rdsl 0.1.3

A powerful Domain Specific Language (DSL) for expressive molecule selection and extraction in RDKit.

RDSL: RDKit Domain Specific Language

rdsl is a domain-specific language (DSL) for selecting atoms and extracting sub-molecules from RDKit molecules. Heavily inspired by PyMOL's selection syntax.

Installation

pip install rdsl

Usage

CLI

rdsl /tmp/7RPZ.pdb /tmp/7RPZ.selected.sdf "resn 6IC"

Atom Selection

The select_atom_ids function returns a numpy array of indices for atoms matching the expression.

from rdkit import Chem
from rdsl import select_atom_ids

mol = Chem.MolFromSmiles("Cc1ccccc1O")

# Simple keyword selections
aromatic_atoms = select_atom_ids(mol, "aromatic")

# Complex logical expressions
carbon_rings = select_atom_ids(mol, "elem C and ring")

# Geometric and distance-based queries
near_oxygen = select_atom_ids(mol, "all within 3.0 of elem O")

# Custom SMARTS matching
benzene_matches = select_atom_ids(mol, 'smarts "c1ccccc1"')

Molecule Extraction

The select_molecule function extracts the selected atoms into a new Molecule object.

from rdsl import select_molecule

# Extract the benzene ring, automatically capping broken bonds with hydrogens
result = select_molecule(mol, "aromatic")
submol = result.mol

# Track where atoms came from
original_idx = result.atom_mapping[0]

# Handle broken bonds with wildcards (useful for fragments)
result = select_molecule(mol, "aromatic", broken_bonds="wildcards")

Functional Group Detection

Identify functional groups with built-in patterns that respect chemical hierarchies.

from rdsl import get_functional_group_matches

# Returns a pandas DataFrame with identified groups
df = get_functional_group_matches(mol)
print(df[["name", "atom_ids", "group"]])

For an online web server from the original authors, see SmartChemist.

Syntax Guide

rdsl supports a wide range of operators. See examples.ipynb for a comprehensive list of selection functionality and examples. A non-exhaustive list of operators is shown below:

Category	Operators / Keywords
Logic	and, or, not, ( )
Selection	first, last, in
Basic Flags	all, none, heavy, hydrogens
Atom Attributes	elem, atomic_number, isotope, mass, index, formal_charge, partial_charge, valence, degree, hybridization, stereo, ring, aromatic, aliphatic
Pharmacophore	donors, acceptors, hydrophobes, pos_ionizable, neg_ionizable, zn_binders
MedChem Alerts	alerts
Functional Groups	functional "<name>"
Custom SMARTS	smarts "<pattern>"
Topology	neighbor, bound_to, ringsize, inring
Expansions	bymolecule, byring, byres, bychain, byfunctional
Proximity	within <dist> of <expr>, beyond <dist> of <expr>, around <dist>, gap <dist> of <expr>
PDB	resi, resn, resv, chain, name, alt, id, b, q, hetatm
PDB Classification	sidechain, backbone,protein, nucleic, polymer, solvent, metals, organic, inorganic, artifact

Acknowledgements

• Functional Groups: The SMARTS patterns used for functional group detection are taken from SmartChemist by Torben Gutermuth. NB: Make sure to cite SmartChemist in any publications that use this functionality, and do not modify the SMARTS patterns in a way that violates the license.
• Selection Parser: The core DSL parser architecture is a port of the pyparser implementation found in mdtop, originally inspired by PyMOL.
• Inspiration: This project was inspired by Alex Binnie, who developed a similar DSL for OpenEye toolkit.

License

MIT