AtomisticSkills

Quantify prediction uncertainty of MACE MLIPs using committee (ensemble) models; flag high-uncertainty structures for DFT verification.

Compute phonon-limited carrier mobility and mode-resolved electron-phonon coupling in 2D materials from first principles with Quantum ESPRESSO and EPW.

GPU-accelerated batched inference for MACE, MatGL (TensorNet/M3GNet/CHGNet), and FairChem MLIPs using NValchemi, enabling parallel static, relax, and MD workflows across multiple structures simultaneously.

Extract structured synthesis procedures from a folder of PDFs using the LeMat-Synth GeneralSynthesisOntology schema, producing one JSON file per paper with per-material synthesis records.

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.

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.

Generate crystal structures with exact composition control using DiffCSP++ (space group + Wyckoff positions), or unconditionally from trained distributions.

Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.

Review a manuscript or code repository for FAIR data compliance (Findable, Accessible, Interoperable, Reusable), producing a structured report with pass/fail per principle and actionable remediation steps.

Act as a reviewer to critically review research plans, manuscripts, or task summaries, pointing out missing baselines, statistical flaws, and weak assumptions.

Sample off-equilibrium potential energy surface (PES), used for benchmarking and fine-tuning MLIPs.

Iteratively optimize expensive black-box objectives — such as materials properties, experimental yields, or simulation outputs — by learning from past evaluations to select the most promising next candidates.

Prepare small-molecule ligands for docking and analysis via optional state enumeration, 3D conformer generation, MMFF/UFF minimization, and export to SDF + AutoDock PDBQT.

Simulate long-time kinetics using rejection-free kinetic Monte Carlo (KMC) with event catalog construction, rate assignment via TST/Arrhenius, detailed-balance validation, superbasin handling, and transport analysis.

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

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

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.

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

Extract explicit safety warnings, GHS classifications, and LD50 profiles from PubChem PUG VIEW.

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

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

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

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

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.

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

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

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

Search, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads.

Search and retrieve research papers from ArXiv API for scientific research.

Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.

Retrieves averaged elemental prices and provides direct vendor purchase links for elements and precursor compounds.

Generate and iteratively refine PowerPoint presentations from simulation results using python-pptx.

Reference guide for energy, force, and stress units across MLIPs, DFT codes, and ASE, including conversion factors.

Hierarchically decompose high-level scientific workflows (from literature or user-proposed) into executable sequences of existing SKILLs and MCP tools for the research plan.

Generate amorphorized structures from crystalline starting points using a melt-quench MD protocol.

Calculate and plot multi-component temperature-composition phase diagrams from Thermodynamic Database (.tdb) files using CALPHAD methods.

Calculate temperature-dependent thermodynamic properties like Equilibrium Phase Fractions for a specific alloy composition using CALPHAD models.

Query Materials Project database for crystal structures, computed properties, elastic/magnetic data, and structurally similar materials using the MP API.

Query the NIST Chemistry WebBook (which includes JANAF thermochemical tables) for standard experimental thermochemistry properties.

Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures.