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"""Core definition of Structure and Molecule metadata."""
from __future__ import annotations
from typing import List, Optional, Type, TypeVar
from pydantic import Field
from pymatgen.core.composition import Composition
from pymatgen.core.periodic_table import Element
from pymatgen.core.structure import Molecule, Structure
from emmet.core.base import EmmetBaseModel
from emmet.core.symmetry import PointGroupData, SymmetryData
T = TypeVar("T", bound="StructureMetadata")
S = TypeVar("S", bound="MoleculeMetadata")
class StructureMetadata(EmmetBaseModel):
"""Mix-in class for structure metadata."""
# Structure metadata
nsites: Optional[int] = Field(
None, description="Total number of sites in the structure."
)
elements: Optional[List[Element]] = Field(
None, description="List of elements in the material."
)
nelements: Optional[int] = Field(None, description="Number of elements.")
composition: Optional[Composition] = Field(
None, description="Full composition for the material."
)
composition_reduced: Optional[Composition] = Field(
None,
title="Reduced Composition",
description="Simplified representation of the composition.",
)
formula_pretty: Optional[str] = Field(
None,
title="Pretty Formula",
description="Cleaned representation of the formula.",
)
formula_anonymous: Optional[str] = Field(
None,
title="Anonymous Formula",
description="Anonymized representation of the formula.",
)
chemsys: Optional[str] = Field(
None,
title="Chemical System",
description="dash-delimited string of elements in the material.",
)
volume: Optional[float] = Field(
None,
title="Volume",
description="Total volume for this structure in Angstroms^3.",
)
density: Optional[float] = Field(
None, title="Density", description="Density in grams per cm^3."
)
density_atomic: Optional[float] = Field(
None,
title="Packing Density",
description="The atomic packing density in atoms per cm^3.",
)
symmetry: Optional[SymmetryData] = Field(
None, description="Symmetry data for this material."
)
@classmethod
def from_composition(
cls: Type[T],
composition: Composition,
fields: Optional[List[str]] = None,
**kwargs,
) -> T:
fields = (
[
"elements",
"nelements",
"composition",
"composition_reduced",
"formula_pretty",
"formula_anonymous",
"chemsys",
]
if fields is None
else fields
)
composition = composition.remove_charges()
elsyms = sorted({e.symbol for e in composition.elements})
data = {
"elements": elsyms,
"nelements": len(elsyms),
"composition": composition,
"composition_reduced": composition.reduced_composition.remove_charges(),
"formula_pretty": composition.reduced_formula,
"formula_anonymous": composition.anonymized_formula,
"chemsys": "-".join(elsyms),
}
return cls(**{k: v for k, v in data.items() if k in fields}, **kwargs)
@classmethod
def from_structure(
cls: Type[T],
meta_structure: Structure,
fields: Optional[List[str]] = None,
**kwargs,
) -> T:
fields = (
[
"nsites",
"elements",
"nelements",
"composition",
"composition_reduced",
"formula_pretty",
"formula_anonymous",
"chemsys",
"volume",
"density",
"density_atomic",
"symmetry",
]
if fields is None
else fields
)
comp = meta_structure.composition.remove_charges()
elsyms = sorted({e.symbol for e in comp.elements})
symmetry = SymmetryData.from_structure(meta_structure)
data = {
"nsites": meta_structure.num_sites,
"elements": elsyms,
"nelements": len(elsyms),
"composition": comp,
"composition_reduced": comp.reduced_composition,
"formula_pretty": comp.reduced_formula,
"formula_anonymous": comp.anonymized_formula,
"chemsys": "-".join(elsyms),
"volume": meta_structure.volume,
"density": meta_structure.density,
"density_atomic": meta_structure.volume / meta_structure.num_sites,
"symmetry": symmetry,
}
kwargs.update({k: v for k, v in data.items() if k in fields})
return cls(**kwargs)
class MoleculeMetadata(EmmetBaseModel):
"""Mix-in class for molecule metadata."""
charge: Optional[int] = Field(None, description="Charge of the molecule")
spin_multiplicity: Optional[int] = Field(
None, description="Spin multiplicity of the molecule"
)
natoms: Optional[int] = Field(
None, description="Total number of atoms in the molecule"
)
elements: Optional[List[Element]] = Field(
None, description="List of elements in the molecule"
)
nelements: Optional[int] = Field(None, title="Number of Elements")
nelectrons: Optional[int] = Field(
None,
title="Number of electrons",
description="The total number of electrons for the molecule",
)
composition: Optional[Composition] = Field(
None, description="Full composition for the molecule"
)
composition_reduced: Optional[Composition] = Field(
None,
title="Reduced Composition",
description="Simplified representation of the composition",
)
formula_alphabetical: Optional[str] = Field(
None,
title="Alphabetical Formula",
description="Alphabetical molecular formula",
)
formula_pretty: Optional[str] = Field(
None,
title="Pretty Formula",
description="Cleaned representation of the formula.",
)
formula_anonymous: Optional[str] = Field(
None,
title="Anonymous Formula",
description="Anonymized representation of the formula",
)
chemsys: Optional[str] = Field(
None,
title="Chemical System",
description="dash-delimited string of elements in the molecule",
)
symmetry: Optional[PointGroupData] = Field(
None, description="Symmetry data for this molecule"
)
@classmethod
def from_composition(
cls: Type[S],
comp: Composition,
fields: Optional[List[str]] = None,
**kwargs,
) -> S:
"""
Create a MoleculeMetadata model from a composition.
Parameters
----------
comp : .Composition
A pymatgen composition.
fields : list of str or None
Composition fields to include.
**kwargs
Keyword arguments that are passed to the model constructor.
Returns
-------
T
A molecule metadata model.
"""
fields = (
[
"elements",
"nelements",
"composition",
"composition_reduced",
"formula_alphabetical",
"formula_pretty",
"formula_anonymous",
"chemsys",
]
if fields is None
else fields
)
elsyms = sorted({e.symbol for e in comp.elements})
data = {
"elements": elsyms,
"nelements": len(elsyms),
"composition": comp,
"composition_reduced": comp.reduced_composition,
"formula_alphabetical": comp.alphabetical_formula,
"formula_pretty": comp.reduced_formula,
"formula_anonymous": comp.anonymized_formula,
"chemsys": "-".join(elsyms),
}
return cls(**{k: v for k, v in data.items() if k in fields}, **kwargs)
@classmethod
def from_molecule(
cls: Type[S],
meta_molecule: Molecule,
fields: Optional[List[str]] = None,
**kwargs,
) -> S:
fields = (
[
"charge",
"spin_multiplicity",
"natoms",
"elements",
"nelements",
"nelectrons",
"composition",
"composition_reduced",
"formula_alphabetical",
"formula_pretty",
"formula_anonymous",
"chemsys",
"symmetry",
]
if fields is None
else fields
)
comp = meta_molecule.composition
elsyms = sorted({e.symbol for e in comp.elements})
symmetry = PointGroupData.from_molecule(meta_molecule)
data = {
"charge": int(meta_molecule.charge),
"spin_multiplicity": meta_molecule.spin_multiplicity,
"natoms": len(meta_molecule),
"elements": elsyms,
"nelements": len(elsyms),
"nelectrons": int(meta_molecule.nelectrons),
"composition": comp,
"composition_reduced": comp.reduced_composition,
"formula_alphabetical": comp.alphabetical_formula,
"formula_pretty": comp.reduced_formula,
"formula_anonymous": comp.anonymized_formula,
"chemsys": "-".join(elsyms),
"symmetry": symmetry,
}
return cls(**{k: v for k, v in data.items() if k in fields}, **kwargs)
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