Updated chemistry-rdkit/SKILL.md with additional chemistry functions

.claude/skills/chemistry-rdkit/SKILL.md

@@ -36,20 +36,24 @@ metadata:
 4. Tanimoto similarity: `DataStructs.TanimotoSimilarity(fp1, fp2)`
 5. Use radius=2 (ECFP4 equivalent) as default for most applications
 6. For virtual screening, Tanimoto > 0.7 suggests structural similarity
+7. To filter for unique structures, use `Chem.MolToInchiKey`
 
 ### Substructure Search
 1. SMARTS patterns: `pattern = Chem.MolFromSmarts('[OH]')`
 2. Check match: `mol.HasSubstructMatch(pattern)`
 3. Get all matches: `mol.GetSubstructMatches(pattern)`
-4. Common SMARTS: `[#6](=O)[OH]` (carboxylic acid), `[NH2]` (primary amine)
-5. Filter compound libraries by functional group presence
+5. Common SMARTS: `[#6](=O)[OH]` (carboxylic acid), `[NH2]` (primary amine)
+6. Find maximum common substructure with `mcs = rdFMCS.FindMCS(mols)`
+7. Filter compound libraries by functional group presence
 
 ### Property Calculation Patterns
 1. Batch processing: iterate over SDMolSupplier, skip None entries
 2. Use `Chem.Descriptors.descList` for all available descriptors
 3. For ADMET filtering, calculate Lipinski, Veber, and PAINS filters
-4. Generate 3D coordinates: `AllChem.EmbedMolecule(mol, AllChem.ETKDG())`
-5. Minimize energy: `AllChem.MMFFOptimizeMolecule(mol)`
+4. For general druglikeness, use `Descriptors.qed`, for synthesizability `from SA_Score import sascorer`
+5. For `sascorer`, append the contrib path first: `sys.path.append(os.path.join(os.environ['CONDA_PREFIX'],'share','RDKit','Contrib'))`
+6. Generate 3D coordinates: `AllChem.EmbedMolecule(mol, AllChem.ETKDG())`
+7. Minimize energy: `AllChem.MMFFOptimizeMolecule(mol)`
 
 ### Common Pitfalls
 1. Always sanitize molecules (default behavior) — disable only when needed

researchclaw/literature/semantic_scholar.py

@@ -236,6 +236,14 @@ def _request_with_retry(
             if exc.code == 429:
                 if _cb_on_429():
                     return None  # breaker tripped
+                # On first 429, don't retry S2 — fall through to next backend
+                # immediately so arXiv/OpenAlex can run without waiting.
+                if attempt == 0:
+                    logger.warning(
+                        "S2 rate-limited (429) on first attempt — "
+                        "skipping S2 for this query, trying next backend"
+                    )
+                    return None
                 delay = min(2 ** (attempt + 1), _MAX_WAIT_SEC)
                 jitter = random.uniform(0, delay * 0.3)
                 wait = delay + jitter

researchclaw/llm/__init__.py

@@ -30,7 +30,8 @@
         "base_url": "https://api.novita.ai/openai",
     },
     "minimax": {
-        "base_url": "https://api.minimaxi.com/v1",
+        "base_url": "https://api.minimax.io/anthropic",
+        "wire_api": "anthropic",
     },
     "volcengine": {
         "base_url": "https://ark.cn-beijing.volces.com/api/v3",