Iterative enumeration¶

crem.utils.enumerate_compounds applies generation repeatedly: molecules produced in one iteration become the inputs to the next. It has two modes:

• mode="scaffold" — scaffold decoration, built on grow_mol (hydrogens are replaced with fragments).
• mode="analogs" — analog enumeration, built on mutate_mol.

It returns the distinct molecules generated across all iterations (as Mol objects, or SMILES with return_smi=True).

Scaffold decoration¶

Decorate specific positions of a scaffold over several rounds. In scaffold mode, protect_added_frag is forced to True, so fragments are never attached to fragments added on a previous iteration — growth happens only at the chosen positions.

from rdkit import Chem
from crem.utils import enumerate_compounds

mol = Chem.MolFromSmiles("Cc1cccc(Cl)c1")  # 1-chloro-3-methylbenzene

mols = enumerate_compounds(
    mol,
    db_fname="fragments.db",
    mode="scaffold",
    n_iterations=3,
    radius=3,
    max_replacements=2,
    replace_ids=[2, 4, 6],     # only these atoms are decorated
    return_smi=True,
)
print(mols)

Analog enumeration¶

In analogs mode the molecule is mutated. Supply explicit hydrogens (Chem.AddHs) if you also want hydrogens replaced. Set protect_added_frag=True to keep newly added fragments from being mutated further.

mol = Chem.MolFromSmiles("c1ccccc1C")
analogs = enumerate_compounds(
    mol,
    db_fname="fragments.db",
    mode="analogs",
    n_iterations=2,
    max_replacements=50,
    return_smi=True,
)

Key parameters¶

Parameter	Meaning
mode	"scaffold" (decorate) or "analogs" (mutate). Default "scaffold".
n_iterations	Number of generation rounds. Default 1.
max_replacements	Max replacements per molecule per iteration (random subset). Default None = all.
replace_ids / protected_ids	Restrict the editable atoms.
protect_added_frag	Prevent edits to previously added fragments. Forced True in scaffold mode. Default False.
min_freq	Minimum fragment frequency. Default 0.
return_smi	Return SMILES instead of Mol objects. Default False.
ncpu	Number of cores. None = all CPUs.

Extra keyword arguments are forwarded to grow_mol (scaffold mode) or mutate_mol (analogs mode) — for example min_atoms / max_atoms for decoration, or min_size / max_size / min_inc / max_inc / replace_cycles for analogs. See crem.utils for the full signature.