rdkit-buildutils 0.3.1

RDKit utilities: placeholder substitution, matching, R-group decomposition, scaffold normalization

rdkit_buildutils

Utilities built on top of RDKit for constructing, normalizing and decomposing molecules with placeholder substitution.

The package supports workflows involving monomers, R-group decomposition, query matching, and scaffold normalization. All helpers are general-purpose and RDKit-only.

⚠️ Developed in a personal context for scientific support. Not affiliated with RDKit or any specific organization.

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✨ Features

Core (rdkit_buildutils/core.py)

• convert_r_to_atom_map(smiles_r): [R1] → [*:1].
• build_molecule_final(base_smiles, **substituents): substitute placeholders (r1="CC", …).

R-group (rdkit_buildutils/rgroup_core.py)

• to_core, normalize_rgroup_smiles, to_peptidic_scaffold.
• anchored_smiles, build_code_map.
• decompose_with_cores, decompose_for_monomer.

Scaffold normalization (rdkit_buildutils/scaffold_normalize.py)

• canonical_ranks, r_to_atommap, relabel_dummies_canonically.
• normalize_scaffold_chiral (D/L preserving).

New in 0.3

• Logging: silence_rdkit, silence_rdkit_all
• Standardization: standardize_for_matching
• HELM: helm_to_query_mol
• Query variants: make_scaffold_variants (strict/nostereo/kekule/dropR/peptidic*)
• R-group extraction: extract_rgroup_smiles
• Filters: is_aminoacid_like_scaffold, keep_targets_with_single_aa_core
• Matching: prepare_targets, find_monomer_matches
• RGD assign: assign_rgroups_for_matches, build_code_map_from_table
• Datatypes: MonomerScaffold, MatchRecord, RAssignment

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📦 Installation

# pip-only (uses rdkit-pypi)
pip install rdkit_buildutils
# or, if you install RDKit via conda-forge, install rdkit separately and then:
pip install rdkit_buildutils

Optional extras:

pip install rdkit_buildutils[pandas]   # pandas helpers
pip install rdkit_buildutils[db]       # adapters you may write externally

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🔬 Examples

from rdkit_buildutils import convert_r_to_atom_map, build_molecule_final
from rdkit import Chem

scaffold = "[R1]NCC(=O)[R2]"
core = convert_r_to_atom_map(scaffold)  # -> [*:1]NCC(=O)[*:2]
mol = build_molecule_final(core, r1="C", r2="OC")
print(Chem.MolToSmiles(mol))

R-group assignment with matching (sketch):

from rdkit_buildutils import (
  helm_to_query_mol, MonomerScaffold, prepare_targets, find_monomer_matches,
  assign_rgroups_for_matches
)
# build MonomerScaffold list...
# prepare targets...
# matches = find_monomer_matches(...)
# assignments = assign_rgroups_for_matches(...)

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✅ License

MIT © 2025 Fabio Nelli