@pikaa-ai/pikaa 0.3.23 → 0.3.24

package/skills/molfeat/SKILL.md

@@ -1,348 +0,0 @@
----
-name: molfeat
-description: Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
-license: Apache-2.0 license
-allowed-tools: Read Write Edit Bash
-compatibility: Requires Python 3.9–3.10 (molfeat 0.11.0 does not support 3.11+). Requires datamol, PyTorch, and optional extras for GNN/transformer models.
-metadata:
-  version: "1.1"
-  skill-author: K-Dense Inc.
----
-
-# Molfeat - Molecular Featurization Hub
-
-## Overview
-
-Molfeat is a comprehensive Python library for molecular featurization that unifies 100+ pre-trained embeddings and hand-crafted featurizers. Convert chemical structures (SMILES strings or RDKit molecules) into numerical representations for machine learning tasks including QSAR modeling, virtual screening, similarity searching, and deep learning applications. Features fast parallel processing, scikit-learn compatible transformers, and built-in caching.
-
-**Version note:** Examples target **molfeat 0.11.0** (PyPI stable, May 2025). Requires **Python 3.9–3.10** (`requires-python` caps below 3.11). Depends on **datamol ≥0.8.0** and **PyTorch ≥1.13**. Since 0.8.7, prefer datamol `Mol` objects over raw `rdkit.Chem.Mol`. Since 0.10.1, fingerprint calculators use RDKit's `rdFingerprintGenerator` API internally. Since 0.11.0, pretrained models load in memory and base models are set to PyTorch evaluation mode automatically.
-
-## When to Use This Skill
-
-This skill should be used when working with:
-- **Molecular machine learning**: Building QSAR/QSPR models, property prediction
-- **Virtual screening**: Ranking compound libraries for biological activity
-- **Similarity searching**: Finding structurally similar molecules
-- **Chemical space analysis**: Clustering, visualization, dimensionality reduction
-- **Deep learning**: Training neural networks on molecular data
-- **Featurization pipelines**: Converting SMILES to ML-ready representations
-- **Cheminformatics**: Any task requiring molecular feature extraction
-
-## Installation
-
-Use a Python 3.9 or 3.10 environment (molfeat does not install on 3.11+ as of 0.11.0):
-
-```bash
-uv pip install "molfeat==0.11.0"
-
-# With all pip-installable optional dependencies
-uv pip install "molfeat[all]==0.11.0"
-```
-
-**Optional dependency extras (PyPI):**
-- `molfeat[dgl]` — GNN models (GIN variants); upstream recommends `dgl<=2.0` (graphbolt issues in newer DGL)
-- `molfeat[graphormer]` — Graphormer models
-- `molfeat[transformer]` — ChemBERTa, ChemGPT, MolT5
-- `molfeat[fcd]` — FCD descriptors
-- `molfeat[pyg]` — PyTorch Geometric featurizers
-- `molfeat[viz]` — NGLView visualization widgets
-
-**External featurizers:** MAP4 is not bundled in molfeat extras — install from [reymond-group/map4](https://github.com/reymond-group/map4) separately. Some heavy deps (DGL, dgllife, graphormer-pretrained) are easier via conda-forge; see [optional dependencies](https://molfeat-docs.datamol.io/stable/).
-
-## Core Concepts
-
-Molfeat organizes featurization into three hierarchical classes:
-
-### 1. Calculators (`molfeat.calc`)
-
-Callable objects that convert individual molecules into feature vectors. Accept RDKit `Chem.Mol` objects or SMILES strings.
-
-**Use calculators for:**
-- Single molecule featurization
-- Custom processing loops
-- Direct feature computation
-
-**Example:**
-```python
-from molfeat.calc import FPCalculator
-
-calc = FPCalculator("ecfp", radius=3, fpSize=2048)
-features = calc("CCO")  # Returns numpy array (2048,)
-```
-
-### 2. Transformers (`molfeat.trans`)
-
-Scikit-learn compatible transformers that wrap calculators for batch processing with parallelization.
-
-**Use transformers for:**
-- Batch featurization of molecular datasets
-- Integration with scikit-learn pipelines
-- Parallel processing (automatic CPU utilization)
-
-**Example:**
-```python
-from molfeat.trans import MoleculeTransformer
-from molfeat.calc import FPCalculator
-
-transformer = MoleculeTransformer(FPCalculator("ecfp"), n_jobs=-1)
-features = transformer(smiles_list)  # Parallel processing
-```
-
-### 3. Pretrained Transformers (`molfeat.trans.pretrained`)
-
-Specialized transformers for deep learning models with batched inference and caching.
-
-**Use pretrained transformers for:**
-- State-of-the-art molecular embeddings
-- Transfer learning from large chemical datasets
-- Deep learning feature extraction
-
-**Example:**
-```python
-from molfeat.trans.pretrained import PretrainedMolTransformer
-
-transformer = PretrainedMolTransformer("ChemBERTa-77M-MLM", n_jobs=-1)
-embeddings = transformer(smiles_list)  # Deep learning embeddings
-```
-
-## Quick Start Workflow
-
-### Basic Featurization
-
-```python
-import datamol as dm
-from molfeat.calc import FPCalculator
-from molfeat.trans import MoleculeTransformer
-
-# Load molecular data
-smiles = ["CCO", "CC(=O)O", "c1ccccc1", "CC(C)O"]
-
-# Create calculator and transformer
-calc = FPCalculator("ecfp", radius=3)
-transformer = MoleculeTransformer(calc, n_jobs=-1)
-
-# Featurize molecules
-features = transformer(smiles)
-print(f"Shape: {features.shape}")  # (4, 2048)
-```
-
-### Save and Load Configuration
-
-```python
-# Save featurizer configuration for reproducibility
-transformer.to_state_yaml_file("featurizer_config.yml")
-
-# Reload exact configuration
-loaded = MoleculeTransformer.from_state_yaml_file("featurizer_config.yml")
-```
-
-### Handle Errors Gracefully
-
-```python
-# Process dataset with potentially invalid SMILES
-transformer = MoleculeTransformer(
-    calc,
-    n_jobs=-1,
-    ignore_errors=True,  # Continue on failures
-    verbose=True          # Log error details
-)
-
-features = transformer(smiles_with_errors)
-# Returns None for failed molecules
-```
-
-## Choosing a Featurizer and Common Workflows
-
-Featurizer choice by task — traditional ML (RF, SVM, XGBoost), deep learning, similarity
-searching, and pharmacophore-based approaches — plus worked workflows for QSAR model
-building, virtual screening, similarity search, scikit-learn pipeline integration, and
-comparing multiple featurizers, are in
-[references/choosing_a_featurizer.md](references/choosing_a_featurizer.md).
-
-The full featurizer list is in
-[references/available_featurizers.md](references/available_featurizers.md); more examples
-are in [references/examples.md](references/examples.md).
-
-## Discovering Available Featurizers
-
-Use the ModelStore to explore all available featurizers:
-
-```python
-from molfeat.store.modelstore import ModelStore
-
-store = ModelStore()
-
-# List all available models
-all_models = store.available_models
-print(f"Total featurizers: {len(all_models)}")
-
-# Search for specific models
-chemberta_models = store.search(name="ChemBERTa")
-for model in chemberta_models:
-    print(f"- {model.name}: {model.description}")
-
-# Get usage information
-model_card = store.search(name="ChemBERTa-77M-MLM")[0]
-model_card.usage()  # Display usage examples
-
-# Load model
-transformer = store.load("ChemBERTa-77M-MLM")
-```
-
-## Advanced Features
-
-### Custom Preprocessing
-
-```python
-class CustomTransformer(MoleculeTransformer):
-    def preprocess(self, mol):
-        """Custom preprocessing pipeline"""
-        if isinstance(mol, str):
-            mol = dm.to_mol(mol)
-        mol = dm.standardize_mol(mol)
-        mol = dm.remove_salts(mol)
-        return mol
-
-transformer = CustomTransformer(FPCalculator("ecfp"), n_jobs=-1)
-```
-
-### Batch Processing Large Datasets
-
-```python
-import numpy as np
-
-def featurize_in_chunks(smiles_list, transformer, chunk_size=10000):
-    """Process large datasets in chunks to manage memory"""
-    all_features = []
-    for i in range(0, len(smiles_list), chunk_size):
-        chunk = smiles_list[i:i+chunk_size]
-        features = transformer(chunk)
-        all_features.append(features)
-    return np.vstack(all_features)
-```
-
-### Caching Expensive Embeddings
-
-Prefer molfeat's built-in pretrained-model cache when possible. For custom embedding caches, use NumPy arrays instead of pickle (pickle can execute arbitrary code when loading untrusted files):
-
-```python
-import numpy as np
-from pathlib import Path
-
-cache_file = Path("embeddings_cache.npz")  # fixed path under your project
-transformer = PretrainedMolTransformer("ChemBERTa-77M-MLM", n_jobs=-1)
-
-if cache_file.exists():
-    embeddings = np.load(cache_file)["embeddings"]
-else:
-    embeddings = transformer(smiles_list)
-    np.savez(cache_file, embeddings=embeddings)
-```
-
-## Performance Tips
-
-1. **Use parallelization**: Set `n_jobs=-1` to utilize all CPU cores
-2. **Batch processing**: Process multiple molecules at once instead of loops
-3. **Choose appropriate featurizers**: Fingerprints are faster than deep learning models
-4. **Cache pretrained models**: Leverage built-in caching for repeated use
-5. **Use float32**: Set `dtype=np.float32` when precision allows
-6. **Handle errors efficiently**: Use `ignore_errors=True` for large datasets
-
-## Common Featurizers Reference
-
-**Quick reference for frequently used featurizers:**
-
-| Featurizer | Type | Dimensions | Speed | Use Case |
-|------------|------|------------|-------|----------|
-| `ecfp` | Fingerprint | 2048 | Fast | General purpose |
-| `maccs` | Fingerprint | 167 | Very fast | Scaffold similarity |
-| `desc2D` | Descriptors | 200+ | Fast | Interpretable models |
-| `mordred` | Descriptors | 1800+ | Medium | Comprehensive features |
-| `map4` | Fingerprint | 1024 | Fast | Large-scale screening |
-| `ChemBERTa-77M-MLM` | Deep learning | 768 | Slow* | Transfer learning |
-| `gin-supervised-masking` | GNN | Variable | Slow* | Graph-based models |
-
-*First run is slow; subsequent runs benefit from caching
-
-## Resources
-
-This skill includes comprehensive reference documentation:
-
-### references/api_reference.md
-Complete API documentation covering:
-- `molfeat.calc` - All calculator classes and parameters
-- `molfeat.trans` - Transformer classes and methods
-- `molfeat.store` - ModelStore usage
-- Common patterns and integration examples
-- Performance optimization tips
-
-**When to load:** Reference when implementing specific calculators, understanding transformer parameters, or integrating with scikit-learn/PyTorch.
-
-### references/available_featurizers.md
-Comprehensive catalog of all 100+ featurizers organized by category:
-- Transformer-based language models (ChemBERTa, ChemGPT)
-- Graph neural networks (GIN, Graphormer)
-- Molecular descriptors (RDKit, Mordred)
-- Fingerprints (ECFP, MACCS, MAP4, and 15+ others)
-- Pharmacophore descriptors (CATS, Gobbi)
-- Shape descriptors (USR, ElectroShape)
-- Scaffold-based descriptors
-
-**When to load:** Reference when selecting the optimal featurizer for a specific task, exploring available options, or understanding featurizer characteristics.
-
-**Search tip:** Use grep to find specific featurizer types:
-```bash
-grep -i "chembert" references/available_featurizers.md
-grep -i "pharmacophore" references/available_featurizers.md
-```
-
-### references/examples.md
-Practical code examples for common scenarios:
-- Installation and quick start
-- Calculator and transformer examples
-- Pretrained model usage
-- Scikit-learn and PyTorch integration
-- Virtual screening workflows
-- QSAR model building
-- Similarity searching
-- Troubleshooting and best practices
-
-**When to load:** Reference when implementing specific workflows, troubleshooting issues, or learning molfeat patterns.
-
-## Troubleshooting
-
-### Invalid Molecules
-Enable error handling to skip invalid SMILES:
-```python
-transformer = MoleculeTransformer(
-    calc,
-    ignore_errors=True,
-    verbose=True
-)
-```
-
-### Memory Issues with Large Datasets
-Process in chunks or use streaming approaches for datasets > 100K molecules.
-
-### Pretrained Model Dependencies
-Some models require additional packages. Install specific extras (pin version for reproducibility):
-```bash
-uv pip install "molfeat[transformer]==0.11.0"  # For ChemBERTa/ChemGPT
-uv pip install "molfeat[dgl]==0.11.0"          # For GIN models
-uv pip install "molfeat[graphormer]==0.11.0"   # For Graphormer
-```
-
-### Reproducibility
-Save exact configurations and document versions:
-```python
-transformer.to_state_yaml_file("config.yml")
-import molfeat
-print(f"molfeat version: {molfeat.__version__}")
-```
-
-## Additional Resources
-
-- **Official Documentation**: https://molfeat-docs.datamol.io/
-- **GitHub Repository**: https://github.com/datamol-io/molfeat
-- **PyPI Package**: https://pypi.org/project/molfeat/
-- **Tutorial**: https://portal.valencelabs.com/datamol/post/types-of-featurizers-b1e8HHrbFMkbun6

package/skills/ncats-arax/SKILL.md

@@ -1,178 +0,0 @@
----
-name: ncats-arax
-description: Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 lookup, explicit selected-provider ARAX federation, separate entity normalization, qualifier-aware graph traversal, and inspection of TRAPI edge bindings, publications, and knowledge-source provenance. Do not use for inference, ranking, open-ended pathfinding, clinical guidance, or sensitive queries.
-allowed-tools: Read Bash
-license: MIT
-compatibility: Requires Python 3.10+ and outbound HTTPS access to arax.transltr.io. The client uses only the Python standard library and needs no API key. Queries and caller metadata may be publicly visible; never submit sensitive or patient-specific content.
-metadata:
-  version: "1.0"
-  skill-author: neuroepithelial
----
-
-# NCATS ARAX
-
-Use ARAX as a constrained knowledge-graph lookup service. Submit reviewed CURIEs and explicit
-Biolink types, preserve the exact TRAPI exchange, inspect query-edge bindings and provenance, and
-treat every returned path as a candidate for subsequent verification.
-
-Read [query-contract.md](references/query-contract.md) before constructing a query. Read
-[output-schema.md](references/output-schema.md) when interpreting saved artifacts, warnings,
-provenance, or partial results.
-
-## Safety boundary
-
-- Use only public, nonsensitive research questions. ARAX status facilities may expose query and
-  caller metadata even when `store=false` is requested.
-- Do not submit patient information, confidential research questions, unpublished compound
-  programs, or proprietary target hypotheses.
-- Do not present a returned path as a validated mechanism or clinical recommendation.
-- Report a zero as "not returned under these constraints," never as evidence that no relationship
-  exists.
-- Describe position as unscored response order, never rank.
-- Verify important candidates with literature and authoritative databases separately.
-
-## Workflow
-
-1. Normalize free text separately, then review and report the proposed CURIE and category.
-2. Choose a typed one-hop query or an exactly two-hop query with both endpoints pinned.
-3. Use default RTX-KG2 lookup unless the user explicitly names two to five providers.
-4. Acknowledge that the biomedical query is public and choose a new or empty output directory.
-5. Run the client once. Do not silently change provider selection or expansion order after a
-   failure or empty result.
-6. Inspect `summary.json` for bounded bindings and provenance and `response.json` for the exact
-   TRAPI payload.
-7. Verify scientifically important paths outside ARAX.
-
-## Preflight
-
-Check the production OpenAPI without making a biomedical query:
-
-```bash
-python skills/ncats-arax/scripts/arax_client.py preflight
-```
-
-The client verifies that the service identifies itself as ARAX, exposes `/query`, and reports a
-supported TRAPI version. A nonproduction endpoint or untested TRAPI series requires an explicit
-override; neither override changes the fixed query shapes or operations.
-
-## Normalize an entity
-
-Normalization is review-only and never triggers a graph query:
-
-```bash
-python skills/ncats-arax/scripts/arax_client.py normalize "primary myelofibrosis" \
-  --expected-category biolink:Disease \
-  --max-synonyms 10 \
-  --acknowledge-public-query \
-  --output-dir outputs/normalize-myelofibrosis
-```
-
-Review the canonical identifier, name, category, and synonym preview before using a CURIE. Report
-all CURIEs and categories regardless of query outcome. A category warning or zero result is a
-reason to curate the identifier, not to chain automatically to `/query`.
-
-## One-hop lookup
-
-Pin at least one endpoint and type both nodes:
-
-```bash
-python skills/ncats-arax/scripts/arax_client.py one-hop \
-  --subject-id CHEBI:31690 \
-  --subject-category biolink:SmallMolecule \
-  --predicate biolink:affects \
-  --object-id NCBIGene:25 \
-  --object-category biolink:Gene \
-  --qualifier biolink:object_aspect_qualifier=activity_or_abundance \
-  --qualifier biolink:object_direction_qualifier=decreased \
-  --acknowledge-public-query \
-  --output-dir outputs/imatinib-abl1
-```
-
-Lookup mode is the default and fixes expansion to `infores:rtx-kg2`. It defaults to 20 results.
-Use `--result-limit N` to request 1-50 results; 50 is the hard cap in either mode.
-
-## Endpoint-pinned two-hop lookup
-
-Use exactly one typed, unpinned intermediate node:
-
-```bash
-python skills/ncats-arax/scripts/arax_client.py two-hop \
-  --subject-id CHEBI:66901 \
-  --subject-category biolink:SmallMolecule \
-  --predicate-1 biolink:affects \
-  --intermediate-category biolink:Gene \
-  --predicate-2 biolink:associated_with \
-  --object-id MONDO:0009061 \
-  --object-category biolink:Disease \
-  --qualifier-1 biolink:object_aspect_qualifier=activity_or_abundance \
-  --qualifier-1 biolink:object_direction_qualifier=increased \
-  --expand-order right-first \
-  --acknowledge-public-query \
-  --output-dir outputs/ivacaftor-cystic-fibrosis
-```
-
-Right-first expansion is the default. If an empty result merits another attempt, run a new query
-explicitly with `--expand-order left-first` and keep the runs separate.
-
-## Selected-provider federation
-
-Federation is explicit and accepts two to five named providers:
-
-```bash
-python skills/ncats-arax/scripts/arax_client.py one-hop \
-  --subject-id CHEBI:31690 \
-  --subject-category biolink:SmallMolecule \
-  --predicate biolink:affects \
-  --object-id NCBIGene:25 \
-  --object-category biolink:Gene \
-  --mode federated \
-  --kp infores:rtx-kg2 \
-  --kp infores:molepro \
-  --acknowledge-public-query \
-  --output-dir outputs/federated-imatinib-abl1
-```
-
-Federation defaults to the hard maximum of 50 results. Provider errors may coexist with useful
-results; such a run exits 7 after retaining its artifacts and is marked partial.
-
-## Inspect saved provenance
-
-Rebuild a bounded summary without network access:
-
-```bash
-python skills/ncats-arax/scripts/arax_client.py summarize \
-  --request outputs/ivacaftor-cystic-fibrosis/request.json \
-  --response outputs/ivacaftor-cystic-fibrosis/response.json \
-  --format text
-```
-
-The inspector accepts only the same constrained request shapes and fixed operations that the live
-commands generate. Use `--format json` for the normalized view on standard output.
-
-## Interpret results
-
-- Follow each analysis's query-edge bindings; do not summarize every knowledge-graph edge.
-- Preserve the physical edge subject, predicate, object, and qualifier values returned by ARAX.
-  Returned predicates or qualifier aspects may be more specific than the query constraint.
-- Inspect all source objects, including primary, aggregator, supporting-data, upstream-resource,
-  and source-record URL fields.
-- Treat `publication_availability: not_returned` as missing metadata, not evidence that no
-  publications exist.
-- Treat missing auxiliary-graph references and provider failures as explicit warnings.
-- Consult the raw response whenever the bounded summary omits detail or the service response is
-  partial, unfamiliar, or scientifically surprising.
-
-## Deliberate exclusions
-
-The client has no raw-query, workflow, operation, overlay, ranking, inference, link-prediction,
-Pathfinder, ARS, batch, all-provider, three-hop, cache, daemon, SDK, MCP, or
-natural-language-to-TRAPI surface. Do not work around those limits with direct HTTP calls under
-this skill.
-
-## Official references
-
-- [ARAX documentation](https://ncatstranslator.github.io/TranslatorTechnicalDocumentation/architecture/ara/arax/)
-- [ARAX production OpenAPI](https://arax.transltr.io/api/arax/v1.4/openapi.json)
-- [ARAXi operation documentation](https://github.com/RTXteam/RTX/blob/master/code/ARAX/Documentation/DSL_Documentation.md)
-- [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI)
-- [Biolink Model](https://biolink.github.io/biolink-model/)