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name: conformers-drawing description: "Generate/optimize RDKit 3D conformers, compute alignment/RMSD, create 2D coordinates, and render molecule/reaction/grid depictions as SVG or PNG." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

RDKit Conformers and Drawing

Use this sub-skill when a task asks for RDKit 3D conformer generation, force-field optimization, conformer alignment/RMSD, 2D coordinate generation, or molecule/reaction drawing. Route basic parsing, validation, suppliers, and molecule editing to molecule-io-core; route reaction semantics and product chemistry to reactions-standardization; route descriptor/fingerprint features to descriptors-fingerprints.

Fast Routing

• 3D conformers: add hydrogens, embed with AllChem.ETKDGv3() or AllChem.EmbedMolecule, optimize with MMFF or UFF, then remove hydrogens only if the caller wants heavy-atom output.
• Multiple conformers: use AllChem.EmbedMultipleConfs, optimize with AllChem.MMFFOptimizeMoleculeConfs or per-conformer UFF/MMFF, then align with AllChem.AlignMolConformers and inspect RMS values.
• Molecule-to-molecule RMSD: use rdkit.Chem.rdMolAlign.AlignMol for a fixed atom map and rdMolAlign.GetBestRMS for symmetry-aware best RMSD.
• 2D depictions: use AllChem.Compute2DCoords / rdDepictor.Compute2DCoords before drawing when molecules lack depiction coordinates, or GenerateDepictionMatching2DStructure for template-aligned drawings.
• SVG drawing: prefer Draw.MolToSVG, Draw.MolsToGridImage(..., useSVG=True), or direct rdMolDraw2D.MolDraw2DSVG for headless, portable output.
• PNG drawing: use Draw.MolToImage, Draw.MolToFile(..., imageType='png'), or rdMolDraw2D.MolDraw2DCairo only when Cairo/Pillow support is available.

Standard Workflow

1. Parse and validate molecules with molecule-io-core; never continue with None molecules.
2. For conformers, make a hydrogenated working copy: mol_h = Chem.AddHs(mol).
3. Configure embedding parameters: params = AllChem.ETKDGv3(); params.randomSeed = 0xF00D; params.numThreads = 0 where supported.
4. Check embedding return values: EmbedMolecule returns 0 on success and negative values on failure; EmbedMultipleConfs returns conformer ids.
5. Prefer MMFF when parameters exist; fall back to UFF when MMFF properties cannot be built.
6. For drawings, compute 2D coordinates on a display copy and write SVG for robust non-GUI automation.

References

• references/conformers.md covers embedding, optimization, hydrogens, alignment, RMSD, and retry patterns.
• references/drawing.md covers 2D coordinates, SVG/PNG output, grids, legends, highlights, and reactions.
• references/troubleshooting.md covers embedding failures, missing conformers, force-field parameter failures, and drawing backend issues.
• scripts/conformer_draw_smoke.py is a bundled smoke CLI that embeds a tiny molecule and writes an SVG without requiring the source checkout.

Minimal Examples

from rdkit import Chem
from rdkit.Chem import AllChem

mol = Chem.AddHs(Chem.MolFromSmiles('CCO'))
params = AllChem.ETKDGv3()
params.randomSeed = 0xF00D
status = AllChem.EmbedMolecule(mol, params)
if status < 0:
    raise RuntimeError(f'RDKit embedding failed: {status}')
if AllChem.MMFFHasAllMoleculeParams(mol):
    AllChem.MMFFOptimizeMolecule(mol)
else:
    AllChem.UFFOptimizeMolecule(mol)

from rdkit import Chem
from rdkit.Chem import AllChem, Draw

mol = Chem.MolFromSmiles('c1ccccc1O')
AllChem.Compute2DCoords(mol)
svg = Draw.MolsToGridImage([mol], legends=['phenol'], useSVG=True)

Validation Checklist

• Confirm every molecule is non-null before embedding or drawing.
• Confirm expected conformer count with mol.GetNumConformers() before optimization, alignment, RMSD, or shape work.
• Record and handle optimization return codes instead of assuming convergence.
• Prefer deterministic seeds in examples, tests, and reproducible bug reports.
• Choose SVG for headless workflows; use PNG only after verifying Cairo/Pillow support.