def fetch_local_file(save_dir, save_name): import preferences if not preferences.get(FETCH_PREFERENCES, FETCH_LOCAL): return None dir = preferences.get(FETCH_PREFERENCES, FETCH_DIRECTORY) if not dir: return None from os.path import join, isfile path = join(dir, save_dir, save_name) if not isfile(path): return None return path
def fetch_local_file(save_dir, save_name):
import preferences
if not preferences.get(FETCH_PREFERENCES, FETCH_LOCAL):
return None
dir = preferences.get(FETCH_PREFERENCES, FETCH_DIRECTORY)
if not dir:
return None
from os.path import join, isfile
path = join(dir, save_dir, save_name)
if not isfile(path):
return None
return path
def show_message(text, append = 0, blankAfter=None, color='black',
followWith="", followTime=20, clickCallback=None,
showNow = True):
status = status_line()
if not status:
return
global _statusBlankHandle
if _statusBlankHandle:
status.frame.after_cancel(_statusBlankHandle)
_statusBlankHandle = None
status.message(text, append, color, clickCallback, showNow)
blankTime = blankAfter
if blankAfter is None:
import preferences
from chimera.replyobj import REPLY_PREFERENCES, STATUS_CLEARING
blankTime = preferences.get(REPLY_PREFERENCES, STATUS_CLEARING)
if blankTime != 0:
if not followWith:
followTime = 0
_statusBlankHandle = status.frame.after(1000 * blankTime, lambda:
show_message(followWith, blankAfter=followTime))
def show_message(text,
append=0,
blankAfter=None,
color='black',
followWith="",
followTime=20,
clickCallback=None,
showNow=True):
status = status_line()
if not status:
return
global _statusBlankHandle
if _statusBlankHandle:
status.frame.after_cancel(_statusBlankHandle)
_statusBlankHandle = None
status.message(text, append, color, clickCallback, showNow)
blankTime = blankAfter
if blankAfter is None:
import preferences
from chimera.replyobj import REPLY_PREFERENCES, STATUS_CLEARING
blankTime = preferences.get(REPLY_PREFERENCES, STATUS_CLEARING)
if blankTime != 0:
if not followWith:
followTime = 0
_statusBlankHandle = status.frame.after(
1000 * blankTime,
lambda: show_message(followWith, blankAfter=followTime))
def _bgCheckColor(cat, opt, c):
oc = preferences.get(cat, opt)
if c is None:
if oc is not None:
preferences.set(cat, opt, None)
else:
nc = c.rgba()
if oc != nc:
preferences.set(cat, opt, nc)
def save_location(save_dir, save_name): import preferences if not preferences.get(FETCH_PREFERENCES, FETCH_SAVE): return None dir = preferences.get(FETCH_PREFERENCES, FETCH_DIRECTORY) from os.path import isdir, join, dirname if not dir or not isdir(dir): return None spath = join(dir, save_dir, save_name) sdir = dirname(spath) if not isdir(sdir): import os try: os.makedirs(sdir) except IOError: return None return spath
def _bgCheckColor(cat, opt, c): oc = preferences.get(cat, opt) if c is None: if oc is not None: preferences.set(cat, opt, None) else: nc = c.rgba() if oc != nc: preferences.set(cat, opt, nc)
def save_location(save_dir, save_name):
import preferences
if not preferences.get(FETCH_PREFERENCES, FETCH_SAVE):
return None
dir = preferences.get(FETCH_PREFERENCES, FETCH_DIRECTORY)
from os.path import isdir, join, dirname
if not dir or not isdir(dir):
return None
spath = join(dir, save_dir, save_name)
sdir = dirname(spath)
if not isdir(sdir):
import os
try:
os.makedirs(sdir)
except IOError:
return None
return spath
def status(self, msg, blankAfter=None, echoToMain=False, log=False,
followWith="", followTime=20, color='black'):
"""Display a status message
'blankAfter' controls how long (in seconds) before the
status area is automatically cleared. Use zero to disable
auto-clearing this message. 'None' uses the user preference.
'echoToMain' and 'log' control sending an identical message
to the main window status line and the reply log,
respectively.
'followWith' is a message to follow the first one with.
'followTime' is how long until the followup message is
cleared (ala blankAfter).
Show the text in 'color' color.
"""
from chimera import replyobj
if not self.provideStatus:
raise ValueError("no status support in dialog")
if self._statusBlankHandle:
self.statusLine.after_cancel(self._statusBlankHandle)
self._statusBlankHandle = None
if echoToMain:
replyobj.status(msg, blankAfter=blankAfter, color=color)
if log:
replyobj.info(msg)
if followWith:
if not msg.endswith("\n"):
msg += "\n"
msg += "[above message copied to Reply Log]"
self.statusLine.configure(text=msg.strip(), fg=color)
self.statusLine.update_idletasks()
blankTime = blankAfter
if blankAfter is None:
import preferences
from replyobj import REPLY_PREFERENCES, STATUS_CLEARING
blankTime = preferences.get(REPLY_PREFERENCES,
STATUS_CLEARING)
if blankTime != 0:
if followWith:
nextMsg = followWith
nextTime = followTime
elif log:
nextMsg = "Previous message also written" \
" to reply log"
nextTime = 20
else:
nextMsg = ""
nextTime = 0
self._statusBlankHandle = self.statusLine.after(
1000 * blankTime, lambda:
self.status(nextMsg, blankAfter=nextTime))
def imageArgs(units, width=None, height=None, supersample=None): """return 3-tuple with horizontal pixels, vertical pixels, supersample""" if not width: width, height = chimera.viewer.windowSize if units == 'pixels': scale = 1 elif preferences.get(IMAGE_SETUP, USE_PRINT_UNITS): adjust = convert[units] / convert['inches'] scale = preferences.get(IMAGE_SETUP, DPI) * adjust else: # use screen resolution scale = convert[units] / convert['pixels'] if supersample is None: supersample = preferences.get(IMAGE_SETUP, SUPERSAMPLE) else: supersample = int(supersample) horizPixels = int(scale * width + 0.5) vertPixels = int(scale * height + 0.5) return horizPixels, vertPixels, supersample
def set_selections(self):
# Construct selection icon by tinting the b/w version with
# the selection color
if self.image_selection is None:
from bgprefs import BACKGROUND, HCOLOR
import preferences
sel_color = [ int(i * 255) for i in preferences.get(BACKGROUND, HCOLOR) ]
self.image_selection = tint(self.pil_selection, tuple(sel_color),
self.frame)
del self.pil_selection
if self._any_selected():
self.selections_button.config(image=self.image_selection)
else:
self.selections_button.config(image=self.image_selection_bw)
def set_selections(self):
# Construct selection icon by tinting the b/w version with
# the selection color
if self.image_selection is None:
from bgprefs import BACKGROUND, HCOLOR
import preferences
sel_color = [
int(i * 255) for i in preferences.get(BACKGROUND, HCOLOR)
]
self.image_selection = tint(self.pil_selection, tuple(sel_color),
self.frame)
del self.pil_selection
if self._any_selected():
self.selections_button.config(image=self.image_selection)
else:
self.selections_button.config(image=self.image_selection_bw)
def popMode(self, log=0, **kw):
"""Exit a message mode"""
if len(self._mode) == 1:
return
if self._mode[0] == STATUS:
if log:
info("".join(self._messages[0]))
if 'followWith' not in kw:
kw['followWith'] = \
"Previous message also written to reply log\n"
self._showStatus(**kw)
del self._messages[0]
elif self._mode[0] != NORMAL:
import preferences
p = preferences.get(REPLY_PREFERENCES, self._mode[0])
if p == DisplayDialog:
self._showDialog()
del self._messages[0]
del self._mode[0]
self._setMode(self._mode[0])
def popMode(self, log=0, **kw):
"""Exit a message mode"""
if len(self._mode) == 1:
return
if self._mode[0] == STATUS:
if log:
info("".join(self._messages[0]))
if 'followWith' not in kw:
kw['followWith'] = \
"Previous message also written to reply log\n"
self._showStatus(**kw)
del self._messages[0]
elif self._mode[0] != NORMAL:
import preferences
p = preferences.get(REPLY_PREFERENCES, self._mode[0])
if p == DisplayDialog:
self._showDialog()
del self._messages[0]
del self._mode[0]
self._setMode(self._mode[0])
def checkPovrayLicense():
if preferences.get(POVRAY_AGREE, LICENSE_AGREE):
return True
if not chimera.nogui:
dialog = PovrayCheckLicense()
agree = dialog.run(chimera.tkgui.app)
else:
text = PovrayLicenseText()
if text:
text = ("You must read and accept the following"
" license agreement before raytracing an image"
" with POV-Ray:\n\n") + text
if not text:
text = "You must read and accept the POV-Ray End-User License at <http://www.povray.org/povlegal.html>."
print text
import sys
sys.stdout.write("\nDo you agree to the Pov-Ray End-User License (y/n)? [n] ")
yesno = sys.stdin.readline()
agree = yesno[0] in "yY"
preferences.set(POVRAY_AGREE, LICENSE_AGREE, agree)
return agree
def updateImageUnits(self, *args): units = self.units.get() if units == 'pixels': self.printRes.disable() self.adjustFOV.disable() else: self.printRes.enable() self.adjustFOV.enable() if units != preferences.get(IMAGE_SETUP, UNITS): preferences.set(IMAGE_SETUP, UNITS, units) try: adjust = convert[units] except KeyError: adjust = -1 if adjust == self.adjust: return if self.adjust != -1 and adjust != -1: factor = self.adjust / adjust w = self.iWidth.get() * factor self.iWidth.set(w) h = self.iHeight.get() * factor self.iHeight.set(h) if adjust == -1: # entering pixel mode w, h = chimera.viewer.windowSize self.iWidth.set(w) self.iHeight.set(h) elif self.adjust == -1: pass # leaving pixel mode, sanity check #w, h = paper_types[preferences.get(PAGE_SETUP, PAPER_TYPE)] #if self.iWidth.get() > w: # self.iWidth.set(w) #if self.iHeight.get() > h: # self.iHeight.set(h) self.adjust = adjust self._computeMaxLineWidth()
def _bgCheckOpt(cat, opt, b): ob = preferences.get(cat, opt) if ob != b: preferences.set(cat, opt, b)
def status(self,
msg,
blankAfter=None,
echoToMain=False,
log=False,
followWith="",
followTime=20,
color='black'):
"""Display a status message
'blankAfter' controls how long (in seconds) before the
status area is automatically cleared. Use zero to disable
auto-clearing this message. 'None' uses the user preference.
'echoToMain' and 'log' control sending an identical message
to the main window status line and the reply log,
respectively.
'followWith' is a message to follow the first one with.
'followTime' is how long until the followup message is
cleared (ala blankAfter).
Show the text in 'color' color.
"""
from chimera import replyobj
if not self.provideStatus:
raise ValueError("no status support in dialog")
if self._statusBlankHandle:
self.statusLine.after_cancel(self._statusBlankHandle)
self._statusBlankHandle = None
if echoToMain:
replyobj.status(msg, blankAfter=blankAfter, color=color)
if log:
replyobj.info(msg)
if followWith:
if not msg.endswith("\n"):
msg += "\n"
msg += "[above message copied to Reply Log]"
self.statusLine.configure(text=msg.strip(), fg=color)
self.statusLine.update_idletasks()
blankTime = blankAfter
if blankAfter is None:
import preferences
from replyobj import REPLY_PREFERENCES, STATUS_CLEARING
blankTime = preferences.get(REPLY_PREFERENCES, STATUS_CLEARING)
if blankTime != 0:
if followWith:
nextMsg = followWith
nextTime = followTime
elif log:
nextMsg = "Previous message also written" \
" to reply log"
nextTime = 20
else:
nextMsg = ""
nextTime = 0
self._statusBlankHandle = self.statusLine.after(
1000 * blankTime,
lambda: self.status(nextMsg, blankAfter=nextTime))
def test_get(self):
self.assertEqual(
preferences.get(default=None, key='suspend - Electron'), None)
subproc.setProgress(progress)
info = 'running "%s"' % '" "'.join(cmd)
if not chimera.nogui and statusMessages:
from chimera import dialogs, tkgui
dialogs.display(tkgui._ReplyDialog.name)
replyobj.info(info + '\n')
task.updateStatus(info)
subprog = SM.monitor('running POV-Ray', subproc,
title="POV-Ray progress",
task=task,
afterCB=afterCB)
if raytraceWait:
subprog.wait()
return
status("Rendering high resolution image...", blankAfter=0)
artist = preferences.get(IMAGE_CREDITS, ARTIST).strip()
copyright = preferences.get(IMAGE_CREDITS, COPYRIGHT).strip()
if raiseWindow and not chimera.nogui:
from chimera import tkgui
import CGLtk
CGLtk.raiseWindow(tkgui.app)
# guarantee label balloon is gone (for command line interface)
tkgui.app.cancelLabelBalloon()
# encourage raise to take place
if hideDialogs and not chimera.nogui:
tkgui._hideChildren(tkgui.app, None)
chimera.tkgui.update_windows()
# if background has opacity then save opacity
opacity = chimera.bgopacity
try:
images = chimera.viewer.pilImages(horizPixels, vertPixels,
def chimeraLabel(item, showModel=None, modelName=False, style=None,
diffWith=None, bondSep="-"):
"""Return preferred chimera label for atom/bond/residue/molecule
'showModel' controls whether the model ID is part of the label
If the value type is boolean, then the model is shown if the value
is true. If the value is None, then the model is shown if there
are multiple models, otherwise the model is omitted.
'modelName' controls whether the model name is part of the label.
Has no effect if atom specs are being returned.
'diffWith' can either be a string or of the same type as 'item';
the returned label will not include any leading components that
are the same as those in 'diffWith'
'style' controls whether the label uses atom specs, quasi-
English-like contents, or serial numbers. It is either 'simple',
'command'/'command-line'/'osl', 'serial number', or None.
If None, then the user's preferences controls the contents.
'bondSep' controls the text separator between parts of a bond
when using English-like contents.
"""
if diffWith and not isinstance(diffWith, basestring):
diffWith = chimeraLabel(diffWith, showModel, modelName, style)
if not style:
if chimera.nogui:
style = "osl"
else:
import preferences
from tkgui import GENERAL, ATOMSPEC_CONTENTS, \
ATOMSPEC_SERIAL, ATOMSPEC_SIMPLE
preferred = preferences.get(GENERAL, ATOMSPEC_CONTENTS)
if preferred == ATOMSPEC_SERIAL:
style = "serial number"
elif preferred == ATOMSPEC_SIMPLE:
style = "simple"
else:
# ATOMSPEC_MIDAS doesn't match value used
# in NamingStyleOption, so make this the
# 'else' case
style = "osl"
if style.startswith('command'):
style = "osl"
elif style.startswith('serial'):
# command keyword values might only be 'serial'
style = "serial number"
if style == "serial number" and (not isinstance(item, chimera.Atom)
or not hasattr(item, 'serialNumber')):
style = "simple"
if isinstance(item, chimera.Bond) \
or isinstance(item, chimera.PseudoBond):
l1 = chimeraLabel(item.atoms[0], showModel, modelName,
style, diffWith)
l2 = chimeraLabel(item.atoms[1], showModel,
modelName, style, l1)
if not l2:
l2 = item.atoms[1].name
return l1 + bondSep + l2
doShowModel = False
if showModel:
doShowModel = True
if not doShowModel and isinstance(item, chimera.Model):
doShowModel = True
if not doShowModel and showModel == None \
and len(chimera.openModels.list()) > 1:
doShowModel = True
if style == "osl":
return chimeraOslLabel(item, diffWith, doShowModel)
components = []
if doShowModel:
if hasattr(item, 'molecule') and item.molecule:
mol = item.molecule
else:
mol = item
if showModel or not modelName:
components.append(mol.oslIdent())
if modelName:
if doShowModel:
components.append("%s(%s)" % (mol.name,
mol.oslIdent()))
else:
components.append(mol.name)
if style == "serial number":
if components and diffWith and diffWith.startswith(
components[0] + " "):
components = []
return " ".join(components + [str(item.serialNumber)])
res = None
if isinstance(item, chimera.Residue):
res = item
elif isinstance(item, chimera.Atom):
res = item.residue
if res:
components.append("%s %s" % (res.type, res.id))
if isinstance(item, chimera.Atom):
components.append(item.oslIdent(chimera.SelAtom)[1:])
if len(components) == 0:
retVal = chimeraOslLabel(item) # Non-molecular object
else:
retVal = " ".join(components)
full = retVal
if diffWith:
if full == diffWith:
return ""
for i in range(len(components)):
if diffWith.startswith(" ".join(components[:i+1])+" "):
retVal = " ".join(components[i+1:])
return retVal
def saveImage(filename=None, width=None, height=None, format=None,
units="pixels", description=None, supersample=None,
master=None, printMode=None, raytrace=False,
raytracePreview=None, raytraceWait=None,
raytraceKeepInput=None,
hideDialogs=True, statusMessages=True, raiseWindow=True,
task=None):
if chimera.nogui and chimera.opengl_platform() != 'OSMESA':
raise chimera.UserError, "Need graphics to save images (or use headless Linux version)"
if statusMessages:
from replyobj import status
else:
def status(*args, **kw):
pass
if printMode is None:
printMode = chimera.viewer.camera.mode()
horizPixels, vertPixels, supersample = \
imageArgs(units, width, height, supersample)
savedSD = None # saved screen distance
if units != 'pixels':
adjustFOV = preferences.get(IMAGE_SETUP, ADJUST_FOV)
if adjustFOV == 1 or (adjustFOV == ONLY_STEREO_CAMERAS
and printMode != 'mono'):
# if image is twice as wide as screen,
# screenDistance is half as much
savedSD = chimera.viewer.camera.screenDistance
adjust = convert[units] / convert['millimeters']
image_width = width * adjust
adjust = chimera.viewer.camera.windowWidth / image_width
chimera.viewer.camera.screenDistance *= adjust
if raytrace:
if not checkPovrayLicense():
return
# TODO: make default an argument or preference
if raytraceWait is None:
raytraceWait = preferences.get(POVRAY_SETUP, WAIT_POVRAY)
if raytraceKeepInput is None:
raytraceKeepInput = preferences.get(POVRAY_SETUP, KEEP_INPUT)
if raytracePreview is None:
raytracePreview = preferences.get(POVRAY_SETUP, SHOW_PREVIEW)
quality = DEFAULT_JPEG_QUALITY
format = 'PNG'
if not chimera.nogui and not filename:
if not master:
master = tkgui.app
chooseDialog = _ChooseFileDialog(filterSet='povray',
format=format)
result = chooseDialog.run(master)
if result is None:
status("Image save cancelled.")
return
filename, format = result[0]
quality = chooseDialog.quality.get()
if not filename:
replyobj.error("Need filename for POV-Ray output")
return
if filename.endswith('.png') or filename.endswith('.jpg'):
povfilename = filename[:-4] + '.pov'
inifilename = filename[:-4] + '.ini'
else:
povfilename = filename + '.pov'
inifilename = filename + '.ini'
if task is None:
from chimera.tasks import Task
task = Task("raytrace image", None)
task.updateStatus("Generating POV-Ray data file")
import exports
exports.doExportCommand('POV-Ray', povfilename)
task.updateStatus("Generating POV-Ray parameter file")
if savedSD is not None:
chimera.viewer.camera.screenDistance = savedSD
import SubprocessMonitor as SM
cmd = [
preferences.get(POVRAY_SETUP, POVRAY_EXE),
inifilename,
"+I%s" % povfilename,
"+O%s" % filename,
"+V" # need verbose to monitor progress
]
inifile = open(inifilename, 'w')
print >> inifile, (
"Width=%d\n"
"Height=%d\n"
# add font path, CHIMERA/share/fonts
"Library_Path=\"%s\"\n"
"Bounding=On\n"
"Bounding_Threshold=1\n"
"Split_Unions=On\n"
"Remove_Bounds=On\n"
"Quality=%d"
) % (
horizPixels,
vertPixels,
os.path.join(os.environ['CHIMERA'], 'share', 'fonts'),
preferences.get(POVRAY_SETUP, POV_QUALITY)
)
if not preferences.get(POVRAY_SETUP, ANTIALIAS):
print >> inifile, "Antialias=Off"
else:
print >> inifile, (
"Antialias=On\n"
"Antialias_Threshold=%f\n"
"Antialias_Depth=%d\n"
"Sampling_Method=%d"
) % (
preferences.get(POVRAY_SETUP, ANTIALIAS_THRESHOLD),
preferences.get(POVRAY_SETUP, ANTIALIAS_DEPTH),
preferences.get(POVRAY_SETUP, ANTIALIAS_METHOD)
)
if not preferences.get(POVRAY_SETUP, JITTER):
print >> inifile, "Jitter=Off"
else:
print >> inifile, (
"Jitter=On\n"
"Jitter_Amount=%f\n"
) % (
preferences.get(POVRAY_SETUP, JITTER_AMOUNT),
)
oa = preferences.get(POVRAY_SETUP, OUTPUT_ALPHA)
if oa == 1 or (oa == 2 and chimera.bgopacity):
if chimera.viewer.depthCue:
replyobj.warning("Depth-cueing disables transparent background")
print >> inifile, "Output_Alpha=On"
if format in ('PNG', 'Stereo PNG'):
print >> inifile, ("; output PNG\n"
"Output_File_Type=N8")
elif format in ('JPEG', 'Stereo JPEG'):
print >> inifile, ("; output JPEG\n"
"Output_File_Type=J%d") % quality
elif format in ('PPM'):
print >> inifile, ("; output PPM\n"
"Output_File_Type=P")
if chimera.nogui or not raytracePreview:
print >> inifile, "Display=Off"
else:
print >> inifile, "Display=On"
if not raytraceWait:
print >> inifile, "Pause_when_Done=On"
inifile.close()
if raytraceKeepInput:
inputs = []
else:
inputs = [ povfilename, inifilename ]
def afterCB(aborted, inputs=inputs, outputs=[filename]):
import os
for fn in inputs:
try:
os.remove(fn)
except OSError:
pass
if aborted:
for fn in outputs:
try:
os.remove(fn)
except OSError:
pass
task.updateStatus("Starting POV-Ray")
try:
subproc = SM.Popen(cmd, stdin=None, stdout=None,
stderr=SM.PIPE, daemon=True)
except OSError, e:
raise chimera.UserError, "Unable run POV-Ray executable: %s" % e
progress = povrayProgress(subproc)
progress.start()
subproc.setProgress(progress)
info = 'running "%s"' % '" "'.join(cmd)
if not chimera.nogui and statusMessages:
from chimera import dialogs, tkgui
dialogs.display(tkgui._ReplyDialog.name)
replyobj.info(info + '\n')
task.updateStatus(info)
subprog = SM.monitor('running POV-Ray', subproc,
title="POV-Ray progress",
task=task,
afterCB=afterCB)
if raytraceWait:
subprog.wait()
return
def get_suspend_preference(pid):
return preferences.get("suspend - %s" % process.get_name(pid))
def fillInUI(self, master):
self._ModelTrigger = None
#self._SetupTrigger = None
self._SizeTrigger = None
self.raytrace = None
# Image Size
imageSetup = Tix.LabelFrame(master, label="Image Size")
imageSetup.pack(fill=Tk.X, ipadx=2, ipady=2)
subframe = imageSetup.frame
#subframe = Tk.Frame(imageSetup.frame)
#subframe.pack(fill=Tk.BOTH, expand=1)
# add in conversion factor for pixels and graphics screen
from chimera import tkgui
win = tkgui.app.graphics
res = tkgui.getScreenMMWidth() / win.winfo_screenwidth()
convert['pixels'] = mm2pt(res)
self.matchAspect = Tk.BooleanVar(master)
self.matchAspect.set(1)
self.usePrint = Tk.BooleanVar(master)
self.usePrint.set(preferences.get(IMAGE_SETUP, USE_PRINT_UNITS))
import itertools
row = itertools.count()
self.showUsePrint = Tk.Checkbutton(subframe, indicatoron=1,
variable=self.usePrint, highlightthickness=0,
text=USE_PRINT_UNITS,
command=self._updateUsePrint)
self.showUsePrint.grid(columnspan=2, row=row.next(), sticky=Tk.W)
w, h = chimera.viewer.windowSize
self.units = ImageUnitsOption(subframe, row.next(), UNITS,
'pixels', self.updateImageUnits)
self.iWidth = FloatOption(subframe, row.next(), 'Image width',
w, self.updateImageWidth, min=1e-10)
self.iHeight = FloatOption(subframe, row.next(), 'Image height',
h, self.updateImageHeight, min=1e-10)
matchAspect = Tk.Checkbutton(subframe, indicatoron=1,
variable=self.matchAspect, highlightthickness=0,
text="Maintain current aspect ratio",
command=self.updateMatchAspect)
matchAspect.grid(columnspan=2, row=row.next(), sticky=Tk.W)
self.grow = Tk.Button(imageSetup.frame, text="Grow to Fit",
command=self.Resize, state=Tk.DISABLED)
fitrow = row.next()
self.grow.grid(row=fitrow, column=0, padx=2, pady=2,
sticky=Tk.NSEW)
self.shrink = Tk.Button(imageSetup.frame, text="Shrink to Fit",
command=lambda f=self.Resize: f(False),
state=Tk.DISABLED)
self.shrink.grid(row=fitrow, column=1, padx=2, pady=2,
sticky=Tk.NSEW)
#fetch = Tk.Button(imageSetup.frame, text="Get Pixels",
# command=self.fetchWindowSize)
#fetch.grid(row=row.next(), column=0, padx=2, pady=2, sticky=Tk.NSEW)
#calc = Tk.Button(imageSetup.frame, text="Image Setup",
# command=self.showImageSetupDialog)
#calc.grid(row=row.next(), column=1, padx=2, pady=2, sticky=Tk.NSEW)
self.printRes = FloatOption(subframe, row.next(), DPI,
preferences.get(IMAGE_SETUP, DPI),
self._updatePrint, min=1)
# Image Information
info = Tix.LabelFrame(master, label="Image Information")
info.pack(fill=Tk.X)
d = Tk.Label(info.frame, text="Description:")
d.grid(columnspan=2, row=0, column=0, sticky=Tk.W, padx=2,
pady=1)
self.description = Tk.Entry(info.frame)
info.frame.grid_columnconfigure(0, weight=1)
info.frame.grid_columnconfigure(1, weight=1)
self.description.grid(columnspan=2, row=1, column=0,
sticky=Tk.EW, padx=2, pady=2)
imageCredits = Tk.Button(info.frame,
text="Image Credits",
command=self.showImageCreditsDialog)
imageCredits.grid(row=2, column=0, padx=2, pady=2)
credit = Tk.Button(info.frame, text="Citing Chimera",
command=lambda: help.display("credits.html"))
credit.grid(row=2, column=1, padx=2, pady=2)
# Image camera
self.raytrace = BooleanOption(master, -1,
'Raytrace with POV-Ray', False,
self._updateRaytrace)
self.raytraceOptions = Tk.Button(master, text=POVRAY_SETUP,
command=self.showPOVRayOptions)
self.raytraceOptions.pack()
self.raytraceOptions.pack_forget()
self.supersample = SupersampleOption(master, -1, SUPERSAMPLE,
preferences.get(IMAGE_SETUP, SUPERSAMPLE),
self._updateSS)
self.adjustFOV = AdjustFOVOption(master, -1, ADJUST_FOV,
preferences.get(IMAGE_SETUP, ADJUST_FOV),
self._updateAdjustFOV)
self.printMode = _PrintModeOption(master, -1,
'Image camera mode', _PrintModeOption.SAME,
self._updatePrintMode)
self.lenticular = IntOption(master, -1,
'Number of lenticular images',
chimera.Camera.lenticularImageCount(),
self._updateLenticular, min=2, width=4)
self.lenticular.forget()
# switch to user's prefered units
self.adjust = convert['pixels']
units = preferences.get(IMAGE_SETUP, UNITS)
self._updateUsePrint()
self.units.set(units)
self.updateImageUnits()
def _bgCheckOpt(cat, opt, b):
ob = preferences.get(cat, opt)
if ob != b:
preferences.set(cat, opt, b)
def chimeraLabel(item,
showModel=None,
modelName=False,
style=None,
diffWith=None,
bondSep="-"):
"""Return preferred chimera label for atom/bond/residue/molecule
'showModel' controls whether the model ID is part of the label
If the value type is boolean, then the model is shown if the value
is true. If the value is None, then the model is shown if there
are multiple models, otherwise the model is omitted.
'modelName' controls whether the model name is part of the label.
Has no effect if atom specs are being returned.
'diffWith' can either be a string or of the same type as 'item';
the returned label will not include any leading components that
are the same as those in 'diffWith'
'style' controls whether the label uses atom specs, quasi-
English-like contents, or serial numbers. It is either 'simple',
'command'/'command-line'/'osl', 'serial number', or None.
If None, then the user's preferences controls the contents.
'bondSep' controls the text separator between parts of a bond
when using English-like contents.
"""
if diffWith and not isinstance(diffWith, basestring):
diffWith = chimeraLabel(diffWith, showModel, modelName, style)
if not style:
if chimera.nogui:
style = "osl"
else:
import preferences
from tkgui import GENERAL, ATOMSPEC_CONTENTS, \
ATOMSPEC_SERIAL, ATOMSPEC_SIMPLE
preferred = preferences.get(GENERAL, ATOMSPEC_CONTENTS)
if preferred == ATOMSPEC_SERIAL:
style = "serial number"
elif preferred == ATOMSPEC_SIMPLE:
style = "simple"
else:
# ATOMSPEC_MIDAS doesn't match value used
# in NamingStyleOption, so make this the
# 'else' case
style = "osl"
if style.startswith('command'):
style = "osl"
elif style.startswith('serial'):
# command keyword values might only be 'serial'
style = "serial number"
if style == "serial number" and (not isinstance(item, chimera.Atom)
or not hasattr(item, 'serialNumber')):
style = "simple"
if isinstance(item, chimera.Bond) \
or isinstance(item, chimera.PseudoBond):
l1 = chimeraLabel(item.atoms[0], showModel, modelName, style, diffWith)
l2 = chimeraLabel(item.atoms[1], showModel, modelName, style, l1)
if not l2:
l2 = item.atoms[1].name
return l1 + bondSep + l2
doShowModel = False
if showModel:
doShowModel = True
if not doShowModel and isinstance(item, chimera.Model):
doShowModel = True
if not doShowModel and showModel == None \
and len(chimera.openModels.list()) > 1:
doShowModel = True
if style == "osl":
return chimeraOslLabel(item, diffWith, doShowModel)
components = []
if doShowModel:
if hasattr(item, 'molecule') and item.molecule:
mol = item.molecule
else:
mol = item
if showModel or not modelName:
components.append(mol.oslIdent())
if modelName:
if doShowModel:
components.append("%s(%s)" % (mol.name, mol.oslIdent()))
else:
components.append(mol.name)
if style == "serial number":
if components and diffWith and diffWith.startswith(components[0] +
" "):
components = []
return " ".join(components + [str(item.serialNumber)])
res = None
if isinstance(item, chimera.Residue):
res = item
elif isinstance(item, chimera.Atom):
res = item.residue
if res:
components.append("%s %s" % (res.type, res.id))
if isinstance(item, chimera.Atom):
components.append(item.oslIdent(chimera.SelAtom)[1:])
if len(components) == 0:
retVal = chimeraOslLabel(item) # Non-molecular object
else:
retVal = " ".join(components)
full = retVal
if diffWith:
if full == diffWith:
return ""
for i in range(len(components)):
if diffWith.startswith(" ".join(components[:i + 1]) + " "):
retVal = " ".join(components[i + 1:])
return retVal
import utils
import os
import preferences
APP_LOCATION = "/Applications/tempo.app"
SETUP_SCRIPT = 'tell application "System Events" to make login item at end with properties {path:"%s", hidden:false}' % APP_LOCATION
LAUNCH_AT_LOGIN_KEY = "ENABLE_LAUNCH_AT_LOGIN"
if os.path.exists(APP_LOCATION):
if preferences.get(LAUNCH_AT_LOGIN_KEY):
preferences.set(LAUNCH_AT_LOGIN_KEY, "true")
utils.run_osa_script(SETUP_SCRIPT)
def get_license():
try:
return preferences.get("license") or download_license()
except:
error.error("Cannot find license")
