Class representing a compact JSON serialization of a molecule. More...

#include <Serialization.h>

Public Types
Public types
enum	BinaryFormat { CBOR, BSON, MsgPack, UBJSON }
	Binary formats that JSON can be encoded into and decoded from.

using	BinaryType = std::vector< std::uint8_t >
	Type used to represent binary JSON formats.

Public Member Functions
Special member functions
	JsonSerialization (JsonSerialization &&other) noexcept

JsonSerialization &	operator= (JsonSerialization &&other) noexcept

	JsonSerialization (const JsonSerialization &other)

JsonSerialization &	operator= (const JsonSerialization &other)

	~JsonSerialization ()

Constructors
	JsonSerialization ()=delete
	Construct a serialization from a JSON string.

	JsonSerialization (const std::string &jsonString)
	Construct a serialization from a JSON string.

	JsonSerialization (const Molecule &molecule)
	Construct a serialization from a Molecule.

	JsonSerialization (const BinaryType &binary, BinaryFormat format)
	Construct a serialization from a binary JSON format.

Conversions
	operator std::string () const
	Dump the unprettified JSON notation as a string.

	operator Molecule () const
	Deserialize the JSON serialization into a Molecule.

BinaryType	toBinary (BinaryFormat format) const
	Serialize the JSON serialization into a binary JSON format.

Modification
JsonSerialization &	standardize ()
	Eliminate all notational freedom of the JSON serialization. More...

Static Public Member Functions
Static members
static std::string	base64Encode (const BinaryType &binary)
	Compare two molecules/complexes encoded as base64 strings. The molecule order is irrelevant. More...

static BinaryType	base64Decode (const std::string &base64String)
	Compare two molecules/complexes encoded as base64 strings. The molecule order is irrelevant. More...

static bool	base64EqualMolecules (const std::string &stringA, const std::string &stringB, BinaryFormat binaryFormat=BinaryFormat::CBOR)
	Compare two molecules/complexes encoded as base64 strings. The molecule order is irrelevant. More...

static bool	equalDecisionLists (const std::string &listStringA, const std::string &listStringB)
	Compare two decision lists encoded as strings. More...

Static Private Member Functions
static std::vector< std::tuple < int, int, int, int > >	unpackDecisionListString (const std::string &listString)

static std::tuple< int, int, int, int >	canonicalizeDecisionListElement (const std::tuple< int, int, int, int > &decisionListElement)

static bool	equalVersions (const std::vector< unsigned > versionA, const std::vector< unsigned > versionB)

static std::vector< std::string >	splitBase64StringIntoMoleculeStrings (std::string base64String)

static bool	compareMoleculeDecisionList (const std::vector< std::tuple< int, int, int, int >> &listA, const std::vector< std::tuple< int, int, int, int >> &listB)

Private Attributes
std::unique_ptr< Impl >	pImpl_

Detailed Description

Class representing a compact JSON serialization of a molecule.

The JSON representation, although principally human readable, is very compact. Keys are heavily shortened. Each Molecule JSON Object has the following structure:

* - a: List of AtomStereopermutator Objects
*   - a: Assignment index (key omitted if unassigned)
*   - c: Central index
*   - r: Ranking
*     - s: Sorted subtituents
*     - l: Ligands
*     - lr: Ranked ligands
*     - lnk: Links (key omitted if empty)
*   - s: Shape name index
*   - o:(optional) Position groups of the ligands
* - b: List of BondStereopermutator Objects
*   - a: Assignment index (key omitted if unassigned)
*   - e: Edge on which it is placed
* - c: Canonicalization state
* - g: Graph Object
*   - Z: List of atomic numbers
*   - E: List of edges, each a List
*     - 0: Source vertex
*     - 1: Target vertex
*     - 2: Bond type index
* - v: Library version List
*   - 0: Major
*   - 1: Minor
*   - 2: Patch
*

For std::string - Molecule interconversions, you can implicitly call the converting operators:

Molecule mol;
std::string jsonSerialization = JsonSerialization(mol);
Molecule reverted = JsonSerialization(jsonSerialization);

For BinaryType - Molecule interconversions, only the implicit Molecule conversion operator is available since the binary JSON format must be specified:

Molecule mol;
JsonSerialization::BinaryType bson = JsonSerialization(mol).toBinary(JsonSerialization::BinaryFormat::BSON);
Molecule reverted = JsonSerialization(bson, JsonSerialization::BinaryFormat::BSON);

Warning: Serializations of molecules have substantial notational freedom. Using lexicographical comparison on serializations does not have the same semantics as calling Molecule's relational operators.

Member Function Documentation

static BinaryType Scine::Molassembler::JsonSerialization::base64Decode ( const std::string & base64String )

static

Compare two molecules/complexes encoded as base64 strings. The molecule order is irrelevant.

Returns: True if both strings encode the same molecule(s).

static std::string Scine::Molassembler::JsonSerialization::base64Encode ( const BinaryType & binary )

static

Compare two molecules/complexes encoded as base64 strings. The molecule order is irrelevant.

Returns: True if both strings encode the same molecule(s).

static bool Scine::Molassembler::JsonSerialization::base64EqualMolecules	(	const std::string &	stringA,
		const std::string &	stringB,
		BinaryFormat	binaryFormat = `BinaryFormat::CBOR`
	)

static

Compare two molecules/complexes encoded as base64 strings. The molecule order is irrelevant.

Returns: True if both strings encode the same molecule(s).

static bool Scine::Molassembler::JsonSerialization::equalDecisionLists	(	const std::string &	listStringA,
		const std::string &	listStringB
	)

static

Compare two decision lists encoded as strings.

The string format is expected to be
"(-100, -95, -90, 1):(10, 15, 20, 4);(1, 6, 11, 1)"
Multiple molecules have to be separated by ";". The molecule order is irrelevant.

JsonSerialization& Scine::Molassembler::JsonSerialization::standardize ( )

Eliminate all notational freedom of the JSON serialization.

The Molecule's JSON representation notational freedoms are removed:

Edges have ordered indices
The graph edge list is sorted
The lists of atom and bond stereopermutators are sorted by their placement atoms and bonds, respectively
Ranking information notational freedom is removed

Complexity \(\Theta(V + E + A + B)\)

Exceptions

std::logic_error If the underlying molecule is not fully canonical. It makes zero sense to standardize the JSON representation if the molecule itself is not canonicalized since then JSON representation comparison will still not yield the same behavior as Molecule comparison.

Returns: *this for method chaining

The documentation for this class was generated from the following file:

Molassembler/Serialization.h

Public Types

Public Member Functions

Static Public Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Member Function Documentation