"""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)