Serialization

class scine_molassembler.JsonSerialization

Class representing a compact JSON serialization of a molecule

>>> # Demonstrate a serialize-deserialize loop
>>> spiro = io.experimental.from_smiles("C12(CCCC1)CCC2")
>>> serializer = JsonSerialization(spiro)
>>> bson_format = JsonSerialization.BinaryFormat.BSON
>>> spiro_as_bson = serializer.to_binary(bson_format)
>>> bson_in_b64 = serializer.base_64_encode(spiro_as_bson)
>>> reverted_bson = JsonSerialization.base_64_decode(bson_in_b64)
>>> serializer = JsonSerialization(reverted_bson, bson_format)
>>> reverted = serializer.to_molecule()
>>> reverted == spiro # Compare the deserialized molecule
True

class BinaryFormat

Specifies the type of JSON binary format

Members:

CBOR : Compact Binary Object Representation

BSON : Binary JSON

MsgPack : MsgPack

UBJSON : Universal Binary JSON

BSON = <BinaryFormat.BSON: 1>

CBOR = <BinaryFormat.CBOR: 0>

MsgPack = <BinaryFormat.MsgPack: 2>

UBJSON = <BinaryFormat.UBJSON: 3>

__init__(self: scine_molassembler.JsonSerialization.BinaryFormat, value: int) → None

property name

property value

__init__(*args, **kwargs)

Overloaded function.

__init__(self: scine_molassembler.JsonSerialization, json_string: str) -> None

Parse a JSON molecule serialization

__init__(self: scine_molassembler.JsonSerialization, molecule: scine_molassembler.Molecule) -> None

Serialize a molecule into JSON

__init__(self: scine_molassembler.JsonSerialization, bytes: bytes, binary_format: scine_molassembler.JsonSerialization.BinaryFormat) -> None

Parse a binary JSON molecule serialization

static base_64_decode(base_64_string: str) → bytes: Decode base-64 string into binary

static base_64_encode(binary: bytes) → str: Encode binary format as base-64 string

static equal_decision_lists(string_a: str, string_b: str) → bool: Compare the decision lists given as strings. For each of the decision list elements,the symmetry number has to be identical and the angle has to be within the intervalof the corresponding other decision list entry.

static equal_molecules(string_a: str, string_b: str, binary_format: scine_molassembler.JsonSerialization.BinaryFormat = <BinaryFormat.CBOR: 0>) → bool: Compare the molecules given by the string representation.

standardize(self: scine_molassembler.JsonSerialization) → scine_molassembler.JsonSerialization: Standardize the internal JSON serialization (only for canonical molecules)

to_binary(self: scine_molassembler.JsonSerialization, binary_format: scine_molassembler.JsonSerialization.BinaryFormat) → bytes: Serialize a molecule into a binary format

to_molecule(self: scine_molassembler.JsonSerialization) → scine_molassembler.Molecule: Construct a molecule from the serialization

to_string(self: scine_molassembler.JsonSerialization) → str: Dump the JSON serialization into a string