Displaying molecular orbitals with chemlab and chemview

In [1]:

    

from chemview import enable_notebook, MolecularViewer
enable_notebook()


    

In [7]:

    

from chemlab.io import remotefile
# pull the file
df = remotefile('https://raw.githubusercontent.com/cclib/cclib/master/data/GAMESS/basicGAMESS-US2012/water_mp2.out', 'gamess')

mo_coefficients = df.read('mocoeffs')
gbasis = df.read('gbasis')
molecule = df.read('molecule')
molecule.guess_bonds()


    

In [14]:

    

from chemlab.qc import molecular_orbital

f = molecular_orbital(molecule.r_array, mo_coefficients[0][-1], gbasis)

mv = MolecularViewer(molecule.r_array, {'atom_types': molecule.type_array,
                                        'bonds': molecule.bonds})
mv.wireframe()
mv.add_isosurface(f, isolevel=0.3, color=0xff0000)
mv.add_isosurface(f, isolevel=-0.3, color=0x0000ff)

mv


    

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