MolSysDict#

molsysmt.MolSysDict is the native declarative dictionary representation of a complete molecular system in MolSysMT.

Overview and Role#

molsysmt.MolSysDict provides a pure Python dictionary schema capable of representing an entire molecular system without instantiating complex class structures. It is wrapped by the MolSysDict dataclass, making it ideal for JSON serialization, network transport, configuration files, and inter-process message passing.

Declarative Schema#

The underlying data dictionary of MolSysDict contains standard header envelope fields and nested core aspect dictionaries:

Top-Level Key	Value Type	Description
`"format"`	String (`"molsysmt"`)	Framework format identifier tag.
`"kind"`	String (`"molsys"`)	System object category classifier.
`"version"`	String (`"0.1"`)	Schema specification version string.
`"metadata"`	Dictionary	User-defined or system provenance metadata dictionary.
`"topology"`	Dictionary (`TopologyDict`)	Declarative dictionary defining `atoms`, `groups`, `bonds`, `chains`, `molecules`, and `entities`.
`"structures"`	Dictionary (`StructuresDict`)	Declarative dictionary holding `structure_id`, `time`, `box`, `coordinates`, and observable trajectory fields.

Usage and Workflow#

import molsysmt as msm
import json

# 1. Convert a native system to a MolSysDict object
sys_dict = msm.convert(system, to_form='molsysmt.MolSysDict')

# 2. Extract underlying dictionary data and serialize to JSON string
json_str = json.dumps(sys_dict.to_dict())

# 3. Reconstruct native MolSys from MolSysDict
reconstructed_system = msm.convert(sys_dict, to_form='molsysmt.MolSys')

Invariants and Performance#

Pure JSON Compatibility: Primitive Python types (dict, list, str, int, float, None) suitable for lossless JSON serialization.
Deep Copy Safety: sys_dict.to_dict(copy=True) and sys_dict.copy() ensure deep copy isolation during message passing.

API Documentation#

Methods and form conversions for molsysmt.MolSysDict are documented in the [molsysmt.MolSysDict API Reference].