AtomisticSkills

In the author's own words, from each skill's SKILL.md — showing the first 30 of 130 files.

• chem-bond-dissociation

  Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.

  .agents/skills/chem-bond-dissociation/SKILL.md on GitHub (opens in a new tab)

• chem-conformer-search

  Generate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.

  .agents/skills/chem-conformer-search/SKILL.md on GitHub (opens in a new tab)

• chem-db-mof

  Query multiple MOF databases (QMOF via MPContribs; ARC-MOF DB7/Majumdar et al. via Zenodo) and download CIF structures with optional element or identifier filters.

  .agents/skills/chem-db-mof/SKILL.md on GitHub (opens in a new tab)

• chem-db-qmof

  Query the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.

  .agents/skills/chem-db-qmof/SKILL.md on GitHub (opens in a new tab)

• chem-db-spectra

  Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.

  .agents/skills/chem-db-spectra/SKILL.md on GitHub (opens in a new tab)

• chem-dft-orca-advanced-calculation

  Write and run custom ORCA input files for advanced electronic structure methods or settings not available through the SCINE wrapper, including multi-reference methods, excited states, relativistic effects, advanced SCF, NMR/EPR, and more.

  .agents/skills/chem-dft-orca-advanced-calculation/SKILL.md on GitHub (opens in a new tab)

• chem-dft-orca-optimization

  Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.

  .agents/skills/chem-dft-orca-optimization/SKILL.md on GitHub (opens in a new tab)

• chem-dft-orca-singlepoint

  Run a DFT or Coupled Cluster single-point energy calculation (with optional gradients/Hessian) on a molecular structure with ORCA through SCINE wrapper.

  .agents/skills/chem-dft-orca-singlepoint/SKILL.md on GitHub (opens in a new tab)

• chem-docking-void

  Dock small-molecule guests into a porous host material using the VOID library (Voronoi Clustering), generating multiple 3D conformers with RDKit and ranking generated complexes.

  .agents/skills/chem-docking-void/SKILL.md on GitHub (opens in a new tab)

• chem-hazard-toxicity

  Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.

  .agents/skills/chem-hazard-toxicity/SKILL.md on GitHub (opens in a new tab)

• chem-irc-verification

  Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.

  .agents/skills/chem-irc-verification/SKILL.md on GitHub (opens in a new tab)

• chem-msms-predict

  Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.

  .agents/skills/chem-msms-predict/SKILL.md on GitHub (opens in a new tab)

• chem-neb-barrier

  Calculate activation barrier using Nudged Elastic Band (NEB) method with MLIPs.

  .agents/skills/chem-neb-barrier/SKILL.md on GitHub (opens in a new tab)

• chem-nmr-analysis

  Scripts for Wasserstein deconvolution of 1H NMR mixture spectra against reference spectra, reaction product prediction, time-series kinetics, and spectral plotting.

  .agents/skills/chem-nmr-analysis/SKILL.md on GitHub (opens in a new tab)

• chem-nmr-predict

  Predict 1H NMR spectra from SMILES strings via NMRdb.org SPINUS neural network prediction and nmrsim quantum mechanical spin simulation.

  .agents/skills/chem-nmr-predict/SKILL.md on GitHub (opens in a new tab)

• chem-react-ot

  Generate transition state structures for chemical reactions using React-OT.

  .agents/skills/chem-react-ot/SKILL.md on GitHub (opens in a new tab)

• chem-similarity-search

  Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.

  .agents/skills/chem-similarity-search/SKILL.md on GitHub (opens in a new tab)

• chem-solution-md

  Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.

  .agents/skills/chem-solution-md/SKILL.md on GitHub (opens in a new tab)

• chem-sorption-gcmc

  Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.

  .agents/skills/chem-sorption-gcmc/SKILL.md on GitHub (opens in a new tab)

• chem-sorption-relax

  Prepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools.

  .agents/skills/chem-sorption-relax/SKILL.md on GitHub (opens in a new tab)

• chem-sorption-widom

  Calculates Henry coefficient and heat of adsorption for a gas in a porous framework using Widom insertion with any supported MLIP.

  .agents/skills/chem-sorption-widom/SKILL.md on GitHub (opens in a new tab)

• chem-spectrum-matcher

  Match an experimental spectrum (1H NMR, 13C NMR, IR) against predicted or database reference spectra for candidate ranking and structure confirmation. Supports local catalog lookup, public database fallback, and pluggable similarity metrics.

  .agents/skills/chem-spectrum-matcher/SKILL.md on GitHub (opens in a new tab)

• chem-thermochemistry

  Compute gas-phase thermodynamic quantities (H, S, G) and reaction thermochemistry (ΔH, ΔS, ΔG) using MLIPs with the ideal-gas/rigid-rotor/harmonic-oscillator approximation.

  .agents/skills/chem-thermochemistry/SKILL.md on GitHub (opens in a new tab)

• chem-ts-optimization

  Optimize non-periodic molecular TS guesses and verify first-order saddle point from vibrational modes.

  .agents/skills/chem-ts-optimization/SKILL.md on GitHub (opens in a new tab)

• chem-vibration

  Calculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.

  .agents/skills/chem-vibration/SKILL.md on GitHub (opens in a new tab)

• drug-admet-prediction

  Compute RDKit physicochemical descriptors and rule-based drug-likeness heuristics (Ro5, Veber, QED) from SMILES.

  .agents/skills/drug-admet-prediction/SKILL.md on GitHub (opens in a new tab)

• drug-binding-site-definition

  Define a docking search box (center coordinates + box dimensions in Angstroms) from a co-crystal ligand, binding-site residues, or a saved JSON specification. Use this skill whenever the user mentions binding site, docking box, search box, grid box, active site definition, or pocket definition, or needs to specify where to dock ligands on a protein. Also use when the user has a protein target but…

  .agents/skills/drug-binding-site-definition/SKILL.md on GitHub (opens in a new tab)

• drug-bioactivity-assay

  Fetch biological assays and target proteins a chemical has been tested against via PubChem.

  .agents/skills/drug-bioactivity-assay/SKILL.md on GitHub (opens in a new tab)

• drug-complex-system-builder

  Build a solvated, charge-neutralized protein-ligand complex for OpenMM molecular dynamics simulation. Combines a prepared receptor PDB and ligand SDF, parameterizes the ligand with OpenFF Sage or GAFF (AM1-BCC charges), applies Amber ff14SB to the protein, solvates with explicit water, and adds counterions. Use this skill when the user wants to solvate a complex, set up a system for MD, prepare f…

  .agents/skills/drug-complex-system-builder/SKILL.md on GitHub (opens in a new tab)

• drug-db-chembl

  Query ChEMBL web services for targets, molecules, and curated bioactivity measurements (IC50, Ki, EC50, etc.).

  .agents/skills/drug-db-chembl/SKILL.md on GitHub (opens in a new tab)

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