rem stringlengths 0 322k | add stringlengths 0 2.05M | context stringlengths 8 228k |
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"Reorients the model so that it is viewed from the top."\ | "Orients the view to the Top View."\ | 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... |
"Reorients the model so that it is viewed from the bottom."\ | "Orients the view to the Bottom View."\ | 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... |
"Reorients the model so that it is viewed from the left side."\ | "Orients the view to the Left View."\ | 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... |
"Reorients the model so that it is viewed from the right side."\ | "Orients the view to the Right View."\ | 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... |
"Reorients the model so that it is viewed from the opposite side of the current view."\ | "Rotates the view 180 degrees."\ | 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... |
"<b>Fuse Chunks</b> creates bonds between two or more chunks.</p>" | "<b>Fuse Chunks</b> can be used to interactively join two or more "\ "chunks by dragging chunks around and fusing them together. "\ "Two types of fusing are supported:<br><br>"\ "<b>Make Bonds</b> creates bonds between the existing open bonds) "\ "of two or more chunks. Bonds are drawn (and undrawn) as chunks "\ "are... | 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... |
spf.write("Version: %s\n" % version) | def createSpecFile(self, specFile, appName, version, releaseNo, sourceDir): """Create the spec file to build rpm package on Linux. Here is some information about what goes inside a RPM spec file: http://www.rpm.org/max-rpm/s1-rpm-build-creating-spec-file.html http://www.rpm.org/max-rpm/s1-rpm-inside-scripts.html """ sp... | |
fields = version.split(".") earlyVersion = ".".join(fields[:-1]) lateVersion = fields[-1] spf.write("Version: %s\n" % earlyVersion) spf.write("Release: %s\n" % lateVersion) | spf.write("Release: 0\n") | def createSpecFile(self, specFile, appName, version, releaseNo, sourceDir): """Create the spec file to build rpm package on Linux. Here is some information about what goes inside a RPM spec file: http://www.rpm.org/max-rpm/s1-rpm-build-creating-spec-file.html http://www.rpm.org/max-rpm/s1-rpm-inside-scripts.html """ sp... |
self.mirrorDistance = self.getMirrorDistance(m.center, jigs[0].center) mirrorChunk.move(2*(self.mirrorDistance)) | self.mirrorDistance, self.wid = orthodist(m.center, self.mirrorAxis, jigs[0].center) mirrorChunk.move(2*(self.mirrorDistance)*self.mirrorAxis) | #def Invert(self): "Mirror the selected chunk(s) about a selected grid plane." #ninad060812--: As of 060812 (11 PM EST) it creates mirror chunks about a selected grid plane #This has some known bugs. listed below ninad060812: #What it does: #- Mirrors selected chunks about a selected Grid plane but keeps the mirrored c... |
def getMirrorDistance(self, chunkCenter, mirrorPlaneCenter): "return the distance between the chunk center and the mirror plane center" return vlen(chunkCenter - mirrorPlaneCenter) | def getMirrorDistance(self, chunkCenter, mirrorPlaneCenter): "return the distance between the chunk center and the mirror plane center" return vlen(chunkCenter - mirrorPlaneCenter) | |
((a0,d0,s0,x0,y0,z0,e0), \ (a1,d1,s1,x1,y1,z1,e1), \ (a2,d2,s2,x2,y2,z2,e2)) = glpane.getLighting() | (((r0,g0,b0),a0,d0,s0,x0,y0,z0,e0), \ ( (r1,g1,b1),a1,d1,s1,x1,y1,z1,e1), \ ( (r2,g2,b2),a2,d2,s2,x2,y2,z2,e2)) = glpane.getLighting() | def writepovlighting(f, glpane): '''Writes a light source record for each light (if enabled) and the 'Atomic' finish record. These records impact the lighting affect. ''' # Get the lighting parameters for the 3 lights. ((a0,d0,s0,x0,y0,z0,e0), \ (a1,d1,s1,x1,y1,z1,e1), \ (a2,d2,s2,x2,y2,z2,e2)) = glpane.getLighting() ... |
"\n color <" + str(d0) + ", " + str(d0) + ", " + str(d0) + ">" + | "\n color <" + str(r0*d0) + ", " + str(g0*d0) + ", " + str(b0*d0) + ">" + | def writepovlighting(f, glpane): '''Writes a light source record for each light (if enabled) and the 'Atomic' finish record. These records impact the lighting affect. ''' # Get the lighting parameters for the 3 lights. ((a0,d0,s0,x0,y0,z0,e0), \ (a1,d1,s1,x1,y1,z1,e1), \ (a2,d2,s2,x2,y2,z2,e2)) = glpane.getLighting() ... |
"\n color <" + str(d1) + ", " + str(d1) + ", " + str(d1) + ">" + | "\n color <" + str(r1*d1) + ", " + str(g1*d1) + ", " + str(b1*d1) + ">" + | def writepovlighting(f, glpane): '''Writes a light source record for each light (if enabled) and the 'Atomic' finish record. These records impact the lighting affect. ''' # Get the lighting parameters for the 3 lights. ((a0,d0,s0,x0,y0,z0,e0), \ (a1,d1,s1,x1,y1,z1,e1), \ (a2,d2,s2,x2,y2,z2,e2)) = glpane.getLighting() ... |
"\n color <" + str(d2) + ", " + str(d2) + ", " + str(d2) + ">" + | "\n color <" + str(r2*d2) + ", " + str(g2*d2) + ", " + str(b2*d2) + ">" + | def writepovlighting(f, glpane): '''Writes a light source record for each light (if enabled) and the 'Atomic' finish record. These records impact the lighting affect. ''' # Get the lighting parameters for the 3 lights. ((a0,d0,s0,x0,y0,z0,e0), \ (a1,d1,s1,x1,y1,z1,e1), \ (a2,d2,s2,x2,y2,z2,e2)) = glpane.getLighting() ... |
assert item | if not item: if platform.atom_debug: print "atom_debug: fyi: MT node with no item (still waiting for MT.update Qt event?)" try: item.text(0) except: if platform.atom_debug: print "atom_debug: fyi: MT node with invalid item (still waiting for MT.update Qt event?)" | def update_items_from_nodes_open_selected(self, node, _guard_ = None, do_setOpen = True, do_invisible_nodes = True): # bruce 050110 temporary; deprecated, only call from above method and not for long! ###@@@ """set the properties in the model tree widget to match those in the tree datastructure #redoc """ assert _guard... |
self._insert(line1) | self._append(line1) | def __init__(self, parent, line1 = None): """###doc this; optional arg line1 should be a string, generally not ending in '\n' """ ###stub -- we'll likely turn this widget into a frame with buttons self.widget = QTextEdit(parent) # public member, private value (except that it's a Qt widget) if line1 == None: line1 = tim... |
def _insert(self, something): "Insert some text. We might deprecate this interface!" self.widget.insert(something) | def _append(self, something): "Append some text. We might deprecate this interface!" self.widget.append(something) self.widget.scrollToBottom() | def _insert(self, something): "Insert some text. We might deprecate this interface!" self.widget.insert(something) |
self._insert("\n") self._insert(line) | self._append(line) | def _print(self, line): self._insert("\n") self._insert(line) |
self._print(text.replace('\r','\n')) | self._print(text) | def set_status_text(self, text, **options): """Compatibility method -- pretend we're a statusbar and this is its "set text" call. [The following is not yet implemented as of the initial commit:] In reality, make sure the new end of the history looks basically like the given text, but use semi-heuristics to decide how t... |
except: print_compact_traceback("problem removing old tracefile, continuing anyway: ") env.history.message(orangemsg("problem removing old tracefile, continuing anyway")) try: | def sim_loop_using_dylib(self): #bruce 051231; compare to sim_loop_using_standalone_executable # 051231 6:29pm: works, except no trace file is written so results in history come from prior one (if any) """#doc """ movie = self._movie if platform.atom_debug and movie.duration: print "atom_debug: possible bug: movie.dura... | |
raise Exception, "Cannot find a web browser for wiki help" | env.history.message(redmsg("Wiki Help cannot find a web browser")) try: webbrowser.open(url) except webbrowser.Error: pass | def register(pathname, key): webbrowser._tryorder += [ key ] webbrowser.register(key, None, webbrowser.GenericBrowser("%s '%%s'" % pathname)) |
webbrowser.open( url) | webbrowser_open( url) | def open_wiki_help_URL(url, whosdoingthis = "Wiki help"): #bruce 051229 split this out of open_wiki_help_page (which is misnamed) """Try to open the given url in the user's browser (unless they've set preferences to prevent this (NIM)), first emitting a history message containing the url (which is described as coming f... |
webbrowser.open(name) | webbrowser_open(name) | def data(self, name, context=None): # [obs comment:] You'll always get a warning like this: # QTextBrowser: no mimesource for http://.... # This could be avoided with QApplication.qInstallMsgHandler, # but I don't think that's supported until PyQt 3.15. Also this falls # victim to all the problems swarming around webbr... |
def _readpdb(assy, filename, isInsert = False): f=open(filename,"rU").readlines() dir, nodename = os.path.split (filename) if not isInsert: assy.filename=filename ndix={} mol=molecule(assy, nodename) for card in f: key=card[:6].lower().replace(" ", "") | def _readpdb(assy, filename, isInsert = False): """Read a Protein DataBank-format file into a single new chunk, which is returned, unless there are no atoms in the file, in which case a warning is printed and None is returned. (The new chunk (if returned) is in assy, but is not yet added into any Group or Part in assy ... | def getname(str, default): x= nampat.search(str) if x: return x.group(1) return gensym(default) |
try: PeriodicTable.getElement(sym) except KeyError: print 'unknown element "',sym,'" in: ',card | try: PeriodicTable.getElement(sym) except: assy.w.history.message( redmsg( "Warning: Pdb file: unknown element %s in: %s" % (sym,card) )) | def _readpdb(assy, filename, isInsert = False): f=open(filename,"rU").readlines() dir, nodename = os.path.split (filename) if not isInsert: assy.filename=filename ndix={} mol=molecule(assy, nodename) for card in f: key=card[:6].lower().replace(" ", "") if key in ["atom", "hetatm"]: sym = capitalize(card[12:14].repla... |
a1=ndix[int(card[6:11])] for i in range(11, 70, 5): try: a2=ndix[int(card[i:i+5])] except ValueError: break mol.bond(a1, a2) | try: a1 = ndix[int(card[6:11])] except: assy.w.history.message( redmsg( "Warning: Pdb file: can't find atom at column %d in: %s" % (6,card) )) else: for i in range(11, 70, 5): try: a2 = ndix[int(card[i:i+5])] except: assy.w.history.message( redmsg( "Warning: Pdb file: can't find atom at column %d in: %s" % (i,card)... | def _readpdb(assy, filename, isInsert = False): f=open(filename,"rU").readlines() dir, nodename = os.path.split (filename) if not isInsert: assy.filename=filename ndix={} mol=molecule(assy, nodename) for card in f: key=card[:6].lower().replace(" ", "") if key in ["atom", "hetatm"]: sym = capitalize(card[12:14].repla... |
assy.addmol(mol) | if mol: assy.addmol(mol) return | def readpdb(assy,filename): """Reads a pdb file""" mol = _readpdb(assy, filename, isInsert = False) assy.addmol(mol) |
assy.addmol(mol) | if mol: assy.addmol(mol) return | def insertpdb(assy,filename): """Reads a pdb file and inserts it into the existing model """ mol = _readpdb(assy, filename, isInsert = True) assy.addmol(mol) |
self.glplane.setViewProjection(1) | self.glpane.setViewProjection(ORTHOGRAPHIC) | def setViewOrtho(self): self.glplane.setViewProjection(1) |
self.glplane.setViewProjection(0) | self.glpane.setViewProjection(PERSPECTIVE) | def setViewPerspec(self): self.glplane.setViewProjection(0) |
msg = redmsg("Movie file [" + self.filename + "] not valid for the current part") | msg = redmsg("Movie file [" + self.filename + "] not valid for the current part.") | def _setup(self, hflag = True): """Setup this movie for playing """ if DEBUG1: print "movie._setup() called. filename = [" + self.filename + "]" r = self._checkMovieFile() if r == 1: msg = redmsg("Cannot play movie file [" + self.filename + "]. It does not exist.") self.assy.w.history.message(msg) return r elif r ==... |
self.fileobj.close() self.assy.movend() | self._pause(0) self.fileobj.close() self.assy.movend() | def _close(self): """Close movie file and adjust atom positions. """ if DEBUG1: print "movie._close() called. self.isOpen =", self.isOpen if not self.isOpen: return # Close the movie file. self.fileobj.close() # Unfreeze atoms. self.assy.movend() # Delete the array containing the original atom positions for the mode... |
"<p><img source=\"setViewOrtho\"><br> "\ "Sets nonperspective (or parallel) projection, with no foreshortening."\ | "<p>Sets nonperspective (or parallel) projection, with no foreshortening."\ | 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><img source=\"setViewPerspec\"><br> "\ "Set perspective projection, drawing objects slightly larger "\ | "<p>Set perspective projection, drawing objects slightly larger "\ | 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... |
self.water_enabled = False | def Enter(self): basicMode.Enter(self) self.water_enabled = False # mark 060219. self.o.assy.selectAtoms() self.w.elemFilterComboBox.setCurrentItem(0) ## Disable filter by default # Reinitialize previously picked atoms (ppas). self.o.assy.ppa2 = self.o.assy.ppa3 = None #self.o.assy.permit_pick_atoms() #bruce 050517 ... | |
self.w.elemFilterComboBox.setCurrentItem(0) | self.set_selection_filter(0) | def Enter(self): basicMode.Enter(self) self.water_enabled = False # mark 060219. self.o.assy.selectAtoms() self.w.elemFilterComboBox.setCurrentItem(0) ## Disable filter by default # Reinitialize previously picked atoms (ppas). self.o.assy.ppa2 = self.o.assy.ppa3 = None #self.o.assy.permit_pick_atoms() #bruce 050517 ... |
self.w.elemFilterComboBox.setCurrentItem(line) | self.set_selection_filter(line) | def keyPress(self,key): '''keypress event handler for selectAtomsMode. ''' from MWsemantics import eCCBtab2 basicMode.keyPress(self, key) |
self.do('rm -rf ' + self.workdir + '/*') | self.do('rm -rf ' + self.workdir) self.do('mkdir -p ' + self.workdir) | def run(self): global all_workers_stop self.do('mkdir -p ' + self.workdir) while not all_workers_stop: job = self.jobqueue.get() if job is None: return try: job.go(self) self.do('rm -rf ' + self.workdir + '/*') except: all_workers_stop = True raise |
for ch in sequence: if ch not in 'GACT': raise UserError('Unknown DNA base (not G, A, C, or T): ' + ch) | def insertmmp(filename, subgroup, tfm, position=position): try: grouplist = _readmmp(assy, filename, isInsert=True) except IOError: raise PluginBug("Cannot read file: " + filename) if not grouplist: raise PluginBug("No atoms in DNA base? " + filename) viewdata, mainpart, shelf = grouplist for member in mainpart.member... | |
env.history.message(redmsg('Bogus DNA base: ' + ch + ' (should be C, G, A, or T)')) return '' | raise UserError('Bogus DNA base: ' + ch + ' (should be C, G, A, or T)') | def get_sequence(self, reverse=False, complement=False, cdict={'C':'G', 'G':'C', 'A':'T', 'T':'A'}): seq = '' for ch in str(self.base_textedit.text()).upper(): if ch in 'CGAT': if complement: ch = cdict[ch] seq += ch elif ch in '\ \t\r\n': pass else: env.history.message(redmsg('Bogus DNA base: ' + ch + ' (should be C, ... |
"<p>Specify the bond length between carbon atoms in angstroms.</p>")) | "<p>Specify the bond length between atoms in angstroms.</p>")) | def languageChange(self): self.setCaption(self.__tr("Nanotube")) self.heading_label.setText(self.__tr("Nanotube")) self.sponsor_btn.setText(QString.null) self.done_btn.setText(QString.null) QToolTip.add(self.done_btn,self.__tr("OK")) self.abort_btn.setText(QString.null) QToolTip.add(self.abort_btn,self.__tr("Cancel")) ... |
"""create an atom of element sym (e.g. 'C') | """Create an atom of element sym (e.g. 'C') | def __init__(self, sym, where, mol): """create an atom of element sym (e.g. 'C') at location where (e.g. V(36, 24, 36)) belonging to molecule mol, which is part of assembly assy """ # unique key for hashing self.key = atKey.next() # element-type object self.element = PeriodicTable.getElement(sym) # 'where' is atom's ab... |
belonging to molecule mol, which is part of assembly assy | belonging to molecule mol (can be None). Atom initially has no bonds and default hybridization type. | def __init__(self, sym, where, mol): """create an atom of element sym (e.g. 'C') at location where (e.g. V(36, 24, 36)) belonging to molecule mol, which is part of assembly assy """ # unique key for hashing self.key = atKey.next() # element-type object self.element = PeriodicTable.getElement(sym) # 'where' is atom's ab... |
self.molecule.assy.changed() | self.changed() | def setDisplay(self, disp): self.display = disp self.molecule.changeapp(1) self.molecule.assy.changed() # bruce 041206 bugfix (unreported bug) # bruce 041109 comment: # atom.setDisplay changes appearance of this atom's bonds, # so: do we need to invalidate the bonds? No, they don't store display # info, and the geometr... |
self.cookieCutterToolbar.setGeometry(QRect(0,0,532,29)) | self.cookieCutterToolbar.setGeometry(QRect(0,0,533,29)) | def __init__(self,parent = None,name = None,fl = 0): QMainWindow.__init__(self,parent,name,fl) self.statusBar() |
self.unnamed.setAccel(QString.null,self.unnamed.insertItem(self.viewDefviewAction.iconSet(),self.__tr("&Default Views"),self.popupMenu_32)) | self.unnamed.setAccel(QString.null,self.unnamed.insertItem(self.viewDefviewAction.iconSet(),self.__tr("Orientations"),self.popupMenu_32)) | def __init__(self,parent = None,name = None,fl = 0): QMainWindow.__init__(self,parent,name,fl) self.statusBar() |
self.resize(QSize(1062,835).expandedTo(self.minimumSizeHint())) | self.resize(QSize(1062,838).expandedTo(self.minimumSizeHint())) | def __init__(self,parent = None,name = None,fl = 0): QMainWindow.__init__(self,parent,name,fl) self.statusBar() |
self.viewDefviewAction.setText(self.__tr("&Default Views")) self.viewDefviewAction.setMenuText(self.__tr("&Default Views")) | self.viewDefviewAction.setText(self.__tr("Orientations")) self.viewDefviewAction.setMenuText(self.__tr("Orientations")) | def languageChange(self): self.setCaption(self.__tr("Atom")) self.fileNewAction.setText(self.__tr("New")) self.fileNewAction.setMenuText(self.__tr("&New")) self.fileNewAction.setAccel(self.__tr("Ctrl+N")) self.fileOpenAction.setText(self.__tr("Open")) self.fileOpenAction.setMenuText(self.__tr("&Open...")) self.fileOpen... |
self.setViewFrontAction.setText(self.__tr("Front View")) self.setViewFrontAction.setMenuText(self.__tr("&Front View")) self.setViewFrontAction.setToolTip(self.__tr("Front View")) self.setViewBackAction.setText(self.__tr("Back View")) self.setViewBackAction.setMenuText(self.__tr("&Back View")) self.setViewTopAction.setT... | self.setViewFrontAction.setText(self.__tr("&Front")) self.setViewFrontAction.setMenuText(self.__tr("&Front")) self.setViewFrontAction.setToolTip(self.__tr("Front")) self.setViewBackAction.setText(self.__tr("Back")) self.setViewBackAction.setMenuText(self.__tr("&Back")) self.setViewTopAction.setText(self.__tr("Top")) se... | def languageChange(self): self.setCaption(self.__tr("Atom")) self.fileNewAction.setText(self.__tr("New")) self.fileNewAction.setMenuText(self.__tr("&New")) self.fileNewAction.setAccel(self.__tr("Ctrl+N")) self.fileOpenAction.setText(self.__tr("Open")) self.fileOpenAction.setMenuText(self.__tr("&Open...")) self.fileOpen... |
self.unnamed.changeItem(self.unnamed.idAt(7),self.__tr("&Default Views")) | self.unnamed.changeItem(self.unnamed.idAt(7),self.__tr("Orientations")) | def languageChange(self): self.setCaption(self.__tr("Atom")) self.fileNewAction.setText(self.__tr("New")) self.fileNewAction.setMenuText(self.__tr("&New")) self.fileNewAction.setAccel(self.__tr("Ctrl+N")) self.fileOpenAction.setText(self.__tr("Open")) self.fileOpenAction.setMenuText(self.__tr("&Open...")) self.fileOpen... |
self.win.enableViews(False) | def rotateView(self, q2): "Rotate current view to quat (viewpoint) q2" # Check User Preference "General | Standard Views: Animate" if not env.prefs[animateStandardViews_prefs_key]: self.quat = Q(q2) self.gl_update() return wxyz1 = V(self.quat.w, self.quat.x, self.quat.y, self.quat.z) wxyz2 = V(q2.w, q2.x, q2.y, q2.z)... | |
self.win.enableViews(False) | def animateView(self, q2, s2, p2, z2, animate=True): "Animate current view to quat (viewpoint) q2, scale s2, pov p2, and zoom factor z2" # Check User Preference "General | Standard Views: Animate" if not animate or not env.prefs[animateStandardViews_prefs_key]: self.quat = Q(q2) self.pov = V(p2[0], p2[1], p2[2]) self.... | |
deltap = p2 - self.pov pf = int(vlen(deltap)*.2) deltas = abs(s2 - self.scale) | pf = int(deltap * .2) | def animateView(self, q2, s2, p2, z2, animate=True): "Animate current view to quat (viewpoint) q2, scale s2, pov p2, and zoom factor z2" # Check User Preference "General | Standard Views: Animate" if not animate or not env.prefs[animateStandardViews_prefs_key]: self.quat = Q(q2) self.pov = V(p2[0], p2[1], p2[2]) self.... |
deltaz = abs(z2 - self.zoomFactor) | def animateView(self, q2, s2, p2, z2, animate=True): "Animate current view to quat (viewpoint) q2, scale s2, pov p2, and zoom factor z2" # Check User Preference "General | Standard Views: Animate" if not animate or not env.prefs[animateStandardViews_prefs_key]: self.quat = Q(q2) self.pov = V(p2[0], p2[1], p2[2]) self.... | |
debug_menu = None | def debug_runpycode_from_a_dialog( source = "some debug menu??"): title = "debug: run py code" label = "one line of python to exec in debug.py's globals()\n(or use @@@ to fake \\n for more lines)\n(or use execfile)" from qt import QInputDialog # bruce 041216 bugfix text, ok = QInputDialog.getText(title, label) if ok: #... | |
self.debug_menu = self.makemenu( self.debug_menu_items() ) | def _init1(self, win = None): # figure out this mixin's idea of main window if not win: try: self.win # no need: assert isinstance( self.win, QWidget) except AttributeError: pass else: win = self.win self._debug_win = win # figure out classname for #doc try: self._debug_classname = "class " + self.__class__.__name__ ex... | |
"[subclasses can in theory override this, but probably needn't and shouldn't]" | def debug_menu_items(self): "[subclasses can in theory override this, but probably needn't and shouldn't]" import debug res = [ ('(debugging menu)', noop, 'disabled'), # None, # separator ] if self._debug_win: res.extend( [ ('load window layout', self._debug_load_window_layout ), ('save window layout', self._debug_save... | |
('enable ATOM_DEBUG', self._debug_enable_atom_debug ), ('disable ATOM_DEBUG', self._debug_disable_atom_debug ), | def debug_menu_items(self): "[subclasses can in theory override this, but probably needn't and shouldn't]" import debug res = [ ('(debugging menu)', noop, 'disabled'), # None, # separator ] if self._debug_win: res.extend( [ ('load window layout', self._debug_load_window_layout ), ('save window layout', self._debug_save... | |
menu = self.debug_menu self.current_event = event | menu = None try: lis = self.debug_menu_items() menu = self.makemenu( lis ) except: print_compact_traceback("bug in do_debug_menu ignored; menu_spec is %r" % (lis,) ) menu = None | def do_debug_menu(self, event): "[public method for subclasses] #doc" menu = self.debug_menu self.current_event = event # (so debug commands can see it) # this code written from Qt/PyQt docs... note that some Atom # modules use menu.exec_loop() but others use menu.popup(); I # don't know for sure whether this matters ... |
menu.exec_loop(event.globalPos(), 1) self.current_event = None | if menu: menu.exec_loop(event.globalPos(), 1) | def do_debug_menu(self, event): "[public method for subclasses] #doc" menu = self.debug_menu self.current_event = event # (so debug commands can see it) # this code written from Qt/PyQt docs... note that some Atom # modules use menu.exec_loop() but others use menu.popup(); I # don't know for sure whether this matters ... |
seq = self.get_sequence(complement=True) self.base_textedit.setText(seq) | def thunk(): seq = self.get_sequence(complement=True) self.base_textedit.setText(seq) self.handlePluginExceptions(thunk) | def complement_btn_clicked(self): seq = self.get_sequence(complement=True) self.base_textedit.setText(seq) |
seq = self.get_sequence(reverse=True) self.base_textedit.setText(seq) | def thunk(): seq = self.get_sequence(reverse=True) self.base_textedit.setText(seq) self.handlePluginExceptions(thunk) | def reverse_btn_clicked(self): seq = self.get_sequence(reverse=True) self.base_textedit.setText(seq) |
self.setTabOrder(self.display_compass_checkbox,self.display_origin_axis_checkbox) | self.setTabOrder(self.display_compass_checkbox,self.display_compass_labels_checkbox) self.setTabOrder(self.display_compass_labels_checkbox,self.display_origin_axis_checkbox) | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) |
self.setTabOrder(self.upper_right_btn,self.radioButton12) self.setTabOrder(self.radioButton12,self.animate_views_checkbox) self.setTabOrder(self.animate_views_checkbox,self.atom_hilite_color_btn) self.setTabOrder(self.atom_hilite_color_btn,self.hotspot_color_btn) | self.setTabOrder(self.upper_right_btn,self.watch_min_in_realtime_checkbox) self.setTabOrder(self.watch_min_in_realtime_checkbox,self.radioButton12) self.setTabOrder(self.radioButton12,self.high_quality_graphics_checkbox) self.setTabOrder(self.high_quality_graphics_checkbox,self.animate_views_checkbox) self.setTabOrder(... | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) |
self.setTabOrder(self.cpk_atom_rad_spinbox,self.vwd_rbtn) self.setTabOrder(self.vwd_rbtn,self.cpk_rbtn) self.setTabOrder(self.cpk_rbtn,self.tubes_rbtn) self.setTabOrder(self.tubes_rbtn,self.lines_rbtn) self.setTabOrder(self.lines_rbtn,self.bond_hilite_color_btn) | self.setTabOrder(self.cpk_atom_rad_spinbox,self.cpk_scale_factor_linedit) self.setTabOrder(self.cpk_scale_factor_linedit,self.cpk_scale_factor_slider) self.setTabOrder(self.cpk_scale_factor_slider,self.level_of_detail_combox) self.setTabOrder(self.level_of_detail_combox,self.bond_hilite_color_btn) | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) |
self.setTabOrder(self.reset_bond_colors_btn,self.bond_line_thickness_spinbox) self.setTabOrder(self.bond_line_thickness_spinbox,self.cpk_cylinder_rad_spinbox) self.setTabOrder(self.cpk_cylinder_rad_spinbox,self.radioButton11) | self.setTabOrder(self.reset_bond_colors_btn,self.cpk_cylinder_rad_spinbox) self.setTabOrder(self.cpk_cylinder_rad_spinbox,self.bond_line_thickness_spinbox) self.setTabOrder(self.bond_line_thickness_spinbox,self.radioButton11) | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) |
self.setTabOrder(self.show_valence_errors_checkbox,self.default_mode_combox) self.setTabOrder(self.default_mode_combox,self.startup_mode_combox) self.setTabOrder(self.startup_mode_combox,self.mode_combox) self.setTabOrder(self.mode_combox,self.fill_type_combox) | self.setTabOrder(self.show_valence_errors_checkbox,self.startup_mode_combox) self.setTabOrder(self.startup_mode_combox,self.default_mode_combox) self.setTabOrder(self.default_mode_combox,self.mode_combox) self.setTabOrder(self.mode_combox,self.display_mode_combox) self.setTabOrder(self.display_mode_combox,self.fill_typ... | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) |
self.setTabOrder(self.restore_bgcolor_btn,self.light_checkbox) | self.setTabOrder(self.restore_bgcolor_btn,self.vwd_rbtn) self.setTabOrder(self.vwd_rbtn,self.cpk_rbtn) self.setTabOrder(self.cpk_rbtn,self.tubes_rbtn) self.setTabOrder(self.tubes_rbtn,self.lines_rbtn) self.setTabOrder(self.lines_rbtn,self.autobond_checkbox) self.setTabOrder(self.autobond_checkbox,self.buildmode_highlig... | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) |
self.setTabOrder(self.light_z_linedit,self.lighting_restore_defaults_btn) | self.setTabOrder(self.light_z_linedit,self.ms_on_checkbox) self.setTabOrder(self.ms_on_checkbox,self.ms_finish_linedit) self.setTabOrder(self.ms_finish_linedit,self.ms_finish_slider) self.setTabOrder(self.ms_finish_slider,self.ms_shininess_linedit) self.setTabOrder(self.ms_shininess_linedit,self.ms_shininess_slider) se... | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) |
self.setTabOrder(self.nanohive_choose_btn,self.msg_serial_number_checkbox) | self.setTabOrder(self.nanohive_choose_btn,self.undo_restore_view_checkbox) self.setTabOrder(self.undo_restore_view_checkbox,self.undo_automatic_checkpoints_checkbox) self.setTabOrder(self.undo_automatic_checkpoints_checkbox,self.undo_stack_memory_limit_spinbox) self.setTabOrder(self.undo_stack_memory_limit_spinbox,self... | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) |
self.setTabOrder(self.msg_timestamp_checkbox,self.caption_prefix_linedit) | self.setTabOrder(self.msg_timestamp_checkbox,self.current_width_spinbox) self.setTabOrder(self.current_width_spinbox,self.current_height_spinbox) self.setTabOrder(self.current_height_spinbox,self.save_current_btn) self.setTabOrder(self.save_current_btn,self.saved_width_lineedit) self.setTabOrder(self.saved_width_lineed... | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) |
self.setTabOrder(self.caption_fullpath_checkbox,self.ok_btn) | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) | |
bytes = self.process.readStdout() if bytes: self.fwThread.putData(bytes) | def processTimeout(self): if self.process.isRunning(): if not self.progressDialog.isShown() or self.progressDialog.Rejected: return msgLabel = self.progressDialog.getMsgLabel() duration = time.time() - self.stime elapmsg = "Elasped Time: " + self.progressDialog.hhmmss_str(int(duration)) msgLabel.setText(elapmsg) byte... | |
self.fwThread.stop() | def processDone(self): self.fwThread.stop() self.jobTimer.stop() if self.process.normalExit(): print "The process is done!" self.retValue = 0 self.progressDialog.accept() else: print "The process is cancelled!" self.retValue = 1 ###Don't know why I can't call reject() here. self.progressDialog.accept()#reject() | |
self.retValue = 0 self.progressDialog.accept() | QDialog.accept(self.progressDialog) | def processDone(self): self.fwThread.stop() self.jobTimer.stop() if self.process.normalExit(): print "The process is done!" self.retValue = 0 self.progressDialog.accept() else: print "The process is cancelled!" self.retValue = 1 ###Don't know why I can't call reject() here. self.progressDialog.accept()#reject() |
self.retValue = 1 self.progressDialog.accept() | QDialog.reject(self.progressDialog) | def processDone(self): self.fwThread.stop() self.jobTimer.stop() if self.process.normalExit(): print "The process is done!" self.retValue = 0 self.progressDialog.accept() else: print "The process is cancelled!" self.retValue = 1 ###Don't know why I can't call reject() here. self.progressDialog.accept()#reject() |
self.outputFile = QFile(self.job_outputfile) self.outputFile.open( IO_WriteOnly | IO_Append ) | def _launch_gamess(self): oldir = os.getcwd() # Save current directory jobDir = os.path.dirname(self.job_batfile) os.chdir(jobDir) # Change directory to the GAMESS temp directory. print "Current directory is: ", jobDir #DATfile = os.path.join(jobDir, "PUNCH") #if os.path.exists(DATfile): # Remove any previous DAT (PU... | |
args = [self.server.program, jobInputFile] | jobOutputfile = self.job_outputfile args = [self.server.program, jobInputFile, jobOutputfile] | def _launch_gamess(self): oldir = os.getcwd() # Save current directory jobDir = os.path.dirname(self.job_batfile) os.chdir(jobDir) # Change directory to the GAMESS temp directory. print "Current directory is: ", jobDir #DATfile = os.path.join(jobDir, "PUNCH") #if os.path.exists(DATfile): # Remove any previous DAT (PU... |
self.process.setCommunication(QProcess.Stdout) self.fwThread = FileWriting(self.outputFile) | print "The params for the QProcess run are: ", args | def _launch_gamess(self): oldir = os.getcwd() # Save current directory jobDir = os.path.dirname(self.job_batfile) os.chdir(jobDir) # Change directory to the GAMESS temp directory. print "Current directory is: ", jobDir #DATfile = os.path.join(jobDir, "PUNCH") #if os.path.exists(DATfile): # Remove any previous DAT (PU... |
self.fwThread.start() | def _launch_gamess(self): oldir = os.getcwd() # Save current directory jobDir = os.path.dirname(self.job_batfile) os.chdir(jobDir) # Change directory to the GAMESS temp directory. print "Current directory is: ", jobDir #DATfile = os.path.join(jobDir, "PUNCH") #if os.path.exists(DATfile): # Remove any previous DAT (PU... | |
self.progressDialog.exec_loop() retValue = self.retValue self.fwThread.wait() bytes = self.process.readStdout() if bytes: self.outputFile.writeBlock(bytes) self.outputFile.flush() | ret = self.progressDialog.exec_loop() if ret == QDialog.Accepted: retValue = 0 else: retValue = 1 | def _launch_gamess(self): oldir = os.getcwd() # Save current directory jobDir = os.path.dirname(self.job_batfile) os.chdir(jobDir) # Change directory to the GAMESS temp directory. print "Current directory is: ", jobDir #DATfile = os.path.join(jobDir, "PUNCH") #if os.path.exists(DATfile): # Remove any previous DAT (PU... |
self.outputFile.close() | def _launch_gamess(self): oldir = os.getcwd() # Save current directory jobDir = os.path.dirname(self.job_batfile) os.chdir(jobDir) # Change directory to the GAMESS temp directory. print "Current directory is: ", jobDir #DATfile = os.path.join(jobDir, "PUNCH") #if os.path.exists(DATfile): # Remove any previous DAT (PU... | |
title = "debug: run py code" label = "one line of python to exec in GLPane.py's globals()\n(or use @@@ to fake \\n for more lines)\n(or use execfile)" text, ok = QInputDialog.getText(title, label) if ok: command = str(text) command = command.replace("@@@",'\n') debug_run_command(command, source = "debug menu") else: p... | from debug import debug_runpycode_from_a_dialog debug_runpycode_from_a_dialog( source = "GLPane debug menu") | def _debug_runpycode(self): title = "debug: run py code" label = "one line of python to exec in GLPane.py's globals()\n(or use @@@ to fake \\n for more lines)\n(or use execfile)" text, ok = QInputDialog.getText(title, label) if ok: # fyi: type(text) == <class '__main__.qt.QString'> command = str(text) #k not yet well t... |
def debug_run_command(command, source = "user debug input"): """Execute a python command, supplied by the user via some sort of debugging interface (named by source), in GLPane.py's globals. Return 1 for ok (incl empty command), 0 for any error. Caller should not print diagnostics -- this function should be extended to... | def debug_run_command(command, source = "user debug input"): #bruce 040913-16 #e move this to somewhere more general? """Execute a python command, supplied by the user via some sort of debugging interface (named by source), in GLPane.py's globals. Return 1 for ok (incl empty command), 0 for any error. Caller should not... | |
mol.changeapp(0) | def _stateDoneOrCancel(self, cancelling = 0): #e rename? revise? #bruce 050228 to help fix bug 314 and unreported bugs "common method for StateDone and StateCancel" ## self.update_from_controls() #k 041017 night - will this help or hurt? since hard to know, not adding it now. # restore normal appearance for mol in self... | |
if self.alter_name: | if alter_name: | def deepcopy(self, alter_name = True): #bruce 051003 added alter_name, but I don't know if passing False is ever legal. ###@@@ #bruce 050704; don't know whether this is complete [needs review by Mark; is it ok it only sets .ui?] "Make a copy of self (a gamessParms object), which shares no mutable state with self. (Used... |
if not os.path.exists(env.prefs[nanohive_path_prefs_key]): | if not os.path.exists(env.prefs[povray_path_prefs_key]): | def raytrace_scene_using_povray(assy, pov, width, height, output_type="png"): '''Render the POV-Ray scene file <pov>. The output image is placed next to <pov> with the extension based on <output_type>. <width>, <height> are the width and height of the rendered image. (int) <output_type> is the extension of the output i... |
program = "\""+povray_exe+"\"" | if sys.platform == 'win32': program = "\""+povray_exe+"\"" else: program = povray_exe | def raytrace_scene_using_povray(assy, pov, width, height, output_type="png"): '''Render the POV-Ray scene file <pov>. The output image is placed next to <pov> with the extension based on <output_type>. <width>, <height> are the width and height of the rendered image. (int) <output_type> is the extension of the output i... |
self.resize(QSize(212,544).expandedTo(self.minimumSizeHint())) | self.resize(QSize(255,591).expandedTo(self.minimumSizeHint())) | def __init__(self,parent = None,name = None,modal = 0,fl = 0): QDialog.__init__(self,parent,name,modal,fl) |
def __init__(self): | def __init__(self, debug_name = None): self.debug_name = debug_name | def __init__(self): self._subs = {} # map from id(func) to list of (zero or more identical elements) func (which are of course strongrefs to func). # (We need the dict for efficient removal, and multiple copies of func in case duplicate funcs are provided # (which is quite possible), but that doesn't need to be optimi... |
print "atom_debug: fyi: %r's event already occurred, fulfilling new subs %r immediately" % (self, func) | print_compact_stack( "atom_debug: fyi: %r's event already occurred, fulfilling new subs %r immediately: " % (self, func)) | def subscribe(self, func): try: subs = self._subs except AttributeError: # our event already occurred (as indicated by fulfill_all removing this attribute). # [not sure if this ever happens in initial uses of this class] # (note: if subscribe could come before __init__, e.g. due to some sort of bug # in which this obj... |
subslist = self.__subslist = OneTimeSubsList() | debug_name = platform.atom_debug and ("%r" % self) or None subslist = self.__subslist = OneTimeSubsList(debug_name) | def track_use(self): """#doc [some callers might inline this method] [must be called on every use, not just first one after a change, in case env.track points to different objects for different uses] """ try: subslist = self.__subslist except AttributeError: # this is the only way self.__subslist gets created; # it mea... |
obj = usage_tracker_obj() | debug_name = platform.atom_debug and ("%r" % self) or None obj = usage_tracker_obj(debug_name) | def begin_tracking_usage(self): #e there's a docstring for this in an outtakes file, if one is needed obj = usage_tracker_obj() match_checking_code = usage_tracker.begin( obj) # don't store match_checking_code in self -- that would defeat the error-checking # for bugs in how self's other code matches up these begin and... |
comCenter = V(0.0, 0.0, 0.0) | def setViewZoomToSelection(self, fast = False): #Nnad 60903 '''Change the view so that only selected atoms, chunks and Jigs fit in the GLPane. (i.e. Zoom to the selection) If <fast> is True, then snap to the view ''' #ninad060903: # I am not using bounding box object as used in fit to selection. I am using only self.sc... | |
numMovables = len(movables) | pointList = [] | def setViewZoomToSelection(self, fast = False): #Nnad 60903 '''Change the view so that only selected atoms, chunks and Jigs fit in the GLPane. (i.e. Zoom to the selection) If <fast> is True, then snap to the view ''' #ninad060903: # I am not using bounding box object as used in fit to selection. I am using only self.sc... |
comCenter += atm.posn() comCenter /= len(self.assy.selatoms_list()) | pointList += [atm.posn()] | def setViewZoomToSelection(self, fast = False): #Nnad 60903 '''Change the view so that only selected atoms, chunks and Jigs fit in the GLPane. (i.e. Zoom to the selection) If <fast> is True, then snap to the view ''' #ninad060903: # I am not using bounding box object as used in fit to selection. I am using only self.sc... |
comCenter += obj.center if self.assy.selatoms_list(): comCenter /= (numMovables + 1) else: comCenter /= numMovables | pointList += [obj.center] | def setViewZoomToSelection(self, fast = False): #Nnad 60903 '''Change the view so that only selected atoms, chunks and Jigs fit in the GLPane. (i.e. Zoom to the selection) If <fast> is True, then snap to the view ''' #ninad060903: # I am not using bounding box object as used in fit to selection. I am using only self.sc... |
center = comCenter | bbox = BBox(pointList) center = bbox.center() scale = float( bbox.scale() * 0.85) aspect = float(self.width) / self.height if aspect < 1.0: scale /= aspect | def setViewZoomToSelection(self, fast = False): #Nnad 60903 '''Change the view so that only selected atoms, chunks and Jigs fit in the GLPane. (i.e. Zoom to the selection) If <fast> is True, then snap to the view ''' #ninad060903: # I am not using bounding box object as used in fit to selection. I am using only self.sc... |
self.snapToView(self.quat, self.scale, pov, 1.0) | self.snapToView(self.quat, scale, pov, 1.0) | def setViewZoomToSelection(self, fast = False): #Nnad 60903 '''Change the view so that only selected atoms, chunks and Jigs fit in the GLPane. (i.e. Zoom to the selection) If <fast> is True, then snap to the view ''' #ninad060903: # I am not using bounding box object as used in fit to selection. I am using only self.sc... |
self.animateToView(self.quat, self.scale, pov, 1.0) | self.animateToView(self.quat, scale, pov, 1.0) | def setViewZoomToSelection(self, fast = False): #Nnad 60903 '''Change the view so that only selected atoms, chunks and Jigs fit in the GLPane. (i.e. Zoom to the selection) If <fast> is True, then snap to the view ''' #ninad060903: # I am not using bounding box object as used in fit to selection. I am using only self.sc... |
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