learningmatter-mit/atomisticskills
60 skills · 99 total installs
$npx skills add learningmatter-mit/atomisticskillsSkillInstalls
chem-db-qmofQuery the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of…mat-calphad-phase-diagramCalculate and plot multi-component temperature-composition phase diagrams from Thermodynamic Database (.tdb) files using CALPHAD methods.chem-bond-dissociationCalculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.chem-conformer-searchGenerate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.chem-db-spectraSearch and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.chem-hazard-toxicityExtract explicit safety warnings, GHS classifications, and LD50 profiles from PubChem PUG VIEW.chem-neb-barrierCalculate activation barrier using Nudged Elastic Band (NEB) method with MLIPs.chem-react-otGenerate transition state structures for chemical reactions using React-OT.chem-similarity-searchFind structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.chem-solution-mdSet up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.chem-thermochemistryCompute gas-phase thermodynamic quantities (H, S, G) and reaction thermochemistry (ΔH, ΔS, ΔG) using MLIPs with the ideal-gas/rigid-rotor/harmonic-oscillator…chem-vibrationCalculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.drug-bioactivity-assayFetch biological assays and target proteins a chemical has been tested against via PubChem.general-arxiv-searchSearch and retrieve research papers from ArXiv API for scientific research.general-biorxiv-searchSearch and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.general-chemical-literatureRetrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.general-chemical-pricingRetrieves averaged elemental prices and provides direct vendor purchase links for elements and precursor compounds.general-fair-data-reviewReview a manuscript or code repository for FAIR data compliance (Findable, Accessible, Interoperable, Reusable), producing a structured report with pass/fail…general-peer-reviewAct as a reviewer to critically review research plans, manuscripts, or task summaries, pointing out missing baselines, statistical flaws, and weak assumptions.general-presentationGenerate and iteratively refine PowerPoint presentations from simulation results using python-pptx.general-property-unitsReference guide for energy, force, and stress units across MLIPs, DFT codes, and ASE, including conversion factors.general-workflow-plannerHierarchically decompose high-level scientific workflows (from literature or user-proposed) into executable sequences of existing SKILLs and MCP tools for the…mat-amorphizationGenerate amorphorized structures from crystalline starting points using a melt-quench MD protocol.mat-calphad-property-diagramCalculate temperature-dependent thermodynamic properties like Equilibrium Phase Fractions for a specific alloy composition using CALPHAD models.chem-db-mofQuery multiple MOF databases (QMOF via MPContribs; ARC-MOF DB7/Majumdar et al.chem-dft-orca-advanced-calculationWrite and run custom ORCA input files for advanced electronic structure methods or settings not available through the SCINE wrapper, including multi-reference…chem-dft-orca-optimizationRun DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.chem-dft-orca-singlepointRun a DFT or Coupled Cluster single-point energy calculation (with optional gradients/Hessian) on a molecular structure with ORCA through SCINE wrapper.chem-docking-voidDock small-molecule guests into a porous host material using the VOID library (Voronoi Clustering), generating multiple 3D conformers with RDKit and ranking…chem-irc-verificationVerify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.chem-msms-predictPredict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network.chem-nmr-analysisScripts for Wasserstein deconvolution of 1H NMR mixture spectra against reference spectra, reaction product prediction, time-series kinetics, and spectral…chem-nmr-predictPredict 1H NMR spectra from SMILES strings via NMRdb.org SPINUS neural network prediction and nmrsim quantum mechanical spin simulation.chem-sorption-gcmcCalculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.chem-sorption-relaxPrepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools.chem-sorption-widomCalculates Henry coefficient and heat of adsorption for a gas in a porous framework using Widom insertion with any supported MLIP.chem-spectrum-matcherMatch an experimental spectrum (1H NMR, 13C NMR, IR) against predicted or database reference spectra for candidate ranking and structure confirmation.chem-ts-optimizationOptimize non-periodic molecular TS guesses and verify first-order saddle point from vibrational modes.drug-admet-predictionCompute RDKit physicochemical descriptors and rule-based drug-likeness heuristics (Ro5, Veber, QED) from SMILES.drug-binding-site-definitionDefine a docking search box (center coordinates + box dimensions in Angstroms) from a co-crystal ligand, binding-site residues, or a saved JSON specification.drug-complex-system-builderBuild a solvated, charge-neutralized protein-ligand complex for OpenMM molecular dynamics simulation.drug-db-chemblQuery ChEMBL web services for targets, molecules, and curated bioactivity measurements (IC50, Ki, EC50, etc.).drug-db-pdbSearch, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional…drug-db-pubchemQuery PubChem via PUG-REST to retrieve CIDs, computed properties, synonyms, and 2D/3D SDF structures.drug-docking-analysisPost-docking analysis of virtual screening results including score distributions, enrichment metrics (ROC AUC, enrichment factors), and ligand efficiency…drug-docking-vinaDock small-molecule ligands into a protein receptor using AutoDock Vina (Python API) and save ranked poses + docking metadata for reproducible virtual…drug-ligand-prepPrepare small-molecule ligands for docking and analysis via optional state enumeration, 3D conformer generation, MMFF/UFF minimization, and export to SDF +…drug-mmpbsa-gbsaCompute single-trajectory MM-GBSA and / or MM-PBSA binding free energy estimates from a protein-ligand MD trajectory.drug-molecular-fingerprintsCompute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.drug-pocket-detectionIdentify and rank ligandable pockets on a protein structure or model using geometry (fpocket) or an ML predictor (P2Rank).drug-pose-validationValidate docked or generated ligand poses for physical plausibility using PoseBusters, filtering out chemically invalid or clashing poses before downstream…drug-protein-ligand-mdRun a protein-ligand MD simulation in OpenMM with energy minimization, restrained equilibration, and production NPT, producing trajectory and checkpoint files…drug-protein-prepPrepare macromolecular receptor structures (PDB/mmCIF or RCSB PDB ID) for docking or simulation by fixing common structure issues and adding hydrogens.drug-redocking-rmsdCompute symmetry-corrected heavy-atom RMSD between docked poses and a reference crystal ligand to validate docking protocols.drug-retrosynthesisPredict synthetic accessibility and retrosynthetic pathways for novel molecules using the IBM RXN API.drug-trajectory-analysisAnalyze a protein-ligand MD trajectory to compute ligand RMSD, pocket RMSF, hydrogen bonds, contact occupancy, and protein-ligand interaction fingerprints over…general-deep-researchPerform iterative, deep, and comprehensive literature research on a specific materials/chemistry topic.general-patent-searchSearch for patents by keyword, material name, or assignee using free data sources (Google Patents).general-plot-digitizerExtract 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-query-literature-databaseFind relevant simulation workflows in the in-house literature database.