Molecule

Molecule#

There are several different ways to create molecule objects such as using SMILES strings, xyz-strings, molecule strings, or xyz-files.

By default, coordinates are given in units of Ångström but atomic units is also available.

Python script

aspirin = vlx.Molecule.read_smiles("CC(=O)OC1=CC=CC=C1C(=O)O")

xyz_str = """
3
water
O    0.0000000    0.0000000   -0.1653507
H    0.7493682    0.0000000    0.4424329
H   -0.7493682    0.0000000    0.4424329
"""

h2o = vlx.Molecule.read_xyz_string(xyz_str)

mol_str = """
C    0.0  0.0  0.0
O    0.0  0.0  1.128
"""

co = vlx.Molecule.read_molecule_string(mol_str)

tq = vlx.Molecule.read_xyz_file("../input_files/tq-polymer.xyz")

3D illustrations of molecular structures are available with the show method.

aspirin.show(atom_indices=True, atom_labels=True)

tq.show()

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Conformation of the molecule can be altered using the set_dihedral_in_degrees function as explained in the next cell.

h2o2 = vlx.Molecule.read_smiles("OO")
h2o2.set_dihedral_in_degrees([3, 1, 2, 4], 180.0)

h2o2.show(atom_indices=True)

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The molecular charge and spin multiplicity can be adjusted using the set_charge and set_multiplicity functions. In the example below, we create a molecule object for the phenyl radical cation.

phenyl = vlx.Molecule.read_smiles("c1ccccc1")
phenyl.set_charge(1)
phenyl.set_multiplicity(2)

Text file

Using a input text file, a molecule specification is exemplified below.

A detailed list of keywords is available.

@molecule
charge: 0
multiplicity: 1
xyz:
O    0.0000000    0.0000000   -0.1653507
H    0.7493682    0.0000000    0.4424329
H   -0.7493682    0.0000000    0.4424329                     
@end

@molecule
charge: 0
multiplicity: 1
xyz_file: "../input_files/tq-polymer.xyz"