Overview of available features

Data Sources

DataSource: Base class for data sources.

Data sources are used to load data from a source programmatically.

Storage

ChemStore: Interface for storing and managing chemical data.

Data storage classes are used to store and manage chemical data. More information can be found in the basic data representation tutorial and the advanced data representation tutorial.

SMILES Standardizers

ChemStandardizer: Base class for SMILES standardizers.

Standardizers to convert SMILES to a standardized form.

Data Filters

DataFilter: Base class for data filters.

Data filters are used to filter data based on some criteria. Examples can be found in the data preparation tutorial.

Descriptor Sets

DescriptorSet: Base class for descriptor sets.

Descriptor sets are used to calculate molecular descriptors for a set of molecules. Examples can be found in the descriptor calculation tutorial.

  • ExtendedValenceSignature: ExtendedValenceSignature

  • Mold2: Mold2

  • Mordred: Mordred

  • PaDEL: PaDEL

  • ProteinDescriptorSet: ProteinDescriptorSet

    • ProDec: ProDec

  • Fingerprint: Fingerprint

    • CDKAtomPairs2DFP: CDKAtomPairs2DFP

    • CDKEStateFP: CDKEStateFP

    • CDKExtendedFP: CDKExtendedFP

    • CDKFP: CDKFP

    • CDKGraphOnlyFP: CDKGraphOnlyFP

    • CDKKlekotaRothFP: CDKKlekotaRothFP

    • CDKMACCSFP: CDKMACCSFP

    • CDKPubchemFP: CDKPubchemFP

    • CDKSubstructureFP: CDKSubstructureFP

Data Splitters

DataSplit: Base class for data splitters.

Data splitters are used to split data into training and test sets. Examples can be found in the data splitting tutorial.

  • LeaveTargetsOut: LeaveTargetsOut

  • PCMSplit: PCMSplit

    • TemporalPerTarget: TemporalPerTarget

Data Filters

DataFilter: Base class for Data Filters.

Data filters are used to filter rows from a dataframe. Examples can be found in the data preparation tutorial.

Feature Filters

FeatureFilter: Base class for feature filters.

Feature filters are used to filter features based on some criteria. Examples can be found in the data preparation tutorial.

Feature Transformers

FeatureTransformer: Base class for feature transformers.

Feature transformers are used for feature standardization and transformation Examples can be found in the data preparation tutorial.

Target Transformers

TargetTransformer: Base class for target transformers.

Target transformers are used for target discretization and transformation.

Imputers

Imputer: Base class for imputers.

Imputers are used for filling missing values in the descriptor or target values. Examples can be found in the data preparation tutorial and the multi task modelling tutorial.

Models

QSPRModel: Base class for models.

Models are used to predict properties of molecules. A general example can be found in the quick start tutorial. More detailed information can be found throughout the basic and advanced modelling tutorials.

More information can be found in the deep learning tutorial.

  • DNNModel: DNNModel

  • ChempropModel: ChempropModel (See Chemprop tutorial.)

  • PyBoostModel: PyBoostModel

Metrics

Metric: Base class for metrics

Metrics are used to evaluate the performance of models. More information can be found in the model assessment tutorial.

Model Assessors

ModelAssessor: Base class for model assessors.

Model assessors are used to assess the performance of models. More information be found in the model assessment tutorial.

Hyperparameter Optimizers

HyperparameterOptimization: Base class for hyperparameter optimizers.

Hyperparameter optimizers are used to optimize the hyperparameters of models. More information can be found in the hyperparameter optimization tutorial.

Model Plots

ModelPlot: Base class for model plots.

Model plots are used to visualize the performance of models. Examples can be found throughout the basic and advanced modelling tutorials.

Monitors

Monitors are used to monitor the training of models. More information can be found in the model monitoring tutorial.

Scaffolds

Scaffold: Base class for scaffolds.

Class for calculating molecular scaffolds of different kinds

Clustering

MoleculeClusters: Base class for clustering molecules.

Classes for clustering molecules