ChimeraX-RDKitConformer

Generate 3D conformers from molecular notations using RDKit ETKDGv3, directly in ChimeraX.

Two installable bundles are provided. Both register the same rdkconf command — install one OR the other.

Option	Bundle	How RDKit runs	ChimeraX pollution
A	bundle-direct	Imported directly into ChimeraX Python	rdkit added
B	bundle-uv	Isolated subprocess via uv (installed in ChimeraX)	uv added
C	bundle-uv	Isolated subprocess via external uv	None

Requirements

• ChimeraX 1.6+ (1.11+ for minimize keyword)

Installation

Option A: Direct RDKit (recommended for simplicity)

Install RDKit into ChimeraX's Python, then install the bundle.

From ChimeraX command line (GUI):

pip install rdkit
cd /path/to/chimerax-rdkit-conformer/bundle-direct
devel install .

From terminal:

ChimeraX --nogui --exit --cmd 'pip install rdkit'
cd /path/to/chimerax-rdkit-conformer/bundle-direct
ChimeraX --nogui --exit --cmd 'devel install .'

Note: devel install must be run from the bundle directory (cd then devel install .). Passing an absolute path does not work due to a ChimeraX bundle builder limitation.

Option B: uv subprocess (uv installed in ChimeraX)

Install uv into ChimeraX's Python, then install the bundle. RDKit itself runs in an isolated subprocess — only uv is added to ChimeraX.

From ChimeraX command line (GUI):

pip install uv
cd /path/to/chimerax-rdkit-conformer/bundle-uv
devel install .

From terminal:

ChimeraX --nogui --exit --cmd 'pip install uv'
cd /path/to/chimerax-rdkit-conformer/bundle-uv
ChimeraX --nogui --exit --cmd 'devel install .'

Option C: uv subprocess (zero ChimeraX pollution)

If uv is already installed on your system, you can skip pip install uv entirely — nothing is added to ChimeraX's Python.

From ChimeraX command line (GUI):

cd /path/to/chimerax-rdkit-conformer/bundle-uv
devel install .
rdkconf uvPath ~/.local/bin/uv

From terminal:

cd /path/to/chimerax-rdkit-conformer/bundle-uv
ChimeraX --nogui --exit --cmd 'devel install .'
ChimeraX --nogui --exit --cmd 'rdkconf uvPath ~/.local/bin/uv'

The uvPath setting is saved persistently — you only need to set it once.

Usage

rdkconf CCO                                        # SMILES (default)
rdkconf c1ccccc1                                   # Benzene
rdkconf "CC(=O)Oc1ccccc1C(=O)O"                   # Aspirin
rdkconf "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"      # InChI (auto-detected)
rdkconf GGG format sequence                        # Peptide sequence
rdkconf ACGT format dna                            # DNA sequence
rdkconf ACGU format rna                            # RNA sequence
rdkconf ">seq\nGGG" format fasta                   # FASTA format
rdkconf "PEPTIDE1{G.G.G}$$$$" format helm          # HELM notation
rdkconf CCO name EtOH                              # Custom residue name
rdkconf CCO hydrogen false                         # Hide hydrogens
rdkconf CCO optimize true                          # RDKit MMFF optimization
rdkconf CCO minimize true                          # ChimeraX minimization (1.11+)
rdkconf CCO optimize true minimize true            # Both: MMFF then minimize
rdkconf c1ccccc1 conformers 5                     # Multiple conformers
rdkconf CCO conformers 10 name EtOH               # Named multi-conformers

Supported Formats

Format	format keyword	Auto-detected
SMILES	smiles (default)	Yes (fallback)
InChI	inchi	Yes (InChI= prefix)
Protein sequence	sequence	No
DNA sequence	dna	No
RNA sequence	rna	No
FASTA	fasta	No
HELM	helm	No

How It Works

ChimeraX's built-in SMILES support (open smiles:CCO) depends on NCI's web service (requires internet, no control over 3D generation quality). This bundle uses RDKit ETKDGv3 locally for high-quality 3D coordinate generation without network dependency. The 3D structure is built directly in memory using ChimeraX's AtomicStructure API — no intermediate files are written.

Development

# Build and install (must cd into the bundle directory first)
cd bundle-direct
ChimeraX --nogui --exit --cmd 'devel install .'

# Run tests (either bundle)
cd bundle-direct && uv run --no-project --with pytest --with rdkit pytest tests/ -v
cd bundle-uv && uv run --no-project --with pytest --with rdkit pytest tests/ -v

License

MIT