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"which is the angle between the three atoms.</p>"\ "<p>The Measure Angle jig will write the angle value to the trace file "\	"which is the angle between the three atoms."\ "</p>"\ "<p>The Measure Angle Jig will write the angle value to the trace file "\	def createWhatsThis(self): ############################################## # File Toolbar ############################################## #### Open File #### fileOpenText = "<u><b>Open File</b></u> (Ctrl + O)</b></p><br> "\ "<p><img source=\"fileopen\"><br> "\ "Opens a new file."\ "</p>" QMimeSourceFactory.default...
jigsDihedralActionText = "<u><b>Measure Dihedral</b></u></b></p><br>"\	jigsDihedralActionText = "<u><b>Measure Dihedral Jig</b></u></b></p><br>"\	def createWhatsThis(self): ############################################## # File Toolbar ############################################## #### Open File #### fileOpenText = "<u><b>Open File</b></u> (Ctrl + O)</b></p><br> "\ "<p><img source=\"fileopen\"><br> "\ "Opens a new file."\ "</p>" QMimeSourceFactory.default...
"A <b>Measure Dihedral</b> jig functions as a dimension to display the "\	"A <b>Measure Dihedral Jig</b> functions as a dimension to display the "\	def createWhatsThis(self): ############################################## # File Toolbar ############################################## #### Open File #### fileOpenText = "<u><b>Open File</b></u> (Ctrl + O)</b></p><br> "\ "<p><img source=\"fileopen\"><br> "\ "Opens a new file."\ "</p>" QMimeSourceFactory.default...
"<p>To create the Measure Dihedral jig, enter <b>Select Atoms</b> mode, "\ "select four atoms and then select this jig. The Measure Dihedral jig is "\	"<p>To create the Measure Dihedral Jig, enter <b>Select Atoms</b> mode, "\ "select four atoms and then select this jig. The Measure Dihedral Jig is "\	def createWhatsThis(self): ############################################## # File Toolbar ############################################## #### Open File #### fileOpenText = "<u><b>Open File</b></u> (Ctrl + O)</b></p><br> "\ "<p><img source=\"fileopen\"><br> "\ "Opens a new file."\ "</p>" QMimeSourceFactory.default...
"which is the dihedral angle value.</p>"\ "<p>The Measure Dihedral jig will write the dihedral angle value to the trace file "\	"which is the dihedral angle value."\ "</p>"\ "<p>The Measure Dihedral Jig will write the dihedral angle value to the trace file "\	def createWhatsThis(self): ############################################## # File Toolbar ############################################## #### Open File #### fileOpenText = "<u><b>Open File</b></u> (Ctrl + O)</b></p><br> "\ "<p><img source=\"fileopen\"><br> "\ "Opens a new file."\ "</p>" QMimeSourceFactory.default...
mol.setDisplay(diDEFAULT)		def _readmmp(assy, filnam, isInsert = False): """The routine to actually reading a mmp file and save data into data structure """ #bruce 041011: added 'U' to file mode, for universal newline support. l=open(filnam,"rU").readlines() if not isInsert: assy.filename=filnam mol = None ndix={} assy.alist = [] #assy.tree = Gr...
self.history.message( orangemsg( "Warning: this movie has no atoms."))	self.warning( "this movie has no atoms. Playing it anyway (no visible effect).")	def warn_if_other_part(self, part): #bruce 050427; to call when play is pressed, more or less... "warn the user if playing this movie won't move any (or all) atoms in the given part (or about other weird conditions too)." if self.alist == None: return # like .touches_part() in a subobject, but can be called sooner... y...
self.history.message( orangemsg( "Warning: all of this movie's atoms have been deleted.")) if not yes: self.history.message( orangemsg( "Warning: to see this movie playing, you must display a different Part.")) elif other or killed: if killed: self.history.message( orangemsg( "Warning: some of this movie's atoms have b...	self.warning( "all of this movie's atoms have been deleted. Playing it anyway (no visible effect).") else: if not yes: self.warning( "to see this movie playing, you must display a different Part.") elif other or killed: if killed: self.warning( "some of this movie's atoms have been deleted. (Playing it still moves the ...	def warn_if_other_part(self, part): #bruce 050427; to call when play is pressed, more or less... "warn the user if playing this movie won't move any (or all) atoms in the given part (or about other weird conditions too)." if self.alist == None: return # like .touches_part() in a subobject, but can be called sooner... y...
	def warning(self, text): self.history.message( orangemsg( "Warning: " + text))	def warn_if_other_part(self, part): #bruce 050427; to call when play is pressed, more or less... "warn the user if playing this movie won't move any (or all) atoms in the given part (or about other weird conditions too)." if self.alist == None: return # like .touches_part() in a subobject, but can be called sooner... y...
QToolTip.add(self.megapov_checkbox,self.__tr("Enable POV-Ray")) QWhatsThis.add(self.megapov_checkbox,self.__tr("This enables POV-Ray as a plug-in. POV-Ray is a free raytracing program available from http://www.povray.org/. POV-Ray must be installed on your computer before you can enable the POV-Ray plug-in."))	QToolTip.add(self.megapov_checkbox,self.__tr("Enable MegaPOV")) QWhatsThis.add(self.megapov_checkbox,self.__tr("This enables MegaPOV as a plug-in. MegaPOV is a free addon raytracing program available from http://megapov.inetart.net/. Both MegaPOV and POV-Ray must be installed on your computer before you can enable the ...	def languageChange(self): self.setCaption(self.__tr("Preferences")) self.ok_btn.setText(self.__tr("OK")) self.groupBox7_2.setTitle(self.__tr("Axes")) self.display_origin_axis_checkbox.setText(self.__tr("Display Origin Axis")) QToolTip.add(self.display_origin_axis_checkbox,self.__tr("Show/Hide Origin Axis")) QWhatsThis....
QToolTip.add(self.megapov_lbl,self.__tr("Enable POV-Ray")) QWhatsThis.add(self.megapov_lbl,self.__tr("This enables POV-Ray as a plug-in. POV-Ray is a free raytracing program available from http://www.povray.org/. POV-Ray must be installed on your computer before you can enable the POV-Ray plug-in."))	QToolTip.add(self.megapov_lbl,self.__tr("Enable MegaPOV")) QWhatsThis.add(self.megapov_lbl,self.__tr("This enables MegaPOV as a plug-in. MegaPOV is a free addon raytracing program available from http://megapov.inetart.net/. Both MegaPOV and POV-Ray must be installed on your computer before you can enable the MegaPOV pl...	def languageChange(self): self.setCaption(self.__tr("Preferences")) self.ok_btn.setText(self.__tr("OK")) self.groupBox7_2.setTitle(self.__tr("Axes")) self.display_origin_axis_checkbox.setText(self.__tr("Display Origin Axis")) QToolTip.add(self.display_origin_axis_checkbox,self.__tr("Show/Hide Origin Axis")) QWhatsThis....
QToolTip.add(self.megapov_path_linedit,self.__tr("The full path to the POV-Ray executable file.")) QWhatsThis.add(self.megapov_path_linedit,self.__tr("The full path to the POV-Ray executable file."))	QToolTip.add(self.megapov_path_linedit,self.__tr("The full path to the MegaPOV executable file (megapov.exe).")) QWhatsThis.add(self.megapov_path_linedit,self.__tr("The full path to the MegaPOV executable file (megapov.exe)."))	def languageChange(self): self.setCaption(self.__tr("Preferences")) self.ok_btn.setText(self.__tr("OK")) self.groupBox7_2.setTitle(self.__tr("Axes")) self.display_origin_axis_checkbox.setText(self.__tr("Display Origin Axis")) QToolTip.add(self.display_origin_axis_checkbox,self.__tr("Show/Hide Origin Axis")) QWhatsThis....
QToolTip.add(self.megapov_choose_btn,self.__tr("Choose POV-Ray executable")) QWhatsThis.add(self.megapov_choose_btn,self.__tr("This opens up a file chooser dialog so that you can specify the location of the POV-Ray executable."))	QToolTip.add(self.megapov_choose_btn,self.__tr("Choose MegaPOV executable (megapov.exe)")) QWhatsThis.add(self.megapov_choose_btn,self.__tr("This opens up a file chooser dialog so that you can specify the location of the MegaPOV executable (megapov.exe)."))	def languageChange(self): self.setCaption(self.__tr("Preferences")) self.ok_btn.setText(self.__tr("OK")) self.groupBox7_2.setTitle(self.__tr("Axes")) self.display_origin_axis_checkbox.setText(self.__tr("Display Origin Axis")) QToolTip.add(self.display_origin_axis_checkbox,self.__tr("Show/Hide Origin Axis")) QWhatsThis....
os.rmdir(os.path.join(root, name))	fname = os.path.join(root, name) if os.path.isdir(fname): os.rmdir(fname) else: os.remove(fname)	def clean(self, rootPath, cleanAll=False): """Clean everything created temporaly""" for root, dirs, files in os.walk(rootPath, topdown=False): for name in files: if cleanAll: os.remove(os.path.join(root, name)) elif not (name.endswith('w32.exe') or name.endswith('.dmg') or name.endswith('.tar.gz')): os.remove(os.path.j...
def __init__(self, part, mflag, simaspect = None):	def __init__(self, part, mflag, simaspect = None, use_dylib_sim = False):	def __init__(self, part, mflag, simaspect = None): "set up external relations from the part we'll operate on; take mflag since someday it'll specify the subclass to use" self.assy = assy = part.assy # needed? #self.tmpFilePath = assy.w.tmpFilePath self.win = assy.w # might be used only for self.win.progressbar.launch ...
if not os.path.exists(program): msg = redmsg("The simulator program [" + program + "] is missing. Simulation aborted.") env.history.message(cmd + msg) return -1	if self.use_dylib_sim: self.dylib_path = os.path.dirname(program) worked = self.import_dylib_sim(self.dylib_path) if not worked: msg = redmsg("The simulator dynamic library [sim.so or sim.dylib or so, in " + self.dylib_path + "] is missing or could not be imported. Simulation aborted.") env.history.message(cmd + msg...	def set_options_errQ(self): #e maybe split further into several setup methods? #bruce 051115 removed unused 'options' arg """Set movie alist (from simaspect or entire part); debug-msg if it was already set (and always ignore old value). Figure out and set filenames, including sim executable path. All inputs and outputs...
ff = open(tfile, "rU")	try: ff = open(tfile, "rU") except: print_compact_traceback("exception opening trace file %r: " % tfile) env.history.message( redmsg( "Error: simulator trace file not found at [%s]." % tfile )) self.mentioned_sim_trace_file = True return	def print_sim_warnings(self): #bruce 050407; soon we should do this continuously instead "#doc; might change self.said_we_are_done to False or True, or leave it alone" try: tfile = self.traceFileName except AttributeError: return # sim never ran (not always an error, I suspect) if not tfile: return # no trace file was ...
env.history.message( redmsg( "Warning: simulator trace file should normally end with \"	env.history.message( orangemsg( "Warning: simulator trace file should normally end with \"	def print_sim_warnings(self): #bruce 050407; soon we should do this continuously instead "#doc; might change self.said_we_are_done to False or True, or leave it alone" try: tfile = self.traceFileName except AttributeError: return # sim never ran (not always an error, I suspect) if not tfile: return # no trace file was ...
mol.changed_attr('atpos', skip = ('basepos',) )	mol.changed_attr('atpos')	def setposn_batch(self, pos): #bruce 050513; I wonder if almost all calls of setposn should be this instead? maybe... "use this in place of setposn, for speed, if you will run it a lot on atoms in the same chunk" mol = self.molecule try: del mol.atpos except: pass else: mol.changed_attr('atpos', skip = ('basepos',) ) #...
def __init__(self, xoff, yoff, right, up, rot90): self.outOfScreen = cross(right, up) if rot90: self.xflip = xflip = right[1] < 0.0	def __init__(self, xoff=0, yoff=0, right=None, up=None, rot90=False, glBegin=False): self.glBegin = glBegin if glBegin: assert right is not None and up is not None self.outOfScreen = cross(right, up) if rot90: self.xflip = xflip = right[1] < 0.0 else: self.xflip = xflip = right[0] < 0.0 xgap = WIDTH halfheight = 0...	def __init__(self, xoff, yoff, right, up, rot90):
self.xflip = xflip = right[0] < 0.0 xgap = WIDTH halfheight = 0.5 * HEIGHT if xflip: xgap = -SCALE def fx(x): return SCALE (WIDTH - 1 - x) else: xgap = SCALE def fx(x): return SCALE x if rot90: yoff += xgap xoff -= halfheight * SCALE def tfm(x, y, yoff1, yflip): if yflip: y1 = SCALE * (HEIGHT - 1 - y) else: y1...	assert tfm is not None def tfmgen(i): def tfm2(x, y): return tfm(x + i * (WIDTH+1), y) return tfm2	def __init__(self, xoff, yoff, right, up, rot90):
def tfm2(x, y): return self.tfm(x + (WIDTH+1) * fi(i), y, yoff, yflip) self.drawCharacter(str[i], tfm2) def drawCharacter(char, color, xfm): def drawSeq(seq, drawline=drawline): if type(seq[0][0]) in (types.TupleType, types.ListType): for subseq in seq: drawSeq(subseq) else: seq = map(lambda tpl,xfm=xfm: apply(xfm,tpl...	def drawSequence(seq, tfm=tfmgen(i)): if type(seq[0][0]) is not types.IntType: for x in seq: drawSequence(x) return seq = map(lambda tpl: apply(tfm,tpl), seq) for i in range(len(seq) - 1): pos1, pos2 = seq[i], seq[i+1] if self.glBegin: glVertex(pos1[0], pos1[1], pos1[2]) glVertex(pos2[0], pos2[1], pos2[2]) else: ...	def tfm2(x, y): return self.tfm(x + (WIDTH+1) * fi(i), y, yoff, yflip)
drawString(text, color, tfm)	f3d = Font3D() f3d.drawString(text, tfm=tfm, color=color)	def tfm(x, y): return csys.xyz((10 + y / (1. * HEIGHT), 0, 0.9 - csys.zinv * x / (1. * WIDTH)))
drawString(text, color, tfm)	f3d = Font3D() f3d.drawString(text, tfm=tfm, color=color)	def tfm(x, y): x = (x / (1. * WIDTH)) * textx y = (y / (1. * HEIGHT)) * texty return textxyz + x + y
if self.part != part:	if self.part is not part:	def set_part(self, part): """change our current part to the one given, and take on that part's view; ok if old or new part is None; note that when called on our current part, effect is to store our view into it (which might not actually be needed, but is fast enough and harmless) """ if self.part != part: self.gl_updat...
"[public] if you know about this part, forget about it (call this from dying parts)" if self.part == part:	"[public] if you know about this part, forget about it (call this from dying parts)" if self.part is part:	def forget_part(self, part): "[public] if you know about this part, forget about it (call this from dying parts)" ###@@@ doit if self.part == part: self.set_part(None) return
m.basepos = m.curpos = + m._savedbasepos	assert m.basepos is m.curpos m.basepos = m.curpos = m.atpos = + m._savedbasepos m.changed_attr('atpos', skip = ('basepos',) )	def restorebasepos(self): """Restore atom positions copied earlier by savebasepos(). """ # restore that later (without erasing it, so no need to save it # again right now) # (only valid when every molecule is "frozen", i.e. basepos and # curpos are same object): for m in self.molecules: m.basepos = m.curpos = + m._save...
self.pset.scf.maxvt = self.pset.ui.iterations		def _save_parms(self): '''Save parameter set values. This is always called by save_ui_settings, since it depends on the ui setting values. This should propbably be a private method.''' # $CONTRL group ########################################### # Parms Values self.pset.contrl.runtyp = runtyp[self.pset.ui.runtyp] # ...
	def open_tmp_inputfile(self): '''Writes a temporary GAMESS inputfile of the current Gamess jig and opens the file in an editor. ''' from platform import find_or_make_Nanorex_subdir tmpdir = find_or_make_Nanorex_subdir('temp') basename = self.gamessJig.name + "-" + self.gamessJig.gms_parms_info('_') tmp_inputfile = os....	def set_ecmethod(self, val): '''Enable/disable widgets when user changes Electron Correlation Method. '''
	if self.edit_input_file_cbox.isChecked(): self.open_tmp_inputfile()	def accept(self): """The slot method for the 'Save' button.""" self._save_ui_settings() QDialog.accept(self)
"""	Note: when atoms are selected, only affects atoms as permitted by the selection filter. """	def selectInvert(self): """If some parts are selected, select the other parts instead. If some atoms are selected, select the other atoms instead (even in chunks with no atoms selected, which end up with all atoms selected). (And unselect all currently selected parts or atoms.) """ self.begin_select_cmd() #bruce 051031...
msg = fix_plurals(str(len(contract_list)) + " atom(s) unselected.")	msg = fix_plurals(str(natoms) + " atom(s) unselected.")	def selectContract(self): """Unselects any atom which has a bond to an unselected atom, or which has any open bonds. """ # Added by Mark 050923. self.begin_select_cmd() #bruce 051031 cmd = "Contract Selection: " env.history.message(greenmsg(cmd)) if not self.selatoms: env.history.message(greenmsg(cmd) + redmsg("No at...
is under the mouse at event get un-selected,	is under the mouse at event get un-selected (subject to selection filter),	def unpick_at_event(self, event): #renamed from unpick; modified """Make whatever visible atom or chunk (depending on self.selwhat) is under the mouse at event get un-selected, but don't change whatever else is selected. """ self.begin_select_cmd() #bruce 051031 if self.o.mode.modename == 'DEPOSIT': atm = self.findAtom...
appnamever = appName + " v" + version + "." + releaseNo	if releaseNo: appnamever = appName + " v" + version + "." + releaseNo ver = "v%s.%s" % (version, releaseNo) else: appnamever = appName + " v" + version ver = "v%s" % version	def createIssFile(self, issFile, appName, version, releaseNo, sourceDir, status): """Create the iss file (script) to build package on Windows. The iss script contains all the instructions for the installation package. """ print "\n------------------------------------------------------\nCreating Inno Setup configuratio...
isf.write("AppVerName=%s v%s.%s\n" % (appName, version, releaseNo))	isf.write("AppVerName=%s %s\n" % (appName, version))	def createIssFile(self, issFile, appName, version, releaseNo, sourceDir, status): """Create the iss file (script) to build package on Windows. The iss script contains all the instructions for the installation package. """ print "\n------------------------------------------------------\nCreating Inno Setup configuratio...
isf.write("AppVerName=%s v%s.%s %s\n" % (appName, version, releaseNo, status))	isf.write("AppVerName=%s %s %s\n" % (appName, ver, status))	def createIssFile(self, issFile, appName, version, releaseNo, sourceDir, status): """Create the iss file (script) to build package on Windows. The iss script contains all the instructions for the installation package. """ print "\n------------------------------------------------------\nCreating Inno Setup configuratio...
self.image90 = QPixmap() self.image90.loadFromData(image90_data,"PNG")	self.image81 = QPixmap() self.image81.loadFromData(image81_data,"PNG")	def __init__(self,parent = None,name = None,fl = 0): QMainWindow.__init__(self,parent,name,fl) self.statusBar()
self.image81 = QPixmap(image81_data)		def __init__(self,parent = None,name = None,fl = 0): QMainWindow.__init__(self,parent,name,fl) self.statusBar()
self.modifyStretchAction.setIconSet(QIconSet(self.image80))	self.modifyStretchAction.setIconSet(QIconSet(self.image81))	def __init__(self,parent = None,name = None,fl = 0): QMainWindow.__init__(self,parent,name,fl) self.statusBar()
self.moveMolXAction.setIconSet(QIconSet(self.image81))	self.moveMolXAction.setIconSet(QIconSet(self.image82))	def __init__(self,parent = None,name = None,fl = 0): QMainWindow.__init__(self,parent,name,fl) self.statusBar()