SALI

calculate_sali(data_frame, smiles_col='SMILES', activity_col='Activity')[source]

Calculate the Structure-Activity Landscape Index (SALI) for a dataframe of molecules and activities.

Parameters:

  • data_frame (DataFrame) – DataFrame with columns for SMILES and Activity.

  • smiles_col (str) – The name of the column containing SMILES strings.

  • activity_col (str) – The name of the column containing activity values.

Return type:

DataFrame

Returns:

DataFrame containing pairwise SALI values and metadata.

plot_sali_pairs(data_frame, smiles_col='SMILES', activity_col='Activity', similarity_col='Tanimoto_Similarity', delta_activity_col='Delta_Activity', sali_col='SALI', similarity_cutoff=0.5, delta_activity_cutoff=1.0, mols_per_row=4, pairs_to_show=10)[source]

Filters and visualizes molecule pairs from a SALI results DataFrame in a grid. Ensures the more active compound of each pair is always displayed on the left.

Parameters:

  • data_frame (DataFrame) – DataFrame containing pairwise SALI results.

  • smiles_col (str) – Base name of the SMILES column.

  • activity_col (str) – Base name of the activity column.

  • similarity_col (str) – Column name for Tanimoto similarity.

  • delta_activity_col (str) – Column name for the activity difference.

  • sali_col (str) – Column name for the SALI index.

  • similarity_cutoff (float) – Minimum similarity threshold for inclusion.

  • delta_activity_cutoff (float) – Minimum activity difference threshold for inclusion.

  • mols_per_row (int) – Number of molecules to display per row in the grid image.

  • pairs_to_show (int) – Maximum number of top SALI pairs to visualize.

Return type:

object

Returns:

An RDKit grid image showing aligned molecule pairs.