xtalmet 0.1.0__tar.gz

xtalmet-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Materials Design Group
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

xtalmet-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: xtalmet
+Version: 0.1.0
+Summary: Python package containing a variety of distance functions for crystals, as well as evaluation metrics for crystal generation.
+Author: Masahiro Negishi
+Author-email: Masahiro Negishi <m.negishi25@imperial.ac.uk>
+License: MIT License
+         
+         Copyright (c) 2025 Materials Design Group
+         
+         Permission is hereby granted, free of charge, to any person obtaining a copy
+         of this software and associated documentation files (the "Software"), to deal
+         in the Software without restriction, including without limitation the rights
+         to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+         copies of the Software, and to permit persons to whom the Software is
+         furnished to do so, subject to the following conditions:
+         
+         The above copyright notice and this permission notice shall be included in all
+         copies or substantial portions of the Software.
+         
+         THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+         IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+         FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+         AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+         SOFTWARE.
+Requires-Dist: pymatgen>=2025.5.28
+Requires-Dist: torch>=2.7.0
+Requires-Dist: matminer>=0.9.3
+Requires-Dist: average-minimum-distance>=1.5.3
+Requires-Dist: smact>=3.1.0
+Requires-Dist: mace-torch>=0.3.13
+Requires-Dist: huggingface-hub
+Requires-Python: >=3.12
+Project-URL: Documentation, https://wmd-group.github.io/xtalmets/
+Project-URL: Repository, https://github.com/WMD-group/xtalmet/
+Description-Content-Type: text/markdown
+
+# xtalmet
+[![License: MIT](https://img.shields.io/badge/license-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Formatter: Ruff](https://img.shields.io/badge/formatter-Ruff-D7FF64.svg?logo=ruff)](https://docs.astral.sh/ruff/)
+[![Linter: Ruff](https://img.shields.io/badge/linter-Ruff-D7FF64.svg?logo=ruff)](https://docs.astral.sh/ruff/)
+[![Packaging: uv](https://img.shields.io/badge/packaging-uv-DE5FE9.svg?logo=uv)](https://docs.astral.sh/uv/)
+[![Docs: Sphinx](https://img.shields.io/badge/docs-Sphinx-000000.svg?logo=sphinx)](https://www.sphinx-doc.org/en/master/index.html)
+[![GitHub issues](https://img.shields.io/github/issues-raw/WMD-Group/xtalmet)](https://github.com/WMD-group/xtalmet/issues)
+[![CI Status](https://github.com/WMD-group/xtalmet/actions/workflows/sphinx.yml/badge.svg)](https://github.com/WMD-group/xtalmet/actions/workflows/sphinx.yml)
+
+The **xtalmet** package offers a variety of distance functions for comparing crystal structures. 
+These include both binary and continuous as well as compositional and structural functions. 
+It also enables you to evaluate a set of crystals using uniqueness and novelty metrics derived from these distances.
+
+- Documentation: https://wmd-group.github.io/xtalmet/
+- Examples: https://github.com/WMD-group/xtalmet/examples
+
+## Motivation
+A central challenge in materials science is the efficient discovery of functional crystals from the vast chemical space. 
+Recently, the inverse design of crystals using advanced machine learning generative models has emerged as a promising approach due to their ability to rapidly generate numerous candidates. 
+However, while these models have become increasingly sophisticated, their evaluation metrics have remained largely unchanged since the seminal work of Xie et al [1] and Zeni et al [2]. 
+To effectively guide model development, these evaluation metrics must also continue to improve. 
+We aim to refine two primary metrics, uniqueness and novelty, by revising the underlying distance function used to compare crystal structures.
+
+[1] Tian Xie et al. Crystal diffusion variational autoencoder for periodic material generation. International Conference on Learning Representations 2022.
+
+[2] Claudio Zeni et al. A generative model for inorganic materials design. Nature 2025.
+
+## Installation
+The latest stable version can be installed via pip:
+```bash
+pip install xtalmet
+```
+
+## Usage
+Two primary features of xtalmet are the calculation of distances between crystals and the uniqueness/novelty evaluation.
+For the former usage, suppose you have two crystals `xtal_1` and `xtal_2` (`pymatgen.core.Structure`) whose distance you want to measure.
+You can do so with one line of code:
+```python
+from xtalmet.distance import d_amd
+distance = d_amd(xtal_1, xtal_2)
+```
+Here, d_amd is a type of continuous distance based on structural fingerprints.
+For a complete list of available distances, please refer to the [documentation](https://wmd-group.github.io/xtalmet/api/xtalmet.distance.html).
+
+For the uniqueness/novelty evaluation, imagine that you want to assess a set of crystals `gen_xtals` (`list[pymatgen.core.Structure]`) generated from a model trained on the MP20 dataset.
+This can be done with just a few lines of code:
+```python
+from xtalmet.evaluator import Evaluator
+evaluator = Evaluator(gen_xtals)
+uniqueness = evaluator.uniqueness(distance="d_amd")
+novelty = evaluator.novelty(train_xtals="mp20", distance="d_amd")
+```
+A more detailed tutorial notebook is provided in the [examples directory](https://github.com/WMD-group/xtalmet/tree/main/examples).
+
+## Acknowledgements
+Although we have argued that the progress on evaluation metrics is slower than that on generative models, we are not the sole contributors to this field. 
+Our work builds upon several influential studies. 
+We particularly acknowledge the following contributions:
+
+- Zeni et al. [2]: For their implementation of the S.U.N. (Stability / Uniqueness / Novelty) metric.
+
+- Baird et al. [3]: For their code for uniqueness and novelty, and their framework for creating a Python benchmarking package.
+
+- Widdowson et al. [4, 5]: For their work on a continuous structural distance between crystals.
+
+Other studies, while not directly related, were also inspiring in shaping our approach to measuring distances between crystals.  
+These include the work of Onwuli et al. [6] on distances between compositional embeddings, as well as Hargreaves et al.'s [7] development of optimal transport-based methods for inorganic compositions.
+
+[3] Baird et al. matbench-genmetrics: A Python library for benchmarking crystal structure generative models using time-based splits of Materials Project structures. Journal of Open Source Software 2024.
+
+[4] Widdowson et al. Resolving the data ambiguity for periodic crystals. Advances in Neural Information Processing Systems 2022.
+
+[5] Widdson et al. Average Minimum Distances of periodic point sets - foundational invariants for mapping periodic crystals. MATCH Communications in Mathematical and in Computer Chemistry 2022.
+
+[6] A. Onwuli et al. Element similarity in high-dimensional materials representations. Digital Discovery 2023.
+
+
+[7] Hargreaves et al. The earth mover’s distance as a metric for the space of inorganic compositions. Chemistry of Materials 2020.
+
+## Citation
+If you find xtalmet useful in your research, please consider citing:
+```bibtex
+@misc{negishi2025continuousuniquenessnoveltymetrics,
+      title={Continuous Uniqueness and Novelty Metrics for Generative Modeling of Inorganic Crystals}, 
+      author={Masahiro Negishi and Hyunsoo Park and Kinga O. Mastej and Aron Walsh},
+      year={2025},
+      eprint={2510.12405},
+      archivePrefix={arXiv},
+      primaryClass={cs.LG},
+      url={https://arxiv.org/abs/2510.12405}, 
+}
+```

xtalmet-0.1.0/README.md

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+# xtalmet
+[![License: MIT](https://img.shields.io/badge/license-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Formatter: Ruff](https://img.shields.io/badge/formatter-Ruff-D7FF64.svg?logo=ruff)](https://docs.astral.sh/ruff/)
+[![Linter: Ruff](https://img.shields.io/badge/linter-Ruff-D7FF64.svg?logo=ruff)](https://docs.astral.sh/ruff/)
+[![Packaging: uv](https://img.shields.io/badge/packaging-uv-DE5FE9.svg?logo=uv)](https://docs.astral.sh/uv/)
+[![Docs: Sphinx](https://img.shields.io/badge/docs-Sphinx-000000.svg?logo=sphinx)](https://www.sphinx-doc.org/en/master/index.html)
+[![GitHub issues](https://img.shields.io/github/issues-raw/WMD-Group/xtalmet)](https://github.com/WMD-group/xtalmet/issues)
+[![CI Status](https://github.com/WMD-group/xtalmet/actions/workflows/sphinx.yml/badge.svg)](https://github.com/WMD-group/xtalmet/actions/workflows/sphinx.yml)
+
+The **xtalmet** package offers a variety of distance functions for comparing crystal structures. 
+These include both binary and continuous as well as compositional and structural functions. 
+It also enables you to evaluate a set of crystals using uniqueness and novelty metrics derived from these distances.
+
+- Documentation: https://wmd-group.github.io/xtalmet/
+- Examples: https://github.com/WMD-group/xtalmet/examples
+
+## Motivation
+A central challenge in materials science is the efficient discovery of functional crystals from the vast chemical space. 
+Recently, the inverse design of crystals using advanced machine learning generative models has emerged as a promising approach due to their ability to rapidly generate numerous candidates. 
+However, while these models have become increasingly sophisticated, their evaluation metrics have remained largely unchanged since the seminal work of Xie et al [1] and Zeni et al [2]. 
+To effectively guide model development, these evaluation metrics must also continue to improve. 
+We aim to refine two primary metrics, uniqueness and novelty, by revising the underlying distance function used to compare crystal structures.
+
+[1] Tian Xie et al. Crystal diffusion variational autoencoder for periodic material generation. International Conference on Learning Representations 2022.
+
+[2] Claudio Zeni et al. A generative model for inorganic materials design. Nature 2025.
+
+## Installation
+The latest stable version can be installed via pip:
+```bash
+pip install xtalmet
+```
+
+## Usage
+Two primary features of xtalmet are the calculation of distances between crystals and the uniqueness/novelty evaluation.
+For the former usage, suppose you have two crystals `xtal_1` and `xtal_2` (`pymatgen.core.Structure`) whose distance you want to measure.
+You can do so with one line of code:
+```python
+from xtalmet.distance import d_amd
+distance = d_amd(xtal_1, xtal_2)
+```
+Here, d_amd is a type of continuous distance based on structural fingerprints.
+For a complete list of available distances, please refer to the [documentation](https://wmd-group.github.io/xtalmet/api/xtalmet.distance.html).
+
+For the uniqueness/novelty evaluation, imagine that you want to assess a set of crystals `gen_xtals` (`list[pymatgen.core.Structure]`) generated from a model trained on the MP20 dataset.
+This can be done with just a few lines of code:
+```python
+from xtalmet.evaluator import Evaluator
+evaluator = Evaluator(gen_xtals)
+uniqueness = evaluator.uniqueness(distance="d_amd")
+novelty = evaluator.novelty(train_xtals="mp20", distance="d_amd")
+```
+A more detailed tutorial notebook is provided in the [examples directory](https://github.com/WMD-group/xtalmet/tree/main/examples).
+
+## Acknowledgements
+Although we have argued that the progress on evaluation metrics is slower than that on generative models, we are not the sole contributors to this field. 
+Our work builds upon several influential studies. 
+We particularly acknowledge the following contributions:
+
+- Zeni et al. [2]: For their implementation of the S.U.N. (Stability / Uniqueness / Novelty) metric.
+
+- Baird et al. [3]: For their code for uniqueness and novelty, and their framework for creating a Python benchmarking package.
+
+- Widdowson et al. [4, 5]: For their work on a continuous structural distance between crystals.
+
+Other studies, while not directly related, were also inspiring in shaping our approach to measuring distances between crystals.  
+These include the work of Onwuli et al. [6] on distances between compositional embeddings, as well as Hargreaves et al.'s [7] development of optimal transport-based methods for inorganic compositions.
+
+[3] Baird et al. matbench-genmetrics: A Python library for benchmarking crystal structure generative models using time-based splits of Materials Project structures. Journal of Open Source Software 2024.
+
+[4] Widdowson et al. Resolving the data ambiguity for periodic crystals. Advances in Neural Information Processing Systems 2022.
+
+[5] Widdson et al. Average Minimum Distances of periodic point sets - foundational invariants for mapping periodic crystals. MATCH Communications in Mathematical and in Computer Chemistry 2022.
+
+[6] A. Onwuli et al. Element similarity in high-dimensional materials representations. Digital Discovery 2023.
+
+
+[7] Hargreaves et al. The earth mover’s distance as a metric for the space of inorganic compositions. Chemistry of Materials 2020.
+
+## Citation
+If you find xtalmet useful in your research, please consider citing:
+```bibtex
+@misc{negishi2025continuousuniquenessnoveltymetrics,
+      title={Continuous Uniqueness and Novelty Metrics for Generative Modeling of Inorganic Crystals}, 
+      author={Masahiro Negishi and Hyunsoo Park and Kinga O. Mastej and Aron Walsh},
+      year={2025},
+      eprint={2510.12405},
+      archivePrefix={arXiv},
+      primaryClass={cs.LG},
+      url={https://arxiv.org/abs/2510.12405}, 
+}
+```

xtalmet-0.1.0/pyproject.toml

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+[project]
+name = "xtalmet"
+version = "0.1.0"
+description = "Python package containing a variety of distance functions for crystals, as well as evaluation metrics for crystal generation."
+readme = "README.md"
+authors = [
+    { name = "Masahiro Negishi", email = "m.negishi25@imperial.ac.uk" }
+]
+requires-python = ">=3.12"
+dependencies = [
+    "pymatgen>=2025.5.28",
+    "torch>=2.7.0",
+    "matminer>=0.9.3",
+    "average-minimum-distance>=1.5.3",
+    "smact>=3.1.0",
+    "mace-torch>=0.3.13",
+    "huggingface_hub"
+]
+license = { file = "LICENSE" }
+
+[project.urls]
+Repository = "https://github.com/WMD-group/xtalmet/"
+Documentation = "https://wmd-group.github.io/xtalmets/"
+
+[dependency-groups]
+dev = [
+    "pytest",
+    "colorama",
+    "seaborn",
+    "ipykernel",
+    "sphinx",
+    "sphinx-rtd-theme",
+    "sphinx-github-style",
+]
+
+[build-system]
+requires = ["uv_build>=0.8.22,<0.9.0"]
+build-backend = "uv_build"
+
+[tool.ruff]
+line-length = 88
+
+[tool.ruff.lint]
+select = [
+    "F", # flake8
+    "E", # pycodestyle
+    "W", # pycodestyle
+    "UP", # pyupgrade
+    "B", # flake8-bugbear
+    "SIM", # flake8-simplify
+    "I", # isort
+    "D", # pydocstyle
+]
+ignore = ["E101", "E501", "W191", "E111", "E114", "E117", "D206", "D300"]
+fixable = ["ALL"]
+pycodestyle.max-doc-length = 88
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "tab"
+docstring-code-format = true

xtalmet-0.1.0/src/xtalmet/crystal.py

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+"""This module defines the Crystal class to store information about a single crystal."""
+
+import warnings
+from collections.abc import Sequence
+
+import amd
+import numpy as np
+from amd import periodicset_from_pymatgen_structure
+from ase import Atoms
+from matminer.featurizers.composition.composite import ElementProperty
+from numpy.typing import ArrayLike
+from pymatgen.core import Composition, Lattice, Species, Structure
+from pymatgen.io.ase import AseAtomsAdaptor
+from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+from pymatgen.util.typing import CompositionLike
+
+
+class Crystal(Structure):
+	"""Container for a single crystal structure."""
+
+	def __init__(
+		self,
+		lattice: ArrayLike | Lattice,
+		species: Sequence[CompositionLike],
+		coords: Sequence[ArrayLike],
+		charge: float | None = None,
+		validate_proximity: bool = False,
+		to_unit_cell: bool = False,
+		coords_are_cartesian: bool = False,
+		site_properties: dict | None = None,
+		labels: Sequence[str | None] | None = None,
+		properties: dict | None = None,
+	) -> None:
+		"""Initialize a Crystal object.
+
+		The parameters are the same as those used in the __init__() method of the
+		pymatgen.core.Structure class.
+
+		Args:
+			lattice (Lattice/3x3 array): The lattice, either as a
+				pymatgen.core.Lattice or
+				simply as any 2D array. Each row should correspond to a lattice
+				vector. e.g. [[10,0,0], [20,10,0], [0,0,30]] specifies a
+				lattice with lattice vectors [10,0,0], [20,10,0] and [0,0,30].
+			species ([Species]): Sequence of species on each site. Can take in
+				flexible input, including:
+
+				i.  A sequence of element / species specified either as string
+					symbols, e.g. ["Li", "Fe2+", "P", ...] or atomic numbers,
+					e.g. (3, 56, ...) or actual Element or Species objects.
+
+				ii. List of dict of elements/species and occupancies, e.g.
+					[{"Fe" : 0.5, "Mn":0.5}, ...]. This allows the setup of
+					disordered structures.
+			coords (Nx3 array): list of fractional/Cartesian coordinates of
+				each species.
+			charge (int): overall charge of the structure. Defaults to behavior
+				in SiteCollection where total charge is the sum of the oxidation
+				states.
+			validate_proximity (bool): Whether to check if there are sites
+				that are less than 0.01 Ang apart. Defaults to False.
+			to_unit_cell (bool): Whether to map all sites into the unit cell,
+				i.e. fractional coords between 0 and 1. Defaults to False.
+			coords_are_cartesian (bool): Set to True if you are providing
+				coordinates in Cartesian coordinates. Defaults to False.
+			site_properties (dict): Properties associated with the sites as a
+				dict of sequences, e.g. {"magmom":[5, 5, 5, 5]}. The sequences
+				have to be the same length as the atomic species and
+				fractional_coords. Defaults to None for no properties.
+			labels (list[str]): Labels associated with the sites as a
+				list of strings, e.g. ['Li1', 'Li2']. Must have the same
+				length as the species and fractional coords. Defaults to
+				None for no labels.
+			properties (dict): Properties associated with the whole structure.
+				Will be serialized when writing the structure to JSON or YAML but is
+				lost when converting to other formats.
+
+		Returns:
+			None
+
+		Note:
+			descriptions for args are copied from pymatgen.core.Structure class.
+		"""
+		super().__init__(
+			lattice,
+			[
+				specie.element if isinstance(specie, Species) else specie
+				for specie in species
+			],  # not considering oxidation states
+			coords,
+			charge,
+			validate_proximity,
+			to_unit_cell,
+			coords_are_cartesian,
+			site_properties,
+			labels,
+			properties,
+		)
+
+	@classmethod
+	def from_Structure(cls, structure: Structure) -> "Crystal":
+		"""Create a Crystal object from a pymatgen Structure object.
+
+		Args:
+			structure (Structure): A pymatgen Structure object.
+
+		Returns:
+			Crystal: A Crystal object created from the Structure.
+		"""
+		# internally calls __init__
+		return cls(
+			lattice=structure.lattice,
+			species=structure.species,
+			coords=structure.frac_coords,
+			charge=structure._charge,
+			validate_proximity=False,
+			to_unit_cell=False,
+			coords_are_cartesian=False,
+			site_properties=structure.site_properties,
+			labels=structure.labels,
+			properties=structure.properties,
+		)
+
+	def get_composition_tuple(self) -> tuple[tuple[str, int]]:
+		"""Get the composition of the crystal as a tuple of (element, count).
+
+		Embedding for d_comp.
+
+		Returns:
+			tuple: A tuple containing elements and their counts (divided by gcd).
+		"""
+		composition_unnorm = [
+			(elem, int(count))
+			for elem, count in dict(sorted(self.composition.as_dict().items())).items()
+		]
+		gcd = np.gcd.reduce([count for _, count in composition_unnorm]).item()
+		composition = tuple((elem, count // gcd) for elem, count in composition_unnorm)
+		return composition
+
+	def get_wyckoff(self) -> tuple[int, tuple[str]] | Exception:
+		"""Get the Wyckoff representation of the crystal.
+
+		Embedding for d_wyckoff.
+
+		Returns:
+			tuple | Exception: A tuple containing the space group number and a tuple of
+			Wyckoff letters, or an Exception from SpacegroupAnalyzer.
+		"""
+		sga = SpacegroupAnalyzer(self)
+		sym = sga.get_symmetrized_structure()
+		sg = sga.get_space_group_number()
+		wyckoff_letters = sorted(
+			[x[-1] for x in sym.wyckoff_symbols]
+		)  # Don't use sym.wyckoff_letters
+		return sg, tuple(wyckoff_letters)
+
+	def get_magpie(self) -> list[float]:
+		"""Get the magpie embedding of the crystal.
+
+		Embedding for d_magpie. Not influenced by oxidation states.
+
+		Returns:
+			list[float]: Magpie feature vector of the crystal.
+
+		References:
+			- Ward et al., (2016). A general-purpose machine learning framework for
+			  predicting properties of inorganic materials. npj Computational Materials,
+			  2(1), 1-7. https://doi.org/10.1038/npjcompumats.2016.28
+		"""
+		if not hasattr(self, "featurizer"):
+			self.featurizer = ElementProperty.from_preset("magpie", impute_nan=True)
+		feature = self.featurizer.featurize(self.composition)
+		return [float(x) for x in feature]
+
+	def get_PDD(
+		self, k: int = 100, **kwargs
+	) -> np.ndarray[np.float32 | np.float64] | Exception:
+		"""Get the pointwise distance distribution (PDD) of the crystal.
+
+		Embedding for d_ppd.
+
+		Args:
+			k (int): Number of nearest neighbors to consider.
+			**kwargs: Additional arguments for amd.PDD, except k.
+
+		Returns:
+			np.ndarray[np.float32 | np.float64] | Exception: PDD or an Exception
+			from periodicset_from_pymatgen_structure
+
+		References:
+			- Widdowson et al., (2022). Resolving the data ambiguity for periodic
+			  crystals. Advances in Neural Information Processing Systems, 35,
+			  24625--24638. https://openreview.net/forum?id=4wrB7Mo9_OQ
+		"""
+		if "return_row_data" in kwargs and kwargs["return_row_data"] is True:
+			warnings.warn(
+				"return_row_data=True is not supported. Automatically set to False.",
+				UserWarning,
+				stacklevel=2,
+			)
+			kwargs["return_row_data"] = False
+
+		return amd.PDD(periodicset_from_pymatgen_structure(self), k, **kwargs)
+
+	def get_AMD(self, k: int = 100) -> np.ndarray[np.float32 | np.float64] | Exception:
+		"""Get the average minimum distance (AMD) of the crystal.
+
+		Embedding for d_amd.
+
+		Args:
+			k (int): Number of nearest neighbors to consider. Also the embedding length.
+
+		Returns:
+			np.ndarray[np.float32 | np.float64] | Exception: AMD or an Exception
+			from periodicset_from_pymatgen_structure
+
+		References:
+			- Widdson et al., (2022). Average Minimum Distances of periodic point sets -
+			  foundational invariants for mapping periodic crystals. MATCH
+			  Communications in Mathematical and in Computer Chemistry, 87(3), 529-559,
+			  https://doi.org/10.46793/match.87-3.529W
+		"""
+		return amd.AMD(periodicset_from_pymatgen_structure(self), k)
+
+	def get_composition_pymatgen(self) -> Composition:
+		"""Get the pymatgen composition of the crystal.
+
+		Called when screening using SMACT or E_hull.
+
+		Returns:
+			Composition: Pymatgen Composition object.
+		"""
+		return self.composition
+
+	def get_ase_atoms(self) -> Atoms:
+		"""Get the ASE Atoms object of the crystal.
+
+		Called when screening using E_hull. Not influenced by oxidation states.
+
+		Returns:
+			Atoms: ASE Atoms object.
+		"""
+		return AseAtomsAdaptor.get_atoms(self)