Actions
auroris.curation.actions.BaseAction
Bases: BaseModel, ABC
An action in the curation process.
The importance of reproducibility
One of the main goals in designing auroris is to make it easy to reproduce the curation process.
Reproducibility is key to scientific research. This is why a BaseAction needs to be serializable and
uniquely identified by a name.
Attributes:
| Name | Type | Description |
|---|---|---|
name |
str
|
The name that uniquely identifies the action. This is used to serialize and deserialize the action. |
prefix |
str
|
This prefix is used when an action adds columns to a dataset. If not set, it defaults to the name in uppercase. |
StereoIsomerACDetection
Bases: BaseAction
Automatic detection of activity shift between stereoisomers.
See auroris.curation.functional.detect_streoisomer_activity_cliff for the docs of the
stereoisomer_id_col, y_cols and threshold attributes
Attributes:
| Name | Type | Description |
|---|---|---|
mol_col |
Optional[str]
|
Column with the SMILES or RDKit Molecule objects. If specified, will be used to render an image for the activity cliffs. |
Deduplication
Bases: BaseAction
Automatic detection of outliers.
See auroris.curation.functional.deduplicate for the docs of the
deduplicate_on, y_cols, keep and method attributes
Discretization
Bases: BaseAction
Thresholding bioactivity columns to binary or multiclass labels.
See auroris.curation.functional.discretize for the docs of the
thresholds, inplace, allow_nan and label_order attributes
Attributes:
| Name | Type | Description |
|---|---|---|
input_column |
str
|
The column to discretize. |
log_scale |
bool
|
Whether a visual depiction of the discretization should be on a log scale. |
ContinuousDistributionVisualization
Bases: BaseAction
Visualize one or more continuous distribution(s).
See auroris.visualization.visualize_continuous_distribution for the docs of the
log_scale and bins attributes
Attributes:
| Name | Type | Description |
|---|---|---|
y_cols |
List[str]
|
The columns whose distributions should be visualized. |
MoleculeCuration
Bases: BaseAction
Automated molecule curation and chemistry space distribution.
See auroris.curation.functional.curate_molecules for the docs of the
remove_stereo, fix_mol, count_stereoisomers, and count_stereocenters attributes
Attributes:
| Name | Type | Description |
|---|---|---|
input_column |
str
|
The name of the column that has the molecules (either |
X_col |
Optional[str]
|
Column with custom features for each of the molecules. If None, will use ECFP. |
y_cols |
Optional[Union[str, List[str]]]
|
Column names for bioactivities, which will be used to colorcode the chemical space visualization. |
OutlierDetection
Bases: BaseAction
Automatic detection of outliers.
See auroris.curation.functional.detect_outliers for the docs of the
method and kwargs attributes
Attributes:
| Name | Type | Description |
|---|---|---|
columns |
List[str]
|
The columns for which to detect outliers. |