Use when when processing in-silico or experimental MS spectra records from databases with incomplete metadata, specifically when the adduct field is null or absent but the ionmode…
Use when you have raw mass spectrometry instrument output (mzML, vendor binary formats, or mzPeak archives) and need to load spectrum metadata, chromatogram data, or signal arrays…
Use when you have mass spectrometry data available in multiple identifier formats (GNPS Task ID, Universal Spectrum Identifier, or Feature-Based Molecular Networking task…
Use when you have raw mass spectrometry data in mzML or Bruker .d format and need to ingest it into a tabular format (pandas DataFrame) for visualization, statistical analysis, or…
Use when after RAMClustR clustering and molecular weight inference via do.findmain, when you need to export deconvoluted cluster spectra for import into external annotation tools…
Use when you have a normalized abundance matrix from LC-MS/MS profiling with sample class assignments (e.g., phenotypic groups, disease states, treatment conditions) and need to…
Use when when you have raw or processed TWIM-MS data (arrival time and m/z values) from a mass spectrometry instrument and need to organize it into a feature table before…
Use when when you have Thermo Fisher Scientific Orbitrap .raw files (e.g., from Q Exactive HF instruments) and need to extract spectral, chromatographic, or metadata directly into…
Use when you have experimental fragment m/z peaklists from Q-Exactive orbitrap, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF UHPLC-HRMS/MS instruments (in CSV or mzML-derived table…
Use when you have raw MS imaging data in imzML (continuous or processed) or Analyze 7.5 format and need to load it into R for spectral processing, normalization, peak-picking, or…
Use when when you have preprocessed MALDI-MSI data (in msimat format) and want to determine whether abundant peaks are actually molecular adducts of simpler parent ions rather…
Use when you have raw or processed MSI data (in imzML or rMSIproc formats) and need to identify and annotate matrix-related peaks before statistical analysis or metabolite…
Use when when extracting and validating chromatographic peaks for target molecules from centroided mzML files, particularly when working with multiple isotopologues and adducts…
Use when when you have aligned peak data from molecular networking (with m/z, intensity, retention time, and alignment quality metrics across multiple spectra) and need to…
Use when you have raw mzML files and feature tables (CSV format from mzMine or XCMS) from untargeted LCMS experiments and need to distinguish true metabolite peaks from false…
Use when you have preprocessed MSI data (as a CSV intensity matrix or Cardinal MSProcessedImagingExperiment object) and suspect that observed peaks include both parent ions and…
Use when you have a high-resolution LC-MS/MS experiment with a measured [M+H]+ or [M-H]− ion mass and optionally a parent ion fragmentation spectrum (peak list with m/z and…
Use when you have generated or obtained a two-dimensional mass-spectrometry intensity matrix (m/z × retention time scan points) with simulated or experimental peak shapes, noise,…
Use when you have individual MS/MS spectra or batch .mgf files from untargeted metabolomics experiments and need to search them against domain-specific reference libraries (e.
Use when you have high-resolution LC-MS data processed through both XCMS feature detection and RAMClustR clustering, and you need to verify the reliability of molecular weight…
Use when you have loaded a Bruker Solarix transient file (.d format with .ser or .fid content) and need to generate a processed mass spectrum for peak picking and molecular…
Use when you have raw GC-MS data in netCDF or vendor-specific binary format and need to separate co-eluting compounds and extract clean mass spectra for each individual chemical…
Use when you have an experimental MS/MS spectrum (e.g., from MassBank or acquired data) for a single metabolite with known accurate precursor m/z and adduct type, and you need to…
Use when after computing all pairwise mass differences from a mass spectrometry imaging dataset, when you need to identify which mass differences correspond to real molecular…
Use when when processing raw or centroid mass spectra (e.g., ESI-MS or FT-ICR data from Bruker .d or Thermo .raw formats) and you need to remove instrument noise and low-abundance…
States of matter, phase transitions, kinetic molecular theory, atmospheric chemistry, green chemistry, and sustainable synthesis.
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library fi — from…
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library fi — from…
Use when targeting Nature Chemistry (Nat Chem) or deciding whether a chemistry manuscript fits this Springer Nature venue.
Use when targeting Nature Reviews Chemistry (Nat Rev Chem) or deciding whether a chemistry review proposal fits this commissioned, authoritative-review venue.
NEB-IRC activation energy pipeline for reaction barriers using GFN2-xTB and pysisyphus. Optimize reactant and product geometries, run CI-NEB path search, optimize the transition…
Use when you have negative-mode MS/MS spectra with annotated molecular formulas and negative adducts (from repositories like MassIVE or MetaboLights), and your current formula…
Use when you have raw floating-point m/z and intensity arrays extracted from mass-spectrometry experiments (e.g., from mzML or mzXML files) and need to compress them for storage…
Carbon chemistry, functional groups, IUPAC nomenclature, isomerism, reaction mechanisms (substitution, elimination, addition), polymers, and biochemistry basics.
Hundreds of chemistry and scientific computing tools. Molecular weight, LogP, TPSA, SMILES validation, thermodynamics, polymer analysis, electrochemistry, DOE, and more.
Use when a task needs the judgment of an anatomic/clinical pathologist — writing or reviewing a surgical pathology synoptic report, working a differential from gross or…
Use when a task needs the judgment of a Photographic Process Worker — calculating a time-temperature compensation when processing chemistry runs off standard temperature,…
Chemical equilibrium, chemical kinetics, and electrochemistry — the quantitative core of physical chemistry.
Use when working with the non-metallic engineering materials — polymers, ceramics, or composites — and you need to reason about structure, processing, or properties.
Use when a task needs the judgment of a Power Plant Operator — diagnosing whether a drum-level change during a load ramp is real or shrink/swell by cross-checking feedwater…
物性計算とMD後処理を扱うスキルです。 ElasticTensorFeature, PostElasticPropertiesFeature, 弾性定数, elastic, Young率, バルク弾性率, ForceConstantFeature, PostPhononBandFeature, PostPhononDOSFeature,…
Geochemistry data analysis and visualization for igneous, metamorphic, and sedimentary rocks. Use when Claude needs to: (1) Create ternary diagrams for compositional data, (2)…
Use when you have raw CE-MS or LC-MS instrument files (stored as OnDiskMSnExp objects or similar Bioconductor containers) and need to extract quantitative features (migration…
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similar — from…
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similar — from…
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similar — from…
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similar — from…
Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity,…
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similar — from…
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similar — from…
Balancing chemical equations, reaction classification, stoichiometric calculations, acid-base chemistry, oxidation-reduction (redox) reactions, and thermochemistry.
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptor — from…
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, finger — from…
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library fi — from…
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similar — from…
鲁科版高中化学同步 Skill是面向课前预习、课后作业、同步巩固、单元复习、错题巩固、期中期末复习、高考复习的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: senior_chemistry_lk_textbook_sync.run.
高中化学快速巩固 Skill是面向每日打卡、同步巩固的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: senior_chemistry_quick_practice.run.
人教版高中化学同步 Skill是面向课前预习、课后作业、同步巩固、单元复习、错题巩固、期中期末复习、高考复习的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: senior_chemistry_rj_textbook_sync.run.
Skill de Química Básica para resolución de problemas de estructura atómica, tabla periódica, enlaces, estequiometría y reacciones químicas a nivel de Secundaria y Bachillerato.
Use when when preprocessing raw SMILES strings from external chemistry databases (e.g., CCSBase, METLIN-CCS, or custom compound libraries) that may contain multiple valid but…