Hello,
I have been writing a python extension to add ORCA support to Avogadro. The
extension so far consists of a input generator, which works nicely, and an
output-file reader, which I can't seem to get to work satisfactorily.
The dialog for the output reader is working nicely, but I have become a bit
stuck when it comes to making the extracted molecular geometries visible in the
GLWidget.
Initially my approach was to extract the coordinates into lists, where the
first item was a string that acted as a "title" for that set of coordinates
(for example, "OPT CYCLE 5" or "SINGLE POINT"), followed by a list for every
atom, consisting of its atomicNumber as an int and x, y, z coordinates as
floats.
This was then translated into Avogadro with the function below:
@pyqtSignature("")
def renderCartesians(self):
molecule = Avogadro.molecules.addMolecule()
atom_index = 0
for info in self.cartesians[-1][1:]:
molecule.addAtom()
molecule.atom(atom_index).atomicNumber = info[0]
molecule.atom(atom_index).pos = numpy.array(info[1:])
atom_index += 1
self.glwidget.molecule = molecule
This seemed to work, except that the molecule only consists of atoms (no
bonds), and does not seem to be recognised by any of avogadro's other
extensions or plugins.
To avoid using the openbabel python bindings, my solution to the bond problem
was to extract the coordinates and format them as a string in the .xyz format;
then create a temporary .xyz file, write the coordinates to the file and read
them back into Avogadro using MoleculeFile.readMolecule():
@pyqtSignature("")
def renderCartesians(self):
tempxyz = tempfile.NamedTemporaryFile(suffix=".xyz")
tempxyz.write(self.cartesians_xyz[-1])
tempxyz.seek(0)
molecule = Avogadro.MoleculeFile.readMolecule(tempxyz.name)
tempxyz.close()
self.glwidget.molecule = molecule
This procedure seemed to work when I tried it in the avogadro python terminal
(although the molecule is still not recognised by the other plugins) but when
implemented, as shown above, through my Extension script, Avogadro just crashes
when the line "self.glwidget.molecule = molecule" is executed.
I feel like I should be using setMolecule(), but I am not sure how to use it.
I have also been reading about "Avogadro::Extension::moleculeChanged", but this
does not seem to be included in the python Extension class.
Does anyone have any tips on how to render a molecule object and have it
recognised by the other avogadro plugins (Such as View>Properties>Molecular
properties..)? I am using Avogadro 1.1.0 on Mac OS X 10.8.
thanks,
Nick
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