Constructed Molecule JSONizer

class ConstructedMoleculeJsonizer(key_makers=(InchiKey(),))

Bases: object

Abstract base class for creating JSONs of constructed molecules.

See also

MoleculeJsonizer

Notes

You might notice that the public methods of this abstract base class are implemented. These are just default implementations, which can be safely ignored or overridden, when implementing subclasses. However, the default implementation can be used directly, if it suits your needs.

Examples

Converting a Constructed Molecule to JSON

You want get a JSON representation of a ConstructedMolecule

import stk

# Make the molecule you want jsonize.
polymer = stk.ConstructedMolecule(
    topology_graph=stk.polymer.Linear(
        building_blocks=(
            stk.BuildingBlock('BrCCBr', [stk.BromoFactory()]),
        ),
        repeating_unit='A',
        num_repeating_units=3,
    )
)

# Make a JSONizer.
jsonizer = stk.ConstructedMoleculeJsonizer()
# Get the JSON.
json = jsonizer.to_json(polymer)

Adding Additional Molecular Keys

Apart from atoms, bonds and the position matrix, the JSON representation holds additional fields, one for each MoleculeKeyMaker provided to the initializer

import stk

# Make the molecule you want jsonize.
polymer = stk.ConstructedMolecule(
    topology_graph=stk.polymer.Linear(
        building_blocks=(
            stk.BuildingBlock('BrCCBr', [stk.BromoFactory()]),
        ),
        repeating_unit='A',
        num_repeating_units=3,
    )
)

# Make a JSONizer.
jsonizer = stk.ConstructedMoleculeJsonizer()
# Get the JSON.
json = jsonizer.to_json(polymer)

In this case, json will look something like

{
    # A tuple of JSON atom representations.
    'atoms': (...),

    # A tuple of JSON bond representations.
    'bonds': (...),

    'InChI': 'The InChI of the molecule',
    'InChIKey': 'The InChIKey of the molecule',
}

For every MoleculeKeyMaker provided to key_makers, a new key will be added to the JSON representation, with its name given by MoleculeKeyMaker.get_key_name() and the value given by MoleculeKeyMaker.get_key().

Methods

to_json(molecule)

Serialize molecule.

__init__(key_makers=(InchiKey(),))

Initializes a ConstructedMoleculeJsonizer.

Parameters

key_makers (tuple of MoleculeKeyMaker) – Used to make the keys of molecules, which should be included in their JSON representations. Keys allow molecular data to reference itself when split across multiple JSONs.

to_json(molecule)

Serialize molecule.

Parameters

molecule (ConstructedMolecule) – The constructed molecule to serialize.

Returns

A JSON representation of molecule.

Return type

dict