labmate-mcp 7.0.0__py3-none-any.whl

labmate_mcp-7.0.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: labmate-mcp
+Version: 7.0.0
+Summary: Your AI lab companion — 78 MCP tools from literature search to benchwork to publication
+Author: Jonas Rackl
+License: MIT
+Project-URL: Homepage, https://github.com/JonasRackl/labmate-mcp
+Project-URL: Repository, https://github.com/JonasRackl/labmate-mcp
+Project-URL: Issues, https://github.com/JonasRackl/labmate-mcp/issues
+Project-URL: Changelog, https://github.com/JonasRackl/labmate-mcp/blob/main/CHANGELOG.md
+Keywords: mcp,model-context-protocol,claude,anthropic,ai-assistant,chemistry,research,scientific-tools,literature-search,crossref,openalex,semantic-scholar,bibtex,citation,bibliography,pubchem,cas,nist,thermochemistry,mass-spectrometry,crystal-structures,materials-project,protein-structures,pdb,retrosynthesis,rxn4chemistry,pka,admet,solubility,nmr-prediction,computational-chemistry,rowan,peptide,peptide-design,isoelectric-point,spps,named-reactions,protecting-groups,molarity,dilution,tlc,chromatography,bench-chemistry,workup,isotope-pattern,cas-validation,unit-conversion,buffer-recipes,amino-acids,nmr-solvents,periodic-table,citation-formatting,journal-guides,thesis-writing,experimental-templates,supporting-information,iupac-nomenclature,molecular-formula
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mcp[cli]>=1.0.0
+Requires-Dist: httpx>=0.27.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: p2smi>=1.1.0
+Requires-Dist: pichemist>=2.1.0
+Provides-Extra: rowan
+Requires-Dist: rowan-python>=2.0.0; extra == "rowan"
+Dynamic: license-file
+
+<div align="center">
+
+# 🧪 labmate-mcp
+
+**Your AI lab companion — from literature search to benchwork to publication.**
+
+[![PyPI](https://img.shields.io/pypi/v/labmate-mcp?color=blue&label=PyPI)](https://pypi.org/project/labmate-mcp/)
+[![Python](https://img.shields.io/badge/Python-3.10+-blue)](https://python.org)
+[![License](https://img.shields.io/badge/License-MIT-green)](LICENSE)
+[![Tools](https://img.shields.io/badge/Tools-78-orange)](#-tool-reference)
+[![Named Reactions](https://img.shields.io/badge/Named_Reactions-151-purple)](#-bench-chemistry--reference-10-tools)
+
+**78 tools** · **25+ scientific APIs** · **151 named reactions** · **Zero config required**
+
+[Install](#-install) · [What Can I Do?](#-what-can-i-do-with-this) · [All Tools](#-tool-reference) · [Configuration](#%EF%B8%8F-configuration) · [Examples](#-examples)
+
+</div>
+
+---
+
+labmate-mcp is an [MCP server](https://modelcontextprotocol.io) that plugs into Claude and gives it deep access to scientific databases, computational chemistry, bench references, and writing utilities. **One install covers the entire research workflow.**
+
+```
+📚 Literature        ⚗️ Synthesis         🧪 Bench             📊 Analysis          ✍️ Publication
+Search papers        Retrosynthesis       Named reactions      Isotope patterns     Format citations
+Citation graphs      Forward prediction   Reagent calculator   Mass spectra         Build bibliography
+Author profiles      Atom mapping         Protecting groups    Binding data         Experimental templates
+Preprints            pKa / ADMET          Solvent reference    Crystal structures   Journal guides
+Open access PDFs     NMR prediction       TLC / Column         Safety data          SI checklist
+     15 tools             11 tools             27 tools             15 tools             10 tools
+```
+
+---
+
+## 💬 What Can I Do With This?
+
+Once installed, just talk to Claude naturally. Here are real things you can ask:
+
+> **"Search for recent papers on copper-catalyzed C–H activation and show me the top 5 most cited"**
+>
+> → Searches Crossref + OpenAlex + Semantic Scholar, ranks by citations, shows abstracts
+
+> **"I need to do a Suzuki coupling with 150 mg of my aryl bromide (MW 261). Calculate the amounts for Pd(PPh₃)₄ (5 mol%), boronic acid (1.3 eq), and K₂CO₃ (2.5 eq)"**
+>
+> → Returns exact masses, mmol, with the substrate as limiting reagent
+
+> **"What's the best protecting group for a primary amine if I need it stable to acidic conditions but removable with Pd/C hydrogenation?"**
+>
+> → Searches 30 PGs with stability matrix, suggests Cbz
+
+> **"Format these DOIs as an ACS-style bibliography: 10.1021/jacs.1c12345, 10.1002/anie.202112345"**
+>
+> → Returns numbered, journal-formatted reference list
+
+> **"I'm writing up my experimental section. Give me a template for a Buchwald-Hartwig amination"**
+>
+> → Fill-in-the-blank template following journal conventions, with safety notes
+
+> **"Look up the NMR solvent peaks for DMSO-d6 — I see something at 2.50 ppm and want to make sure it's just residual solvent"**
+>
+> → Residual ¹H: 2.50 ppm (quintet), ¹³C: 39.52 ppm, water: 3.33 ppm
+
+> **"Generate a peptide library of 20 cyclic pentapeptides with at least one D-amino acid"**
+>
+> → Creates SMILES strings with properties (MW, logP, TPSA) for each
+
+> **"I'm submitting to JACS. What are the formatting requirements and word limits?"**
+>
+> → Full guide: 5000-word limit, superscript numerals, 300-word abstract, graphical abstract specs
+
+---
+
+## 📦 Install
+
+```bash
+pip install labmate-mcp
+```
+
+That's it. **58 of 78 tools work immediately — no API keys, no configuration.**
+
+### Connect to Claude
+
+Add this to your Claude config file:
+
+<details>
+<summary><b>Claude Desktop</b> — <code>claude_desktop_config.json</code></summary>
+
+On macOS: `~/Library/Application Support/Claude/claude_desktop_config.json`
+On Windows: `%APPDATA%\Claude\claude_desktop_config.json`
+
+```json
+{
+  "mcpServers": {
+    "labmate": {
+      "command": "labmate-mcp"
+    }
+  }
+}
+```
+
+</details>
+
+<details>
+<summary><b>Claude Code</b> — <code>.mcp.json</code> in your project root</summary>
+
+```json
+{
+  "mcpServers": {
+    "labmate": {
+      "command": "labmate-mcp"
+    }
+  }
+}
+```
+
+</details>
+
+<details>
+<summary><b>Docker</b></summary>
+
+```bash
+docker build -t labmate-mcp .
+docker run -it labmate-mcp
+```
+
+</details>
+
+Restart Claude after adding the config. You should see labmate's 78 tools available.
+
+### Optional: Add API keys for more tools
+
+```json
+{
+  "mcpServers": {
+    "labmate": {
+      "command": "labmate-mcp",
+      "env": {
+        "SEMANTIC_SCHOLAR_API_KEY": "your-key",
+        "UNPAYWALL_EMAIL": "you@university.edu"
+      }
+    }
+  }
+}
+```
+
+See [Configuration](#%EF%B8%8F-configuration) for the full list.
+
+---
+
+## 🔧 Tool Reference
+
+### 📚 Literature & Discovery (15 tools)
+
+Search papers across multiple databases, explore citation graphs, find open access PDFs, and track research trends.
+
+<details>
+<summary>Show all 15 tools</summary>
+
+| Tool | Source | What it does |
+|:-----|:-------|:-------------|
+| `search_papers` | Crossref + OpenAlex + S2 | Multi-source paper search with metadata fusion |
+| `get_paper_details` | Crossref + OpenAlex + S2 | Full metadata: abstract, authors, citations, references |
+| `find_similar_papers` | Semantic Scholar | Content-based paper recommendations |
+| `get_paper_citations` | Semantic Scholar | Forward citation graph + context snippets |
+| `get_paper_references` | Semantic Scholar | Backward citation graph (bibliography) |
+| `get_author_profile` | OpenAlex + S2 | h-index, publications, co-authors, topics |
+| `analyze_research_topic` | OpenAlex | Publication volume trends over time |
+| `find_open_access_pdf` | Unpaywall | Legal open access PDF URLs |
+| `search_chemrxiv` | Crossref + OpenAlex | Chemistry preprint search |
+| `get_chemrxiv_categories` | — | List ChemRxiv subject categories |
+| `search_web_of_science` | Web of Science | WoS search *(requires API key)* |
+| `generate_bibtex` | Crossref | DOI → BibTeX (single or batch) |
+| `get_journal_metrics` | OpenAlex | Impact metrics, open access %, policy |
+| `search_protein_structures` | RCSB PDB | Search PDB by keyword, organism, method |
+| `get_protein_structure` | RCSB PDB | Full PDB entry: resolution, ligands, sequence |
+
+</details>
+
+### 🔬 Compound Data & Safety (12 tools)
+
+Look up any compound by name, SMILES, or formula. Get safety data, binding affinities, crystal structures, and more.
+
+<details>
+<summary>Show all 12 tools</summary>
+
+| Tool | Source | What it does |
+|:-----|:-------|:-------------|
+| `search_compound` | PubChem | Name/SMILES/formula → compound data |
+| `get_compound_properties` | PubChem | MW, SMILES, InChI, formula, XLogP, TPSA |
+| `profile_compound` | Multiple | Comprehensive profile combining several databases |
+| `get_safety_data` | PubChem GHS | GHS pictograms, H-statements, P-statements |
+| `translate_compound_ids` | UniChem | Convert PubChem ↔ ChEMBL ↔ DrugBank ↔ ChEBI |
+| `search_crystal_structures` | COD | Crystallography Open Database search |
+| `search_materials_project` | Materials Project | Band gaps, formation energies *(requires key)* |
+| `search_nist_webbook` | NIST | ΔHf, Cp, phase transitions, IR spectra |
+| `search_mass_spectra` | MassBank | Mass spectrum search by exact mass or name |
+| `search_binding_data` | BindingDB | IC₅₀, Ki, Kd binding affinities |
+| `search_toxicity` | EPA CompTox | Toxicity endpoints *(requires key)* |
+| `classify_natural_product` | GNPS | NP superclass / class / pathway |
+
+</details>
+
+### ⚗️ Computational Chemistry (11 tools)
+
+AI-powered retrosynthesis, forward reaction prediction, pKa, solubility, ADMET, and NMR shift prediction.
+
+<details>
+<summary>Show all 11 tools</summary>
+
+| Tool | Source | What it does |
+|:-----|:-------|:-------------|
+| `predict_retrosynthesis` | IBM RXN | Multi-step retrosynthetic analysis |
+| `plan_synthesis` | IBM RXN | Forward synthesis route planning |
+| `predict_product` | IBM RXN | Predict products from reactants + reagents |
+| `predict_atom_mapping` | IBM RXN | Atom-by-atom mapping for mechanisms |
+| `text_to_procedure` | IBM RXN | Natural language → structured procedure |
+| `predict_pka` | Rowan Science | pKa values (any functional group, aqueous) |
+| `predict_solubility` | Rowan Science | Aqueous solubility prediction |
+| `predict_admet` | Rowan Science | Absorption, metabolism, toxicity prediction |
+| `search_tautomers` | Rowan Science | Enumerate tautomeric forms |
+| `compute_descriptors` | Rowan Science | Molecular descriptors from SMILES |
+| `predict_nmr` | Rowan Science | ¹H and ¹³C chemical shift prediction |
+
+*IBM RXN and Rowan tools require free API keys. See [Configuration](#%EF%B8%8F-configuration).*
+
+</details>
+
+### 🧬 Peptide Chemistry (10 tools)
+
+Sequence-to-SMILES conversion with 450+ amino acids, cyclization, library generation, pI calculation, and MS/MS interpretation.
+
+<details>
+<summary>Show all 10 tools</summary>
+
+| Tool | Source | What it does |
+|:-----|:-------|:-------------|
+| `peptide_to_smiles` | p2smi | Sequence → SMILES (450+ AAs, 5 cyclization types) |
+| `peptide_cyclization_options` | p2smi | Which cyclizations does a sequence support? |
+| `generate_peptide_library` | p2smi | Random peptide generation with NCAAs, D-stereo |
+| `peptide_properties` | p2smi + RDKit | MW, logP, TPSA, HBD/HBA, Lipinski |
+| `check_peptide_synthesis` | p2smi | SPPS feasibility: difficult motifs, aggregation |
+| `modify_peptide` | p2smi | Apply N-methylation, PEGylation |
+| `calculate_peptide_pi` | pichemist | Isoelectric point (8 pKa reference sets) |
+| `calculate_peptide_extinction` | pep-calc.com | ε₂₈₀ (Trp/Tyr/Cys contributions) |
+| `get_peptide_ion_series` | pep-calc.com | b/y/a/c/z ion ladders for MS/MS |
+| `assign_peptide_ms_peaks` | pep-calc.com | Match m/z values to fragments |
+
+*pep-calc.com tools fall back to local alternatives if the API is unavailable.*
+
+</details>
+
+### 🧪 Bench Chemistry — Calculators (5 tools)
+
+The calculators every lab needs, built in. Handles unit conversions automatically.
+
+<details>
+<summary>Show all 5 tools</summary>
+
+| Tool | What it does |
+|:-----|:-------------|
+| `calculate_molarity` | Solve for any unknown: mass, moles, volume, or MW |
+| `calculate_dilution` | C₁V₁ = C₂V₂ with automatic unit handling |
+| `calculate_reaction_mass` | Multi-reagent mass calc from equivalents |
+| `calculate_yield` | Percent yield from actual / theoretical |
+| `calculate_concentration` | M ↔ mM ↔ mg/mL ↔ %w/v ↔ ppm ↔ ppb |
+
+</details>
+
+### 📖 Bench Chemistry — Reference (10 tools)
+
+151 named reactions. 30 protecting groups. Solvent tables. Cooling baths. TLC stains. Column guides. Buffers. NMR solvents. Everything you'd normally look up in a textbook or a dog-eared printout taped to the fume hood.
+
+<details>
+<summary>Show all 10 tools</summary>
+
+| Tool | Coverage |
+|:-----|:---------|
+| `lookup_named_reaction` | **151 named reactions** with conditions, mechanism, scope, limitations |
+| `lookup_protecting_group` | **30 PGs** for OH, NH, C=O, COOH with stability/lability matrix |
+| `lookup_workup_procedure` | Step-by-step protocols: LAH quench, aqueous extraction, etc. |
+| `lookup_solvent_properties` | **32 solvents**: bp, mp, density, polarity index, dielectric, miscibility |
+| `lookup_cooling_bath` | **24 recipes** from −196 °C (lN₂) to +100 °C |
+| `lookup_tlc_stain` | **13 stains** organized by functional group selectivity |
+| `lookup_column_chromatography` | Solvent selection, Rf rules, loading, troubleshooting |
+| `lookup_buffer_recipe` | **20+ buffers**: PBS, Tris, HEPES, TAE, TBE, RIPA, citrate, etc. |
+| `lookup_amino_acid_properties` | **20 canonical AAs**: MW, pKa₁/pKa₂/pKaR, pI, hydropathy |
+| `lookup_nmr_solvent` | **12 solvents**: residual ¹H/¹³C shifts, water peak, multiplicity |
+
+</details>
+
+### 🔧 Chemistry Utilities (5 tools)
+
+<details>
+<summary>Show all 5 tools</summary>
+
+| Tool | What it does |
+|:-----|:-------------|
+| `calculate_isotope_pattern` | Isotope distribution from formula/SMILES (Cl, Br, S patterns) |
+| `validate_cas_number` | CAS registry check-digit validation |
+| `convert_units` | Mass, volume, energy, pressure, temperature, length, amount |
+| `lookup_periodic_table` | Z, mass, electron config, electronegativity, radius, group |
+| `calculate_buffer_ph` | Henderson-Hasselbalch solver with built-in pKa database |
+
+</details>
+
+### ✍️ Writing & Publication (10 tools)
+
+Format citations, build bibliographies, generate experimental section templates, check journal requirements, and prepare your SI — all from within Claude.
+
+<details>
+<summary>Show all 10 tools</summary>
+
+| Tool | Source | What it does |
+|:-----|:-------|:-------------|
+| `format_citation` | Crossref | DOI → formatted reference in **20+ styles** (ACS, RSC, Nature, Angew, APA…) |
+| `build_bibliography` | Crossref | Batch DOIs → numbered, styled reference list |
+| `lookup_iupac_name` | PubChem | SMILES → IUPAC systematic name |
+| `name_to_smiles` | PubChem | Common name → SMILES + InChI + InChIKey + MW |
+| `format_molecular_formula` | Local | C6H12O6 → C₆H₁₂O₆ (Unicode) / `\ce{C6H12O6}` (LaTeX) / `<sub>` (HTML) |
+| `lookup_experimental_template` | Local | **18 reaction templates** with fill-in fields and safety notes |
+| `lookup_journal_guide` | Local | Submission requirements for **12 top chemistry journals** |
+| `generate_si_checklist` | Local | SI checklist tailored to compound type |
+| `lookup_abbreviation` | Local | **193 standard abbreviations** (solvents, reagents, spectroscopy) |
+| `get_thesis_guide` | Local | Section-by-section writing guide: abstract → SI |
+
+</details>
+
+---
+
+## 📖 Examples
+
+### Literature workflow
+
+```
+You:    "Find the 5 most cited papers on photoredox catalysis from 2020-2024"
+Claude: [searches Crossref + Semantic Scholar, ranks by citation count]
+
+You:    "Show me who cited paper #2 and what topics they focused on"
+Claude: [retrieves forward citation graph from Semantic Scholar]
+
+You:    "Is there an open access PDF for paper #3?"
+Claude: [checks Unpaywall → returns legal OA link]
+
+You:    "Generate BibTeX for all 5 papers"
+Claude: [fetches structured citation data from Crossref]
+```
+
+### Synthesis planning
+
+```
+You:    "I want to make 4-methoxybiphenyl from 4-bromoanisole. What coupling should I use?"
+Claude: [looks up Suzuki coupling conditions, suggests Pd(PPh₃)₄/K₂CO₃/PhB(OH)₂]
+
+You:    "Calculate amounts for 200 mg scale with 5 mol% catalyst"
+Claude: [reaction mass calculator → exact mg for each reagent]
+
+You:    "What's a good workup for this?"
+Claude: [aqueous workup protocol, extraction with EtOAc, Na₂SO₄ dry]
+```
+
+### Writing a paper
+
+```
+You:    "Format these 12 DOIs as an ACS bibliography"
+Claude: [Crossref content negotiation → numbered reference list]
+
+You:    "I'm writing the experimental section for a Sonogashira coupling. Give me a template"
+Claude: [fill-in template with safety notes]
+
+You:    "What SI do I need for a small molecule paper?"
+Claude: [checklist: ¹H NMR, ¹³C NMR, HRMS, mp, HPLC purity, + formatting tips]
+
+You:    "I want to submit to Angew. Chem. — what are the requirements?"
+Claude: [5000-word Communication, 150-word abstract, endnote citations, graphical abstract]
+```
+
+---
+
+## ⚙️ Configuration
+
+**All environment variables are optional.** The server runs out of the box.
+
+| Variable | Service | Free? | What it unlocks |
+|:---------|:--------|:-----:|:----------------|
+| `SEMANTIC_SCHOLAR_API_KEY` | [Semantic Scholar](https://www.semanticscholar.org/product/api#api-key) | ✅ | Higher rate limits for citations & recommendations |
+| `UNPAYWALL_EMAIL` | [Unpaywall](https://unpaywall.org/) | ✅ | Open access PDF discovery |
+| `RXN4CHEMISTRY_API_KEY` | [IBM RXN](https://rxn.res.ibm.com) | ✅ | Retrosynthesis, product prediction, atom mapping |
+| `ROWAN_API_KEY` | [Rowan Science](https://rowan.ai) | ✅ | pKa, solubility, ADMET, tautomers, NMR prediction |
+| `MATERIALS_PROJECT_API_KEY` | [Materials Project](https://materialsproject.org) | ✅ | Crystal structures, band gaps, formation energies |
+| `WOS_API_KEY` | [Web of Science](https://developer.clarivate.com) | 🏛️ | Web of Science search (institutional) |
+| `COMPTOX_API_KEY` | [EPA CompTox](mailto:ccte_api@epa.gov) | ✅ | Toxicity & environmental data |
+
+**Aliases:** `S2_API_KEY` and `SEMANTIC_SCHOLAR_API_KEY` both work, as do `MP_API_KEY`/`MATERIALS_PROJECT_API_KEY` and `RXN_API_KEY`/`RXN4CHEMISTRY_API_KEY`.
+
+---
+
+## 🗄️ Built-in Databases
+
+These ship with labmate and require no API calls:
+
+| Database | Entries | What's inside |
+|:---------|--------:|:--------------|
+| Named reactions | **151** | Conditions, mechanism type, scope, limitations, references |
+| Protecting groups | **30** | OH/NH/C=O/COOH, install/remove conditions, stability matrix |
+| Solvents | **32** | bp, density, polarity index, dielectric, miscibility, safety |
+| Cooling baths | **24** | Recipes from −196 °C to +100 °C |
+| TLC stains | **13** | Selectivity by functional group, recipe, visualization |
+| Buffer recipes | **20+** | Preparation at specific pH, temperature correction |
+| Amino acids | **20** | pKa, pI, MW, hydropathy, codon, special notes |
+| NMR solvents | **12** | Residual ¹H, ¹³C, water peak, multiplicity, bp |
+| Experimental templates | **18** | Fill-in-the-blank for common reaction types |
+| Journal guides | **12** | JACS, Angew, Nature Chem, JOC, Org Lett, etc. |
+| Abbreviations | **193** | Standard abbreviations across 7 categories |
+| SI requirements | **18** | Per-technique formatting and common mistakes |
+| Thesis writing | **6** | Section-by-section guidance and tips |
+
+<details>
+<summary><b>All 151 named reactions</b> (click to expand)</summary>
+
+Aldol · Appel · Arndt-Eistert · Baeyer-Villiger · Bamford-Stevens · Barton Decarboxylation · Barton-McCombie · Baylis-Hillman · Beckmann · Biginelli · Birch · Bischler-Napieralski · Bouveault-Blanc · Buchner · Buchwald-Hartwig (C–N) · Buchwald-Hartwig (C–O) · Cannizzaro · CBS · Chan-Lam · Chichibabin · Claisen Condensation · Claisen Rearrangement · Clemmensen · CuAAC Click · Comins · Cope Elimination · Corey-Bakshi-Shibata · Corey-Chaykovsky · Corey-Fuchs · Corey-Kim · Corey-Winter · Curtius · Dakin · Darzens · Dess-Martin · Dieckmann · Diels-Alder · Doering-LaFlamme · Enders SAMP/RAMP · Eschweiler-Clarke · Evans Aldol · Favorskii · Ferrier · Finkelstein · Fischer Esterification · Fischer Indole · Friedel-Crafts Acylation · Friedel-Crafts Alkylation · Fukuyama · Gabriel · Grignard · Grubbs Metathesis · Hantzsch Pyridine · Heck · Henry · Hiyama · Hiyama-Denmark · Hofmann · Horner · Horner-Wadsworth-Emmons · IBX · Ireland-Claisen · Jacobsen Epoxidation · Jones · Julia-Lythgoe · Knoevenagel · Kolbe · Kulinkovich · Kumada · Lawesson · Lemieux-Johnson · Ley · Liebeskind-Srogl · Lossen · Luche · Mannich · Matteson · Meerwein · Meerwein-Ponndorf-Verley · Michael · Midland · Minisci · Mitsunobu · Mukaiyama Aldol · Myers · Negishi · Noyori · Nozaki-Hiyama-Kishi · Ohira-Bestmann · Olefin Metathesis · Oppenauer · Oppolzer Sultam · Ozonolysis · Paal-Knorr · Parikh-Doering · Passerini · Paternò-Büchi · Petasis · Peterson · Pictet-Spengler · Pinner · Pinnick · Prins · Ramberg-Bäcklund · Reductive Amination · Reformatsky · Ring-Closing Metathesis · Ritter · Robinson Annulation · Roush · Rubottom · Sakurai-Hosomi · Sandmeyer · Sharpless AD · Sharpless AE · Shi Epoxidation · Shiina · Simmons-Smith · Sonogashira · Staudinger Ligation · Staudinger Reduction · Steglich · Stetter · Still-Gennari · Stille · Stork Enamine · Strecker · Suzuki · Suzuki-Miyaura · Swern · Takai · Tebbe · TEMPO · Tiffeneau-Demjanov · Trost AAA · Tsuji-Trost · Ugi · Ullmann · Upjohn · Vilsmeier-Haack · Wacker · Weinreb Amide · Wharton · Williamson · Wittig · Wittig Rearrangement · Wohl-Ziegler · Wolff · Wolff-Kishner · Yamaguchi · Zincke Aldehyde
+
+</details>
+
+---
+
+## 🏗️ Architecture
+
+```
+labmate_mcp/
+├── server.py       5,116 lines   78 MCP tool definitions + response formatting
+├── bench.py        3,392 lines   Calculators + reference databases (151 reactions, 30 PGs, …)
+├── apis.py         1,744 lines   HTTP clients for 25+ scientific APIs
+├── writing.py      1,488 lines   Citations, templates, journal guides, SI, thesis
+├── chemistry.py      572 lines   Isotope patterns, CAS, units, periodic table, pH
+├── peptide.py        384 lines   p2smi + pichemist + pep-calc.com integration
+└── __init__.py         4 lines   Version
+                  ──────────────
+                  12,700 lines
+```
+
+---
+
+## 🤝 Contributing
+
+Contributions are welcome! See [CONTRIBUTING.md](CONTRIBUTING.md) for details.
+
+High-impact areas: more named reactions, more experimental templates, more journal guides, tests, and bug reports.
+
+---
+
+## 📄 License
+
+[MIT](LICENSE) — use freely in academia and industry.
+
+## 📚 Citations
+
+If labmate-mcp contributes to your research, please cite the underlying tools:
+
+- **p2smi:** Feller, A. (2025). p2smi: Generation and analysis of drug-like peptide SMILES strings. *JOSS*, 10, 8319. [doi:10.21105/joss.08319](https://doi.org/10.21105/joss.08319)
+- **pichemist:** Trastoy, B. *et al.* (2023). pIChemiSt: Structure-based isoelectric point prediction. *J. Chem. Inf. Model.* [AstraZeneca peptide-tools](https://github.com/AstraZeneca/peptide-tools)
+- **OpenAlex:** Priem, J., Piwowar, H., & Orr, R. (2022). OpenAlex: A fully-open index of scholarly works. [arXiv:2205.01833](https://arxiv.org/abs/2205.01833)

labmate_mcp-7.0.0.dist-info/RECORD

@@ -0,0 +1,14 @@
+labmate_mcp/__init__.py,sha256=XN03SO8_l0brKxemaWRduycpmnAywho7wpQJSCgOfKM,151
+labmate_mcp/__main__.py,sha256=DEhydVGp643KaLZatSrKq7-qgqpDH8g7S-E7mj-1hRw,89
+labmate_mcp/apis.py,sha256=UyvMKFObLSUim1lVgVx1LeJ7R_lOmoA4GeJF3Oj6n2M,57153
+labmate_mcp/bench.py,sha256=pLE9Lfujc63ehH-6OxPTpqpIoUzueoh2hufMOxldb2g,229070
+labmate_mcp/chemistry.py,sha256=3tvSR48T9Lx3mj8OroMhhE-1Xg7mzwalSpAsLmb0hcM,31529
+labmate_mcp/peptide.py,sha256=17mjKz8BJ8BUS__TZh6FQMr7EmiydLyYI7RrAI8Zxgg,12691
+labmate_mcp/server.py,sha256=P8I5iIDJfbH-8yN-6fawoxKcI4L5K8aQLh-lJoHv6Ms,208242
+labmate_mcp/writing.py,sha256=WZqgIzplqZgNuhwBHAjXwXQ9A5tz8rxEzktJEl-GVHQ,79511
+labmate_mcp-7.0.0.dist-info/licenses/LICENSE,sha256=apOEJKkENojldUYm_yKVJ-7Bn4t0oPPkdUJtYxQUQO8,1068
+labmate_mcp-7.0.0.dist-info/METADATA,sha256=KWMPjY8dIKTP1I6j3cCzVlLezKbvGYl15izSJY413H4,23995
+labmate_mcp-7.0.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+labmate_mcp-7.0.0.dist-info/entry_points.txt,sha256=NhDC0g-0iSDsd3RYfmNPBAdg_9C2npgVxw9e4AOXpIk,56
+labmate_mcp-7.0.0.dist-info/top_level.txt,sha256=VWDn7cOlUMYcWXhs4Mjax0xHCzDsWH9dgwtO1JiBSbg,12
+labmate_mcp-7.0.0.dist-info/RECORD,,

labmate_mcp-7.0.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.10.2)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

labmate_mcp-7.0.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+labmate-mcp = labmate_mcp.server:main

labmate_mcp-7.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Jonas Rackl
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

labmate_mcp-7.0.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+labmate_mcp