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Using Avogadro from Python
# Developed by Tim Vandermeersch, with a blog post at
# http://timvdm.blogspot.com/2009/05/using-avogadro-library-from-python.html
#
#import openbabel
# needed for OB formats on linux (can be omitted by importing openbabel first)
import sys
if sys.platform.find('linux') != -1:
try:
import dl
except ImportError:
import DLFCN as dl
sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import uic
import Avogadro
import sys
class MainWindow(QMainWindow):
def __init__(self):
QMainWindow.__init__(self)
uiFile = file('mainwindow.ui', 'r')
self.ui = uic.loadUi(uiFile, self)
self.connect(self.ui.actionOpen, SIGNAL('triggered()'), self, SLOT('open()'))
self.connect(self.ui.listWidget, SIGNAL('currentRowChanged(int)'), self, SLOT('load(int)'))
self.objects = []
def newGLWidget(self):
glWidget = Avogadro.GLWidget()
glWidget.loadDefaultEngines()
glWidget.quality = 4
toolGroup = Avogadro.ToolGroup()
tool = Avogadro.PluginManager.instance.tool('Navigate', None)
if tool:
toolGroup.append(tool)
self.objects.append(tool)
glWidget.toolGroup = toolGroup
self.objects.append(glWidget)
self.objects.append(toolGroup)
return glWidget
@pyqtSignature('load(int)')
def load(self, row):
mol = self.molFile.molecule(row)
self.objects.append(mol)
glWidget = self.newGLWidget()
glWidget.molecule = mol
mdiWindow = self.ui.mdiArea.addSubWindow(Avogadro.toPyQt(glWidget))
print glWidget
print Avogadro.toPyQt(glWidget)
mdiWindow.setWindowTitle(self.molFile.titles[row])
mdiWindow.show()
@pyqtSignature('readThreadFinnished()')
def readThreadFinnished(self):
self.ui.listWidget.clear()
self.ui.listWidget.addItems(self.molFile.titles)
self.ui.statusbar.showMessage('Done.', 5)
@pyqtSignature('open()')
def open(self):
filename = str(QFileDialog.getOpenFileName(self, 'Open', QDir.currentPath(),
'Chemistry files (*.cml *.sdf *.mol *.xyz)'))
self.molFile = Avogadro.MoleculeFile.readFile(filename, '', '', False)
self.connect(Avogadro.toPyQt(self.molFile), SIGNAL('ready()'), self, SLOT('readThreadFinnished()'))
self.ui.statusbar.showMessage('Reading file...')
if __name__ == "__main__":
app = QApplication(sys.argv)
window = MainWindow()
window.show()
sys.exit(app.exec_())
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>MainWindow</class>
<widget class="QMainWindow" name="MainWindow">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>681</width>
<height>494</height>
</rect>
</property>
<property name="windowTitle">
<string>MainWindow</string>
</property>
<widget class="QWidget" name="centralwidget">
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
<widget class="QListWidget" name="listWidget">
<property name="minimumSize">
<size>
<width>150</width>
<height>0</height>
</size>
</property>
</widget>
</item>
<item>
<widget class="QMdiArea" name="mdiArea"/>
</item>
</layout>
</widget>
<widget class="QMenuBar" name="menubar">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>681</width>
<height>28</height>
</rect>
</property>
<widget class="QMenu" name="menu_File">
<property name="title">
<string>&amp;File</string>
</property>
<addaction name="actionOpen"/>
</widget>
<addaction name="menu_File"/>
</widget>
<widget class="QStatusBar" name="statusbar"/>
<action name="actionNew">
<property name="text">
<string>New</string>
</property>
</action>
<action name="actionOpen">
<property name="text">
<string>Open</string>
</property>
</action>
</widget>
<resources/>
<connections/>
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