miniCAT — Compound Attachment Tool (mini)

miniCAT is a lightweight tool to attach chemical ligands (from SMILES) to nanocrystal / QD structures. It provides:

• RDKit-based functional-group detection and ionic transforms,
• geometry utilities to place/anchor ligands on specified “dummy” sites (e.g. Cl, Br, I, Rb),
• control over multi-ligand, multi-pass passivations with ratios and spatial distributions.

This repository is a slimmed-down version of CAT (Compound Attachment Tool), focused on just the essentials.

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Installation (conda/mamba recommended)

Create and activate the environment:

mamba env create -f environment.yml
mamba activate minicat

Install the package in editable mode to get the miniCAT CLI:

pip install -e .

Note: RDKit is provided via conda-forge in the environment; keeping it in the conda env avoids pip/rdkit compatibility issues.

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Quick start

Inputs:

• initial_dot.xyz — your QD/nanocrystal with “dummy” attachment sites (e.g. Cl, Rb).
• SMILES strings for ligands.

Example: two-pass passivation — first passivate Cl with a 25/75 segmented mix of two anionic ligands, then passivate Rb with a 40/60 random mix of two cationic ligands.

miniCAT   --qd initial_dot.xyz   --out_prefix final_passivated_dot   --job-ligands "CCCC(=O)O" "CCCCS"   --job-dummy "Cl"   --job-dist "0.25:0.75:segmented"   --job-ligands "C[NH3+]" "C(C)(C)N"   --job-dummy "Rb"   --job-dist "0.40:0.60:random"

Key flags (subset):

• --qd : input .xyz QD structure.
• --out_prefix : base filename for outputs.
• --job-ligands : one or more SMILES strings (repeatable per pass).
• --job-dummy : the target dummy species for that pass (e.g., Cl, Br, I, Rb).
• --job-dist : ratio and distribution strategy; format: r1:r2:mode where mode ∈ {random, segmented}.
• Multiple “passes” are specified by repeating the --job-ligands/--job-dummy/--job-dist triplet.

Special-cased inputs:

• Hydrogen halides can be given as HCl, HBr, HI (or just Cl, Br, I) and are normalized internally.
• H2S may be given as S.

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Package layout

minicat/
  main.py                        # CLI entry point, exposed as the `miniCAT` command
  functional_groups_class.py     # RDKit functional-groups & transforms

Run help:

miniCAT -h

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Development

Optional tooling:

mamba install black isort

Format:

black minicat
isort minicat

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License

See LICENSE.