### Install mofdsribe with all extras

Source: https://mofdscribe.readthedocs.io/en/latest/installation.html

To include all optional utilities, append `[all]` to the pip install command.

```bash
pip install -e ".[all]"
```

--------------------------------

### Install mofdsribe from GitHub

Source: https://mofdscribe.readthedocs.io/en/latest/installation.html

Install the latest code and data directly from GitHub. Use the `-e` flag for an editable installation.

```bash
git clone git+https://github.com/kjappelbaum/mofdscribe.git
cd mofdscribe
pip install -e .
```

--------------------------------

### Initialize BUFeaturizer with RDKitAdaptor

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/bu_featurizer.html

Example of initializing BUFeaturizer with RDKitAdaptor and specifying aggregation methods. This setup is useful for calculating features like asphericity on MOF BUs.

```python
from mofdscribe.bu import BUFeaturizer, MOFBBs
from mofdscribe.bu.rdkitadaptor import RDKitAdaptor
from rdkit.Chem.Descriptors3D import Asphericity
from pymatgen.core import Molecule
from pymatgen.io.babel import BabelMolAdaptor
base_featurizer = RDKitAdaptor(featurizer=Asphericity, feature_labels=["asphericity"])
bu_featurizer = BUFeaturizer(featurizer=base_featurizer, aggregations=("mean", "std", "min", "max"))
bu_featurizer.featurize(
        mofbbs=MOFBBs(nodes=[BabelMolAdaptor.from_string(
            "[CH-]1C=CC=C1.[CH-]1C=CC=C1.[Fe+2]", "smi").pymatgen_mol],
        linkers=[BabelMolAdaptor.from_string("CCCC", "smi").pymatgen_mol]))
```

--------------------------------

### BUFeaturizer Example

Source: https://mofdscribe.readthedocs.io/en/latest/api/featurizers.html

Demonstrates how to use BUFeaturizer with RDKitAdaptor to compute and aggregate features like asphericity for MOF building blocks.

```python
>>> from mofdscribe.bu import BUFeaturizer, MOFBBs
>>> from mofdscribe.bu.rdkitadaptor import RDKitAdaptor
>>> from rdkit.Chem.Descriptors3D import Asphericity
>>> from pymatgen.core import Molecule
>> from pymatgen.io.babel import BabelMolAdaptor
>>> base_featurizer = RDKitAdaptor(featurizer=Asphericity, feature_labels=["asphericity"])
>>> bu_featurizer = BUFeaturizer(featurizer=base_featurizer, aggregations=("mean", "std", "min", "max"))
>>> bu_featurizer.featurize(
        mofbbs=MOFBBs(nodes=[BabelMolAdaptor.from_string(
            "[CH-]1C=CC=C1.[CH-]1C=CC=C1.[Fe+2]", "smi").pymatgen_mol],
        linkers=[BabelMolAdaptor.from_string("CCCC", "smi").pymatgen_mol]))
```

--------------------------------

### Example Custom Model for MOFBench

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/bench/mofbench.html

This example demonstrates how to implement a custom model class that can be used with MOFBench. It includes methods for featurization, fitting, and prediction using scikit-learn pipelines.

```python
class MyDummyModel:
    def __init__(self):
        self.model = Pipeline(
            [("scaler", StandardScaler()), ("lr", LinearRegression(**(lr_kwargs or {})))]
        )

    def featurize(self, s: Structure):
        return s.density

    def fit(self, idx, structures, y):
        x = np.array([self.featurize(s) for s in structures]).reshape(-1, 1)
        self.model.fit(x, y)

    def predict(self, idx, structures):
        x = np.array([self.featurize(s) for s in structures]).reshape(-1, 1)
        return self.model.predict(x)
```

--------------------------------

### Initialize and Featurize with APRDF

Source: https://mofdscribe.readthedocs.io/en/latest/api/featurizers.html

Demonstrates how to initialize the APRDF featurizer and use it to compute features for a given structure. Ensure pymatgen and mofdscribe are installed.

```python
from mofdscribe.chemistry.aprdf import APRDF
from pymatgen.core.structure import Structure
s = Structure.from_file("tests/test_files/LiTiO3.cif")
aprdf = APRDF()
features = aprdf.featurize(s)
```

--------------------------------

### PHVect Initialization with Default Settings

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/topology/ph_vect.html

Demonstrates the initialization of the PHVect featurizer using its default parameters. This is useful for a quick start or when default behavior is desired.

```python
PHVect()
```

--------------------------------

### Install RASPA and Zeo++ dependencies

Source: https://mofdscribe.readthedocs.io/en/latest/installation.html

Install RASPA and Zeo++ using conda for energy grid/Henry coefficient and pore descriptor calculations.

```bash
# RASPA and Zeo++ (if you want to use energy grid/Henry coefficient and pore descriptors)
conda install -c conda-forge raspa2 zeopp-lsmo
```

--------------------------------

### Instantiate a MOF-Dscribe Dummy Model for Benchmarking

Source: https://mofdscribe.readthedocs.io/en/latest/getting_started.html

Use a pre-implemented dummy model from MOF-Dscribe for testing or as a reference. This example uses `DensityRegressor` for a linear regression task.

```python
from mofdscribe.bench.dummy_models import DensityRegressor
from mofdscribe.bench.logKHCO2 import LogkHCO2IDBench

logkHCO2_interpolation_density = LogkHCO2IDBench(
    DensityRegressor(),
    version="v0.0.1",
    name="linear density",
    features="density",
    model_type="linear regression /w polynomial features",
    implementation="mofdscribe",
    reference="mofdscribe",
)

```

--------------------------------

### Install Open Babel dependency

Source: https://mofdscribe.readthedocs.io/en/latest/installation.html

Install Open Babel using conda for SBU-centered features with moffragmentor.

```bash
# openbabel dependency for moffragmentor (if you want to use SBU-centered features)
conda install -c conda-forge openbabel
```

--------------------------------

### QMOF Dataset Initialization

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/datasets/qmof_dataset.html

Demonstrates how to initialize the QMOF dataset with various options.

```APIDOC
## QMOF Dataset Initialization

### Description
This section describes how to instantiate the QMOF dataset object, allowing users to specify version, flavor, and data filtering options.

### Method
```python
QMOF(version: str = "v0.0.1", flavor: str = "all", drop_basename_duplicates: bool = True, drop_graph_duplicates: bool = True, subset: Optional[Collection[int]] = None, drop_nan: bool = False)
```

### Parameters
#### Arguments
- **version** (str): The version of the dataset to use. Defaults to "v0.0.1".
- **flavor** (str): The flavor of the dataset. Accepted values are "all", "csd", "gcmc", and "csd-gcmc". Defaults to "all".
- **drop_basename_duplicates** (bool): If True, removes duplicate structures based on CSD basename. Defaults to True.
- **drop_graph_duplicates** (bool): If True, removes duplicate structures based on graph hash. Defaults to True.
- **subset** (Optional[Collection[int]]): A collection of indices to load a subset of the dataset. Defaults to None.
- **drop_nan** (bool): If True, rows with NaN values in features or hashes are dropped. Defaults to False.

### Raises
- **ValueError**: If an unavailable version is specified.
```

--------------------------------

### Install CGAL and Dionysus dependencies

Source: https://mofdscribe.readthedocs.io/en/latest/installation.html

Install CGAL and Dionysus using conda for persistent-homology based features. May require system-level package manager installation on some systems.

```bash
# cgal dependency for moltda (if you want to use persistent-homology based features)
# on some systems, you might need to replace this with sudo apt-get install libcgal-dev or brew install cgal
conda install -c conda-forge cgal dionysus
```

--------------------------------

### LSOP Featurizer Initialization and Usage

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/lsop_featurizer.html

This snippet demonstrates how to initialize and use the LSOP featurizer. It covers the constructor arguments and the featurization process.

```APIDOC
## LSOP Class

### Description
Compute shape parameters for a fragment. The fragments can be a molecule or a molecule that only contains important part (e.g. binding sites) of a molecule. The shape parameters are then supposed to quantify the shape of the fragment. For instance, a triangular molecule will have a `tri_plan` parameter close to 1.

While there is a site-based LSOP featurizer in matminer there is none that uses LSOP to quantify the shape of some fragment. This featurizers just does that.

It does so by placing a dummy site at the center of mass of the fragment and then computes the LSOP considering all other sites as neighbors.

### Methods

#### `__init__(self, types: Tuple[str] = _default_types, parameters: Optional[List[dict]] = None)`
Initialize the featurizer.

Args:
    types (Tuple[str]): The types of LSOP to compute. For the full list of types see: :py:attr:`pymatgen.analysis.local_env.LocalStructOrderParams.__supported_types`. Defaults to: ["tet", "oct", "bcc", "sq_pyr", "sq_pyr_legacy", "tri_bipyr", "sq_bipyr", "oct_legacy", "tri_plan", "sq_plan", "pent_plan", "tri_pyr", "pent_pyr", "hex_pyr", "pent_bipyr", "hex_bipyr", "T", "cuboct", "oct_max", "tet_max", "tri_plan_max", "sq_plan_max", "pent_plan_max", "cuboct_max", "bent", "see_saw_rect", "hex_plan_max", "sq_face_cap_trig_pris"]
    parameters(List[dict], optional): The parameters to pass to the LocalStructOrderParams object.

#### `feature_labels(self) -> List[str]`
Returns the feature labels for the computed LSOP types.

#### `featurize(self, s: Union[Structure, IStructure, Molecule, IMolecule]) -> np.ndarray`
Computes the LSOP values for the given structure or molecule.

Args:
    s (Union[Structure, IStructure, Molecule, IMolecule]): The input structure or molecule.

Returns:
    np.ndarray: An array of computed LSOP values.

#### `implementors(self) -> List[str]`
Returns the list of implementors for this featurizer.

#### `citations(self) -> List[str]`
Returns the list of citations relevant to this featurizer.
```

--------------------------------

### get_regression_metrics

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/metrics/regression.html

Get regression metrics.

```APIDOC
## get_regression_metrics

### Description
Get regression metrics.

### Parameters
#### Arguments
- **predictions** (ArrayLike) - predictions for one objective
- **labels** (ArrayLike) - true labels for one objective

### Returns
- **RegressionMetrics**: regression metrics

### Example
```python
predictions = [0.1, 0.2, 0.3, 0.4, 0.5]
labels = [0.1, 0.2, 0.3, 0.4, 0.5]
get_regression_metrics(predictions, labels)
```

```

--------------------------------

### Get Implementors of PartialChargeHistogram

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/chemistry/partialchargehistogram.html

List the individuals who implemented the PartialChargeHistogram featurizer.

```python
from mofdscribe.featurizers.chemistry import PartialChargeHistogram

featurizer = PartialChargeHistogram()
implementors = featurizer.implementors()
print(implementors)
```

--------------------------------

### Initialize EnergyGrid Featurizer

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/chemistry/energygrid.html

Initializes the EnergyGrid featurizer with various parameters controlling the energy grid computation and RASPA simulation settings. Ensure RASPA_DIR is set or provided.

```python
from mofscribe.featurizers.chemistry import EnergyGrid

featurizer = EnergyGrid(
    raspa_dir="/path/to/raspa",
    grid_spacing=0.1,
    bin_size_vdw=0.05,
    min_energy_vdw=-10.0,
    max_energy_vdw=10.0,
    cutoff=12.0,
    mof_ff="cpg",
    mol_ff="TraPPE",
    mol_name="CO2",
    sites=("C_co2",),
    tail_corrections=True,
    mixing_rule="Lorentz-Berthelot",
    shifted=False,
    separate_interactions=True,
    run_eqeq=True,
    primitive=True,
)
```

--------------------------------

### Get Implementors

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/compositionstats_featurizer.html

Returns a list of the developers who implemented the CompositionStats featurizer.

```python
CompositionStats().implementors()
```

--------------------------------

### Get Implementors List

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/pore/geometric_properties.html

Returns a list of the names of the individuals who implemented the featurizer.

```python
def implementors(self) -> List[str]:
        return ["Kevin Maik Jablonka", "Maciej Haranczyk and Zeo++ authors"]
```

--------------------------------

### AtomCenteredPHSite Initialization and Featurization

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/topology/atom_centered_ph.html

Demonstrates how to initialize the AtomCenteredPHSite featurizer with custom parameters and how to use its featurize method to extract features from a structure.

```APIDOC
## AtomCenteredPHSite

### Description
Site featurizer for atom-centered statistics of persistence diagrams. This featurizer computes the persistence diagrams for the neighborhood of every site and then aggregates the diagrams by computing certain statistics.

### Class Signature
```python
AtomCenteredPHSite(
    aggregation_functions: Tuple[str] = ("min", "max", "mean", "std"),
    cutoff: float = 12,
    dimensions: Tuple[int] = (1, 2),
    alpha_weight: Optional[str] = None
)
```

### Parameters
*   **aggregation_functions** (Tuple[str]): Aggregations to compute on the persistence diagrams (over birth/death time and persistence). Defaults to ("min", "max", "mean", "std").
*   **cutoff** (float): Consider neighbors of site within this radius (in Angstrom). Defaults to 12.
*   **dimensions** (Tuple[int]): Betti numbers to consider. 0 describes isolated components, 1 cycles and 2 cavities. Defaults to (1, 2).
*   **alpha_weight** (Optional[str]): If specified, use weighted alpha shapes, i.e., replacing the points with balls of varying radii. For instance `atomic_radius_calculated` or `van_der_waals_radius`.

### Methods
#### `featurize(self, s: Union[Structure, IStructure], idx: int) -> np.ndarray`
Computes the persistence diagrams for the neighborhood of a given site and aggregates them.

*   **Parameters**:
    *   **s** (Union[Structure, IStructure]): The input structure.
    *   **idx** (int): The index of the site to featurize.
*   **Returns**:
    *   np.ndarray: An array of computed features.

### Example Usage
```python
from matminer.featurizers.structure import SiteStatsFingerprint
from mofdscribe.topology.atom_centered_ph import AtomCenteredPHSite

# Initialize the featurizer
featurizer = SiteStatsFingerprint(AtomCenteredPHSite(dimensions=(0, 1), cutoff=10.0))

# Assuming 'structure' is a pymatgen Structure object
# features = featurizer.featurize(structure)
# print(features)
```

### Feature Labels
```python
# Example of how to get feature labels
# atom_centered_ph_site = AtomCenteredPHSite(dimensions=(0, 1))
# print(atom_centered_ph_site.feature_labels())
# Output might look like: ['dim0_birth_min', 'dim0_birth_max', ...]
```

### Implementors
*   Kevin Maik Jablonka

### Citations
*   @article{Jiang2021, doi = {10.1038/s41524-021-00493-w}, url = {https://doi.org/10.1038/s41524-021-00493-w}, year = {2021}, month = feb, publisher = {Springer Science and Business Media {LLC}}, volume = {7}, number = {1}, author = {Yi Jiang and Dong Chen and Xin Chen and Tangyi Li and Guo-Wei Wei and Feng Pan}, title = {Topological representations of crystalline compounds for the machine-learning prediction of materials properties}, journal = {npj Computational Materials}}
*   @article{doi:10.1021/acs.jpcc.0c01167, author = {Krishnapriyan, Aditi S. and Haranczyk, Maciej and Morozov, Dmitriy}, title = {Topological Descriptors Help Predict Guest Adsorption in Nanoporous Materials}, journal = {The Journal of Physical Chemistry C}, volume = {124}, number = {17}, pages = {9360-9368}, year = {2020}, doi = {10.1021/acs.jpcc.0c01167}
```

--------------------------------

### Get BU Featurizer Implementors

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/bu_featurizer.html

Retrieves a list of implementors for the underlying featurizer.

```python
def implementors(self) -> List[str]:
        return self._featurizer.implementors()
```

--------------------------------

### QMOF Dataset Initialization

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/datasets/qmof_dataset.html

Initializes the QMOF dataset with specified version, flavor, and duplicate handling options. Raises ValueError if an invalid version is provided.

```python
from mofds.datasets import QMOF

# Initialize with default settings
dataset = QMOF()

# Initialize with specific flavor and drop NaNs
dataset_gcmc_no_nan = QMOF(flavor="gcmc", drop_nan=True)

# Initialize with a specific version
dataset_v001 = QMOF(version="v0.0.1")
```

--------------------------------

### _PBEBandGapIDBench

Source: https://mofdscribe.readthedocs.io/en/latest/api/bench.html

Benchmarking models for the PBE bandgap under in-distribution conditions. This class initializes the PBE bandgap benchmark.

```APIDOC
## _PBEBandGapIDBench

### Description
Benchmarking models for the PBE bandgap under in-distribution conditions. In-distribution implies that we use a cluster stratified splitter that ensures that the ratios of different clusters in the training and test set are the same.
Initialize the PBE bandgap benchmark.

### Parameters
* **model** (_object_) – The model to be benchmarked. Must implement the fit and predict methods.
* **name** (_str_) – The name of the modeling approach.
* **version** (_str_, optional) – Version of the dataset to use. Defaults to “v0.0.1”.
* **features** (_str_, optional) – Description of the features used in the model. Defaults to None.
* **model_type** (_str_, optional) – Model type (e.g. Conv-Net, BERT, XGBoost). Defaults to None.
* **reference** (_str_, optional) – Reference with more details about modeling approach. Defaults to None.
* **implementation** (_str_, optional) – Link to implementation. Defaults to None.
* **debug** (_bool_) – If True, use a small dataset (1% of full dataset) for debugging. Defaults to False.
* **patch_in_ds** (_bool_) – If True, the dataset will be patched into the model class under the ds attribute.
```

--------------------------------

### Get Groups for HashSplitter

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/splitters/splitters.html

Returns the groups for splitting, which are derived from the hashes of the dataset structures.

```python
def _get_groups(self) -> Collection[int]:
        return self._get_hashes()

```

--------------------------------

### Initialize Model Configuration

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/bench/logkHCO2.html

This snippet shows how to initialize a model configuration object with various parameters. It is used when setting up a new model instance.

```python
features=features,
            name=name,
            model_type=model_type,
            reference=reference,
            implementation=implementation,
            debug=debug,
            patch_in_ds=patch_in_ds,
        )
```

--------------------------------

### Get BU Featurizer Citations

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/bu_featurizer.html

Retrieves a list of citations associated with the underlying featurizer.

```python
def citations(self) -> List[str]:
        return self._featurizer.citations()
```

--------------------------------

### enable_logging

Source: https://mofdscribe.readthedocs.io/en/latest/api/helpers.html

Set up the mofdscribe logging with sane defaults.

```APIDOC
## enable_logging()

### Description
Set up the mofdscribe logging with sane defaults.

### Return Type
`List`[`int`]
```

--------------------------------

### Get Citation Information

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/topology/ph_image.html

Provides a list of bibliographic citations relevant to the Persistence Images method.

```bibtex
@article{doi:10.1021/acs.jpcc.0c01167,
            author = {Krishnapriyan, Aditi S. and Haranczyk, Maciej and Morozov, Dmitriy},
            title = {Topological Descriptors Help Predict Guest Adsorption in Nanoporous Materials},
            journal = {The Journal of Physical Chemistry C},
            volume = {124},
            number = {17},
            pages = {9360-9368},
            year = {2020},
            doi = {10.1021/acs.jpcc.0c01167},
            }
```

```bibtex
@article{krishnapriyan_machine_2021,
            title={Machine learning with persistent homology and chemical word embeddings improves prediction accuracy and interpretability in metal-organic frameworks},
            author={Krishnapriyan, Aditi S and Montoya, Joseph and Haranczyk, Maciej and Hummelsh{\o}j, Jens and Morozov, Dmitriy},
            journal = {Scientific Reports},
            volume = {11},
            numer = {1},
            issn = {2045-2322},
            pages = {8888},
            year={2021},
            doi = {10.1038/s41598-021-88027-8}
            }
```

```bibtex
@article{adams2017persistence,
            title={Persistence images: A stable vector representation of persistent homology},
            author={Adams, Henry and Emerson, Tegan and Kirby, Michael and Neville, Rachel and Peterson, Chris and Shipman, Patrick and Chepushtanova, Sofya and Hanson, Eric and Motta, Francis and Ziegelmeier, Lori},
            }
```

--------------------------------

### Initialize and Use BUMatch Featurizer

Source: https://mofdscribe.readthedocs.io/en/latest/api/featurizers.html

Instantiate the BUMatch featurizer with specified topologies and aggregation functions, then apply it to a MOF structure. Note that edge match values are generally less meaningful than vertex match values.

```python
from mofdscribe.bu import BUMatch
from pymatgen.core import Structure
s = Structure.from_file("tests/test_files/bu_test_1.cif")
bu_match = BUMatch(topos=["tbo", "pcu"], aggregations=["mean", "min"])
bu_match.featurize(s)
```

--------------------------------

### Get Implementors

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/bu_matches.html

Returns a list of the implementors of this featurizer. Currently lists Kevin Maik Jablonka.

```python
def implementors(self):
        return ["Kevin Maik Jablonka"]
```

--------------------------------

### Initialize HostGuestFeaturizer

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/hostguest/host_guest_featurizer.html

Instantiate the HostGuestFeaturizer with a base featurizer and desired aggregation methods. Ensure the base featurizer is compatible and not a MultipleFeaturizer.

```python
from mofdscribe.featurizers.hostguest import HostGuestFeaturizer
from matminer.featurizers.structure.sites import SiteStatsFingerprint
from pymatgen.core import Structure
structure = Structure.from_file("tests/data/structures/Co2O3.cif")
featurizer = HostGuestFeaturizer(featurizer=SiteStatsFingerprint.from_preset("SOAP_formation_energy"),
    aggregations=("mean", "std", "min", "max"))
```

--------------------------------

### Get Citations

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/bu_matches.html

Returns a list of citations associated with this featurizer. Currently lists a placeholder citation.

```python
def citations(self):
        return ["Kevin Maik Jablonka and Berend Smit, TBA."]
```

--------------------------------

### Retrieving Labels

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/datasets/arcmof_dataset.html

Method to get specific label values for a given set of indices and label names.

```APIDOC
## Method

### `get_labels(idx: Collection[int], labelnames: Collection[str] = None) -> np.ndarray`

### Description

Retrieves the label values for the specified indices. If `labelnames` is not provided, it defaults to all available label names.

### Parameters

- **idx** (`Collection[int]`) - Required - A collection of integer indices for which to retrieve labels.
- **labelnames** (`Collection[str]`, optional) - The specific label names to retrieve. Defaults to all available label names if not provided.

### Returns

- **np.ndarray**: A NumPy array containing the requested label values.
```

--------------------------------

### Initialize PHVect Featurizer

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/topology/ph_vect.html

Instantiate the PHVect featurizer with various configuration options. Customize atom types, dimensions, UMAP settings, and periodicity.

```python
PHVect(
        atom_types=(
            "C-H-N-O",
            "F-Cl-Br-I",
            "Cu-Mn-Ni-Mo-Fe-Pt-Zn-Ca-Er-Au-Cd-Co-Gd-Na-Sm-Eu-Tb-V-Ag-Nd-U-Ba-Ce-K-Ga-
            Cr-Al-Li-Sc-Ru-In-Mg-Zr-Dy-W-Yb-Y-Ho-Re-Be-Rb-La-Sn-Cs-Pb-Pr-Bi-Tm-Sr-Ti-
            Hf-Ir-Nb-Pd-Hg-Th-Np-Lu-Rh-Pu",
        ),
        compute_for_all_elements=True,
        dimensions=(1, 2),
        min_size=20,
        n_components=20,
        apply_umap=False,
        umap_n_components=2,
        umap_metric="hellinger",
        p=1,
        random_state=None,
        periodic=False,
        no_supercell=False,
        primitive=False,
        alpha_weight=None,
    )
```

--------------------------------

### Directly use RDKitAdaptor

Source: https://mofdscribe.readthedocs.io/en/latest/featurizers/bu_centered/rdkit_derived.html

Demonstrates how to directly instantiate RDKitAdaptor with an RDKit descriptor and a list of output feature names, avoiding the need for subclassing.

```python
from mofdscribe.bu.rdkitadaptor import RDKitAdaptor
from rdkit.Chem.Descriptors3D import InertialShapeFactor

my_featurizer = RDKitAdaptor(InertialShapeFactor, ["inertial_shape_factor"])

```

--------------------------------

### Get Citations

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/compositionstats_featurizer.html

Returns a list of citations relevant to the CompositionStats featurizer. Currently returns an empty list.

```python
CompositionStats().citations()
```

--------------------------------

### Get SphereLikeness Citations

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/shape_featurizer.html

Retrieve the citation information for the Sphere Likeness descriptor. This includes the relevant publication details.

```python
sphere_likeness.citations()
```

--------------------------------

### Initialize VoxelGrid Featurizer

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/pore/voxelgrid.html

Instantiate the VoxelGrid featurizer with custom parameters for grid dimensions, aggregation methods, and property calculations. Defaults are provided for common use cases.

```python
VoxelGrid(
    min_size=30,
    n_x=25,
    n_y=25,
    n_z=25,
    geometry_aggregations=("binary",),
    properties=("X", "electron_affinity"),
    flatten=True,
    regular_bounding_box=True,
    primitive=False,
)
```

--------------------------------

### Initialize BUMatch Featurizer

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/bu_matches.html

Instantiates the BUMatch featurizer, which quantifies the mismatch between MOF building blocks and topological prototypes. Configure parameters like scaling, mismatch fill value, and aggregation methods.

```python
from mofdscribe.bu import BUMatch
from pymatgen.core import Structure

# Example usage:
s = Structure.from_file("tests/test_files/bu_test_1.cif")
bu_match = BUMatch(topos=["tbo", "pcu"], aggregations=["mean", "min"])

# Featurize a structure:
features = bu_match.featurize(s)
print(features)
```

--------------------------------

### Instantiate a Reference Dataset

Source: https://mofdscribe.readthedocs.io/en/latest/getting_started.html

Load a de-duplicated structure dataset, such as QMOF, for use in machine learning studies. Datasets are downloaded to `~/.data/mofdscribe` on first use.

```python
from mofdscribe.datasets import CoRE, QMOF
qmof = QMOF() # will use no labels and the latest version of the dataset

```

--------------------------------

### Get Stratification Column Values

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/splitters/splitters.html

Retrieves the stratification column from the dataset's DataFrame or returns a pre-defined array-like object.

```python
def _get_stratification_col(self) -> Collection[Union[int, float]]:
        if isinstance(self._stratification_col, str):
            return self._ds._df[self._stratification_col].values
        else:
            return self._stratification_col
```

--------------------------------

### Get Feature Labels

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/chemistry/racs.html

Retrieves the labels for the computed RACS features, indicating the specific combination of parameters used for each feature.

```APIDOC
## Get Feature Labels

### Description
Retrieves the labels for the computed RACS features, indicating the specific combination of parameters used for each feature.

### Method
`feature_labels()`

### Returns
- List[str]: A sorted list of feature labels.
```

--------------------------------

### Initialize PHHist Featurizer

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/topology/ph_hist.html

Initialize the PHHist featurizer with custom parameters for atom types, dimensions, histogram resolution, and periodicity.

```python
from mofdscribe.featurizers.topology.ph_hist import PHHist

featurizer = PHHist(
    atom_types=("C-H-N-O", "F-Cl-Br-I"),
    dimensions=(1, 2),
    min_size=20,
    nx=10,
    ny=10,
    periodic=False,
    normed=True,
    primitive=False,
    alpha_weight="van_der_waals_radius"
)
```

--------------------------------

### Get Feature Labels for LSOP

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/lsop_featurizer.html

Returns a list of feature labels for the computed LSOP types. Each label is prefixed with 'lsop_'.

```python
    def feature_labels(self) -> List[str]:
        return [f"lsop_{val}" for val in self.types]

```

--------------------------------

### AccessibleVolume

Source: https://mofdscribe.readthedocs.io/en/latest/api/featurizers.html

Featurizer for calculating accessible volume. Provides methods to get feature labels, citations, implementors, and set fit requests.

```APIDOC
## AccessibleVolume

### Description
Calculates the accessible volume of a material.

### Methods
- `feature_labels()`: Returns the labels for the features generated by this featurizer.
- `citations()`: Returns the citations associated with this featurizer.
- `implementors()`: Returns the implementors of this featurizer.
- `set_fit_request()`: Sets the request for fitting the featurizer.
```

--------------------------------

### Initialize LSOP Featurizer

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/lsop_featurizer.html

Initializes the LSOP featurizer with specified types and parameters. Supports molecules and structures.

```python
# -*- coding: utf-8 -*-
"""Compute local structure order parameters for a fragment."""
from typing import List, Optional, Tuple, Union

import numpy as np
from matminer.featurizers.base import BaseFeaturizer
from pymatgen.analysis.local_env import LocalStructOrderParams
from pymatgen.core import IMolecule, IStructure, Molecule, Structure
from pymatgen.core.periodic_table import DummySpecies

from mofdscribe.featurizers.utils.extend import (
    operates_on_imolecule,
    operates_on_istructure,
    operates_on_molecule,
    operates_on_structure,
)

_default_types = (
    "cn",
    "tet",
    "oct",
    "bcc",
    "sq_pyr",
    "sq_pyr_legacy",
    "tri_bipyr",
    "sq_bipyr",
    "oct_legacy",
    "tri_plan",
    "sq_plan",
    "pent_plan",
    "tri_pyr",
    "pent_pyr",
    "hex_pyr",
    "pent_bipyr",
    "hex_bipyr",
    "T",
    "cuboct",
    "oct_max",
    "tet_max",
    "tri_plan_max",
    "sq_plan_max",
    "pent_plan_max",
    "cuboct_max",
    "bent",
    "see_saw_rect",
    "hex_plan_max",
    "sq_face_cap_trig_pris",
)




@operates_on_structure
@operates_on_istructure
@operates_on_molecule
@operates_on_imolecule
class LSOP(BaseFeaturizer):
    """Compute shape parameters for a fragment.

    The fragments can be a molecule or a molecule that only contains important part (e.g. binding sites)
    of a molecule. The shape parameters are then supposed to quantify the shape of the fragment.
    For instance, a triangular molecule will have a `tri_plan` parameter close to 1.

    While there is a site-based LSOP featurizer in matminer there is none that uses LSOP
    to quantify the shape of some fragment. This featurizers just does that.

    It does so by placing a dummy site at the center of mass
    of the fragment and then computes the LSOP considering all other sites as neighbors.
    """

    def __init__(
        self,
        types: Tuple[str] = _default_types,
        parameters: Optional[List[dict]] = None,
    ) -> None:
        """Initialize the featurizer.

        Args:
            types (Tuple[str]): The types of LSOP to compute.
                For the full list of types
                see: :py:attr:`pymatgen.analysis.local_env.LocalStructOrderParams. __supported_types`.
                Defaults to: ["tet", "oct", "bcc", "sq_pyr", "sq_pyr_legacy", "tri_bipyr", "sq_bipyr",
                "oct_legacy", "tri_plan", "sq_plan", "pent_plan", "tri_pyr", "pent_pyr", "hex_pyr",
                "pent_bipyr", "hex_bipyr", "T", "cuboct", "oct_max", "tet_max", "tri_plan_max",
                "sq_plan_max", "pent_plan_max", "cuboct_max", "bent", "see_saw_rect", "hex_plan_max",
                "sq_face_cap_trig_pris"]
            parameters(List[dict], optional): The parameters to pass to the LocalStructOrderParams object.
        """
        self._lsop = LocalStructOrderParams(types, parameters)
        self.types = types

```

--------------------------------

### Initialize AMD Featurizer

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/chemistry/amd.html

Initializes the AMD featurizer with custom parameters for nearest neighbors, atom types, aggregation methods, and primitive cell computation.

```python
from mofdscribe.featurizers.chemistry import AMD

# Initialize with default parameters
featurizer_default = AMD()

# Initialize with custom parameters
featurizer_custom = AMD(
    k=50,
    atom_types=("C", "O"),
    compute_for_all_elements=False,
    aggregations=("mean", "std"),
    primitive=False
)
```

--------------------------------

### Get Feature Labels for PHVect

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/topology/ph_vect.html

Retrieves the labels for the computed features from a fitted PHVect object. This is useful for understanding the output of the featurizer.

```python
self._get_feature_labels()
```

--------------------------------

### PHImage Featurizer Initialization

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/topology/ph_image.html

Initializes the PHImage featurizer with various parameters to control the topological analysis.

```APIDOC
## PHImage

### Description
Computes the persistence homology image of a crystal structure.

### Parameters
- **atom_types** (Optional[List[str]]): List of atom types to consider. If None, all atom types are considered.
- **compute_for_all_elements** (bool): Whether to compute features for all elements. Defaults to False.
- **min_size** (float): Minimum size for alpha shapes. Defaults to 1.0.
- **image_size** (Tuple[int, int]): The size of the persistence image (number of bins).
- **spread** (float): Spread parameter for the persistence image. Defaults to 0.1.
- **dimensions** (List[int]): List of topological dimensions to consider (e.g., [0, 1, 2]).
- **weight** (Optional[str]): Weighting scheme for alpha shapes. Defaults to None.
- **max_b** (Union[float, List[float]]): Maximum birth value for persistence diagrams. Can be a single float or a list matching the number of dimensions.
- **max_p** (Union[float, List[float]]): Maximum persistence value for persistence diagrams. Can be a single float or a list matching the number of dimensions.
- **max_fit_tolerence** (float): Tolerance for fitting persistence diagrams. Defaults to 0.01.
- **periodic** (bool): Whether to consider periodic boundary conditions. Defaults to True.
- **no_supercell** (bool): Whether to avoid creating supercells. Defaults to False.
- **alpha_weight** (Optional[str]): If specified, uses weighted alpha shapes based on atomic radii (e.g., 'atomic_radius_calculated' or 'van_der_waals_radius').

### Raises
- **AssertionError**: If the length of `max_b` or `max_p` does not match the number of dimensions.
```

--------------------------------

### Get Implementors of Atom-Centered Features

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/topology/atom_centered_ph.html

Returns a list of names for the individuals who implemented the atom-centered features. This is for attribution and understanding the origin of the code.

```python
return ["Kevin Maik Jablonka", "Aditi Krishnapriyan"]
```

--------------------------------

### Enable Logging with Default Configuration

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/helpers.html

Call this function to set up the mofdscribe logging system with predefined handlers and formats for INFO and WARNING levels. It returns a list of handler IDs.

```python
# -*- coding: utf-8 -*-
"""Convenience functions for mofdscribe."""

import sys
from typing import List

from loguru import logger

__all__ = ["enable_logging"]




def enable_logging() -> List[int]:
    """Set up the mofdscribe logging with sane defaults."""
    logger.enable("mofdscribe")

    config = dict(
        handlers=[
            dict(
                sink=sys.stderr,
                format="<green>{time:YYYY-MM-DD HH:mm:ss.SSS Z UTC}</>" " <red>|</> <lvl>{level}</> <red>|</> <cyan>{name}:{function}:{line}</>" " <red>|</> <lvl>{message}</>",
                level="INFO",
            ),
            dict(
                sink=sys.stderr,
                format="<red>{time:YYYY-MM-DD HH:mm:ss.SSS Z UTC} | {level} | {name}:{function}:{line} | {message}</>",
                level="WARNING",
            ),
        ]
    )
    return logger.configure(**config)

```

--------------------------------

### Get Atom-Centered Feature Labels

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/topology/atom_centered_ph.html

Retrieves the labels for atom-centered topological features. This is useful for understanding the naming convention of generated features.

```python
names = []

for atom_type in self.atom_types:
    for aggregation in self.species_aggregation_functions:
        for fl in self.site_featurizer.feature_labels():
            names.append(f"{atom_type}_{aggregation}_{fl}")

return names
```

--------------------------------

### Initialize BU Matcher

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/bu/bu_matches.html

Initializes the BU matcher with various configuration options. Set `return_only_best` to False and provide `aggregations` if you need detailed statistics beyond the minimum RMSD.

```python
def __init__(self, allow_rescale=True, mismatch_fill_value=1000.0,
             return_only_best=True, aggregations=("max", "min", "mean", "std"),
             topos=ALL_AVAILABLE_TOPOS, match="auto", skip_non_fitting_if_possible=True):
        self.allow_rescale = allow_rescale
        self.mismatch_fill_value = mismatch_fill_value
        self.topos = topos
        self.return_only_best = return_only_best
        if not return_only_best and aggregations is None:
            logger.error("If return_only_best is False, aggregations must be set.")
        self.aggregations = aggregations
        if self.return_only_best:
            self.aggregations = ("min",)

        self.match = match
        self.skip_non_fitting_if_possible = skip_non_fitting_if_possible
```

--------------------------------

### Get Feature Importance

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/metrics/adverserial.html

Determine the importance of each feature in distinguishing between the two datasets using the trained classifier's feature importances.

```python
validator.get_feature_importance()
```

--------------------------------

### EnergyGrid Featurizer Initialization

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/chemistry/energygrid.html

Initializes the EnergyGrid featurizer with various parameters to control the energy grid computation.

```APIDOC
## EnergyGrid(raspa_dir: Optional[str] = None, grid_spacing: float = 0.1, bin_size_vdw: float = 0.05, min_energy_vdw: float = -1.0, max_energy_vdw: float = 1.0, cutoff: float = 12.0, mof_ff: str = 'UFF', mol_ff: str = 'UFF', mol_name: str = 'CO2', sites: Tuple[str] = ('C_co2',), tail_corrections: bool = True, mixing_rule: str = 'Lorentz-Berthelot', shifted: bool = False, separate_interactions: bool = True, run_eqeq: bool = True, primitive: bool = True)

### Description
Initializes the EnergyGrid featurizer. This class computes energy diagrams for specified Van-der-Waals sites within a MOF structure.

### Parameters
- **raspa_dir** (Optional[str]) - Path to the RASPA directory. Defaults to the RASPA_DIR environment variable or auto-detection.
- **grid_spacing** (float) - Spacing for the grid points in the energy diagram. Defaults to 0.1.
- **bin_size_vdw** (float) - Bin size for the Van der Waals energy histogram. Defaults to 0.05.
- **min_energy_vdw** (float) - Minimum energy value for the Van der Waals histogram. Defaults to -1.0.
- **max_energy_vdw** (float) - Maximum energy value for the Van der Waals histogram. Defaults to 1.0.
- **cutoff** (float) - Cutoff distance for interactions. Defaults to 12.0.
- **mof_ff** (str) - Force field for the MOF framework. Defaults to 'UFF'.
- **mol_ff** (str) - Force field for the guest molecule. Defaults to 'UFF'.
- **mol_name** (str) - Name of the guest molecule. Defaults to 'CO2'.
- **sites** (Tuple[str]) - Names of the Van-der-Waals sites for which energy diagrams are computed. Defaults to ('C_co2',).
- **tail_corrections** (bool) - Whether to use analytical tail-correction for interactions beyond the cutoff. Defaults to True.
- **mixing_rule** (str) - Mixing rule for framework and guest molecule force fields. Available options: `Jorgenson`, `Lorentz-Berthelot`. Defaults to "Lorentz-Berthelot".
- **shifted** (bool) - Whether to shift the potential to be zero at the cutoff. Defaults to False.
- **separate_interactions** (bool) - Whether to use the framework's force field for framework-molecule interactions. Defaults to True.
- **run_eqeq** (bool) - Whether to run EqEq to compute charges. Defaults to True.
- **primitive** (bool) - Whether to reduce the structure to its primitive form before computation. Defaults to True.

### Raises
- **ValueError**: If `raspa_dir` is not a valid directory and cannot be detected.
```

--------------------------------

### Get Feature Labels for PartialChargeHistogram

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/chemistry/partialchargehistogram.html

Retrieve the descriptive labels for each bin in the partial charge histogram. These labels correspond to the charge ranges.

```python
from mofdscribe.featurizers.chemistry import PartialChargeHistogram

featurizer = PartialChargeHistogram()
labels = featurizer.feature_labels()
print(labels)
```

--------------------------------

### Initialize PBEBandGapIDBench

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/bench/pbegap.html

Initializes the PBEBandGapIDBench for benchmarking PBE bandgap prediction models. It configures the dataset splitting strategy to ensure similar cluster ratios in training and testing sets for in-distribution evaluation. The `debug` flag allows for using a smaller dataset subset for faster testing.

```python
# -*- coding: utf-8 -*-
"""In-dataset predictions for PBE bandgaps."""
from typing import Optional

from mofdscribe.bench.mofbench import MOFBenchRegression
from mofdscribe.datasets import QMOFDataset
from mofdscribe.splitters.splitters import HashSplitter

__all__ = ("PBEBandGapIDBench",)




class PBEBandGapIDBench(MOFBenchRegression):
    """Benchmarking models for the PBE bandgap under in-distribution conditions.

    In-distribution implies that we use a cluster stratified splitter
    that ensures that the ratios of different clusters in the training
    and test set are the same.
    """

    def __init__(
        self,
        model,
        name: str,
        version: Optional[str] = "v0.0.1",
        features: Optional[str] = None,
        model_type: Optional[str] = None,
        reference: Optional[str] = None,
        implementation: Optional[str] = None,
        debug: bool = False,
        patch_in_ds: bool = False,
    ):
        """Initialize the PBE bandgap benchmark.

        Args:
            model (object): The model to be benchmarked.
                Must implement the `fit` and `predict` methods.
            name (str): The name of the modeling approach.
            version (str, optional): Version of the dataset to use.
                Defaults to "v0.0.1".
            features (str, optional): Description of the features used in the model.
                Defaults to None.
            model_type (str, optional): Model type (e.g. Conv-Net, BERT, XGBoost).
                Defaults to None.
            reference (str, optional): Reference with more details about modeling approach.
                Defaults to None.
            implementation (str, optional): Link to implementation. Defaults to None.
            debug (bool): If True, use a small dataset (1% of full dataset) for debugging.
                Defaults to False.
            patch_in_ds (bool): If True, the dataset will be patched into the model class
                under the `ds` attribute.
        """
        super().__init__(
            model,
            ds=QMOFDataset(version),
            splitter=HashSplitter(
                QMOFDataset(version, flavor="all"),
                stratification_col="outputs.pbe.bandgap",
                sample_frac=0.01 if debug else 1.0,
            ),
            target=["outputs.pbe.bandgap"],
            task="pbe_bandgap_id",
            k=5,
            version=version,
            features=features,
            name=name,
            model_type=model_type,
            reference=reference,
            implementation=implementation,
            debug=debug,
            patch_in_ds=patch_in_ds,
        )

```

--------------------------------

### Get Feature Labels for PartialChargeStats

Source: https://mofdscribe.readthedocs.io/en/latest/_modules/mofdscribe/featurizers/chemistry/partialchargestats.html

Retrieves the descriptive labels for the features generated by the PartialChargeStats featurizer. These labels correspond to the aggregations used.

```python
featurizer.feature_labels()
```