Oximachinerunner API reference

Implements methods to use oximachine as part of a Python package

class oximachinerunner.OximachineRunner(modelname='all', automatic_download=True)[source]

Bases: object

Loads a model and then runs the prediction

__init__(modelname='all', automatic_download=True)[source]
Parameters

  • modelname (str, optional) – [description]. Defaults to ‘all’. Use it to specifiy a model. You can view all available models with the .available_models property

  • automatic_download (bool, optional) – [description]. Defaults to True.

__repr__()[source]

Return repr(self).

__weakref__

list of weak references to the object (if defined)

property available_models

List all the available models.

Return type

List[str]

property default_mapping

Return the default mapping between model name and filename

Return type

Dict[str, str]

property feature_names

Get a list of feature names

Return type

List[str]

property featureset

Return the list of feature names

Return type

List[str]

load_model()[source]

Load the model and populate the namespace with the model objects.

property model

Return the model object with .predict method

run_oximachine(structure)[source]

Runs oximachine after attempting to guess what structure is

Parameters

  • structure (Union[str, os.PathLike, Structure, Atoms]) –

  • be a pymatgen.Structure (can) –

  • or a filepath as str or (ase.Atoms) –

  • os.PathLike –

  • we then attempt to parse with pymatgen. (which) –

Raises

  • ParsingError – In case the format of structure is not implemented or in case we cannot convert the input into a pymatgen Structure object.

  • FeaturizationError – In case the featurization fails.

  • PredictionError – In case the prediction fails.

Returns

with the keys metal_indices, metal_symbols,

prediction, max_probas, base_predictions

Return type

OrderedDict

property scaler

Return the scaler object with .transform method

Some general utility functions for the oxidation state mining project

class oximachinerunner.utils.SymbolNameDict[source]

Bases: object

Parses the periodic table json and returns a dictionary with symbol: longname

__init__()[source]

Initialize self. See help(type(self)) for accurate signature.

__weakref__

list of weak references to the object (if defined)

get_symbol_name_dict(only_metal=True)[source]

Iterates over keys and returns the symbol: name dict.

oximachinerunner.utils.cbk_for_urlretrieve(a, b, c)[source]

Callback function for showing process

oximachinerunner.utils.diff_to_18e(nvalence)[source]

The number of electrons to donate to achieve 18 electrons might be an interesting descriptor, though there are more stable electron configurations

oximachinerunner.utils.download_all()[source]

Download model and scaler

oximachinerunner.utils.download_model(url, destination, md5)[source]
Downloads file from url to destination

and checks md5 hash

Parameters

  • url (str) – URL

  • destination (Union[Path, str]) – Path to which the downloaded file will be saved

  • md5 (str) – Expected md5 hash

Raises

  • Exception – [description]

  • Exception – [description]

oximachinerunner.utils.flatten(items)[source]

Yield items from any nested iterable; see Reference.

oximachinerunner.utils.has_metal_sites(structure)[source]

Returns True if there is a metal in the structure.

oximachinerunner.utils.md5sum(filename)[source]

Gets the md5 hash of a file

oximachinerunner.utils.model_exists(path, md5)[source]

Checks whether a model if the expected md5 hash exists at the path

oximachinerunner.utils.read_pickle(filepath)[source]

Does what it says. Nothing more and nothing less. Takes a pickle file path and unpickles it

Defining custom exceptions for OximachineRunner

exception oximachinerunner.errors.FeaturizationError[source]

Bases: oximachinerunner.errors.OximachineRunnerException

Error that is thrown if the featurization fails

exception oximachinerunner.errors.ModelNotFoundError[source]

Bases: oximachinerunner.errors.OximachineRunnerException

Error that is thrown if the model could not be found

exception oximachinerunner.errors.NoMetalError[source]

Bases: oximachinerunner.errors.OximachineRunnerException

Error that is thrown if there is no metal in the structure

exception oximachinerunner.errors.OximachineRunnerException[source]

Bases: Exception

General class for oximachine errors

__weakref__

list of weak references to the object (if defined)

exception oximachinerunner.errors.ParsingError[source]

Bases: oximachinerunner.errors.OximachineRunnerException

Error that is thrown if we cannot convert the structure into a pymatgen Structure object

exception oximachinerunner.errors.PredictionError[source]

Bases: oximachinerunner.errors.OximachineRunnerException

Error that is thrown if the prediction fails

Tutorials