def loadDataPushed(self):
"""Loads the trajectory data with the chosen initial parameters."""
self.config, result = FileLoaderDialog.getConfig()
if result == 1:
QApplication.processEvents()
self.setInfoLabel(
"Loading trajectory and running atomic contact analysis...")
nproc = int(self.settingsView.coreBox.value())
self.analysis = Analyzer(self.config.psf, self.config.dcd,
self.config.cutoff,
self.config.hbondcutoff,
self.config.hbondcutangle,
self.config.sel1text,
self.config.sel2text)
QApplication.processEvents()
try:
self.analysis.runFrameScan(nproc)
except:
box = ErrorBox(
"Error while loading data: Probably you specified an atom selection with 0 atoms or invalid input files."
)
box.exec_()
self.loadDataPushed()
self.setInfoLabel("%d frames loaded." %
len(self.analysis.contactResults))
self.updateSelectionLabels(self.config.sel1text,
self.config.sel2text)
self.sasaView.setFilePaths(*self.analysis.getFilePaths())
self.exportWidget.setFilePaths(*self.analysis.getFilePaths())
def showStatistics(self):
"""Shows general statistics of the analyzed data over all frames."""
if len(self.contacts) == 0 or self.contacts is None:
box = ErrorBox(ErrorMessages.NOSCORES_PROMPTANALYSIS)
box.exec_()
return
self.statisticsView = Statistics(self.contacts)
self.statisticsView.showNormal()
def savePlot(self):
"""Saves the current plot."""
fileName = QFileDialog.getSaveFileName(self, 'Save Path')
path, file_extension = os.path.splitext(fileName[0])
if file_extension == "":
file_extension = "png"
else:
file_extension = file_extension[1:]
try:
self.contactPlotter.saveFigure(path, file_extension)
except ValueError:
box = ErrorBox("File format " + file_extension + " is not supported.\nPlease choose from eps, pdf, pgf,"
" png, ps, raw, rgba, svg, svgz. ")
box.exec_()
def exportSession(self):
"""Exports the current session to file."""
fileName = QFileDialog.getSaveFileName(self, 'Export file')
filestring = fileName[0]
if filestring == "":
return
if self.contacts is not None and self.analysis is not None:
self.setInfoLabel("Exporting current session...")
DataHandler.writeSessionToFile(filestring, self.analysis)
self.cleanInfoLabel()
else:
box = ErrorBox(ErrorMessages.NOEXPDATA)
box.exec_()
return
def savePlot(self):
"""Saves the generated SASA plot over all frames."""
fileName = QFileDialog.getSaveFileName(self, 'Export Path')
if len(fileName[0]) > 0:
path, file_extension = os.path.splitext(fileName[0])
if file_extension == "":
file_extension = ".png"
file_extension = file_extension[1:]
try:
self.previewPlot.saveFigure(path, file_extension)
except ValueError:
box = ErrorBox("File format " + file_extension + " is not supported.\nPlease choose from eps, pdf, pgf,"
" png, ps, raw, rgba, svg, svgz. ")
box.exec_()
def savePlot(self):
"""Saves the generated SASA plot over all frames."""
fileName = QFileDialog.getSaveFileName(self, 'Export Path')
if len(fileName[0]) > 0:
path, file_extension = os.path.splitext(fileName[0])
if file_extension == "":
file_extension = ".png"
file_extension = file_extension[1:]
try:
self.previewPlot.saveFigure(path, file_extension)
except ValueError:
box = ErrorBox(
"File format " + file_extension +
" is not supported.\nPlease choose from eps, pdf, pgf,"
" png, ps, raw, rgba, svg, svgz. ")
box.exec_()
def savePlot(self):
"""Saves the current plot."""
fileName = QFileDialog.getSaveFileName(self, 'Save Path')
path, file_extension = os.path.splitext(fileName[0])
if file_extension == "":
file_extension = "png"
else:
file_extension = file_extension[1:]
try:
self.contactPlotter.saveFigure(path, file_extension)
except ValueError:
box = ErrorBox(
"File format " + file_extension +
" is not supported.\nPlease choose from eps, pdf, pgf,"
" png, ps, raw, rgba, svg, svgz. ")
box.exec_()
def analyzeDataPushed(self):
"""Handles the Analyzer after the Accumulation maps have been set."""
if self.analysis is None:
box = ErrorBox(ErrorMessages.NODATA_PROMPTLOAD)
box.exec_()
return
self.maps, result = AnalysisDialog.getMapping()
if result == 1:
self.analysis.frameUpdate.connect(self.updateAnalyzedFrames)
self.setInfoLabel("Analyzing contacts...")
map1 = self.maps[0]
map2 = self.maps[1]
nproc = int(self.settingsView.coreBox.value())
self.contacts = self.analysis.runContactAnalysis(map1, map2, nproc)
self.progressBar.setValue(0)
self.setInfoLabel("Updating timeline...")
QApplication.processEvents()
self.updateSettings()
self.updateFilters()
self.cleanInfoLabel()
def plotMap(self):
"""Plots the contact map."""
sip.delete(self.tab3.mapPlot)
self.tab3.mapPlot = MapPlotter(None, width=8, height=5, dpi=60)
self.grid2.addWidget(self.tab3.mapPlot, 3, 0, 1, 4)
if self.map1 is None or self.map2 is None or self.contacts is None or len(
self.contacts) == 0:
box = ErrorBox(ErrorMessages.RESID_REQUIRED)
box.exec_()
return
res = self.tab3.mapPlot.plotMap(self.contacts, self.map1, self.map2,
self.label1, self.label2,
self.tab3.attributeBox.currentText(),
self.threshold, self.nsPerFrame)
if res == -1:
box = ErrorBox(ErrorMessages.RESID_REQUIRED)
box.exec_()
self.tab3.mapPlot.update()
def plotMap(self):
"""Plots the contact map."""
sip.delete(self.tab3.mapPlot)
self.tab3.mapPlot = MapPlotter(None, width=8, height=5, dpi=60)
self.grid2.addWidget(self.tab3.mapPlot, 3, 0, 1, 4)
if self.map1 is None or self.map2 is None or self.contacts is None or len(self.contacts) == 0:
box = ErrorBox(ErrorMessages.RESID_REQUIRED)
box.exec_()
return
res = self.tab3.mapPlot.plotMap(self.contacts, self.map1, self.map2, self.label1, self.label2,
self.tab3.attributeBox.currentText(), self.threshold, self.nsPerFrame)
if res == -1:
box = ErrorBox(ErrorMessages.RESID_REQUIRED)
box.exec_()
self.tab3.mapPlot.update()
def createTclScriptVis(self):
"""Creates the Tcl script for VMD visualization of the selections."""
if len(self.contacts) == 0:
box = ErrorBox(ErrorMessages.NOCONTACTS)
box.exec_()
return
fileName = QFileDialog.getSaveFileName(self, 'Save Path')
if len(fileName[0]) > 0:
path, file_extension = os.path.splitext(fileName[0])
if file_extension != ".tcl":
file_extension = ".tcl"
path += file_extension
f = open(path, 'w')
f.write('mol new %s \n' % self.psf)
f.write('mol addfile %s \n' % self.dcd)
f.write('mol delrep 0 top \n')
f.write('mol representation NewCartoon \n')
f.write('mol Color ColorID 3 \n')
f.write('mol selection {all} \n')
f.write('mol addrep top \n')
if self.tab4.splitVisCheckbox.isChecked():
for cont in self.contacts:
currentSel1 = []
index = 0
for item in cont.key1:
if item != "none":
currentSel1.append(
AccumulationMapIndex.vmdsel[index] + " " +
item)
index += 1
currentSel1String = " and ".join(currentSel1)
currentSel2 = []
index = 0
for item in cont.key2:
if item != "none":
currentSel2.append(
AccumulationMapIndex.vmdsel[index] + " " +
item)
index += 1
currentSel2String = " and ".join(currentSel2)
add1 = ("" if self.tab4.additionalText1.text() == "" else
(" and " + self.tab4.additionalText1.text()))
add2 = ("" if self.tab4.additionalText2.text() == "" else
(" and " + self.tab4.additionalText2.text()))
sel = "(" + currentSel1String + add1 + ") or (" + currentSel2String + add2 + ")"
f.write('mol representation Licorice \n')
f.write('mol Color Name \n')
f.write('mol selection {%s} \n' % sel)
f.write('mol addrep top \n')
else:
total = []
for cont in self.contacts:
currentSel1 = []
index = 0
for item in cont.key1:
if item != "none":
currentSel1.append(
AccumulationMapIndex.vmdsel[index] + " " +
item)
index += 1
currentSel1String = " and ".join(currentSel1)
currentSel2 = []
index = 0
for item in cont.key2:
if item != "none":
currentSel2.append(
AccumulationMapIndex.vmdsel[index] + " " +
item)
index += 1
currentSel2String = " and ".join(currentSel2)
add1 = ("" if self.tab4.additionalText1.text() == "" else
(" and " + self.tab4.additionalText1.text()))
add2 = ("" if self.tab4.additionalText2.text() == "" else
(" and " + self.tab4.additionalText2.text()))
sel = "(" + currentSel1String + add1 + ") or (" + currentSel2String + add2 + ")"
total.append(sel)
seltext = " or ".join(total)
f.write('mol representation Licorice \n')
f.write('mol Color Name \n')
f.write('mol selection {%s} \n' % seltext)
f.write('mol addrep top \n')
f.close()
def calculateSasa(self):
"""Computes the SASA of the given selections."""
print("calculate SASA")
self.allSasas = []
# load psf and trajectory, make lists with radii and coordinates
if self.psf == "" or self.dcd == "":
e = ErrorBox(ErrorMessages.CHOOSEFILE)
e.exec_()
return
try:
u = MDAnalysis.Universe(self.psf, self.dcd)
except IOError:
e = ErrorBox(ErrorMessages.FILE_NOT_FOUND)
e.exec_()
return
probeRadius = 1.4
# seltext = "segid UBQ"
# resseltext = "segid UBQ and same residue as around 5.0 (segid RN11)"
seltext = self.sasaSelection1TextField.text()
seltext2 = self.sasaSelection2TextField.text()
resseltext = self.sasaRestrictionTextField.text()
# 0=spiral, 1=random (VMD)
pointstyle = 1
# number of points to approximate the sphere
surfacePoints = 50
# pair distance
pairdist = 2.0 * (2.0 + 1.4)
if resseltext != "":
restricted = 1
else:
restricted = 0
selection = u.select_atoms(seltext)
# natoms = len(selection.atoms)
radius = []
restrictedList = []
if restricted:
ressel = u.select_atoms(resseltext)
for s in selection.atoms:
if s in ressel.atoms:
restrictedList.append(1)
else:
restrictedList.append(0)
radius.append(vdwRadius(s.name[0]))
else:
restrictedList = [0]
for s in selection.atoms:
radius.append(vdwRadius(s.name[0]))
natoms = len(selection)
nprad = np.array(radius, dtype=np.float32)
restrictedList = np.array(restrictedList, dtype=np.int32)
# TODO: bug if selection is not static for all frames
# TODO: dynamic allocation of positions in every frame!
input_coords = []
for ts in u.trajectory:
# ressel = u.select_atoms(resseltext)
# print("restricted: ", len(ressel.atoms))
input_coords.append(selection.positions)
nprocs = self.coreBox.value()
input_chunks = chunks(input_coords, nprocs)
pool = LoggingPool(nprocs)
results = []
rank = 0
trajLength = len(u.trajectory)
self.totalFramesToProcess = trajLength
for input_coords_chunk in input_chunks:
results.append(pool.apply_async(calculate_sasa_parallel, args=(input_coords_chunk, natoms, pairdist, nprad,
surfacePoints, probeRadius, pointstyle,
restricted, restrictedList, rank)))
rank += 1
print("ranks", rank)
self.state = True
self.sasaEventListener()
pool.close()
pool.join()
self.state = False
for r in results:
self.allSasas.extend(r.get())
del radius
if self.calculateContactAreaCheckbox.isChecked():
print("Calculate contact area")
selection2 = u.select_atoms(seltext2)
# natoms2 = len(selection2.atoms)
radius2 = []
restrictedList2 = []
if restricted:
ressel = u.select_atoms(resseltext)
for s in selection2.atoms:
if s in ressel.atoms:
restrictedList2.append(1)
else:
restrictedList2.append(0)
radius2.append(vdwRadius(s.name[0]))
else:
print("You need a restricted selection for contact areas!")
natoms2 = len(selection2)
nprad = np.array(radius2, dtype=np.float32)
restrictedList2 = np.array(restrictedList2, dtype=np.int32)
input_coords2 = []
for ts in u.trajectory:
input_coords2.append(selection2.positions)
input_chunks2 = chunks(input_coords2, nprocs)
pool = LoggingPool(nprocs)
results = []
rank = 0
trajLength = len(u.trajectory)
self.totalFramesToProcess = trajLength
for input_coords_chunk2 in input_chunks2:
results.append(pool.apply_async(calculate_sasa_parallel, args=(input_coords_chunk2, natoms2, pairdist,
nprad, surfacePoints, probeRadius,
pointstyle, restricted, restrictedList2,
rank)))
rank += 1
print("ranks", rank)
self.state = True
self.sasaEventListener()
pool.close()
pool.join()
all_sasas2 = []
for r in results:
all_sasas2.extend(r.get())
diff_list = []
for sasa_value1, sasa_value2 in zip(self.allSasas, all_sasas2):
diff_list.append(sasa_value1 - sasa_value2)
self.allSasas = diff_list
sip.delete(self.previewPlot)
self.previewPlot = SimplePlotter(None, width=4, height=2, dpi=70)
self.previewPlot.plot(np.arange(0, trajLength, 1), self.allSasas)
self.previewPlot.axes.set_xlabel("frame")
if self.calculateContactAreaCheckbox.isChecked():
self.previewPlot.axes.set_ylabel(r'Contact Area [A$^{\circ}$$^{2}$]')
else:
self.previewPlot.axes.set_ylabel(r'SASA [A$^{\circ}$$^{2}$]')
self.graphGridLayout.addWidget(self.previewPlot)
self.previewPlot.update()
def createTclScriptVis(self):
"""Creates the Tcl script for VMD visualization of the selections."""
if len(self.contacts) == 0:
box = ErrorBox(ErrorMessages.NOCONTACTS)
box.exec_()
return
fileName = QFileDialog.getSaveFileName(self, 'Save Path')
if len(fileName[0]) > 0:
path, file_extension = os.path.splitext(fileName[0])
if file_extension != ".tcl":
file_extension = ".tcl"
path += file_extension
f = open(path, 'w')
f.write('mol new %s \n' % self.psf)
f.write('mol addfile %s \n' % self.dcd)
f.write('mol delrep 0 top \n')
f.write('mol representation NewCartoon \n')
f.write('mol Color ColorID 3 \n')
f.write('mol selection {all} \n')
f.write('mol addrep top \n')
if self.tab4.splitVisCheckbox.isChecked():
for cont in self.contacts:
currentSel1 = []
index = 0
for item in cont.key1:
if item != "none":
currentSel1.append(AccumulationMapIndex.vmdsel[index] + " " + item)
index += 1
currentSel1String = " and ".join(currentSel1)
currentSel2 = []
index = 0
for item in cont.key2:
if item != "none":
currentSel2.append(AccumulationMapIndex.vmdsel[index] + " " + item)
index += 1
currentSel2String = " and ".join(currentSel2)
add1 = ("" if self.tab4.additionalText1.text() == "" else (" and " + self.tab4.additionalText1.text()))
add2 = ("" if self.tab4.additionalText2.text() == "" else (" and " + self.tab4.additionalText2.text()))
sel = "("+currentSel1String + add1 + ") or (" + currentSel2String + add2 + ")"
f.write('mol representation Licorice \n')
f.write('mol Color Name \n')
f.write('mol selection {%s} \n' % sel)
f.write('mol addrep top \n')
else:
total = []
for cont in self.contacts:
currentSel1 = []
index = 0
for item in cont.key1:
if item != "none":
currentSel1.append(AccumulationMapIndex.vmdsel[index] + " " + item)
index += 1
currentSel1String = " and ".join(currentSel1)
currentSel2 = []
index = 0
for item in cont.key2:
if item != "none":
currentSel2.append(AccumulationMapIndex.vmdsel[index] + " " + item)
index += 1
currentSel2String = " and ".join(currentSel2)
add1 = ("" if self.tab4.additionalText1.text() == "" else (" and " + self.tab4.additionalText1.text()))
add2 = ("" if self.tab4.additionalText2.text() == "" else (" and " + self.tab4.additionalText2.text()))
sel = "(" + currentSel1String + add1 + ") or (" + currentSel2String + add2 + ")"
total.append(sel)
seltext = " or ".join(total)
f.write('mol representation Licorice \n')
f.write('mol Color Name \n')
f.write('mol selection {%s} \n' % seltext)
f.write('mol addrep top \n')
f.close()
def calculateSasa(self):
"""Computes the SASA of the given selections."""
print("calculate SASA")
self.allSasas = []
# load psf and trajectory, make lists with radii and coordinates
if self.psf == "" or self.dcd == "":
e = ErrorBox(ErrorMessages.CHOOSEFILE)
e.exec_()
return
try:
u = MDAnalysis.Universe(self.psf, self.dcd)
except IOError:
e = ErrorBox(ErrorMessages.FILE_NOT_FOUND)
e.exec_()
return
probeRadius = 1.4
# seltext = "segid UBQ"
# resseltext = "segid UBQ and same residue as around 5.0 (segid RN11)"
seltext = self.sasaSelection1TextField.text()
seltext2 = self.sasaSelection2TextField.text()
resseltext = self.sasaRestrictionTextField.text()
# 0=spiral, 1=random (VMD)
pointstyle = 1
# number of points to approximate the sphere
surfacePoints = 50
# pair distance
pairdist = 2.0 * (2.0 + 1.4)
if resseltext != "":
restricted = 1
else:
restricted = 0
selection = u.select_atoms(seltext)
# natoms = len(selection.atoms)
radius = []
restrictedList = []
if restricted:
ressel = u.select_atoms(resseltext)
for s in selection.atoms:
if s in ressel.atoms:
restrictedList.append(1)
else:
restrictedList.append(0)
radius.append(vdwRadius(s.name[0]))
else:
restrictedList = [0]
for s in selection.atoms:
radius.append(vdwRadius(s.name[0]))
natoms = len(selection)
nprad = np.array(radius, dtype=np.float32)
restrictedList = np.array(restrictedList, dtype=np.int32)
# TODO: bug if selection is not static for all frames
# TODO: dynamic allocation of positions in every frame!
input_coords = []
for ts in u.trajectory:
# ressel = u.select_atoms(resseltext)
# print("restricted: ", len(ressel.atoms))
input_coords.append(selection.positions)
nprocs = self.coreBox.value()
input_chunks = chunks(input_coords, nprocs)
pool = LoggingPool(nprocs)
results = []
rank = 0
trajLength = len(u.trajectory)
self.totalFramesToProcess = trajLength
for input_coords_chunk in input_chunks:
results.append(
pool.apply_async(calculate_sasa_parallel,
args=(input_coords_chunk, natoms, pairdist,
nprad, surfacePoints, probeRadius,
pointstyle, restricted, restrictedList,
rank)))
rank += 1
print("ranks", rank)
self.state = True
self.sasaEventListener()
pool.close()
pool.join()
self.state = False
for r in results:
self.allSasas.extend(r.get())
del radius
if self.calculateContactAreaCheckbox.isChecked():
print("Calculate contact area")
selection2 = u.select_atoms(seltext2)
# natoms2 = len(selection2.atoms)
radius2 = []
restrictedList2 = []
if restricted:
ressel = u.select_atoms(resseltext)
for s in selection2.atoms:
if s in ressel.atoms:
restrictedList2.append(1)
else:
restrictedList2.append(0)
radius2.append(vdwRadius(s.name[0]))
else:
print("You need a restricted selection for contact areas!")
natoms2 = len(selection2)
nprad = np.array(radius2, dtype=np.float32)
restrictedList2 = np.array(restrictedList2, dtype=np.int32)
input_coords2 = []
for ts in u.trajectory:
input_coords2.append(selection2.positions)
input_chunks2 = chunks(input_coords2, nprocs)
pool = LoggingPool(nprocs)
results = []
rank = 0
trajLength = len(u.trajectory)
self.totalFramesToProcess = trajLength
for input_coords_chunk2 in input_chunks2:
results.append(
pool.apply_async(calculate_sasa_parallel,
args=(input_coords_chunk2, natoms2,
pairdist, nprad, surfacePoints,
probeRadius, pointstyle, restricted,
restrictedList2, rank)))
rank += 1
print("ranks", rank)
self.state = True
self.sasaEventListener()
pool.close()
pool.join()
all_sasas2 = []
for r in results:
all_sasas2.extend(r.get())
diff_list = []
for sasa_value1, sasa_value2 in zip(self.allSasas, all_sasas2):
diff_list.append(sasa_value1 - sasa_value2)
self.allSasas = diff_list
sip.delete(self.previewPlot)
self.previewPlot = SimplePlotter(None, width=4, height=2, dpi=70)
self.previewPlot.plot(np.arange(0, trajLength, 1), self.allSasas)
self.previewPlot.axes.set_xlabel("frame")
if self.calculateContactAreaCheckbox.isChecked():
self.previewPlot.axes.set_ylabel(
r'Contact Area [A$^{\circ}$$^{2}$]')
else:
self.previewPlot.axes.set_ylabel(r'SASA [A$^{\circ}$$^{2}$]')
self.graphGridLayout.addWidget(self.previewPlot)
self.previewPlot.update()