🧬 Graph

In this section, we will describe how to create a molecule graph using a predefined molecule source. The molecule source defines the main chain and any additional chains that are part of the molecule.

Molecule Source 🧪

The molecule source is defined as a dictionary where each key represents a chain, and the value is a list of strings representing the connections between atoms in that chain.

# molecule source
molecule_src = {
    'MainChain': ["C1-C2", "C2-C3", "C3*{Chain1}", "C3-C4", "C4*{Chain2}", "C4-C5", "C5-C6"],
    'Chain1': ["C1=C2", "C2-C3", "C3=*"],
    'Chain2': ["*-C1", "C1=C2", "C2-XX3"]
}

# NOTE: create a molecule
mol_ = mi.generate_molecule(molecule_src, molecule_name='my_molecule')
# construct molecule
constructed_molecule = mol_.constructed_molecules
print(constructed_molecule)
# main chain
chain_info = mol_.chain_info
print(chain_info)
# molecule info
molecule = mol_.molecule
print(molecule)

# NOTE: create a molecule graph (nx.Graph)
graph = mol_.to_graph()
print(graph)

# NOTE: create a molgraph (MolGraph)
mol_graph = mol_.to_molgraph()
# display molecule graph
mol_graph.d()

molecule_src = {
    'MainChain': ["C1-C2", "C2=C3", "C3-C4", "C3*{Chain1}", "C4=C5", "C5*{Chain1}", "C5-C6", "C6=C1", "C6*{Chain2}"],
    'Chain1': ["C1=C2", "C2-C3", "C3=*"],
    'Chain2': ["*-C1", "C1=C2", "C2-XX3"]
}

molecule_src = {
    'MainChain': ["C1*{Chain1}", "C1-C2", "C2*{Chain2}"],
    'Chain1': ["*-C1", "C1=C2", "C2-C3", "C3=*"],
    'Chain2': ["*-C1", "C1=C2", "C2-C3", "C3=*"],
}

molecule_src = {
    'MainChain': ["C1*{Chain1}", "C1-C2", "C2*{Chain2}", "C2-C3", "C3*{Chain3}"],
    'Chain1': ["*-C1", "C1=C2", "C2-C3", "C3=*"],
    'Chain2': ["*-C1", "C1=C2", "C2-C3", "C3=*"],
    'Chain3': ["*-C1", "C1=C2", "C2-C3"],
}

# naphthalene
molecule_src = {
    'MainChain': ["C1-C2", "C2=C3", "C3-C4", "C4=C5", "C5-C6", "C6=C1", "C1*{Chain1}", "C6*{Chain1}"],
    'Chain1': ["*-C1", "C1=C2", "C2-C3", "C3=C4", "C4-**"],
}