pymatgen/molecule format

Aliases

pymatgen/molecule

Implementation: PyMatgenMoleculeFormat

Overview

In-memory pymatgen Molecule objects for nonperiodic systems.

pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis.

Periodic boundary conditions are removed during conversion. The optional pymatgen dependency is required, and writing returns one Molecule object per frame.

Quick examples

The examples use the preferred alias pymatgen/molecule; any alias listed above is equivalent.

import dpdata

from pymatgen.core import Molecule

molecule = Molecule(["H"], [[0.0, 0.0, 0.0]])

# Geometry-only data
system = dpdata.System(molecule, fmt="pymatgen/molecule")

# Write geometry-only data
converted = system.to("pymatgen/molecule")

Conversions

Convert from this format to System

dpdata.System(file_name, fmt: Literal['pymatgen/molecule'] = None, **kwargs) → dpdata.system.System

dpdata.System.from_pymatgen_molecule(file_name, **kwargs) → dpdata.system.System

Convert a pymatgen Molecule into System data.

Parameters:

file_namepymatgen.core.Molecule

In-memory molecule to convert.

**kwargsdict

Additional format arguments accepted for API compatibility.

Returns:

System

converted system

Convert from System to this format

dpdata.System.to(fmt: Literal['pymatgen/molecule'], **kwargs)

dpdata.System.to_pymatgen_molecule(**kwargs)

Convert System frames to pymatgen Molecule objects.

Parameters:

**kwargsdict

Additional format arguments accepted for API compatibility.

Returns:

list[pymatgen.core.Molecule]

One molecule per frame.

Convert from LabeledSystem to this format

dpdata.LabeledSystem.to(fmt: Literal['pymatgen/molecule'], **kwargs)

dpdata.LabeledSystem.to_pymatgen_molecule(**kwargs)

Convert System frames to pymatgen Molecule objects.

Parameters:

**kwargsdict

Additional format arguments accepted for API compatibility.

Returns:

list[pymatgen.core.Molecule]

One molecule per frame.