Plug cclib into Avogadro

cclib is an open source Python library for parsing and analysing computational chemistry log files.

Avogadro is a cross-platform molecular visualiser with a lot of functionality geared towards setting up and analysing computational chemistry calculations. It is an open source project led by Marcus Hanwell and is built on top of OpenBabel.

Although Avogadro has increasing support for parsing comp chem log files from a variety of packages, there may be times when it chokes on a file. If this happens, it's nice to have a backup option. This is where cclib can come in handy.

If you're on Windows, have Avogadro 1.0.0, cclib 1.0, OpenBabel 2.2.3 and its Python bindings (these latter shouldn't be necessary in a future version of Avogadro), just copy the following code into a .py file and save it in C:\Program Files\Avogadro\bin\extensionScripts.

When you next start Avogadro, it will have an "Open with cclib" Option in the Scripts menu.

from PyQt4.QtCore import *
from PyQt4.QtGui import *

import sys
sys.path.append("C:\\Python26\\Lib\\site-packages")
sys.path.append("C:\\Python26\\lib")

import cclib

import numpy
import Avogadro as avo
import openbabel as ob

class Extension(QObject):
  def __init__(self):
    QObject.__init__(self)

  def name(self):                            # Recommended
    return "Open with cclib"

  def description(self):                     # Recommended
    return "Open comp chem files with cclib"

  def actions(self):                         # Required
    actions = []

    # Actions are just instances of the QAction class from PyQt4
    action = QAction(self)
    action.setText("Open with cclib")
    actions.append(action)

    return actions

  def performAction(self, action, glwidget): # Required
    # Only one action so need to check its identity

    filename = str(QFileDialog.getOpenFileName())
    if not filename: # You hit cancel
      return None
   
    logfile = cclib.parser.ccopen(filename)
    data = logfile.parse()

    obmol = ob.OBMol()
    avomol = avo.molecules.addMolecule()
    avoatoms = []
    for atomcoord, atomno in zip(data.atomcoords[-1], data.atomnos):
        coord = atomcoord.tolist()
        obatom = ob.OBAtom()
        obatom.SetAtomicNum(int(atomno))
        obatom.SetVector(*coord)
        obmol.AddAtom(obatom)
       
        newatom = avomol.addAtom()
        newatom.atomicNumber = int(atomno)
        newatom.pos = atomcoord
        avoatoms.append(newatom)   

    obmol.ConnectTheDots()
    obmol.PerceiveBondOrders()
    obmol.SetTotalSpinMultiplicity(data.mult)
    obmol.SetTotalCharge(data.charge)

    for bond in ob.OBMolBondIter(obmol):
        newbond = avomol.addBond()
        newbond.setBegin(avomol.atom(bond.GetBeginAtomIdx() - 1))
        newbond.setEnd(avomol.atom(bond.GetEndAtomIdx() - 1))
        newbond.order = bond.GetBO()
       
    avo.GLWidget.current().molecule = avomol

    return None

Notes:

• There should be no need to have the OpenBabel Python bindings installed separately, but there is no way to access the OpenBabel library in Avogadro (at least on Windows). This prevents me, for example, from calling ConnectTheDots (I had to use my own installation of OpenBabel) or to add Conformers (which was what I wanted to do).
• There are two Script menus after installing this plugin!
• How do I emit a debug message?
• The Python prompt in Avogadro requires you to "print" everything to see its value. This should not be necessary.
• Cutting and pasting multiple lines into the Python prompt works fine, but it looks pretty weird as the prompt (>>>) is missing.