Examples

Creating Random Molecular Graphs

One of the simplest things you can do with vabene, is generate random molecular graphs, which obey your chosen valence restrictions. First, let’s introduce the Atom. It has 3 parameters, the atomic number, the formal charge and the maximum valence it is allowed to have.

import vabene as vb

# Create an uncharged carbon atom, which can have a valence of
# up to 4.
atom = vb.Atom(6, 0 , 4)

With that out of the way, we can use the RandomAtomFactory to generate a random set of atoms, given we provide it with a tuple of atoms we want it to select from

atom_factory = vb.RandomAtomFactory(
    # The atoms, which are randomly picked for use in our molecular
    # graph. Each atom can be picked multiple times.
    atoms=(vb.Atom(6, 0, 4), vb.Atom(7, 0, 3)),
    # The total number of atoms the factory will produce.
    num_atoms=10,
)
# The atoms our molecular graph will use.
atoms = tuple(atom_factory.get_atoms())

Now that we have a random set of atoms for use in our molecular graph, we need to pair them with a random set of bonds. To get a random set of bonds, we use the RandomBondFactory

bond_factory = vb.RandomBondFactory()
bonds = bond_factory.get_bonds(atoms)

Now that we have our atoms and bonds, we can make a Molecule

molecule = vb.Molecule(atoms, bonds)

Done. You made a molecule that looks something like this

Yours will be different, because we didn’t set a random seed. However, you can use the random_seed parameter on the factories to get reproducible results.

Forcing Atoms to be Present in Random Molecular Graphs

Sometimes, we want to have a random molecular graph, subject to the constraint that it is guaranteed to include a specific atom, or group of atoms. The required_atoms parameter of the RandomAtomFactory allows us to do this.

import vabene as vb

atom_factory = vb.RandomAtomFactory(
    atoms=(vb.Atom(6, 0, 4), vb.Atom(7, 0, 3)),
    # The factory is guaranteed to produce these atoms every time
    # get_atoms() is called. These atoms will not be included in
    # the random selection, unless they were provided to the
    # "atoms" parameter too.
    required_atoms=(vb.Atom(35, 0, 1), vb.Atom(35, 0, 1)),
    num_atoms=10,
)
# A random set of carbon and nitrogen atoms, together with 2
# bromine atoms.
atoms = tuple(atom_factory.get_atoms())

Forcing Bonds to be Present in Random Molecular Graphs

Sometimes, we want to have a random molecular graph, but we want to force it to have a certain substructure. For example, let’s assume that we want to make a random molecule graph, but we want to guarantee that it has a BrCCCBr substructure.

First, lets create a RandomAtomFactory, which is forced to yield these atoms

import vabene as vb

atom_factory = vb.RandomAtomFactory(
    atoms=(vb.Atom(6, 0, 4), vb.Atom(7, 0, 3)),
    required_atoms=(
        vb.Atom(35, 0, 1),
        vb.Atom(6, 0, 4),
        vb.Atom(6, 0, 4),
        vb.Atom(6, 0, 4),
        vb.Atom(35, 0, 1),
    ),
    num_atoms=10,
)
atoms = tuple(atom_factory.get_atoms())

Next, lets create a RandomBondFactory, which force to yield the necessary bond, as well as other, random, bonds

bond_factory = vb.RandomBondFactory(
    # We know what atom ids to use for the bonds, because
    # RandomAtomFactory will yield that required_atoms first, in
    # the order that we provided them.
    required_bonds=(
        vb.Bond(0, 1, 1),
        vb.Bond(1, 2, 1),
        vb.Bond(2, 3, 1),
        vb.Bond(3, 4, 1),
    ),
)
bonds = bond_factory.get_bonds(atoms)

Finally, we can make a random Molecule, which is guaranteed to have the BrCCCBr substructure

molecule = vb.Molecule(atoms, bonds)

Here is the one I got: