def new_project(self):
if self.AMDock.state:
msg = QtGui.QMessageBox.warning(
self.AMDock, 'Warning',
'There are processes in the background. Do you want to close them?',
QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
if msg == QtGui.QMessageBox.No:
return
elif msg == QtGui.QMessageBox.Yes:
try:
self.pymol.force_finished()
except:
pass
if self.AMDock.program_body.reset_function():
Variables.__init__(self.AMDock)
self.prot_label.setText('Target: ')
self.prot_labelB.setText('Off-Target: ')
# try:
# self.AMDock.output2file.conclude()
# except:
# pass
try:
os.chdir(self.AMDock.loc_project)
except:
pass
self.clear_result_tab()
self.AMDock.log_widget.textedit.append(80 * '#')
self.AMDock.log_widget.textedit.append(
Ft('NEW PROJECT...\n\n').resetting())
def amdock_load(self):
elements = {
0: 'Working Directory',
1: 'Input Directory',
2: 'Results Directory',
3: 'PDBQT of Target Protein',
4: 'All Poses File of Target Result',
5: 'Best Pose File of Target Result',
6: 'PDBQT of Off-Target Protein',
7: 'All Poses File of Off-Target Result',
8: 'Best Pose File of Off-Target Result'
}
elements_score = {
0: 'Working Directory',
1: 'Input Directory',
2: 'Results Directory',
3: 'PDBQT of Target Protein',
4: 'PDBQT of Ligand'
}
self.AMDock.statusbar.showMessage(" Loading .amdock file...", 2000)
# if self.
self.data = self.AMDock.loader.load_amdock_file()
if self.data:
if self.AMDock.project.mode == 1:
self.table1 = self.data[0]
self.complete = self.data[1]
self.table2 = self.data[2]
else:
self.table1 = self.data[0]
self.complete = self.data[1]
errlist = ''
errlist2 = []
if self.AMDock.project.mode != 2:
for index in range(0, len(self.complete)):
if self.complete[index] == '1':
errlist += '\n-%s' % elements[index]
if len(errlist) != 0:
QtGui.QMessageBox.critical(
self, 'Error',
'Some files defined in .amdock file were not found or '
'they are inaccessible.\nMissing elements:%s' %
errlist)
self.import_text.clear()
Variables.__init__(self.AMDock)
else:
os.chdir(self.AMDock.project.results)
self.prot_label.setText('Target: %s' %
self.AMDock.target.name)
self.prot_label_sel.setText('%s' % self.AMDock.target.name)
self.result_table.setRowCount(len(self.table1))
self.sele1.setRange(1, len(self.table1))
f = 0
for x in self.table1:
c = 0
for item in x:
item = str(item)
self.result_table.setItem(
f, c, QtGui.QTableWidgetItem(item))
self.result_table.item(
f,
c).setTextAlignment(QtCore.Qt.AlignHCenter
| QtCore.Qt.AlignVCenter)
if c == 4:
item_v = float(item)
if item_v <= -0.3:
self.result_table.item(
f, c).setBackgroundColor(
QtGui.QColor(0, 255, 128, 200))
c += 1
f += 1
self.value1 = float(self.result_table.item(0, 1).text())
self.result_table.item(0, 1).setBackgroundColor(
QtGui.QColor('darkGray'))
selection_model = self.result_table.selectionModel()
selection_model.select(
self.result_table.model().index(0, 0),
QtGui.QItemSelectionModel.ClearAndSelect)
if self.AMDock.project.bsd_mode_target == 0:
self.result_table.setHorizontalHeaderLabels(
QtCore.QString(
"Binding Site;Affinity(kcal/mol);Estimated Ki;Ki Units;Ligand Efficiency"
).split(";"))
else:
self.result_table.setHorizontalHeaderLabels(
QtCore.QString(
"Pose;Affinity(kcal/mol);Estimated Ki;Ki Units;Ligand Efficiency"
).split(";"))
if self.AMDock.project.mode == 1:
self.prot_labelB.setText('Off-Target: %s' %
self.AMDock.offtarget.name)
self.prot_label_selB.setText(
'%s' % self.AMDock.offtarget.name)
self.result_tableB.show()
self.selectivity_value_text.show()
self.selectivity.show()
self.sele1.show()
self.sele2.show()
self.prot_label_sel.show()
self.prot_label_selB.show()
self.div.show()
self.equal.show()
self.prot_labelB.show()
self.result_tableB.setRowCount(len(self.table2))
self.sele2.setRange(1, len(self.table2))
f = 0
for x in self.table2:
c = 0
for item in x:
item = str(item)
self.result_tableB.setItem(
f, c, QtGui.QTableWidgetItem(item))
self.result_tableB.item(f, c).setTextAlignment(
QtCore.Qt.AlignHCenter
| QtCore.Qt.AlignVCenter)
if c == 4:
item_v = float(item)
if item_v <= -0.3:
self.result_tableB.item(
f, c).setBackgroundColor(
QtGui.QColor(0, 255, 128, 200))
c += 1
f += 1
self.value2 = float(
self.result_tableB.item(0, 1).text())
self.result_tableB.item(0, 1).setBackgroundColor(
QtGui.QColor('darkGray'))
selection_model = self.result_tableB.selectionModel()
selection_model.select(
self.result_tableB.model().index(0, 0),
QtGui.QItemSelectionModel.ClearAndSelect)
if self.AMDock.project.bsd_mode_offtarget == 0:
self.result_tableB.setHorizontalHeaderLabels(
QtCore.QString(
"Binding Site;Affinity(kcal/mol);Estimated Ki;Ki Units;Ligand Efficiency"
).split(";"))
else:
self.result_tableB.setHorizontalHeaderLabels(
QtCore.QString(
"Pose;Affinity(kcal/mol);Estimated Ki;Ki Units;Ligand Efficiency"
).split(";"))
self.selectivity_value = math.exp(
(self.value2 - self.value1) / (0.001987207 * 298))
self.selectivity_value_text.setText(
'%.01f' % self.selectivity_value)
else:
for index in range(0, len(self.complete)):
if self.complete[index] == '1':
errlist += '\n-%s' % elements_score[index]
errlist2.append(index)
if len(errlist) != 0:
QtGui.QMessageBox.critical(
self, 'Error',
'Some files defined in .amdock file were not found or '
'they are inaccessible.\nMissing elements:%s' %
errlist)
self.import_text.clear()
Variables.__init__(self.AMDock)
else:
os.chdir(self.AMDock.project.results)
self.prot_label.setText('Target: %s' %
self.AMDock.target.name)
self.result_table.setRowCount(len(self.table1))
self.sele1.setRange(1, len(self.table1))
f = 0
for x in self.table1:
c = 0
for item in x:
item = str(item)
self.result_table.setItem(
f, c, QtGui.QTableWidgetItem(item))
self.result_table.item(
f,
c).setTextAlignment(QtCore.Qt.AlignHCenter
| QtCore.Qt.AlignVCenter)
if c == 4:
item_v = float(item)
if item_v <= -0.3:
self.result_table.item(
f, c).setBackgroundColor(
QtGui.QColor(0, 255, 128, 200))
c += 1
f += 1
self.result_table.item(0, 1).setBackgroundColor(
QtGui.QColor('darkGray'))
selection_model = self.result_table.selectionModel()
selection_model.select(
self.result_table.model().index(0, 0),
QtGui.QItemSelectionModel.ClearAndSelect)
# open log if exit
if os.path.exists(
os.path.join(self.AMDock.project.WDIR,
self.AMDock.project.name + '.log')):
self.AMDock.project.log = os.path.join(
self.AMDock.project.WDIR,
self.AMDock.project.name + '.log')
if not self.AMDock.project.log:
return
if os.path.exists(self.AMDock.project.log):
msg = QtGui.QMessageBox.information(
self.AMDock, 'Information', 'This project has a log file.'
' Do you want to open it?',
QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
if msg == QtGui.QMessageBox.Yes:
self.AMDock.log_widget.textedit.append(
Ft('Opening AMDock Log File...').process())
ofile = open(self.AMDock.project.log)
for line in ofile:
line = line.strip('\n')
self.AMDock.log_widget.textedit.append(line)
ofile.close()
self.AMDock.log_widget.textedit.append(
Ft('Opening AMDock Log File... Done.').process())
def __init__(self):
super(AMDock, self).__init__()
QtGui.QMainWindow.__init__(self)
Variables.__init__(self)
# redirect stderr to log window
sys.stderr = EmittingStream(textWritten=self.normalOutputWritten)
self.checker = Checker(self)
self.output2file = OutputFile(self)
self.loader = Loader(self)
self.project = PROJECT()
self.target = BASE()
self.offtarget = BASE()
self.ligand = BASE()
self.log_thread = QtCore.QThreadPool()
self.numeric_version = [1, 5, 2]
self.version = "{}.{}.{} For Windows and Linux".format(*self.numeric_version)
self.spacing_autoligand = 1.0
self.spacing_autodock = 0.375
self.pH = 7.40
self.para_file = None
self.state = 0 # 0 not running, 2 running
self.section = -1 # -1 only PD selected, 0 project, 1 input files, 2 bsd, 3 docking
with open(self.style_file) as f:
self.setStyleSheet(f.read())
self.icon = QtGui.QIcon()
self.icon.addPixmap(QtGui.QPixmap(self.home_icon), QtGui.QIcon.Active, QtGui.QIcon.Off)
self.icon.addPixmap(QtGui.QPixmap(self.home_icon), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.icon.addPixmap(QtGui.QPixmap(self.home_icon), QtGui.QIcon.Selected, QtGui.QIcon.Off)
self.icon.addPixmap(QtGui.QPixmap(self.home_icon), QtGui.QIcon.Disabled, QtGui.QIcon.Off)
self.icon.addPixmap(QtGui.QPixmap(self.home_icon_white), QtGui.QIcon.Selected, QtGui.QIcon.On)
self.icon.addPixmap(QtGui.QPixmap(self.home_icon_white), QtGui.QIcon.Active, QtGui.QIcon.On)
##--TABS
self.main_window = QtGui.QTabWidget(self)
self.setCentralWidget(self.main_window)
##--Tabs for Docking Options
self.lobby = Lobby(self)
self.main_window.addTab(self.lobby, self.icon, "")
self.program_body = Program_body(self)
self.main_window.addTab(self.program_body, "Docking Options")
self.main_window.setTabEnabled(1, False)
##Tabs for result analysis
self.result_tab = Results(self)
self.main_window.addTab(self.result_tab, "Results Analysis")
self.main_window.setTabEnabled(2, False)
# **Configurations_Tab
self.configuration_tab = Configuration_tab(self)
self.main_window.addTab(self.configuration_tab, "Configuration")
# ** Help_Tab
self.help_tab = Help(self)
self.main_window.addTab(self.help_tab, "Info")
# ** log dockwidget
self.log_widget = LogWindow(self)
self.addDockWidget(QtCore.Qt.RightDockWidgetArea, self.log_widget)
if self.configuration_tab.log_view.isChecked():
self.log_widget.show()
else:
self.log_widget.hide()
self.statusbar = QtGui.QStatusBar(self)
self.statusbar.setObjectName("statusbar")
self.setStatusBar(self.statusbar)
QtCore.QMetaObject.connectSlotsByName(self)
self.version_label = QtGui.QLabel("Version: %s" % self.version)
self.statusbar.addPermanentWidget(self.version_label)
