
"freqButs": {},
"executionList": ['attributes...'],
"shownColumns": {},
"showColor": False,
"lastUse": None
}
self.prefs = preferences.addCategory("Model Panel",
preferences.HiddenCategory,
optDict=options)
ModelessDialog.__init__(self)
def destroy(self):
self.regionListing.hlist._widgetCache.clear()
self.seqCanvas.mav.triggers.deleteHandler(DEL_ASSOC,
self.delAssocHandlerID)
if hasattr(self,'_selChangeHandler') and self._selChangeHandler:
chimera.triggers.deleteHandler("selection changed",
self._selChangeHandler)
if self._scfDialog:
self._scfDialog.destroy()
self._scfDialog = None
for rd in self.renameDialogs.values():
rd.destroy()
self.renameDialogs.clear()
ModelessDialog.destroy(self)
def __init__(self, name, molList, tableData=None): self.title = "ModBase: %s" % name self.molList = molList self.tableData = tableData ModelessDialog.__init__(self) self.closeHandler = chimera.openModels.addRemoveHandler( self._modelClosedCB, None) self.selHandler = chimera.triggers.addHandler( "selection changed", self._selectionChangedCB, None) self.sesHandler = chimera.triggers.addHandler( SAVE_SESSION, self._sessionCB, None) chimera.extension.manager.registerInstance(self)
def __init__(self,
title="Add Hydrogens",
models=None,
useHBonds=None,
cb=None,
**kw):
self.title = title
self.cb = cb
self.startModels = models
if useHBonds is None:
self.startUseHBonds = prefs[HBOND_GUIDED]
else:
self.startUseHBonds = useHBonds
ModelessDialog.__init__(self, **kw)
def __init__(self, process=None, models=None, chargeModel=None, cb=None, **kw): if process: self.title = "Assign Charges for %s" % process.title() else: from AddCharge import process self.process = process self.cb = cb self.startModels = models if not chargeModel: from AddCharge import defaultChargeModel chargeModel = defaultChargeModel self.initialChargeModel = chargeModel ModelessDialog.__init__(self, **kw)
def __init__(self, parent=None, mode='atoms'):
# Check
self.title = 'Select {}'.format(mode)
self.mode = mode
# Fire up
ModelessDialog.__init__(self)
if not chimera.nogui: # avoid useless errors during development
chimera.extension.manager.registerInstance(self)
# Fix styles
self._fix_styles(*self.buttonWidgets.values())
self._toplevel.attributes('-topmost', True)
self._toplevel.resizable(width=True, height=False)
def __init__(self, movie, startFrame, stride, endFrame, useSel, minRmsd,
maxRmsd, ignoreBulk, ignoreHyds, recolor):
self.movie = movie
self.movie.subdialogs.append(self)
self.startFrame = startFrame
self.stride = stride
self.endFrame = endFrame
self.useSel = useSel
self.minRmsd = minRmsd
self.maxRmsd = maxRmsd
self.ignoreBulk = ignoreBulk
self.ignoreHyds = ignoreHyds
self.recolor = recolor
self.title = self.titleFmt % (minRmsd, maxRmsd)
ModelessDialog.__init__(self)
def __init__(self, movie, startFrame, stride, endFrame, useSel, minRmsd, maxRmsd, ignoreBulk, ignoreHyds, recolor): self.movie = movie self.movie.subdialogs.append(self) self.startFrame = startFrame self.stride = stride self.endFrame = endFrame self.useSel = useSel self.minRmsd = minRmsd self.maxRmsd = maxRmsd self.ignoreBulk = ignoreBulk self.ignoreHyds = ignoreHyds self.recolor = recolor self.title = self.titleFmt % (minRmsd, maxRmsd) ModelessDialog.__init__(self)
def __init__(self, name, cavities, sessionData=None): self.title = "CASTp: %s" % name self.cavities = cavities from weakref import proxy def wrapper(s=proxy(self)): s._cavityChangeCB() for cav in cavities: cav.pocketInfo["atoms"].selChangedCB = wrapper cav.mouthInfo["atoms"].selChangedCB = wrapper if sessionData: self.tableData = sessionData else: self.tableData = None ModelessDialog.__init__(self) chimera.extension.manager.registerInstance(self)
def __init__(self, model):
self.model = model
self.setInCallback = False
self.title = "%s attributes (model %s)" % (
readableName(model), model.oslIdent()[1:])
self.triggers = [('Model', chimera.triggers.addHandler(
'Model', self._refreshCB, None))]
self.refreshFuncs = {}
self.refreshFuncs['Model'] = []
if isinstance(self.model, chimera.Molecule) \
and len(self.model.pdbHeaders) > 0:
self.buttons = self.buttons + ["PDB Headers..."]
ModelessDialog.__init__(self)
def __init__(self, group):
self.group = group
self.setInCallback = 0
if group.category:
self.title = "%s attributes" % _mapName(group)
self.triggers = [('PseudoBondGroup',
chimera.triggers.addHandler('PseudoBondGroup',
self._refreshCB, None)),
('PseudoBond',
chimera.triggers.addHandler('PseudoBond',
self._refreshCB, None))]
self.refreshFuncs = {}
self.refreshFuncs['PseudoBondGroup'] = []
self.refreshFuncs['PseudoBond'] = []
ModelessDialog.__init__(self)
def __init__(self, refModels, altModels, subSelection, *args, **kw):
#
# Save the subselection (part of model to match)
# as well as the model lists (ordered by subid)
#
self.subSelection = subSelection
l = [ (m.subid, m) for m in refModels ]
l.sort()
self.refModels = [ t[1] for t in l ]
l = [ (m.subid, m) for m in altModels ]
l.sort()
self.altModels = [ t[1] for t in l ]
#
# Grab the atomic coordinates that will be used
# to compute RMSDs and check for errors
#
self.atomDict = {}
counts = []
for ml in self.refModels, self.altModels:
for m in ml:
osl = '%s%s' % (m.oslIdent(), self.subSelection)
s = selection.OSLSelection(osl)
atoms = s.atoms()
self.atomDict[m] = match._coordArray(atoms)
counts.append(len(atoms))
if min(counts) != max(counts):
raise chimera.UserError("Unequal number of atoms "
"found in models")
if counts[0] == 0:
raise chimera.UserError("No atoms match atom specifier")
#
# Add handler to monitor change in display or active
# status changes
#
self.trigger = chimera.triggers.addHandler('check for changes',
self._statusCheck, None)
#
# Initialize dialog
#
ModelessDialog.__init__(self, *args, **kw)
#
# Register with extension manager
#
chimera.extension.manager.registerInstance(self)
def __init__(self, refModels, altModels, subSelection, *args, **kw):
#
# Save the subselection (part of model to match)
# as well as the model lists (ordered by subid)
#
self.subSelection = subSelection
l = [(m.subid, m) for m in refModels]
l.sort()
self.refModels = [t[1] for t in l]
l = [(m.subid, m) for m in altModels]
l.sort()
self.altModels = [t[1] for t in l]
#
# Grab the atomic coordinates that will be used
# to compute RMSDs and check for errors
#
self.atomDict = {}
counts = []
for ml in self.refModels, self.altModels:
for m in ml:
osl = '%s%s' % (m.oslIdent(), self.subSelection)
s = selection.OSLSelection(osl)
atoms = s.atoms()
self.atomDict[m] = match._coordArray(atoms)
counts.append(len(atoms))
if min(counts) != max(counts):
raise chimera.UserError("Unequal number of atoms "
"found in models")
if counts[0] == 0:
raise chimera.UserError("No atoms match atom specifier")
#
# Add handler to monitor change in display or active
# status changes
#
self.trigger = chimera.triggers.addHandler('check for changes',
self._statusCheck, None)
#
# Initialize dialog
#
ModelessDialog.__init__(self, *args, **kw)
#
# Register with extension manager
#
chimera.extension.manager.registerInstance(self)
def __init__(self,
cb,
unchargedResidues,
unchargedAtoms,
method,
status,
gaffType,
showCharges=False):
self.cb = cb
self.unchargedResidues = unchargedResidues
self.unchargedAtoms = unchargedAtoms
self.status = status
self.method = method
self.gaffType = gaffType
self.showCharges = showCharges
ModelessDialog.__init__(self)
def destroy(self): if self.cavities: cav1 = self.cavities[0] atoms = (cav1.mouthInfo["atoms"].atoms() or cav1.pocketInfo["atoms"].atoms()) if atoms: # close surface too... from chimera import openModels mol = atoms[0].molecule openModels.close(openModels.list( id=mol.id, subid=mol.subid)) for chk in [self.doSelect, self.doColor, self.doSurface, self.doZoom, self.excludeMouth]: chk.destroy() chimera.extension.manager.deregisterInstance(self) ModelessDialog.destroy(self)
def __init__(self, viewdock, *args, **kw):
self.viewdock = viewdock
self.results = viewdock.results
self.compounds = Set()
self.selected = None
self.valueCache = {}
self._isMapped = False
self._colAddHandler = None
self._colDelHandler = None
self._colUpdHandler = None
self._needChangeCompounds = False
ModelessDialog.__init__(self, *args, **kw)
self._exitHandler = self.viewdock.triggers.addHandler(
self.viewdock.EXIT, self._exit, None)
self._cpdChgHandler = self.viewdock.triggers.addHandler(
self.viewdock.COMPOUND_STATE_CHANGED, self._compoundStateChanged,
None)
def Close(self):
if self._computing:
self._abort = True
return
self.movie.subdialogs.remove(self)
while self.dependentDialogs:
self.dependentDialogs.Close()
ModelessDialog.Close(self)
def __init__(self, group):
self.group = group
self.setInCallback = 0
if group.category:
self.title = "%s attributes" % _mapName(group)
self.triggers = [
('PseudoBondGroup',
chimera.triggers.addHandler('PseudoBondGroup',
self._refreshCB, None)),
('PseudoBond',
chimera.triggers.addHandler('PseudoBond',
self._refreshCB, None))
]
self.refreshFuncs = {}
self.refreshFuncs['PseudoBondGroup'] = []
self.refreshFuncs['PseudoBond'] = []
ModelessDialog.__init__(self)
def __init__(self,
process=None,
models=None,
chargeModel=None,
cb=None,
**kw):
if process:
self.title = "Assign Charges for %s" % process.title()
else:
from AddCharge import process
self.process = process
self.cb = cb
self.startModels = models
if not chargeModel:
from AddCharge import defaultChargeModel
chargeModel = defaultChargeModel
self.initialChargeModel = chargeModel
ModelessDialog.__init__(self, **kw)
def __init__(self, mol, modes, sesData=None, *args, **kw):
self.showVectors = False
self.vectorModel = None
self.sessionHandler = None
self.movieDialog = None
self.modeNumber = False
self.__recursion = False
self.counter = 0
self.cyl = 0
self.con = 0
self.rel = 0
self.vecSf = 0
self.atoms = list()
self.modeData = list()
self.title = None
self.molecule = None
print modes
self.molecule = mol
self.title = "Normal Modes for %s" % mol.name
cs1 = mol.newCoordSet(0)
for atom in mol.atoms:
atom.setCoord(atom.coord(), cs1)
self.atoms.append(atom)
for index, mode in enumerate(modes):
active = False
displacements = list()
v = mode.getEigvec()
# freq = str((mode.getEigval()/FREQ_CONVERSOR)**0.5)
freq = str(mode.getEigval())
for i in xrange(0, len(v), 3):
x, y, z = v[i:i + 3]
displacements.append(Vector(x, y, z))
self.modeData.append(
_NormalModeProxy(index, active, freq, displacements, self))
self._createMovieDialog(self.molecule)
ModelessDialog.__init__(self, *args, **kw)
self.sessionHandler = chimera.triggers.addHandler(
SAVE_SESSION, self._sessionSaveCB, None)
if not chimera.nogui: # avoid useless errors during development
chimera.extension.manager.registerInstance(self)
def __init__(self, ensemble, **kw):
self.title = "MD Movie: %s" % ensemble.name
self.ensemble = ensemble
self.model = Trajectory.Ensemble(self.ensemble)
self.model.CreateMolecule()
endFrame = ensemble.endFrame
if endFrame == "pipe":
fn = 1
while True:
replyobj.status("Loading trajectory from pipe:"
" frame %d\n" % fn)
try:
self.model.LoadFrame(fn,
makeCurrent=False)
except NoFrameError:
break
fn += 1
replyobj.status("Loading trajectory from pipe: done\n")
endFrame = fn-1
if ensemble.startFrame == None:
self.startFrame = 1
else:
self.startFrame = ensemble.startFrame
if self.startFrame > len(ensemble):
replyobj.warning("Start frame > number of"
" trajectory frames; changing start"
" frame to 1\n")
self.startFrame = 1
if endFrame == None:
self.endFrame = len(ensemble)
else:
self.endFrame = endFrame
if self.endFrame > len(ensemble):
replyobj.warning("End frame > number of"
" trajectory frames; changing end"
" frame to last frame\n")
self.endFrame = len(ensemble)
self.molTrigID = chimera.triggers.addHandler("Molecule",
self._molTrigCB, None)
self.openOpts = kw
self._inTriggerCB = False
ModelessDialog.__init__(self)
del self.openOpts
chimera.extension.manager.registerInstance(self)
def Close(self):
chimera.viewer.background = None
self.entry.resaturate()
for (trigger, key), handler in self.entry._handlers.items():
chimera.triggers.deleteHandler(trigger, handler)
global ui
ui = None
ModelessDialog.Close(self)
chimera.extension.manager.deregisterInstance(self)
self.destroy()
def __init__(self, viewdock, *args, **kw):
self.viewdock = viewdock
self.results = viewdock.results
self.compounds = Set()
self.selected = None
self.valueCache = {}
self._isMapped = False
self._colAddHandler = None
self._colDelHandler = None
self._colUpdHandler = None
self._needChangeCompounds = False
ModelessDialog.__init__(self, *args, **kw)
self._exitHandler = self.viewdock.triggers.addHandler(
self.viewdock.EXIT,
self._exit, None)
self._cpdChgHandler = self.viewdock.triggers.addHandler(
self.viewdock.COMPOUND_STATE_CHANGED,
self._compoundStateChanged,
None)
def __init__(self, ensemble, **kw):
self.title = "MD Movie: %s" % ensemble.name
self.ensemble = ensemble
self.model = Trajectory.Ensemble(self.ensemble)
self.model.CreateMolecule()
endFrame = ensemble.endFrame
if endFrame == "pipe":
fn = 1
while True:
replyobj.status("Loading trajectory from pipe:"
" frame %d\n" % fn)
try:
self.model.LoadFrame(fn, makeCurrent=False)
except NoFrameError:
break
fn += 1
replyobj.status("Loading trajectory from pipe: done\n")
endFrame = fn - 1
if ensemble.startFrame == None:
self.startFrame = 1
else:
self.startFrame = ensemble.startFrame
if self.startFrame > len(ensemble):
replyobj.warning("Start frame > number of"
" trajectory frames; changing start"
" frame to 1\n")
self.startFrame = 1
if endFrame == None:
self.endFrame = len(ensemble)
else:
self.endFrame = endFrame
if self.endFrame > len(ensemble):
replyobj.warning("End frame > number of"
" trajectory frames; changing end"
" frame to last frame\n")
self.endFrame = len(ensemble)
self.molTrigID = chimera.triggers.addHandler("Molecule",
self._molTrigCB, None)
self.openOpts = kw
self._inTriggerCB = False
ModelessDialog.__init__(self)
del self.openOpts
chimera.extension.manager.registerInstance(self)
def __init__(self):
import os.path
myDir, junk = os.path.split(__file__)
addFunction('place text', (self._pickLabel, self._moveLabel,
None), icon=chimage.get(Image.open(os.path.join(myDir,
'ilabel.png')), tkgui.app))
addFunction('place key', (self._startOrGrabKey,
self._sizeOrMoveKey, None), icon=chimage.get(
Image.open(os.path.join(myDir, 'key.png')), tkgui.app))
import Ilabel
if not Ilabel._ilabelModel:
Ilabel.IlabelModel()
self.model = Ilabel._ilabelModel
ModelessDialog.__init__(self)
self._sessionHandlerID = chimera.triggers.addHandler(
SAVE_SESSION, self._saveSession, None)
self._closeHandlerID = chimera.triggers.addHandler(
CLOSE_SESSION, self.destroy, None)
self._beginRestoreHandlerID = chimera.triggers.addHandler(
BEGIN_RESTORE_SESSION, self.destroy, None)
