better-dsh 0.2.5-c → 0.2.5-e

package/docs/80_upstream-docs-and-skills/hermes-dev-skill/src/docs/user-guide/skills/optional/research/research-drug-discovery.md

@@ -1,237 +0,0 @@
----
-title: "Drug Discovery — Drug discovery: ChEMBL search, drug-likeness, interactions"
-sidebar_label: "Drug Discovery"
-description: "Drug discovery: ChEMBL search, drug-likeness, interactions"
----
-
-{/* This page is auto-generated from the skill's SKILL.md by website/scripts/generate-skill-docs.py. Edit the source SKILL.md, not this page. */}
-
-# Drug Discovery
-
-Drug discovery: ChEMBL search, drug-likeness, interactions.
-
-## Skill metadata
-
-| | |
-|---|---|
-| Source | Optional — install with `hermes skills install official/research/drug-discovery` |
-| Path | `optional-skills/research\drug-discovery` |
-| Version | `1.0.0` |
-| Author | bennytimz |
-| License | MIT |
-| Platforms | linux, macos, windows |
-| Tags | `science`, `chemistry`, `pharmacology`, `research`, `health` |
-
-## Reference: full SKILL.md
-
-:::info
-The following is the complete skill definition that Hermes loads when this skill is triggered. This is what the agent sees as instructions when the skill is active.
-:::
-
-# Drug Discovery & Pharmaceutical Research
-
-You are an expert pharmaceutical scientist and medicinal chemist with deep
-knowledge of drug discovery, cheminformatics, and clinical pharmacology.
-Use this skill for all pharma/chemistry research tasks.
-
-## Core Workflows
-
-### 1 — Bioactive Compound Search (ChEMBL)
-
-Search ChEMBL (the world's largest open bioactivity database) for compounds
-by target, activity, or molecule name. No API key required.
-
-```bash
-# Search compounds by target name (e.g. "EGFR", "COX-2", "ACE")
-TARGET="$1"
-ENCODED=$(python -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$TARGET")
-curl -s "https://www.ebi.ac.uk/chembl/api/data/target/search?q=${ENCODED}&format=json" \
-  | python -c "
-import json,sys
-data=json.load(sys.stdin)
-targets=data.get('targets',[])[:5]
-for t in targets:
-    print(f\"ChEMBL ID : {t.get('target_chembl_id')}\")
-    print(f\"Name      : {t.get('pref_name')}\")
-    print(f\"Type      : {t.get('target_type')}\")
-    print()
-"
-```
-
-```bash
-# Get bioactivity data for a ChEMBL target ID
-TARGET_ID="$1"   # e.g. CHEMBL203
-curl -s "https://www.ebi.ac.uk/chembl/api/data/activity?target_chembl_id=${TARGET_ID}&pchembl_value__gte=6&limit=10&format=json" \
-  | python -c "
-import json,sys
-data=json.load(sys.stdin)
-acts=data.get('activities',[])
-print(f'Found {len(acts)} activities (pChEMBL >= 6):')
-for a in acts:
-    print(f\"  Molecule: {a.get('molecule_chembl_id')}  |  {a.get('standard_type')}: {a.get('standard_value')} {a.get('standard_units')}  |  pChEMBL: {a.get('pchembl_value')}\")
-"
-```
-
-```bash
-# Look up a specific molecule by ChEMBL ID
-MOL_ID="$1"   # e.g. CHEMBL25 (aspirin)
-curl -s "https://www.ebi.ac.uk/chembl/api/data/molecule/${MOL_ID}?format=json" \
-  | python -c "
-import json,sys
-m=json.load(sys.stdin)
-props=m.get('molecule_properties',{}) or {}
-print(f\"Name       : {m.get('pref_name','N/A')}\")
-print(f\"SMILES     : {m.get('molecule_structures',{}).get('canonical_smiles','N/A') if m.get('molecule_structures') else 'N/A'}\")
-print(f\"MW         : {props.get('full_mwt','N/A')} Da\")
-print(f\"LogP       : {props.get('alogp','N/A')}\")
-print(f\"HBD        : {props.get('hbd','N/A')}\")
-print(f\"HBA        : {props.get('hba','N/A')}\")
-print(f\"TPSA       : {props.get('psa','N/A')} Ų\")
-print(f\"Ro5 violations: {props.get('num_ro5_violations','N/A')}\")
-print(f\"QED        : {props.get('qed_weighted','N/A')}\")
-"
-```
-
-### 2 — Drug-Likeness Calculation (Lipinski Ro5 + Veber)
-
-Assess any molecule against established oral bioavailability rules using
-PubChem's free property API — no RDKit install needed.
-
-```bash
-COMPOUND="$1"
-ENCODED=$(python -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$COMPOUND")
-curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${ENCODED}/property/MolecularWeight,XLogP,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,TPSA,InChIKey/JSON" \
-  | python -c "
-import json,sys
-data=json.load(sys.stdin)
-props=data['PropertyTable']['Properties'][0]
-mw   = float(props.get('MolecularWeight', 0))
-logp = float(props.get('XLogP', 0))
-hbd  = int(props.get('HBondDonorCount', 0))
-hba  = int(props.get('HBondAcceptorCount', 0))
-rot  = int(props.get('RotatableBondCount', 0))
-tpsa = float(props.get('TPSA', 0))
-print('=== Lipinski Rule of Five (Ro5) ===')
-print(f'  MW   {mw:.1f} Da    {\"✓\" if mw<=500 else \"✗ VIOLATION (>500)\"}')
-print(f'  LogP {logp:.2f}       {\"✓\" if logp<=5 else \"✗ VIOLATION (>5)\"}')
-print(f'  HBD  {hbd}           {\"✓\" if hbd<=5 else \"✗ VIOLATION (>5)\"}')
-print(f'  HBA  {hba}           {\"✓\" if hba<=10 else \"✗ VIOLATION (>10)\"}')
-viol = sum([mw>500, logp>5, hbd>5, hba>10])
-print(f'  Violations: {viol}/4  {\"→ Likely orally bioavailable\" if viol<=1 else \"→ Poor oral bioavailability predicted\"}')
-print()
-print('=== Veber Oral Bioavailability Rules ===')
-print(f'  TPSA         {tpsa:.1f} Ų   {\"✓\" if tpsa<=140 else \"✗ VIOLATION (>140)\"}')
-print(f'  Rot. bonds   {rot}           {\"✓\" if rot<=10 else \"✗ VIOLATION (>10)\"}')
-print(f'  Both rules met: {\"Yes → good oral absorption predicted\" if tpsa<=140 and rot<=10 else \"No → reduced oral absorption\"}')
-"
-```
-
-### 3 — Drug Interaction & Safety Lookup (OpenFDA)
-
-```bash
-DRUG="$1"
-ENCODED=$(python -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$DRUG")
-curl -s "https://api.fda.gov/drug/label.json?search=drug_interactions:\"${ENCODED}\"&limit=3" \
-  | python -c "
-import json,sys
-data=json.load(sys.stdin)
-results=data.get('results',[])
-if not results:
-    print('No interaction data found in FDA labels.')
-    sys.exit()
-for r in results[:2]:
-    brand=r.get('openfda',{}).get('brand_name',['Unknown'])[0]
-    generic=r.get('openfda',{}).get('generic_name',['Unknown'])[0]
-    interactions=r.get('drug_interactions',['N/A'])[0]
-    print(f'--- {brand} ({generic}) ---')
-    print(interactions[:800])
-    print()
-"
-```
-
-```bash
-DRUG="$1"
-ENCODED=$(python -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$DRUG")
-curl -s "https://api.fda.gov/drug/event.json?search=patient.drug.medicinalproduct:\"${ENCODED}\"&count=patient.reaction.reactionmeddrapt.exact&limit=10" \
-  | python -c "
-import json,sys
-data=json.load(sys.stdin)
-results=data.get('results',[])
-if not results:
-    print('No adverse event data found.')
-    sys.exit()
-print(f'Top adverse events reported:')
-for r in results[:10]:
-    print(f\"  {r['count']:>5}x  {r['term']}\")
-"
-```
-
-### 4 — PubChem Compound Search
-
-```bash
-COMPOUND="$1"
-ENCODED=$(python -c "import urllib.parse,sys; print(urllib.parse.quote(sys.argv[1]))" "$COMPOUND")
-CID=$(curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/${ENCODED}/cids/TXT" | head -1 | tr -d '[:space:]')
-echo "PubChem CID: $CID"
-curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/${CID}/property/IsomericSMILES,InChIKey,IUPACName/JSON" \
-  | python -c "
-import json,sys
-p=json.load(sys.stdin)['PropertyTable']['Properties'][0]
-print(f\"IUPAC Name : {p.get('IUPACName','N/A')}\")
-print(f\"SMILES     : {p.get('IsomericSMILES','N/A')}\")
-print(f\"InChIKey   : {p.get('InChIKey','N/A')}\")
-"
-```
-
-### 5 — Target & Disease Literature (OpenTargets)
-
-```bash
-GENE="$1"
-curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
-  -H "Content-Type: application/json" \
-  -d "{\"query\":\"{ search(queryString: \\\"${GENE}\\\", entityNames: [\\\"target\\\"], page: {index: 0, size: 1}) { hits { id score object { ... on Target { id approvedSymbol approvedName associatedDiseases(page: {index: 0, size: 5}) { count rows { score disease { id name } } } } } } } }\"}" \
-  | python -c "
-import json,sys
-data=json.load(sys.stdin)
-hits=data.get('data',{}).get('search',{}).get('hits',[])
-if not hits:
-    print('Target not found.')
-    sys.exit()
-obj=hits[0]['object']
-print(f\"Target: {obj.get('approvedSymbol')} — {obj.get('approvedName')}\")
-assoc=obj.get('associatedDiseases',{})
-print(f\"Associated with {assoc.get('count',0)} diseases. Top associations:\")
-for row in assoc.get('rows',[]):
-    print(f\"  Score {row['score']:.3f}  |  {row['disease']['name']}\")
-"
-```
-
-## Reasoning Guidelines
-
-When analysing drug-likeness or molecular properties, always:
-
-1. **State raw values first** — MW, LogP, HBD, HBA, TPSA, RotBonds
-2. **Apply rule sets** — Ro5 (Lipinski), Veber, Ghose filter where relevant
-3. **Flag liabilities** — metabolic hotspots, hERG risk, high TPSA for CNS penetration
-4. **Suggest optimizations** — bioisosteric replacements, prodrug strategies, ring truncation
-5. **Cite the source API** — ChEMBL, PubChem, OpenFDA, or OpenTargets
-
-For ADMET questions, reason through Absorption, Distribution, Metabolism, Excretion, Toxicity systematically. See references/ADMET_REFERENCE.md for detailed guidance.
-
-## Important Notes
-
-- All APIs are free, public, require no authentication
-- ChEMBL rate limits: add sleep 1 between batch requests
-- FDA data reflects reported adverse events, not necessarily causation
-- Always recommend consulting a licensed pharmacist or physician for clinical decisions
-
-## Quick Reference
-
-| Task | API | Endpoint |
-|------|-----|----------|
-| Find target | ChEMBL | `/api/data/target/search?q=` |
-| Get bioactivity | ChEMBL | `/api/data/activity?target_chembl_id=` |
-| Molecule properties | PubChem | `/rest/pug/compound/name/{name}/property/` |
-| Drug interactions | OpenFDA | `/drug/label.json?search=drug_interactions:` |
-| Adverse events | OpenFDA | `/drug/event.json?search=...&count=reaction` |
-| Gene-disease | OpenTargets | GraphQL POST `/api/v4/graphql` |

package/docs/80_upstream-docs-and-skills/hermes-dev-skill/src/docs/user-guide/skills/optional/research/research-duckduckgo-search.md

@@ -1,255 +0,0 @@
----
-title: "Duckduckgo Search — Free keyless web, news, and image search via ddgs"
-sidebar_label: "Duckduckgo Search"
-description: "Free keyless web, news, and image search via ddgs"
----
-
-{/* This page is auto-generated from the skill's SKILL.md by website/scripts/generate-skill-docs.py. Edit the source SKILL.md, not this page. */}
-
-# Duckduckgo Search
-
-Free keyless web, news, and image search via ddgs.
-
-## Skill metadata
-
-| | |
-|---|---|
-| Source | Optional — install with `hermes skills install official/research/duckduckgo-search` |
-| Path | `optional-skills/research\duckduckgo-search` |
-| Version | `1.3.0` |
-| Author | gamedevCloudy |
-| License | MIT |
-| Platforms | linux, macos, windows |
-| Tags | `search`, `duckduckgo`, `web-search`, `free`, `fallback` |
-| Related skills | [`arxiv`](/docs/user-guide/skills/bundled/research/research-arxiv) |
-
-## Reference: full SKILL.md
-
-:::info
-The following is the complete skill definition that Hermes loads when this skill is triggered. This is what the agent sees as instructions when the skill is active.
-:::
-
-# DuckDuckGo Search
-
-Free web search using DuckDuckGo. **No API key required.**
-
-Preferred when `web_search` is unavailable or unsuitable (for example when `FIRECRAWL_API_KEY` is not set). Can also be used as a standalone search path when DuckDuckGo results are specifically desired.
-
-## Detection Flow
-
-Check what is actually available before choosing an approach:
-
-```bash
-# Check CLI availability
-command -v ddgs >/dev/null && echo "DDGS_CLI=installed" || echo "DDGS_CLI=missing"
-```
-
-Decision tree:
-1. If `ddgs` CLI is installed, prefer `terminal` + `ddgs`
-2. If `ddgs` CLI is missing, do not assume `execute_code` can import `ddgs`
-3. If the user wants DuckDuckGo specifically, install `ddgs` first in the relevant environment
-4. Otherwise fall back to built-in web/browser tools
-
-Important runtime note:
-- Terminal and `execute_code` are separate runtimes
-- A successful shell install does not guarantee `execute_code` can import `ddgs`
-- Never assume third-party Python packages are preinstalled inside `execute_code`
-
-## Installation
-
-Install `ddgs` only when DuckDuckGo search is specifically needed and the runtime does not already provide it.
-
-```bash
-# Python package + CLI entrypoint
-pip install ddgs
-
-# Verify CLI
-ddgs --help
-```
-
-If a workflow depends on Python imports, verify that same runtime can import `ddgs` before using `from ddgs import DDGS`.
-
-## Method 1: CLI Search (Preferred)
-
-Use the `ddgs` command via `terminal` when it exists. This is the preferred path because it avoids assuming the `execute_code` sandbox has the `ddgs` Python package installed.
-
-```bash
-# Text search
-ddgs text -q "python async programming" -m 5
-
-# News search
-ddgs news -q "artificial intelligence" -m 5
-
-# Image search
-ddgs images -q "landscape photography" -m 10
-
-# Video search
-ddgs videos -q "python tutorial" -m 5
-
-# With region filter
-ddgs text -q "best restaurants" -m 5 -r us-en
-
-# Recent results only (d=day, w=week, m=month, y=year)
-ddgs text -q "latest AI news" -m 5 -t w
-
-# JSON output for parsing
-ddgs text -q "fastapi tutorial" -m 5 -o json
-```
-
-### CLI Flags
-
-| Flag | Description | Example |
-|------|-------------|---------|
-| `-q` | Query — **required** | `-q "search terms"` |
-| `-m` | Max results | `-m 5` |
-| `-r` | Region | `-r us-en` |
-| `-t` | Time limit | `-t w` (week) |
-| `-s` | Safe search | `-s off` |
-| `-o` | Output format | `-o json` |
-
-## Method 2: Python API (Only After Verification)
-
-Use the `DDGS` class in `execute_code` or another Python runtime only after verifying that `ddgs` is installed there. Do not assume `execute_code` includes third-party packages by default.
-
-Safe wording:
-- "Use `execute_code` with `ddgs` after installing or verifying the package if needed"
-
-Avoid saying:
-- "`execute_code` includes `ddgs`"
-- "DuckDuckGo search works by default in `execute_code`"
-
-**Important:** `max_results` must always be passed as a **keyword argument** — positional usage raises an error on all methods.
-
-### Text Search
-
-Best for: general research, companies, documentation.
-
-```python
-from ddgs import DDGS
-
-with DDGS() as ddgs:
-    for r in ddgs.text("python async programming", max_results=5):
-        print(r["title"])
-        print(r["href"])
-        print(r.get("body", "")[:200])
-        print()
-```
-
-Returns: `title`, `href`, `body`
-
-### News Search
-
-Best for: current events, breaking news, latest updates.
-
-```python
-from ddgs import DDGS
-
-with DDGS() as ddgs:
-    for r in ddgs.news("AI regulation 2026", max_results=5):
-        print(r["date"], "-", r["title"])
-        print(r.get("source", ""), "|", r["url"])
-        print(r.get("body", "")[:200])
-        print()
-```
-
-Returns: `date`, `title`, `body`, `url`, `image`, `source`
-
-### Image Search
-
-Best for: visual references, product images, diagrams.
-
-```python
-from ddgs import DDGS
-
-with DDGS() as ddgs:
-    for r in ddgs.images("semiconductor chip", max_results=5):
-        print(r["title"])
-        print(r["image"])
-        print(r.get("thumbnail", ""))
-        print(r.get("source", ""))
-        print()
-```
-
-Returns: `title`, `image`, `thumbnail`, `url`, `height`, `width`, `source`
-
-### Video Search
-
-Best for: tutorials, demos, explainers.
-
-```python
-from ddgs import DDGS
-
-with DDGS() as ddgs:
-    for r in ddgs.videos("FastAPI tutorial", max_results=5):
-        print(r["title"])
-        print(r.get("content", ""))
-        print(r.get("duration", ""))
-        print(r.get("provider", ""))
-        print(r.get("published", ""))
-        print()
-```
-
-Returns: `title`, `content`, `description`, `duration`, `provider`, `published`, `statistics`, `uploader`
-
-### Quick Reference
-
-| Method | Use When | Key Fields |
-|--------|----------|------------|
-| `text()` | General research, companies | title, href, body |
-| `news()` | Current events, updates | date, title, source, body, url |
-| `images()` | Visuals, diagrams | title, image, thumbnail, url |
-| `videos()` | Tutorials, demos | title, content, duration, provider |
-
-## Workflow: Search then Extract
-
-DuckDuckGo returns titles, URLs, and snippets — not full page content. To get full page content, search first and then extract the most relevant URL with `web_extract`, browser tools, or curl.
-
-CLI example:
-
-```bash
-ddgs text -q "fastapi deployment guide" -m 3 -o json
-```
-
-Python example, only after verifying `ddgs` is installed in that runtime:
-
-```python
-from ddgs import DDGS
-
-with DDGS() as ddgs:
-    results = list(ddgs.text("fastapi deployment guide", max_results=3))
-    for r in results:
-        print(r["title"], "->", r["href"])
-```
-
-Then extract the best URL with `web_extract` or another content-retrieval tool.
-
-## Limitations
-
-- **Rate limiting**: DuckDuckGo may throttle after many rapid requests. Add a short delay between searches if needed.
-- **No content extraction**: `ddgs` returns snippets, not full page content. Use `web_extract`, browser tools, or curl for the full article/page.
-- **Results quality**: Generally good but less configurable than Firecrawl's search.
-- **Availability**: DuckDuckGo may block requests from some cloud IPs. If searches return empty, try different keywords or wait a few seconds.
-- **Field variability**: Return fields may vary between results or `ddgs` versions. Use `.get()` for optional fields to avoid `KeyError`.
-- **Separate runtimes**: A successful `ddgs` install in terminal does not automatically mean `execute_code` can import it.
-
-## Troubleshooting
-
-| Problem | Likely Cause | What To Do |
-|---------|--------------|------------|
-| `ddgs: command not found` | CLI not installed in the shell environment | Install `ddgs`, or use built-in web/browser tools instead |
-| `ModuleNotFoundError: No module named 'ddgs'` | Python runtime does not have the package installed | Do not use Python DDGS there until that runtime is prepared |
-| Search returns nothing | Temporary rate limiting or poor query | Wait a few seconds, retry, or adjust the query |
-| CLI works but `execute_code` import fails | Terminal and `execute_code` are different runtimes | Keep using CLI, or separately prepare the Python runtime |
-
-## Pitfalls
-
-- **`max_results` is keyword-only**: `ddgs.text("query", 5)` raises an error. Use `ddgs.text("query", max_results=5)`.
-- **Do not assume the CLI exists**: Check `command -v ddgs` before using it.
-- **Do not assume `execute_code` can import `ddgs`**: `from ddgs import DDGS` may fail with `ModuleNotFoundError` unless that runtime was prepared separately.
-- **Package name**: The package is `ddgs` (previously `duckduckgo-search`). Install with `pip install ddgs`.
-- **Don't confuse `-q` and `-m`** (CLI): `-q` is for the query, `-m` is for max results count.
-- **Empty results**: If `ddgs` returns nothing, it may be rate-limited. Wait a few seconds and retry.
-
-## Validated With
-
-Validated examples against `ddgs==9.11.2` semantics. Skill guidance now treats CLI availability and Python import availability as separate concerns so the documented workflow matches actual runtime behavior.