datamol icon indicating copy to clipboard operation
datamol copied to clipboard

lasso only color when using smarts_list but not atom_indices

Open OleinikovasV opened this issue 1 year ago • 0 comments

Really like lasso functionality, but at times I would prefer to pass the atom indices and have them colored, but it seems that it is all grey, as they are not being assigned.

See example below: lasso only color when using smarts_list but not atom_indices

import datamol as dm

input_smiles = "Cc1c(scn1)c2ccc(cc2)CNC(=O)[C@@H]3C[C@H](CN3C(=O)[C@H](C(C)(C)C)NC(=O)C)O"

dm.lasso_highlight_image(
    input_smiles,
    search_molecules = ["N1CC(O)CC1C(=O)"],
    color_list=[(0.9, 0.5, 0.1)],
    mol_size=(500, 400),
    use_svg=False
)

Image

If I instead atom_indices directly, it gives me a gray lasso only (which is not useful when having multiple highlights!):

dm.lasso_highlight_image(
    input_smiles,
    # search_molecules = ["N1CC(O)CC1C(=O)"],
    atom_indices=[[20, 19, 18, 17, 16, 15, 14, 32]],
    color_list=[(0.9, 0.5, 0.1)],
    mol_size=(500, 400),
    use_svg=False
)

Image

OleinikovasV avatar Mar 07 '25 13:03 OleinikovasV