Atomistic Skills

Plugin atomistic-skills from marketplace atomistic-skills in learningmatter-mit/AtomisticSkills. Commands read from the repo's manifest — 17 days ago.

Skills (133)

• chem-bond-dissociation

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

• chem-conformer-search

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

• chem-db-mof

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

• 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.

• chem-db-spectra

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

• 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.

• chem-dft-orca-optimization

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

• 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.

• 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.

• chem-hazard-toxicity

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

• chem-irc-verification

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

• 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.

• chem-neb-barrier

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

• chem-nmr-analysis

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

• chem-nmr-predict

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

• chem-react-ot

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

• chem-similarity-search

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

• 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.

• chem-sorption-gcmc

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

• chem-sorption-relax

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

• chem-sorption-widom

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

• 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.

• 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.

• chem-ts-optimization

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

• chem-vibration

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

• drug-admet-prediction

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

• 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 n

• drug-bioactivity-assay

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

• 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 coun

• drug-db-chembl

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

• drug-db-pdb

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

• drug-db-pubchem

  Query PubChem via PUG-REST to retrieve CIDs, computed properties, synonyms, and 2D/3D SDF structures.

• drug-docking-analysis

  Post-docking analysis of virtual screening results including score distributions, enrichment metrics (ROC AUC, enrichment factors), and ligand efficiency calculations.

• drug-docking-vina

  Dock small-molecule ligands into a protein receptor using AutoDock Vina (Python API) and save ranked poses + docking metadata for reproducible virtual screening.

• drug-ligand-prep

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

• drug-mmpbsa-gbsa

  Compute single-trajectory MM-GBSA and / or MM-PBSA binding free energy estimates from a protein-ligand MD trajectory. Two backends: a fast OpenMM GBn2 path (no extra dependencies) and an AmberTools MMPBSA.py path that supports both GB (multiple igb models) and Poisson-Boltzmann PB on the same trajec

• drug-molecular-fingerprints

  Compute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.

• drug-pocket-detection

  Identify and rank ligandable pockets on a protein structure or model using geometry (fpocket) or an ML predictor (P2Rank). Returns ranked pockets with lining residues, geometric center, volume, and a druggability score per pocket. Excludes docking; pair with drug-binding-site-definition or drug-dock

• drug-pose-validation

  Validate docked or generated ligand poses for physical plausibility using PoseBusters, filtering out chemically invalid or clashing poses before downstream refinement.

• drug-protein-ligand-md

  Run a protein-ligand MD simulation in OpenMM with energy minimization, restrained equilibration, and production NPT, producing trajectory and checkpoint files for downstream analysis.

• drug-protein-prep

  Prepare macromolecular receptor structures (PDB/mmCIF or RCSB PDB ID) for docking or simulation by fixing common structure issues and adding hydrogens.

• drug-redocking-rmsd

  Compute symmetry-corrected heavy-atom RMSD between docked poses and a reference crystal ligand to validate docking protocols.

• drug-retrosynthesis

  Predict synthetic accessibility and retrosynthetic pathways for novel molecules using the IBM RXN API.

• drug-trajectory-analysis

  Analyze a protein-ligand MD trajectory to compute ligand RMSD, pocket RMSF, hydrogen bonds, contact occupancy, and protein-ligand interaction fingerprints over time.

• general-arxiv-search

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

• general-atomisticskills-rules

  Working rules for atomistic research with AtomisticSkills -- how to scope a request, set up a research directory and a plan before simulating, run skills and MCP tools, stay within GPU memory, and report results. Read it before any multi-step simulation, screening, fine-tuning or benchmarking task.

• general-atomisticskills-setup

  Set up, check or troubleshoot how AtomisticSkills runs on this machine -- creating its Python environments, connecting its MCP servers, choosing uv or a container runtime, and configuring API keys. Use it when installing AtomisticSkills, when a skill command or MCP tool fails to start, or before a f

• general-biorxiv-search

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

• general-chemical-literature

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

• general-chemical-pricing

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

• general-deep-research

  Perform iterative, deep, and comprehensive literature research on a specific materials/chemistry topic.

• general-fair-data-review

  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.

• general-patent-search

  Search for patents by keyword, material name, or assignee using free data sources (Google Patents).

• general-peer-review

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

• general-plot-digitizer

  Extract continuous X-Y data from experimental spectrum images (Raman, XRD, UV-Vis, IR, etc.) via hybrid VLM + CV pipeline and agent-in-the-loop workflow.

• general-presentation

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

• general-property-units

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

• general-publisher-access-guard

  Avoid bot-blocking publisher websites by routing paper retrieval through legal open-access APIs and mirrors.

• general-query-literature-database

  Find relevant simulation workflows in the in-house literature database.

• general-workflow-planner

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

• mat-amorphization

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

• mat-calphad-phase-diagram

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

• mat-calphad-property-diagram

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

• mat-db-mp

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

• mat-db-nist-janaf

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

• mat-db-optimade

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

• mat-defect-energy-dft

  Calculate charged defect formation energies and transition level diagrams using pymatgen-analysis-defects and atomate2 VASP workflows.

• mat-defect-energy

  Calculate point-defect formation energies (vacancies, substitutions, interstitials) using MLIPs.

• mat-dft-electron-phonon

  Computes electron-phonon coupling to calculate temperature-dependent bandgap renormalization using atomate2.

• mat-dft-electronic-transport

  Compute electronic transport properties (mobility, conductivity, Seebeck coefficient) using DFT and AMSET via atomate2.

• mat-dft-ferroelectric

  Calculate the spontaneous ferroelectric polarization across a non-polar to polar structure transition using the Berry Phase method.

• mat-dft-lobster

  Construct computational flows for VASP electronic structure projection via LOBSTER to calculate chemical bonding insights (COHP, atomic charges, DOS).

• mat-dft-mixing-functionals

  Energy corrections needed when using certain MLIPs for phase diagram construction / formation energy calculations.

• mat-dft-vasp

  Prepare VASP input files, run DFT calculations (locally or remotely via atomate2), and parse VASP output results.

• mat-dielectric-response

  Calculate frequency-dependent dielectric response using atomate2 OpticsMaker and VASP.

• mat-diffusion-analysis

  Calculate ionic diffusion coefficients and activation energy from MD trajectories using pymatgen.

• mat-disorder

  Generate ordered structures from disordered starting points with partial occupancies.

• mat-edi-mobility

  Compute defect-limited carrier mobility and electron-defect scattering matrix elements in 2D and 3D semiconductors from first principles with Quantum ESPRESSO and the EDI plugin.

• mat-elasticity

  Calculate the full elastic tensor and mechanical properties (bulk modulus, shear modulus, Young's modulus, Poisson's ratio) using MLIPs.

• mat-electrochemical-window

  Calculate the intrinsic electrochemical stability window (ECW) of a material using standard phase diagram thermodynamic methods.

• mat-electronic-structure
• mat-elemental-energies
• mat-epw-mobility
• mat-equation-of-state
• mat-grain-boundary
• mat-grand-canonical-mc
• mat-intercalation-voltage
• mat-ionic-substitution
• mat-kinetic-monte-carlo
• mat-lammps-md
• mat-lattice-thermal-conductivity
• mat-magnetic-density
• mat-md-monitors
• mat-md-probability-density
• mat-melting-point
• mat-phase-diagram
• mat-phase-field-conservative
• mat-phase-field-non-conservative
• mat-phonon
• mat-pourbaix-diagram
• mat-qha-thermal-expansion
• mat-raman-spectra
• mat-random-structure-search
• mat-reaction-network
• mat-sample-pes-by-md
• mat-solid-free-energy
• mat-stability
• mat-structure-novelty
• mat-surface-adsorption
• mat-surface-energy
• mat-synthesis-extraction
• mat-synthesis-recommendation
• mat-wannier-tight-binding
• mat-xrd-calculator
• mat-xrd-digitizer
• mat-xrd-phase-analysis
• mat-xrd-refinement
• ml-bayesian-optimization
• ml-cluster-expansion
• ml-committee-uncertainty
• ml-fairchem-finetune
• ml-foundation-potentials
• ml-generative-adit
• ml-generative-diffcsp
• ml-generative-mattergen
• ml-mace-finetune
• ml-matgl-finetune
• ml-mlip-automl
• ml-mlip-benchmark
• ml-mlip-nvalchemi
• ml-mlip-speed
• ml-property-predict-scd
• ml-property-predictor

MCP servers (10)

• adit

  runs: ${CLAUDE_PLUGIN_ROOT}/venv/run --server adit

• atomate2

  runs: ${CLAUDE_PLUGIN_ROOT}/venv/run --server atomate2

• base

  runs: ${CLAUDE_PLUGIN_ROOT}/venv/run --server base

• diffcsp

  runs: ${CLAUDE_PLUGIN_ROOT}/venv/run --server diffcsp

• drugdisc

  runs: ${CLAUDE_PLUGIN_ROOT}/venv/run --server drugdisc

• fairchem

  runs: ${CLAUDE_PLUGIN_ROOT}/venv/run --server fairchem

• mace

  runs: ${CLAUDE_PLUGIN_ROOT}/venv/run --server mace

• matgl

  runs: ${CLAUDE_PLUGIN_ROOT}/venv/run --server matgl

• mattergen

  runs: ${CLAUDE_PLUGIN_ROOT}/venv/run --server mattergen

• smol

  runs: ${CLAUDE_PLUGIN_ROOT}/venv/run --server smol

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