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, 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 __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, 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, 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, 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, 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, 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, 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, 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 __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, 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 __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, 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, 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,
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, 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, 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, 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, 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, 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 __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, 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,
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, 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, 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 __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, seqCanvas):
self.seqCanvas = seqCanvas
seqCanvas.mainCanvas.bind('<ButtonPress-1>', self._mouseDownCB)
seqCanvas.mainCanvas.bind('<ButtonRelease-1>', self._mouseUpCB)
seqCanvas.mainCanvas.bind('<B1-Motion>', self._mouseDragCB)
seqCanvas.mainCanvas.bind('<Button-3>',
lambda e: self._focusCB(e, pref="residue"))
seqCanvas.mainCanvas.bind('<Shift-Button-3>',
lambda e: self._focusCB(e, pref="region"))
self.title = "Region Browser for " + seqCanvas.mav.title
self._dragLines = []
self._dragRegion = None
self._prevDrag = None
self._bboxes = []
self._afterID = None
self._highlightedRegion = None
self.regions = []
self.associatedRegions = {}
self.renameDialogs = {}
self._scfDialog = None
ModelessDialog.__init__(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)
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)
def __init__(self, num, width, height, img_src, **kw):
"""num is the number of panels the wizard is to contain
width is the desired width of each panel, in pixels
height is the desired height of each panel, in pixels
img_src is the absolute path to a .gif file containing
an image to appear in the left-hand side of the wizard
"""
self.panel_width = width
self.panel_height = height
self.img_src = img_src
if kw.has_key('img_bg_color'):
self.img_bg_color = kw['img_bg_color']
else:
self.img_bg_color = None
self.numPanels = num
self.pCurrent = 0
self.pFrames = [None] * self.numPanels
ModelessDialog.__init__(self)
def __init__(self, num, width, height, img_src, **kw):
"""num is the number of panels the wizard is to contain
width is the desired width of each panel, in pixels
height is the desired height of each panel, in pixels
img_src is the absolute path to a .gif file containing
an image to appear in the left-hand side of the wizard
"""
self.panel_width = width
self.panel_height = height
self.img_src = img_src
if kw.has_key('img_bg_color'):
self.img_bg_color = kw['img_bg_color']
else:
self.img_bg_color = None
self.numPanels = num
self.pCurrent = 0
self.pFrames = [None] * self.numPanels
ModelessDialog.__init__(self)
def __init__(self, mav, *args, **kw):
self.mav = mav
self.title = "Delete Sequences/Gaps of %s" % (mav.title, )
self.handlerID = self.mav.triggers.addHandler(MOD_ALIGN,
self._alignMod, None)
ModelessDialog.__init__(self, *args, **kw)
def __init__(self, fileAttrs, mavStatus): self.fileAttrs = fileAttrs self.mavStatus = mavStatus self.reminder = "Annotations only saved in Stockholm format\n"\ "Comments saved in RSF and Stockholm formats\n" ModelessDialog.__init__(self)
def __init__(self, noteDialog): self.noteDialog = noteDialog ModelessDialog.__init__(self)
def __init__(self, rotDialog):
self.rotDialog = rotDialog
ModelessDialog.__init__(self)
def __init__(self, mav, *args, **kw):
self.mav = mav
self.title = "Match Structures by Sequence for %s" % mav.title
ModelessDialog.__init__(self, *args, **kw)
def __init__(self, mav, *args, **kw): self.mav = mav self.title = "Match Structures by Sequence for %s" % mav.title ModelessDialog.__init__(self, *args, **kw)
def __init__(self, fileName):
self._fileName = fileName
self.title = "Open %s" % fileName
self.Open = self.OK
ModelessDialog.__init__(self)
def __init__(self, models=None): self.initModels = models ModelessDialog.__init__(self)
def __init__(self, controller, movie_ui, *args, **kwargs):
self.title = "OrbiTraj Configuration"
self.controller = controller
self.movie_ui = movie_ui
ModelessDialog.__init__(self, *args, **kwargs)
