CIMtools.preprocessing package

class CIMtools.preprocessing.CGR(cgr_type='0')

Bases: CIMtoolsTransformerMixin

fit(x, y=None)

Do nothing and return the estimator unchanged

This method is just there to implement the usual API and hence work in pipelines.

fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → CGR

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → CGR

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

transform(x)
class CIMtools.preprocessing.CGRToMatrix(charge=True, is_radical=False, isotope=False, hybridization=False, neighbors=False, in_ring=False, adjacent=True)

Bases: GraphToMatrix

fit(x, y=None)

Do nothing and return the estimator unchanged

This method is just there to implement the usual API and hence work in pipelines.

fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → CGRToMatrix

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → CGRToMatrix

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

transform(x)
class CIMtools.preprocessing.Conditions(temperature=298.15, pressure=100000, solvents=None)

Bases: object

property pressure
property solvents
property temperature
class CIMtools.preprocessing.ConditionsToDataFrame(max_solvents=1)

Bases: CIMtoolsTransformerMixin

fit(x, y=None)

Do nothing and return the estimator unchanged

This method is just there to implement the usual API and hence work in pipelines.

fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_feature_names()

Get feature names.

Returns

feature_names – Names of the features produced by transform.

Return type

list of strings

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → ConditionsToDataFrame

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → ConditionsToDataFrame

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

transform(x)
class CIMtools.preprocessing.DictToConditions(temperature=None, pressure=None, solvents=None, amounts=None, default_temperature=298.15, default_pressure=100000, default_first_solvent='water', default_first_amount=1)

Bases: CIMtoolsTransformerMixin

Dictionary to Conditions mapper

Parameters

  • temperature – name of temperature key

  • pressure – name of pressure key

  • solvents – names of solvents keys

  • amounts – names of solvents amounts keys

fit(x, y=None)

Do nothing and return the estimator unchanged

This method is just there to implement the usual API and hence work in pipelines.

fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → DictToConditions

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → DictToConditions

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

transform(x)
class CIMtools.preprocessing.EquationTransformer(equation='x')

Bases: CIMtoolsTransformerMixin

fit(x, y=None)

Do nothing and return the estimator unchanged

This method is just there to implement the usual API and hence work in pipelines.

fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_feature_names()

Get feature names.

Returns

feature_names – Names of the features produced by transform.

Return type

list of strings

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → EquationTransformer

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → EquationTransformer

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

transform(x)
class CIMtools.preprocessing.Fragmentor(fragment_type=3, min_length=2, max_length=10, cgr_dynbonds=0, doallways=False, useformalcharge=False, header=None, workpath='.', version='2017', verbose=False, remove_rare_ratio=0, return_domain=False)

Bases: BaseEstimator, TransformerMixin

ISIDA Fragmentor wrapper

Parameters

  • fragment_type – fragmentation type. see Fragmentor manual (-t)

  • min_length – minimal length of fragments. see Fragmentor manual (-l)

  • max_length – maximal length of fragments. see Fragmentor manual (-u)

  • cgr_dynbonds – see Fragmentor manual (-d)

  • doallways – see Fragmentor manual (–DoAllWays)

  • useformalcharge – see Fragmentor manual (–UseFormalCharge)

  • header –

    if None descriptors will be generated on train set if False Fragmentor will work in headless mode. in this mod fit unusable and Fragmentor return

    all found descriptors

    else path string to existing header file acceptable

  • workpath – path for temp files

  • version – fragmentor version

  • verbose – silent Fragmentor output

  • remove_rare_ratio – if descriptors found on train less then given ratio it will be removed from header. if partial fit used, be sure to use finalize method. unusable if headless mode set

  • return_domain – add AD bool column. False in column is: molecule/CGR has new features

delete_work_path()
finalize()

finalize partial fitting procedure

fit(x, y=None)

Compute the header.

fit_transform(x, y=None)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_feature_names()

Get feature names.

Returns

feature_names – Names of the features produced by transform.

Return type

list of strings

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

partial_fit(x, y=None)
set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → Fragmentor

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_partial_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → Fragmentor

Request metadata passed to the partial_fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to partial_fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to partial_fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in partial_fit.

Returns

self – The updated object.

Return type

object

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → Fragmentor

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

set_work_path(workpath)
transform(x)
class CIMtools.preprocessing.FragmentorFingerprint(fingerprint_size=12, bits_count=4, bits_active=2, fragment_type=3, min_length=2, max_length=10, cgr_dynbonds=0, doallways=False, useformalcharge=False, workpath='.', version='2017', verbose=False)

Bases: BaseEstimator, TransformerMixin

ISIDA Fragmentor fragments to fingerprints

Parameters

  • fingerprint_size – exponent of 2 of fingerprint length

  • bits_count – include number of fragment descriptors into fingerprint. for example by default: if number is one: only one set of bits will be activated. if number is tho: additional set of bits will be activated (totally up to 2*bits_active). if number is four or greater: will be activated up 4*bits_active bits

  • bits_active – number of activated bits for each fragment (need for prevent collision bit lost)

  • workpath – path for temp files.

  • version – fragmentor version. need for selecting Fragmentor executables named as fragmentor-{version}

delete_work_path()
fit(x, y=None)
fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → FragmentorFingerprint

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → FragmentorFingerprint

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

set_work_path(workpath)
transform(x)
transform_bitset(x)
class CIMtools.preprocessing.MoleculesToMatrix(charge=True, is_radical=False, isotope=False, hybridization=False, neighbors=False, implicit_hydrogens=False, total_hydrogens=False, in_ring=False, adjacent=True)

Bases: GraphToMatrix

fit(x, y=None)

Do nothing and return the estimator unchanged

This method is just there to implement the usual API and hence work in pipelines.

fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → MoleculesToMatrix

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → MoleculesToMatrix

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

transform(x)
class CIMtools.preprocessing.RDTool(algorithm='max', verbose=False)

Bases: CIMtoolsTransformerMixin

Parameters

algorithm – ‘max’,’min’,’mixture’

fit(x, y=None)

Do nothing and return the estimator unchanged

This method is just there to implement the usual API and hence work in pipelines.

fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → RDTool

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → RDTool

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

transform(x)
class CIMtools.preprocessing.SolventVectorizer(polarizability_form1=True, polarizability_form2=True, permettivity_form1=True, permettivity_form2=True, permettivity_form3=True, permettivity_form4=True, permettivity_polarizability=True, alpha_kamlet_taft=True, beta_kamlet_taft=True, pi_kamlet_taft=True, spp_katalan=True, sb_katalan=True, sa_katalan=True)

Bases: CIMtoolsTransformerMixin

fit(x, y=None)

Do nothing and return the estimator unchanged

This method is just there to implement the usual API and hence work in pipelines.

fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_feature_names()

Get feature names.

Returns

feature_names – Names of the features produced by transform.

Return type

list of strings

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → SolventVectorizer

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → SolventVectorizer

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

transform(x)
class CIMtools.preprocessing.StandardizeCGR

Bases: CIMtoolsTransformerMixin

Reactions and Molecules standardization

For molecules kekule/thiele and groups standardization procedures will be applied.

fit(x, y=None)

Do nothing and return the estimator unchanged

This method is just there to implement the usual API and hence work in pipelines.

fit_transform(X, y=None, **fit_params)

Fit to data, then transform it.

Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.

Parameters

  • X (array-like of shape (n_samples, n_features)) – Input samples.

  • y (array-like of shape (n_samples,) or (n_samples, n_outputs), default=None) – Target values (None for unsupervised transformations).

  • **fit_params (dict) – Additional fit parameters.

Returns

X_new – Transformed array.

Return type

ndarray array of shape (n_samples, n_features_new)

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns

routing – A MetadataRequest encapsulating routing information.

Return type

MetadataRequest

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, default=True) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params – Parameter names mapped to their values.

Return type

dict

set_fit_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → StandardizeCGR

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in fit.

Returns

self – The updated object.

Return type

object

set_output(*, transform=None)

Set output container.

See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.

Parameters

transform ({"default", "pandas"}, default=None) –

Configure output of transform and fit_transform.

  • ”default”: Default output format of a transformer

  • ”pandas”: DataFrame output

  • None: Transform configuration is unchanged

Returns

self – Estimator instance.

Return type

estimator instance

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**params (dict) – Estimator parameters.

Returns

self – Estimator instance.

Return type

estimator instance

set_transform_request(*, x: Union[bool, None, str] = '$UNCHANGED$') → StandardizeCGR

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config()). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a pipeline.Pipeline. Otherwise it has no effect.

Parameters

x (str, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED) – Metadata routing for x parameter in transform.

Returns

self – The updated object.

Return type

object

transform(x)