StructuresDict#

molsysmt.StructuresDict is the native declarative dictionary representation of structural and trajectory data in MolSysMT.

Overview and Role#

molsysmt.StructuresDict provides a JSON-compatible dictionary schema representing 3D Cartesian atomic coordinates, periodic cell box matrices, frame timestamps, velocities, and thermodynamic observables.

Declarative Schema#

The schema dictionary maps standard structure parameters to nested list arrays or base64 binary encodings:

Top-Level Key

Value Type

Physical Units

Description

"coordinates"

Nested List or Base64

nanometer (nm)

3D Cartesian coordinates array (n_structures, n_atoms, 3).

"velocities"

Nested List or Base64

nm / ps

Atomic velocity vectors (n_structures, n_atoms, 3).

"box"

Nested List

nanometer (nm)

Periodic unit cell box matrices (n_structures, 3, 3).

"time"

Nested List

picosecond (ps)

Frame timestamps array (n_structures,).

"structure_id"

List of Strings

N/A

String identifiers for structural frames or PDB models.

"b_factor"

Nested List

nm²

Crystallographic B-factors (n_structures, n_atoms).

"occupancy"

Nested List

Dimensionless

Crystallographic atom occupancy values (n_structures, n_atoms).

"alternate_location"

List of Dicts

N/A

Alternate location mapping dicts.

"temperature"

Nested List

kelvin (K)

Frame-level temperatures (n_structures,).

"potential_energy"

Nested List

kJ / mol

Frame-level potential energies (n_structures,).

"kinetic_energy"

Nested List

kJ / mol

Frame-level kinetic energies (n_structures,).

Usage and Workflow#

import molsysmt as msm

# Convert native Structures container to StructuresDict
struct_dict = msm.convert(structures, to_form='molsysmt.StructuresDict')

Invariants and Performance#

  • JSON Encodable: Encodable into standard JSON string representations.

API Documentation#

Methods for molsysmt.StructuresDict are documented in the [molsysmt.Structures API Reference].