rem stringlengths 0 322k | add stringlengths 0 2.05M | context stringlengths 8 228k |
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('.', [ 'config.ini', 'docs/license.txt', ]), | ('.', ['docs/license.txt',]), ('.', ['lib/config.ini',]), | def __init__(self, **kw): self.__dict__.update(kw) # for the versioninfo resources self.version = cfg.get('version.number') self.company_name = base_config.APPLICATION_NAME self.copyright = "Copyright " + cfg.get('version.copyright') self.name = base_config.APPLICATION_NAME |
shot.generate(spath.open('wb')) fp.close() | fp = spath.open('wb') try: shot.generate(fp) finally: fp.close() | def doSnapshot(wfile, form, str_rid, item): url = form.getfirst('url') if not url and item: url = item.url shot = snapshot.Snapshot() shot.fetch(url) spath = cfg.getpath('weblibsnapshot')/('%s.mhtml' % str_rid) shot.generate(spath.open('wb')) fp.close() if item: t = datetime.datetime.now() item.cached = str(t)[:10] re... |
if self.moveOption == 'MOVEDEFAULT': wX = event.pos().x() wY = self.o.height - event.pos().y() wZ = glReadPixelsf(wX, wY, 1, 1, GL_DEPTH_COMPONENT) if wZ[0][0] >= 1.0: junk, self.movingPoint = self.o.mousepoints(event) else: self.movingPoint = A(gluUnProject(wX, wY, wZ[0][0])) | wX = event.pos().x() wY = self.o.height - event.pos().y() wZ = glReadPixelsf(wX, wY, 1, 1, GL_DEPTH_COMPONENT) if wZ[0][0] >= 1.0: junk, self.movingPoint = self.o.mousepoints(event) else: self.movingPoint = A(gluUnProject(wX, wY, wZ[0][0])) | def leftDown(self, event): """Move the selected object(s). """ self.o.SaveMouse(event) self.picking = True self.dragdist = 0.0 self.transDelta = 0 # X, Y or Z deltas for translate. self.rotDelta = 0 # delta for constrained rotations. self.moveOffset = [0.0, 0.0, 0.0] # X, Y and Z offset for move. |
else: | if self.moveOption != 'MOVEDEFAULT': | def leftDown(self, event): """Move the selected object(s). """ self.o.SaveMouse(event) self.picking = True self.dragdist = 0.0 self.transDelta = 0 # X, Y or Z deltas for translate. self.rotDelta = 0 # delta for constrained rotations. self.moveOffset = [0.0, 0.0, 0.0] # X, Y and Z offset for move. |
"Resets the display setting for each atom in the selected chunks to Default display mode" if not self.assy.selmols: env.history.message(redmsg("Reset Atoms Display: No chunks selected.")) return self.assy.resetAtomsDisplay() env.history.message(greenmsg("Reset Atoms Display:")) msg = "Display setting for all atoms in ... | "Resets the display setting for each atom in the selected chunks or atoms to Default display mode" cmd = greenmsg("Reset Atoms Display: ") if self.assy.selmols: self.assy.resetAtomsDisplay() msg = "Display setting for all atoms in selected chunk(s) reset to Default (i.e. their parent chunk's display mode)." if self.... | def dispResetAtomsDisplay(self): "Resets the display setting for each atom in the selected chunks to Default display mode" if not self.assy.selmols: env.history.message(redmsg("Reset Atoms Display: No chunks selected.")) return self.assy.resetAtomsDisplay() env.history.message(greenmsg("Reset Atoms Display:")) msg = "... |
"Resets the display setting for each invisible atom in the selected chunks to Default display mode" if not self.assy.selmols: env.history.message(redmsg("Show Invisible Atoms: No chunks selected.")) return nia = self.assy.showInvisibleAtoms() env.history.message(greenmsg("Show Invisible Atoms:")) msg = str(nia) + " in... | "Resets the display setting for each invisible atom in the selected chunks or atoms to Default display mode" cmd = greenmsg("Show Invisible Atoms: ") nia = 0 if self.assy.selmols: nia = self.assy.showInvisibleAtoms() if self.assy.selatoms: for a in self.assy.selatoms.values(): if a.display == diINVISIBLE: a.setDispl... | def dispShowInvisAtoms(self): "Resets the display setting for each invisible atom in the selected chunks to Default display mode" if not self.assy.selmols: env.history.message(redmsg("Show Invisible Atoms: No chunks selected.")) return nia = self.assy.showInvisibleAtoms() # nia = Number of Invisible Atoms env.history.... |
doubleStrand = (double == 'Double') | def build_struct(self, name, params, position): # No error checking in build_struct, do all your error # checking in gather_parameters seq, dnatype, double = params if dnatype == 'A-DNA': dna = A_Dna() elif dnatype == 'B-DNA': dna = B_Dna() elif dnatype == 'Z-DNA': dna = Z_Dna() self.dna = dna # needed for done msg do... | |
return "Done creating a strand of %s." % self.dna.geometry | dna = self.dna if dna.double: dbl = "double " else: dbl = "" return "Done creating a %sstrand of %s." % (dbl, dna.geometry) | def done_msg(self): return "Done creating a strand of %s." % self.dna.geometry |
if self.havelist == (disp,): | eltprefs = PeriodicTable.color_change_counter, PeriodicTable.rvdw_change_counter if self.havelist == (disp, eltprefs): | # global dispdef change (in GLPane.setDisplay).] |
self.havelist = (disp,) | self.havelist = (disp, eltprefs) | # global dispdef change (in GLPane.setDisplay).] |
if self.haveradii != (disp,): | eltprefs = PeriodicTable.rvdw_change_counter if self.haveradii != (disp,eltprefs): | def get_sel_radii_squared(self): #bruce 050419 fix bug 550 by fancifying haveradii # in the same way as for havelist (see 'bruce 050415'). # Note: this must also be invalidated when one atom's display mode changes, # and it is, by atom.setDisplay calling changeapp(1) on its chunk. disp = self.get_dispdef() ##e should c... |
self.haveradii = (disp,) | self.haveradii = (disp,eltprefs) | def get_sel_radii_squared(self): #bruce 050419 fix bug 550 by fancifying haveradii # in the same way as for havelist (see 'bruce 050415'). # Note: this must also be invalidated when one atom's display mode changes, # and it is, by atom.setDisplay calling changeapp(1) on its chunk. disp = self.get_dispdef() ##e should c... |
[As of 040508 this boundary will be changed from thickness 1 to thickness 2 | [As of 050408 this boundary will be changed from thickness 1 to thickness 2 | def __init__(self, part, atoms): """atoms is a list of atoms within the part (e.g. the selected ones, for Minimize Selection); we copy it in case caller modifies it later. We become a simulatable aspect for simulating motion of those atoms (and of any singlets bonded to them, since user has no way to select those expli... |
LIBAQUA_MD5 = "c5e2db5ab38c2af63891cc95c7c1ddf5" | LIBAQUA_MD5 = "c43f7944d0d7ed42f82e2a9ba45687d0" | def makePlatformPackage(self): # linux specFile = os.path.join(self.rootPath, 'setup.spec') destDir = os.path.join('/usr/local', PMMT) self.createSpecFile(specFile, self.appName, self.version, self.releaseNo, destDir) """Before run rpmbuilder, mv self.buildSource to /usr/local, cp spec file into /usr/src/RPM/SPECS/, a... |
def test_atomset_keysIn(self): """\ atomset.add(atm1) atm1.key in atomset --> True atm2.key in atomset --> False """ atomset = AtomDict() atom1 = Atom() atom2 = Atom() atomset.add(atom1) assert atomset.has_key(atom1.key) assert not atomset.has_key(atom2.key) assert atom1.key in atomset assert atom2.key not in atomset | ## def test_atomset_keysIn(self): | |
y -= 58 self.mt.setGeometry(0,0,mmk_geometry.width(),560) | if sys.platform == 'linux2': pass else: y -= 58 self.mt.setGeometry(0,0,mmk_geometry.width(),560) | def _findGoodLocation(self, firstShow): '''Find ideal location for the MMKit. Should only be called after history, and MMKit has been created.''' global MMKitWin if sys.platform == 'linux2': #hist_height = 70 # not needed with new layout. mark 060222. mmk_height = 559 toolbar_height = 25 status_bar_height = 29 else: h... |
name = gensym("DNA-") self.group = grp = Group(name, self.win.assy, part.topnode) | self.group = grp = Group(gensym("DNA-"), self.win.assy, part.topnode) | def build_dna(self): 'Slot for the OK button' seq = self.get_sequence() dnatype = str(self.dna_type_combox.currentText()) double = str(self.endings_combox.currentText()) params = (seq, dnatype, double) if self.previousParams != params: self.remove_dna() self.previousParams = params if self.group == None: if len(seq) > ... |
env.history.message(cmd + "Done.") | env.history.message(cmd + "Done creating a strand of %s." % dna.geometry) | def build_dna(self): 'Slot for the OK button' seq = self.get_sequence() dnatype = str(self.dna_type_combox.currentText()) double = str(self.endings_combox.currentText()) params = (seq, dnatype, double) if self.previousParams != params: self.remove_dna() self.previousParams = params if self.group == None: if len(seq) > ... |
raise | def build_dna(self): 'Slot for the OK button' seq = self.get_sequence() dnatype = str(self.dna_type_combox.currentText()) double = str(self.endings_combox.currentText()) params = (seq, dnatype, double) if self.previousParams != params: self.remove_dna() self.previousParams = params if self.group == None: if len(seq) > ... | |
DEFAULT_INPUT = ("%s.mmp" % base,) DEFAULT_OUTPUT_MIN = ("exitvalue", "stderr", "stdout", base+".trc", base + ".xyz") DEFAULT_OUTPUT_STRUCT = ("exitvalue", "structurematch", "stderr") DEFAULT_PROGRAM_MIN = ("/tmp/testsimulator", "--minimize", "--dump-as-text", base + ".mmp") DEFAULT_PROGRAM_DYN = ("/tmp/testsimulator",... | DEFAULT_INPUT = ["%s.mmp" % base] DEFAULT_OUTPUT_MIN = ["exitvalue", "stderr", "stdout", base+".trc", base + ".xyz"] DEFAULT_OUTPUT_STRUCT = ["exitvalue", "structurematch", "stderr"] DEFAULT_PROGRAM_MIN = "/tmp/testsimulator --minimize " + \ "--dump-as-text " + base + ".mmp" DEFAULT_PROGRAM_DYN = "/tmp/testsimulator --... | def say(str): pass |
ALT_OUTPUT_FOR_STRUCT = ("exitvalue", "structurematch", "stderr", "stdout", base + ".trc", base + ".xyz") | ALT_OUTPUT_FOR_STRUCT = ["exitvalue", "structurematch", "stderr", "stdout", base + ".trc", base + ".xyz"] | def say(str): pass |
userInput = ( ) userOutput = ( ) | userInput = [ ] userOutput = [ ] | def say(str): pass |
userProgram = line[7:].split() userProgram[0] = join(here, userProgram[0]) userProgram = tuple(userProgram) | userProgram = here + os.sep + line[7:].strip() | def say(str): pass |
try: say(repr(prog)) stdout = open("stdout", "a") stderr = open("stderr", "a") p = Popen(prog, stdout=stdout, stderr=stderr) stdout.close() stderr.close() rc = p.wait() say("return code = %d" % rc) return rc except OSError: sys.stderr.write(repr(prog) + os.linesep) raise | prog += " >> stdout 2>> stderr" rc = os.system(prog) rc >>= 8 say(prog + " " + repr(rc)) return rc | def run(prog): # Redirect standard ouput to "stdout" file # Redirect standard error to "stderr" file # Will this work on Windows? try: say(repr(prog)) stdout = open("stdout", "a") stderr = open("stderr", "a") p = Popen(prog, stdout=stdout, stderr=stderr) #p = Popen(prog, stderr=stderr) stdout.close() stderr.close() rc ... |
if DEBUG: say("STDOUT") say(open("stdout").read()) | def run(prog): # Redirect standard ouput to "stdout" file # Redirect standard error to "stderr" file # Will this work on Windows? try: say(repr(prog)) stdout = open("stdout", "a") stderr = open("stderr", "a") p = Popen(prog, stdout=stdout, stderr=stderr) #p = Popen(prog, stderr=stderr) stdout.close() stderr.close() rc ... | |
rc = run(("/tmp/testsimulator", "--base-file=" + base + ".xyzcmp", base + ".xyz")) | rc = run("/tmp/testsimulator --base-file=" + base + ".xyzcmp " + \ base + ".xyz") | def run(prog): # Redirect standard ouput to "stdout" file # Redirect standard error to "stderr" file # Will this work on Windows? try: say(repr(prog)) stdout = open("stdout", "a") stderr = open("stderr", "a") p = Popen(prog, stdout=stdout, stderr=stderr) #p = Popen(prog, stderr=stderr) stdout.close() stderr.close() rc ... |
stdout.close() stderr.close() | def run(prog): # Redirect standard ouput to "stdout" file # Redirect standard error to "stderr" file # Will this work on Windows? try: say(repr(prog)) stdout = open("stdout", "a") stderr = open("stderr", "a") p = Popen(prog, stdout=stdout, stderr=stderr) #p = Popen(prog, stderr=stderr) stdout.close() stderr.close() rc ... | |
say("Copying output from " + f) | def run(prog): # Redirect standard ouput to "stdout" file # Redirect standard error to "stderr" file # Will this work on Windows? try: say(repr(prog)) stdout = open("stdout", "a") stderr = open("stderr", "a") p = Popen(prog, stdout=stdout, stderr=stderr) #p = Popen(prog, stderr=stderr) stdout.close() stderr.close() rc ... | |
say(f + '->' + line) | def run(prog): # Redirect standard ouput to "stdout" file # Redirect standard error to "stderr" file # Will this work on Windows? try: say(repr(prog)) stdout = open("stdout", "a") stderr = open("stderr", "a") p = Popen(prog, stdout=stdout, stderr=stderr) #p = Popen(prog, stderr=stderr) stdout.close() stderr.close() rc ... | |
else: sys.stdout.write(open("results").read()) if DEBUG: | else: sys.stdout.write(open("results").read()) if False and DEBUG: | def run(prog): # Redirect standard ouput to "stdout" file # Redirect standard error to "stderr" file # Will this work on Windows? try: say(repr(prog)) stdout = open("stdout", "a") stderr = open("stderr", "a") p = Popen(prog, stdout=stdout, stderr=stderr) #p = Popen(prog, stderr=stderr) stdout.close() stderr.close() rc ... |
if releaseNo: spf.write("Release: %s\n" % releaseNo) | requirements = [ ] pyver = sys.version[:3] if pyver == '2.4': spf.write("Release: python24\n") requirements.append('python >= 2.4, python < 2.5') elif pyver == '2.3': spf.write("Release: python23\n") requirements.append('python >= 2.3, python < 2.4') 'python = ' + sys.version()[:3] | 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... |
spf.write("Release: 0\n") | raise Exception("Must use Python 2.3 or 2.4") if requirements: requirements = "Requires: " + " ".join(requirements) else: requirements = "" | 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... |
%description | %(requirements)s %%description | 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... |
%prep %setup %build %install | %%prep %%setup %%build %%install | 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... |
%post | %%post | 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... |
%files %defattr(755, root, root, 755) """ | %%files %%defattr(755, root, root, 755) """ % { "requirements": requirements } | 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... |
QToolTip.add(self.watch_min_in_realtime_checkbox,self.__tr("Enable/disable real time graphical updates during adjustments")) QWhatsThis.add(self.watch_min_in_realtime_checkbox,self.__tr("<p><b>Watch In Real Time</b></p>Enables/disables real time graphical updates during adjust operations.")) | QToolTip.add(self.watch_min_in_realtime_checkbox,self.__tr("Enable/disable real time graphical updates for <b>Adjust All</b> or <b>Adjust Selection</b>")) QWhatsThis.add(self.watch_min_in_realtime_checkbox,self.__tr("<p><b>Watch motion in real time</b></p>Enables/disables real time graphical updates during adjust opera... | 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.cutoverrms_linedit,self.__tr("Cutover RMS foce (pN)")) | QToolTip.add(self.cutoverrms_linedit,self.__tr("Cutover RMS force (pN)")) | 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.cutoverrms_lbl,self.__tr("Cutover RMS foce (pN)")) | QToolTip.add(self.cutoverrms_lbl,self.__tr("Cutover RMS force (pN)")) | 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.... |
shortargs = 'ho:i:s:t:v:' longargs = ['help', 'outdir=', 'iconfile=', 'sourcedir=', 'tag=', 'version='] | shortargs = 'ho:i:s:t:v:p' longargs = ['help', 'outdir=', 'iconfile=', 'sourcedir=', 'tag=', 'version=', 'premature-exit'] | def main(): shortargs = 'ho:i:s:t:v:' longargs = ['help', 'outdir=', 'iconfile=', 'sourcedir=', 'tag=', 'version='] try: opts, args = getopt.getopt(sys.argv[1:], shortargs, longargs) except getopt.GetoptError: usage() sys.exit(2) currentDir = os.getcwd() appName = "nanoENGINEER-1" rootDir = None if sys.platform == 'w... |
if is_singlet or v6 <= (atype.valence - min_other_valence) * V_SINGLE: | our_min_other_valence = max(min_other_valence, atype.numbonds - 1) if is_singlet or v6 <= (atype.valence - our_min_other_valence) * V_SINGLE: | def permitted_btypes_for_bond(self, bond): #bruce 060523 """If we are a real atom: Given one of our bonds (either real or open), and considering as fixed only its and our real bonds' existence (not their current bond types or our current atomtype), and ignoring everything else about the given bond (like the other atom ... |
nsteps = int(min(max(self.fps, 2), angle)) | nsteps = int(min(max(self.fps, 2), max(angle, 2))) | 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)... |
if c.logic == 2 or c.logic == 1: | if c.logic == 1 or c.logic == 2 : | def partselect(self, assy): """Loop thru all the atoms that are visible and select any that are 'in' the shape, ignoring the thickness parameter. pick the parts that contain them """ #---This function has been modified by Huaicai on 10/05/04 to fix bugs of shift & Ctrl drag #---selection of molecules #---Some very tric... |
if c.logic == 1: | if c.logic == 2: | def partselect(self, assy): """Loop thru all the atoms that are visible and select any that are 'in' the shape, ignoring the thickness parameter. pick the parts that contain them """ #---This function has been modified by Huaicai on 10/05/04 to fix bugs of shift & Ctrl drag #---selection of molecules #---Some very tric... |
self.fileform = 0 | self.fileform = '' self.mext = '.dpb' | def __init__(self, assy): SimSetupDialog.__init__(self) self.assy = assy self.nframes = 300 self.temp = 300 self.stepsper = 10 self.timestep = 10 self.filename = '' self.fileform = 0 |
args = [filePath + '/../bin/simulator', '-f' + str(self.nframes), '-t' + str(self.temp), '-i' + str(self.stepsper), "simulate.mmp"] | args = [filePath + '/../bin/simulator', '-f' + str(self.nframes), '-t' + str(self.temp), '-i' + str(self.stepsper), str(self.fileform), "simulate.mmp"] | def GoPressed(self): QDialog.accept(self) import os, sys tmpFilePath = self.assy.w.tmpFilePath if not self.assy.filename: self.assy.filename= os.path.join(tmpFilePath, "simulate.mmp") #By writting the current model into simulate.mmp under ~/atom_tmp, no matter # if it is a *.pdb, a *.mmp with model change or not, we'l... |
self.assy.w.msgbarLabel.setText("Movie written to "+ os.path.join(tmpFilePath, "simulate.dpb")) | self.assy.w.msgbarLabel.setText("Movie written to "+ os.path.join(tmpFilePath, "simulate" + self.mext)) | def GoPressed(self): QDialog.accept(self) import os, sys tmpFilePath = self.assy.w.tmpFilePath if not self.assy.filename: self.assy.filename= os.path.join(tmpFilePath, "simulate.mmp") #By writting the current model into simulate.mmp under ~/atom_tmp, no matter # if it is a *.pdb, a *.mmp with model change or not, we'l... |
self.assy.selectAtoms() | def toolsSelectAtoms(self): self.glpane.setMode('SELECT') self.assy.selectAtoms() # Update display with selected atoms | |
self.assy.selectParts() | def toolsSelectMolecules(self): self.glpane.setMode('SELECT') self.assy.selectParts() # Update display with selected molecules | |
self.yflip = yflip = up[0] < 0.0 | def __init__(self, xoff, yoff, right, up, rot90): if rot90: self.xflip = xflip = right[1] < 0.0 self.yflip = yflip = up[0] < 0.0 else: self.xflip = xflip = right[0] < 0.0 self.yflip = yflip = up[1] < 0.0 | |
self.yflip = yflip = up[1] < 0.0 | def __init__(self, xoff, yoff, right, up, rot90): if rot90: self.xflip = xflip = right[1] < 0.0 self.yflip = yflip = up[0] < 0.0 else: self.xflip = xflip = right[0] < 0.0 self.yflip = yflip = up[1] < 0.0 | |
if yflip: def fy(y): return self.SCALE * (self.HEIGHT - 1 - y) else: def fy(y): return self.SCALE * y | def fx(x): return self.SCALE * x | |
def tfm(x, y, yoff1): return Numeric.array((xoff + yoff1 + fy(y), yoff + fx(x), 0.0)) | def tfm(x, y, yoff1, yflip): if yflip: y1 = self.SCALE * (self.HEIGHT - 1 - y) else: y1 = self.SCALE * y return Numeric.array((xoff + yoff1 + y1, yoff + fx(x), 0.0)) | def tfm(x, y, yoff1): return Numeric.array((xoff + yoff1 + fy(y), yoff + fx(x), 0.0)) |
def tfm(x, y, yoff1): return Numeric.array((xoff + fx(x), yoff + yoff1 + fy(y), 0.0)) | def tfm(x, y, yoff1, yflip): if yflip: y1 = self.SCALE * (self.HEIGHT - 1 - y) else: y1 = self.SCALE * y return Numeric.array((xoff + fx(x), yoff + yoff1 + y1, 0.0)) | def tfm(x, y, yoff1): return Numeric.array((xoff + fx(x), yoff + yoff1 + fy(y), 0.0)) |
return self.tfm(x + 5 * fi(i), y, yoff) | return self.tfm(x + 5 * fi(i), y, yoff, yflip) | def tfm2(x, y): return self.tfm(x + 5 * fi(i), y, yoff) |
self.invalidate_attrs('bbox','center') | self.invalidate_attrs(['bbox','center']) | def computeBoundingBox(self): """Compute the bounding box for this Part. This should be called whenever the geometry model has been changed, like new parts added, parts/atoms deleted, parts moved/rotated(not view move/rotation), etc.""" self.invalidate_attrs('bbox','center') self.bbox, self.center return |
PlotToolDialog.__init__(self) | PlotToolDialog.__init__(self, modal=False) | def __init__(self, assy, movie): #bruce 050326 added movie arg PlotToolDialog.__init__(self) ## self.assy = assy self.history = assy.w.history #bruce 050326 self.movie = movie # before bruce 050326 was assy.current_movie if self.setup(): return self.exec_loop() |
self.exec_loop() | self.show() | def __init__(self, assy, movie): #bruce 050326 added movie arg PlotToolDialog.__init__(self) ## self.assy = assy self.history = assy.w.history #bruce 050326 self.movie = movie # before bruce 050326 was assy.current_movie if self.setup(): return self.exec_loop() |
else: msg = redmsg("No jigs in this part. Nothing to plot.") self.history.message(cmd + msg) | else: msg = redmsg("The part contains no jigs that write data to the trace file. Nothing to plot.") self.history.message(cmd + msg) msg = "The following jigs write output to the tracefile: Rotary Motors, Linear Motors, Grounds, Thermostats and Thermometers." self.history.message(msg) | def setup(self): """Setup the Plot Tool dialog, including populating the combobox with plotting options. """ # To setup the Plot Tool, we need to do the following: # 1. Make sure there is a valid DPB file. This is temporary since the Plot Tool will # soon allow the user to open and plot any trace file. # 2. From th... |
_nullMol = molecule("<not an assembly>", 'name-of-_nullMol') | _nullMol = _make_nullMol() | def delatom(self, atm): """Private method; should be the only way atoms can be removed from a molecule (except for optimized callers like molecule.merge). Remove atom atm from molecule self, preparing atm for being destroyed or for later addition to some other mol, doing necessary invals in self, and (for safety and po... |
self.mol = molecule(win.assy, chem.gensym("Nanotube.")) | def __init__(self, win): NanotubeGeneratorDialog.__init__(self, win) # win is parent. Fixes bug 1089. Mark 051119. self.win = win self.mol = molecule(win.assy, chem.gensym("Nanotube.")) # Validator for the length linedit widget. self.validator = QDoubleValidator(self) self.validator.setRange(0.0, 1000.0, 2) # Range ... | |
("debug_flags", BOOLEAN), | ("debug_flags", INT), | def debug_run_command(command, source = "user debug input"): #bruce 040913-16 in GLPane.py; modified 040928 """Execute a python command, supplied by the user via some sort of debugging interface (named by source), in debug.py's globals. Return 1 for ok (incl empty command), 0 for any error. Caller should not print exce... |
"debug_flags": False, | "debug_flags": 0, | def debug_run_command(command, source = "user debug input"): #bruce 040913-16 in GLPane.py; modified 040928 """Execute a python command, supplied by the user via some sort of debugging interface (named by source), in debug.py's globals. Return 1 for ok (incl empty command), 0 for any error. Caller should not print exce... |
('(debugging menu)', noop, 'disabled'), | ('debugging menu (unsupported)', noop, 'disabled'), | def debug_menu_items(self): """#doc; as of 050416 this will be called every time the debug menu needs to be put up, so that the menu contents can be different each time (i.e. so it can be a dynamic menu) [subclasses can override this; best if they call this superclass method and modify its result, e.g. add new items at... |
if self._debug_win: | if 0 and self._debug_win: | def debug_menu_items(self): """#doc; as of 050416 this will be called every time the debug menu needs to be put up, so that the menu contents can be different each time (i.e. so it can be a dynamic menu) [subclasses can override this; best if they call this superclass method and modify its result, e.g. add new items at... |
def _debug_print_object_counts(self): from HistoryWidget import _graymsg msglater = "" for clasname, modulename in ( ('Atom', 'chem'), ('Bond', 'bonds'), ('Node', 'Utility'), ('Part', 'part'), ('Assembly', 'assembly')): if sys.modules.has_key(modulename): module = sys.modules[modulename] clas = getattr(module, clasna... | def _debug_update_parts(self): win = self._debug_win win.assy.update_parts() | |
'test_callWrongSimulatorObject', 'test_badCallback1', 'test_pyrex_minH2', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_enabled_disabled_jigs_005_disabled_measure_distance_jig', | 'test_pyrex_minH2', 'test_badCallback1', 'test_singlebond_stretch_Cl_AlH2', 'test_reordering_jigs_or_chunks_02_thermo_anchor_stat_reordering_6', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_minimize_h2', 'test_reordering_jigs_or_chunks_02_thermo_anchor_stat_reordering_3', 'test_reordering_jigs_or_chunks_02_thermo_anchor_stat_reordering_8', | 'test_reordering_jigs_or_chunks_03_thermo_anchor_reordering', 'test_singlebond_stretch_H_Cl', 'test_temperature_tests_003_thermostat_test_4', 'test_singlebond_stretch_Cl_SH', 'test_minimize_0013', 'test_singlebond_stretch_F_SH', 'test_singlebond_stretch_H_H', 'test_singlebond_stretch_F_CH3', 'test_enabled_disabled_jigs... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_reordering_jigs_or_chunks_01_thermo_anchor_reordering_4', 'test_enabled_disabled_jigs_003_one_thermometer_enabled_other_disabled', | 'test_singlebond_stretch_F_PH2', 'test_reordering_jigs_or_chunks_02_thermo_anchor_stat_reordering_1', 'test_motors_009_linearmotor_Methane_Molecule', 'test_singlebond_stretch_F_SiH3', 'test_singlebond_stretch_Cl_PH2', 'test_singlebond_stretch_Cl_NH2', 'test_singlebond_stretch_F_NH2', 'test_singlebond_stretch_H_BH2', 't... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_reordering_jigs_or_chunks_02_thermo_anchor_stat_reordering_1', 'test_minimize_0013', 'test_singlebond_stretch_F_OH', 'test_reordering_jigs_or_chunks_02_thermo_anchor_stat_reordering_4', 'test_reordering_jigs_or_chunks_01_thermo_anchor_reordering_5', 'test_reordering_jigs_or_chunks_02_thermo_anchor_stat_reordering... | 'test_singlebond_stretch_HS_SH', 'test_singlebond_stretch_F_AlH2', 'test_singlebond_stretch_HO_PH2', 'test_singlebond_stretch_H_PH2', 'test_singlebond_stretch_HS_NH2', 'test_minimize_0010', 'test_temperature_tests_001_two_methanes_9A_apart_vdw_5', 'test_singlebond_stretch_Cl_BH2', 'test_singlebond_stretch_HS_PH2', 'tes... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_singlebond_stretch_Cl_SH', 'test_temperature_tests_003_thermostat_test_2', 'test_reordering_jigs_or_chunks_02_thermo_anchor_stat_reordering_7', 'test_temperature_tests_003_thermostat_test_3', 'test_singlebond_stretch_HS_SH', 'test_rigid_organics_CH4', 'test_reordering_jigs_or_chunks_02_thermo_anchor_stat_reorderi... | 'test_singlebond_stretch_H2P_AlH2', 'test_enabled_disabled_jigs_002_one_anchor_enabled_other_disabled', 'test_motors_025_two_linearmotors_applying_equal_forces_normal_to_each_other', 'test_motors_and_anchors_005_rotorymotor_against_anchor_3', 'test_singlebond_stretch_HO_SiH3', 'test_singlebond_stretch_H_AlH2', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_singlebond_stretch_H3C_CH3', 'test_singlebond_stretch_HS_CH3', 'test_singlebond_stretch_F_NH2', 'test_motors_025_two_linearmotors_applying_equal_forces_normal_to_each_other', 'test_singlebond_stretch_H_AlH2', 'test_enabled_disabled_jigs_004_one_thermostat_enabled_other_disabled', | 'test_motors_012_rotarymotor_0_torque_and_negative_speed', 'test_motors_020_rotarymotor_high_torque_and_speed', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_singlebond_stretch_H_H', 'test_singlebond_stretch_H2Al_SiH3', 'test_singlebond_stretch_H3Si_SiH3', 'test_singlebond_stretch_Cl_AlH2', 'test_singlebond_stretch_F_SiH3', 'test_reordering_jigs_or_chunks_03_thermo_anchor_reordering', 'test_temperature_tests_001_two_methanes_9A_apart_vdw_5', 'test_singlebond_stretch_F... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_motors_and_anchors_005_rotorymotor_against_anchor_3', 'test_singlebond_stretch_F_BH2', 'test_reordering_jigs_or_chunks_02_thermo_anchor_stat_reordering_2', 'test_singlebond_stretch_H2N_SiH3', | 'test_motors_017_rotarymotor_positive_torque_and_negative_speed', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_motors_016_rotarymotor_negative_torque_and_0_speed', 'test_motors_012_rotarymotor_0_torque_and_negative_speed', 'test_singlebond_stretch_HO_SiH3', 'test_motors_026_two_linearmotors_applying_equal_and_opposite_forces', 'test_singlebond_stretch_F_CH3', 'test_singlebond_stretch_F_SH', 'test_reordering_jigs_or_chunks... | 'test_singlebond_stretch_H2N_AlH2', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_singlebond_stretch_Cl_SiH3', 'test_singlebond_stretch_HS_AlH2', 'test_enabled_disabled_jigs_007_one_linearmotor_enabled_and_other_disabled', 'test_singlebond_stretch_Cl_NH2', 'test_singlebond_stretch_H2P_CH3', 'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_6', 'test_singlebond... | 'test_motors_018_rotarymotor_positive_torque_and_0_speed', 'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_3', 'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_7', 'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_5... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_5', 'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_3', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_motors_018_rotarymotor_positive_torque_and_0_speed', | 'test_singlebond_stretch_H2Al_AlH2', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_motors_010_linearmotor_box_of_helium', 'test_heteroatom_organics_CH3OH', 'test_singlebond_stretch_F_AlH2', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_motors_028_bug1306_test2', | 'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_8', 'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_2', 'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_6', 'test_motors_016_rotarymotor_negative_torque_and_0_speed... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_heteroatom_organics_CH3AlH2', 'test_heteroatom_organics_C3H6BH', 'test_motors_017_rotarymotor_positive_torque_and_negative_speed', | 'test_heteroatom_organics_CH3OH', 'test_singlebond_stretch_HO_CH3', 'test_singlebond_stretch_H2B_CH3', 'test_singlebond_stretch_H2N_SiH3', 'test_singlebond_stretch_H2B_SiH3', 'test_singlebond_stretch_H2Al_CH3', 'test_floppy_organics_C2H6', 'test_singlebond_stretch_H2B_AlH2', 'test_floppy_organics_C4H8', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_8', 'test_heteroatom_organics_C3H6O', 'test_singlebond_stretch_H2B_SiH3', 'test_rigid_organics_C8H8', 'test_singlebond_stretch_H2Al_AlH2', 'test_singlebond_stretch_H2B_CH3', 'test_singlebond_stretch_HO_CH3', 'test_floppy_organics_C4H8', | 'test_reordering_jigs_or_chunks_04_thermo_lmotor_anchor_stat_reordering_6', 'test_reordering_jigs_or_chunks_04_thermo_lmotor_anchor_stat_reordering_3', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_singlebond_stretch_H2B_AlH2', 'test_singlebond_stretch_H2N_AlH2', 'test_minimize_0009', 'test_heteroatom_organics_CH3BH2', 'test_heteroatom_organics_C3H6PH', 'test_floppy_organics_C2H6', 'test_singlebond_stretch_H2Al_CH3', 'test_singlebond_stretch_HO_NH2', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_reordering_jigs_or_chunks_04_thermo_lmotor_anchor_stat_reordering_3', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_motors_030_rotarymotor_and_linear_motor_attached_to_same_atoms', 'test_singlebond_stretch_HO_AlH2', | 'test_heteroatom_organics_CH3OCH3', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_heteroatom_organics_CH3OCH3', 'test_reordering_jigs_or_chunks_04_thermo_lmotor_anchor_stat_reordering_6', 'test_reordering_jigs_or_chunks_03_thermo_rmotor_anchor_stat_reordering_3', 'test_reordering_jigs_or_chunks_03_thermo_rmotor_anchor_stat_reordering_6', 'test_reordering_jigs_or_chunks_03_thermo_rmotor_anchor_... | 'test_reordering_jigs_or_chunks_03_thermo_rmotor_anchor_stat_reordering_8', 'test_heteroatom_organics_C3H6PH', 'test_motors_005_linearmotor_negative_force_and_positive_stiffness', 'test_motors_007_linearmotor_positive_force_and_0_stiffness', 'test_motors_002_linearmotor_0_force_and_negative_stiffness', 'test_motors_008... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_singlebond_stretch_H2B_PH2', 'test_motors_007_linearmotor_positive_force_and_0_stiffness', 'test_motors_004_linearmotor_negative_force_and_negative_stiffness', 'test_motors_002_linearmotor_0_force_and_negative_stiffness', 'test_motors_005_linearmotor_negative_force_and_positive_stiffness', 'test_motors_006_linear... | 'test_rigid_organics_C10H12', 'test_motors_001_linearmotor_0_force_and_0_stiffness', 'test_singlebond_stretch_HO_OH', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_singlebond_stretch_H2N_PH2', 'test_reordering_jigs_or_chunks_03_thermo_rmotor_anchor_stat_reordering_8', 'test_motors_001_linearmotor_0_force_and_0_stiffness', 'test_rigid_organics_C10H12', 'test_singlebond_stretch_HO_OH', 'test_singlebond_stretch_H2P_AlH2', | 'test_heteroatom_organics_ADAMframe_S_Cs', 'test_heteroatom_organics_CH3BH2', 'test_floppy_organics_C6H12b', 'test_jigs_to_several_atoms_003_linearmotor_to_50_atoms', 'test_motors_023_rotarymotor_two_planet_gears', 'test_amino_acids_tyr_l_aminoacid', 'test_motors_and_anchors_004_rotorymotor_against_anchor_2', 'test_mot... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_heteroatom_organics_ADAMframe_S_Cs', 'test_heteroatom_organics_C5H10S', 'test_jigs_to_several_atoms_003_linearmotor_to_50_atoms', 'test_heteroatom_organics_ADAMframe_PH_Cs', 'test_motors_023_rotarymotor_two_planet_gears', 'test_floppy_organics_C6H12b', 'test_motors_and_anchors_003_rotorymotor_against_anchor_1', '... | 'test_heteroatom_organics_N_ADAM_C3v', 'test_traceCallbackWithMotor', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_heteroatom_organics_N_ADAM_C3v', 'test_heteroatom_organics_ADAMframe_SiH2_c2v', 'test_heteroatom_organics_B_ADAM_C3v', 'test_heteroatom_organics_ADAMframe_BH_Cs', 'test_motors_and_anchors_001_linearmotor_pulling_against_anchor_1', 'test_motors_024_linearmotor_two_dodecahedranes', 'test_heteroatom_organics_ADAM_SH... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_heteroatom_organics_ADAM_F_c3v', 'test_heteroatom_organics_Al_ADAM_C3v', 'test_singlebond_stretch_HO_BH2', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_jigs_to_several_atoms_006_anchors_to_100_atoms', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_heteroatom_organics_ADAM_Cl_c3v', 'test_jigs_to_several_atoms_005_anchors_to_50_atoms', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_singlebond_stretch_H2N_CH3', | 'test_heteroatom_organics_ADAMframe_AlH_Cs', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_heteroatom_organics_C4H8PH', 'test_minimize_0012', | 'test_floppy_organics_C7H14c', 'test_singlebond_stretch_H2N_CH3', 'test_enabled_disabled_jigs_005_disabled_measure_distance_jig', 'test_heteroatom_organics_C4H8AlH', 'test_heteroatom_organics_CH3PHCH3', 'test_jigs_to_several_atoms_006_anchors_to_100_atoms', 'test_jigs_to_several_atoms_005_anchors_to_50_atoms', 'test_he... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_floppy_organics_C7H14c', 'test_heteroatom_organics_CH3PHCH3', 'test_minimize_0011', 'test_rigid_organics_C14H20', 'test_heteroatom_organics_ADAMframe_AlH_Cs', 'test_enabled_disabled_jigs_002_one_anchor_enabled_other_disabled', 'test_heteroatom_organics_C4H8NH', 'test_floppy_organics_C4H10a', | 'test_heteroatom_organics_CH3SiH2CH3', 'test_heteroatom_organics_C_CH3_3_OH', 'test_heteroatom_organics_C_CH3_3_SH', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_heteroatom_organics_C4H8BH', 'test_heteroatom_organics_C4H8AlH', 'test_heteroatom_organics_C_CH3_3_SiH3', | 'test_heteroatom_organics_C5H10SiH2', 'test_singlebond_stretch_HS_BH2', 'test_heteroatom_organics_C5H10AlH', 'test_heteroatom_organics_C_CH3_3_BH2', 'test_heteroatom_organics_Al_ADAM_C3v', 'test_heteroatom_organics_ADAM_BH2', 'test_heteroatom_organics_C_CH3_3_NH2', 'test_heteroatom_organics_C4H8PH', 'test_heteroatom_or... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
'test_pyrex_minimize0001', 'test_floppy_organics_C5H12b', 'test_floppy_organics_C3H8', 'test_heteroatom_organics_CH3PH2', 'test_heteroatom_organics_C5H10SiH2', 'test_heteroatom_organics_C4H8O', 'test_heteroatom_organics_CH3SiH3', 'test_heteroatom_organics_C_CH3_3_NH2', 'test_heteroatom_organics_CH3NHCH3', 'test_heteroa... | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) | |
'test_floppy_organics_C7H14a', 'test_heteroatom_organics_C_CH3_3_BH2', 'test_floppy_organics_C5H12e', 'test_heteroatom_organics_ADAM_AlH2_Cs', 'test_rigid_organics_C8H14', | 'test_heteroatom_organics_ADAM_PH2_Cs', 'test_heteroatom_organics_ADAM_NH2_Cs', 'test_minimize_0012', | def lastLineOfReadings(f): lines = readlines(f) n = None for i in range(len(lines)): if lines[i].startswith("# Done:"): n = i - 1 break if n == None: return None return map(string.atof, lines[n].split()) |
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