def buildANM(self):
if self.anmDlg.cutoffCheckbox.isChecked():
anmMethod = 'cutoff'
elif self.anmDlg.pfCheckBox.isChecked():
anmMethod = 'pf'
if self.anmDlg.caCheckBox.isChecked():
useCA = True
else:
useCA = False
cutoff = self.anmDlg.cutoffSpinBox.value()
power = self.anmDlg.pfSpinBox.value()
try:
self.anm = ANM(self.tempModel.model0, cutoff, useCA, anmMethod, power)
self.anm.calcModes()
self.painter.populateAnm(self.anm)
self.plotContrl.msfButton.setEnabled(True)
self.plotContrl.cxButton.setEnabled(True)
self.plotContrl.internalDButton.setEnabled(True)
self.plotContrl.clusterButton.setEnabled(True)
self.pymolControl.springButton.setEnabled(True)
self.pymolControl.springColorButton.setEnabled(True)
self.pymolControl.arrowButton.setEnabled(True)
self.pymolControl.arrowColorButton.setEnabled(True)
self.pymolControl.arrowSizeSlider.setEnabled(True)
self.pymolControl.movieButton.setEnabled(True)
self.pymolControl.movieColorButton.setEnabled(True)
self.pymolControl.movieSizeSlider.setEnabled(True)
self.pymolControl.msfButton.setEnabled(True)
except ValueError or TypeError:
QMessageBox.warning(self, 'ANM Failed',
'Failed to build an ANM',
QMessageBox.Ok, QMessageBox.NoButton)
class mainWindow(QMainWindow):
def __init__(self, parent = None):
super(mainWindow, self).__init__(parent)
self.painter = anmPainter()
self.plotContrl = plotControl()
self.centralSplitter = QSplitter(Qt.Vertical)
self.centralSplitter.addWidget(self.painter)
self.centralSplitter.addWidget(self.plotContrl)
self.setCentralWidget(self.centralSplitter)
self.anmDlg = anmDlg()
self.anmDlg.buildButton.setEnabled(False)
self.strDlg = structureDlg()
self.splitter1 = QSplitter(Qt.Vertical)
self.splitter1.addWidget(self.strDlg)
self.splitter1.addWidget(self.anmDlg)
basicDockWidget = QDockWidget('Structure Panel', self)
basicDockWidget.setObjectName('basicDockWidget')
basicDockWidget.setAllowedAreas(Qt.LeftDockWidgetArea)
basicDockWidget.setWidget(self.splitter1)
self.addDockWidget(Qt.LeftDockWidgetArea, basicDockWidget)
QApplication.setStyle(QStyleFactory.create('Cleanlooks'))
self.pdbViewer = pdbViewer()
viewerDockWidget = QDockWidget('Pdb Viewer', self)
viewerDockWidget.setObjectName('PdbViewer')
viewerDockWidget.setAllowedAreas(Qt.TopDockWidgetArea|
Qt.BottomDockWidgetArea)
viewerDockWidget.setWidget(self.pdbViewer)
self.addDockWidget(Qt.TopDockWidgetArea, viewerDockWidget)
self.setWindowTitle('ENM Visualizer')
self.setCorner(Qt.TopRightCorner, Qt.RightDockWidgetArea)
self.pymolWidget = PyMolWidget()
self.pymolWidget.setMinimumSize(250, 250)
self.pymolControl = pymolControl()
self.pymolSplitter = QSplitter(Qt.Vertical)
self.pymolSplitter.addWidget(self.pymolWidget)
self.pymolSplitter.addWidget(self.pymolControl)
pymolDockWidget = QDockWidget('PyMol', self)
pymolDockWidget.setObjectName('Pymol')
pymolDockWidget.setAllowedAreas(Qt.RightDockWidgetArea)
pymolDockWidget.setWidget(self.pymolSplitter)
self.addDockWidget(Qt.RightDockWidgetArea, pymolDockWidget)
self.statusBar = self.statusBar()
self.statusBar.showMessage('Ready')
self.setWindowIcon(QIcon('/image/AppIcon.png'))
self.connect(self.strDlg.submitButton, SIGNAL('clicked()'),
self.submitStructure)
self.connect(self.anmDlg.buildButton, SIGNAL('clicked()'),
self.buildANM)
self.connect(self.pdbViewer, SIGNAL('itemSelectionChanged()'),
self.selectInPymol)
self.connect(self.plotContrl.msfButton, SIGNAL('clicked()'),
self.painter.plotFreqAndMSF)
self.connect(self.plotContrl.cxButton, SIGNAL('clicked()'),
self.painter.plotCX)
self.connect(self.plotContrl.internalDButton, SIGNAL('clicked()'),
self.painter.plotInternalD)
self.connect(self.plotContrl.clusterButton, SIGNAL('clicked()'),
self.painter.plotCluster)
self.connect(self.pymolControl.cmdLineEdit, SIGNAL('returnPressed()'),
self.passCmdToPymol)
self.connect(self.pymolControl.cmdLineEdit, SIGNAL('upPressed()'),
self.previousCmd)
self.connect(self.pymolControl.cmdLineEdit, SIGNAL('downPressed()'),
self.nextCmd)
self.connect(self.pymolControl.cmdSubmitButton, SIGNAL('clicked()'),
self.passCmdToPymol)
self.connect(self.pymolControl.springButton, SIGNAL('clicked()'),
self.buildSprings)
self.connect(self.pymolControl.springColorButton, SIGNAL('clicked()'),
self.changeSpringColor)
self.connect(self.pymolControl.msfButton, SIGNAL('clicked()'),
self.colorByMSF)
self.connect(self.pymolControl.arrowButton, SIGNAL('clicked()'),
self.drawArrows)
self.connect(self.pymolControl.arrowSizeSlider, SIGNAL('valueChanged(int)'),
self.drawArrows)
self.connect(self.pymolControl.arrowColorButton, SIGNAL('clicked()'),
self.changeArrowColor)
self.connect(self.pymolControl.movieButton, SIGNAL('clicked()'),
self.makeMovie)
self.strDlg.structureLineEdit.setFocus()
self.cmdHistory = []
self.cmdPointer = -1
self.arrowColor = None
@waitingEffects
def submitStructure(self):
fileName = str(self.strDlg.structureLineEdit.text())
try:
self.tempModel = pdbParser(fileName)
self.pdbViewer.populateTable(self.tempModel.model0)
tempModel = self.tempModel.toCA().writePDB('tempp.pdb')
if self.tempModel._getMethod == 'local':
self.pymolWidget.loadMolFile(fileName)
elif self.tempModel._getMethod == 'online':
self.pymolWidget.loadMolFile('temp.pdb')
self.anmDlg.buildButton.setEnabled(True)
self.pymolWidget.setFocus()
except ValueError:
QMessageBox.warning(self, 'Initialization Failed',
'Failed to read %s' % fileName,
QMessageBox.Ok, QMessageBox.NoButton)
self.strDlg.structureLineEdit.setFocus()
self.strDlg.structureLineEdit.selectAll()
@waitingEffects
def buildANM(self):
if self.anmDlg.cutoffCheckbox.isChecked():
anmMethod = 'cutoff'
elif self.anmDlg.pfCheckBox.isChecked():
anmMethod = 'pf'
if self.anmDlg.caCheckBox.isChecked():
useCA = True
else:
useCA = False
cutoff = self.anmDlg.cutoffSpinBox.value()
power = self.anmDlg.pfSpinBox.value()
try:
self.anm = ANM(self.tempModel.model0, cutoff, useCA, anmMethod, power)
self.anm.calcModes()
self.painter.populateAnm(self.anm)
self.plotContrl.msfButton.setEnabled(True)
self.plotContrl.cxButton.setEnabled(True)
self.plotContrl.internalDButton.setEnabled(True)
self.plotContrl.clusterButton.setEnabled(True)
self.pymolControl.springButton.setEnabled(True)
self.pymolControl.springColorButton.setEnabled(True)
self.pymolControl.arrowButton.setEnabled(True)
self.pymolControl.arrowColorButton.setEnabled(True)
self.pymolControl.arrowSizeSlider.setEnabled(True)
self.pymolControl.movieButton.setEnabled(True)
self.pymolControl.movieColorButton.setEnabled(True)
self.pymolControl.movieSizeSlider.setEnabled(True)
self.pymolControl.msfButton.setEnabled(True)
except ValueError or TypeError:
QMessageBox.warning(self, 'ANM Failed',
'Failed to build an ANM',
QMessageBox.Ok, QMessageBox.NoButton)
def passCmdToPymol(self):
cmd = str(self.pymolControl.cmdLineEdit.text())
self.cmdHistory.append(cmd)
self.cmdPointer = -1
self.pymolWidget._pymol.cmd.do(cmd)
self.pymolControl.cmdLineEdit.clear()
self.pymolWidget.setFocus()
self.pymolControl.cmdLineEdit.setFocus()
def previousCmd(self):
try:
self.pymolControl.cmdLineEdit.setText(self.cmdHistory[self.cmdPointer])
self.cmdPointer -= 1
except IndexError:
pass
def nextCmd(self):
if self.cmdPointer == -1:
self.pymolControl.cmdLineEdit.clear()
else:
self.cmdPointer += 1
self.pymolControl.cmdLineEdit.setText(self.cmdHistory[self.cmdPointer])
def buildSprings(self):
springFileName = 'springs_temp.pdb'
objName = 'springs_temp'
objList = self.pymolWidget._pymol.cmd.get_names()
if objName in objList:
self.pymolWidget._pymol.cmd.delete(objName)
tempCAModel = self.tempModel.toCA()
tempCAModel.writePDB(springFileName)
springFile = open(springFileName, 'a')
for i in xrange(len(self.anm.contactPair_x)):
springFile.write('CONECT %4d %4d\n' %
(tempCAModel.getModel().atom_number[self.anm.contactPair_x[i]],
tempCAModel.getModel().atom_number[self.anm.contactPair_y[i]]))
springFile.close()
self.pymolWidget._pymol.cmd.hide('everything')
self.pymolWidget._pymol.cmd.load(springFileName)
self.pymolWidget.setFocus()
self.pymolControl.springColorButton.setFocus()
os.remove(springFileName)
def changeSpringColor(self):
color = QColorDialog.getColor(Qt.blue)
if color.isValid():
rgb = color.getRgbF()
self.pymolWidget._pymol.cmd.set_color('tempColor',
[rgb[0], rgb[1], rgb[2]])
self.pymolWidget._pymol.cmd.color('tempColor', 'springs_temp')
def changeArrowColor(self):
color = QColorDialog.getColor(Qt.white)
if color.isValid():
rgb = color.getRgbF()
self.arrowColor = [rgb[0], rgb[1], rgb[2]]
self.drawArrows()
def colorByMSF(self):
msf = self.anm.getMSF().tolist()[0]
msfFileName = 'msf_temp.pdb'
objName = 'msf_temp'
objList = self.pymolWidget._pymol.cmd.get_names()
if objName in objList:
self.pymolWidget._pymol.cmd.delete(objName)
tempCAModel = self.tempModel.toCA()
tempCAModel.model0.b_factor = msf
tempCAModel.writePDB(msfFileName)
self.pymolWidget._pymol.cmd.hide('everything')
self.pymolWidget._pymol.cmd.load(msfFileName)
self.pymolWidget._pymol.cmd.set('cartoon_trace', 1)
self.pymolWidget._pymol.cmd.show('cartoon', objName)
self.pymolWidget._pymol.cmd.spectrum('b', 'cyan_yellow', objName)
self.pymolWidget.setFocus()
self.pymolControl.msfButton.setFocus(True)
def drawArrows(self):
if self.arrowColor is None:
self.arrowColor = [1, 1, 1]
objName = 'arrows'
objList = self.pymolWidget._pymol.cmd.get_names()
if objName in objList:
self.pymolWidget._pymol.cmd.delete(objName)
arrowSize = self.pymolControl.arrowSizeSlider.value()
mode = int(self.pymolControl.arrowModeLineEdit.text())
self.anm.arrowGenerator(mode = mode, color = self.arrowColor, size = arrowSize)
self.pymolWidget._pymol.cmd.hide('everything')
self.pymolWidget._pymol.cmd.set('cartoon_trace', 1)
self.pymolWidget._pymol.cmd.load('tempp.pdb')
self.pymolWidget._pymol.cmd.do('as cartoon, tempp')
self.pymolWidget._pymol.cmd.load_cgo(self.anm.arrows, objName)
self.pymolWidget.setFocus()
self.pymolControl.arrowButton.setFocus(True)
def makeMovie(self):
objName = 'movie'
objList = self.pymolWidget._pymol.cmd.get_names()
if objName in objList:
self.pymolWidget._pymol.cmd.delete(objName)
movieSize = self.pymolControl.movieSizeSlider.value()
mode = int(self.pymolControl.movieModeLineEdit.text())
self.anm.modeAnimator(modes = [mode], scaler = movieSize)
self.pymolWidget._pymol.cmd.hide('everything')
self.pymolWidget._pymol.cmd.load('movie.pdb')
self.pymolWidget.setFocus()
self.pymolWidget.playMovie()
#self.pymolControl.movieButton.setFocus()
def selectInPymol(self):
rowsToSelect = []
allSelectedIndexes = self.pdbViewer.selectedIndexes()
if len(allSelectedIndexes) == 0:
return
for item in allSelectedIndexes:
if item.row() not in rowsToSelect:
rowsToSelect.append(item.row())
if len(rowsToSelect) == 1:
self.pymolWidget._pymol.cmd.do('select aa, resi %d and chain a' %int(rowsToSelect[0]))
self.pymolWidget._pymolProcess()
self.ax4.set_xlim([0, len(self.anm.getInternalDis())])
self.ax4.set_ylim([0, len(self.anm.getInternalDis())])
self.ax4.set_title('Internal Distance Matrix')
self.ax4.pcolor(self.anm.getInternalDis(), cmap = plt.cm.Blues)
self.canvas.draw()
def plotCluster(self):
if self.anm is None:
return
self.figure.clf()
self.ax5 = self.figure.add_subplot(111)
self.ax5.imshow('cluster.png')
self.canvas.draw()
if __name__ == '__main__':
import sys
from PdbParser import *
app = QApplication(sys.argv)
gln = pdbParser('1t3r.pdb')
anm = ANM(gln)
anm.calcModes()
main = anmPainter()
main.show()
sys.exit(app.exec_())