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Estimate small molecule solubility, permeability, and lipophilicity with Boltz using SMILES, a text notation for molecular structures. Process individual molecules or lists, review costs before submission, and receive results mapped to each input.

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• Estimate properties for a molecule from its SMILES
• Evaluate a molecule list from a CSV file
• Compare predicted properties during initial screening

Predict how a small molecule may sit within a protein using structural inputs. Generate ranked 3D poses without defining a search region, then use those poses as starting points for further evaluation.

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• Predicting ligand poses from a protein structure and SMILES
• Generating ranked poses for a small fragment library
• Preparing starting poses for downstream rescoring

Performs root-cause analysis of a bug — from a GitHub issue, an issue URL, or a free-text description — before any reproduction or fix is written. TRIGGER when: triaging or diagnosing a bug, investigating why something misbehaves, an issue number/URL handed over for analysis, needing the root cause before touching code. DO NOT TRIGGER when: a failing reproduction test already exists and you are ready to fix → opsmill-dev-fixing-bugs; writing that reproduction test → opsmill-dev-test-driving-bugs; capturing a new bug as a ticket → opsmill-dev-creating-issues.

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Create animated lesson diagrams, sliders that update figures, and interactive panels that explain how systems work. It also builds moving dot patterns for page headers, with rules for readability, themes, and reduced motion.

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• Animate a process in a lesson
• Explore a formula with a slider
• Show a system's behavior through one control

Generate candidate positions and orientations for small molecules binding to proteins with DiffDock and DiffDock-L. Prepare single or batch docking runs, organize predicted poses by model confidence, and review validation needs without treating confidence as binding affinity.

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• Predicting binding poses for a protein and small molecule
• Preparing and validating batch docking inputs
• Comparing poses across receptor conformations

Process molecular datasets in Python through a simpler interface to RDKit, a chemistry toolkit. Convert and standardize structures, calculate molecular properties, compare and cluster compounds, generate 3D conformations, and visualize results for drug discovery workflows.

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• Load and standardize molecular datasets
• Calculate molecular properties and similarities
• Cluster compounds and select diverse subsets

Screen an existing compound library against a protein target with Boltz. Rank candidates by binding confidence or lead optimization score, download predicted structures, and review solubility, permeability, and lipophilicity results alongside the ranked hits.

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• Screening an existing compound library against a protein
• Finding candidates with high binding confidence
• Comparing candidates for lead optimization

Implements and validates the fix for a bug once a failing reproduction test exists. TRIGGER when: a bug has a failing reproduction test and you are ready to make it pass, implementing the root-cause fix, the final step of the bug-fixing pipeline. DO NOT TRIGGER when: no reproduction test exists yet → opsmill-dev-test-driving-bugs; still diagnosing, or asked to fix a bug with no analysis or reproduction test yet → opsmill-dev-analyzing-bugs.

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Writes a single failing test that reproduces a bug after its root-cause analysis is complete, before any fix is written. TRIGGER when: a bug has a completed root-cause analysis and you need the failing reproduction test, writing a test that proves a bug exists, the second step of the bug-fixing pipeline. DO NOT TRIGGER when: still triaging or diagnosing the bug → opsmill-dev-analyzing-bugs; implementing the fix once the test exists → opsmill-dev-fixing-bugs; general feature test-first work → superpowers test-driven-development.

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Read, analyze, modify, and visualize molecular structures with RDKit in Python. Calculate molecular properties, search for similar structures or specific structural patterns, apply reaction rules, and generate 2D or 3D coordinates with detailed control over processing.

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• Calculating properties for a collection of molecules
• Searching for molecules with similar structures
• Filtering molecules by specific structural patterns

Turn small-molecule structures into numerical features for similarity searches and models that predict activity or properties. Using Molfeat, the skill covers representation choices, invalid inputs, alignment with experimental labels, and saving feature-generation settings for reuse.

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• Prepare molecular features for activity or property prediction
• Choose molecular representations for similarity searches
• Keep experimental labels aligned after rejecting invalid molecules

Build molecular property prediction workflows with DeepChem for solubility, toxicity, and related chemistry tasks. Prepare molecular representations, choose compatible models, handle missing labels, and evaluate predictions using data splits designed for the intended scientific question.

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• Predicting solubility from molecular structures
• Comparing graph models on MoleculeNet datasets
• Checking data splits for information leakage

Look up compound–target binding data in BindingDB using PDB or UniProt identifiers, or search for similar chemical structures. Receive concise summaries of matching records, with full API responses saved to a file when requested.

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• Find ligands linked to a PDB identifier
• Look up binding data for a UniProt entry
• Search for compounds with similar structures

Use Boltz-2 to predict structures of complexes containing proteins, DNA, RNA, and small molecules. Obtain structure files and confidence scores to assess designed binders, with optional predictions of binding strength between a protein and a small molecule.

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• Assessing a designed binder against its target
• Predicting a protein and small-molecule complex
• Predicting complexes containing DNA or RNA

Strict SMILES validation, structural comparison, and modification verification. Catches invalid LLM-generated molecules.

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Train and run Uni-Mol Tools models to predict molecular properties from CSV data. Organize experiments into projects, compare model performance, rank results, and manage storage through interactive commands or machine-readable JSON output.

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• Train molecular property models from CSV data
• Predict properties with a trained model
• Organize experiments and compare model performance

Predict three-dimensional structures of complexes containing proteins, RNA, DNA, and small molecules with Chai-1. Compare candidate structures using confidence scores and clash indicators, or run repeated predictions from Python to evaluate designed binders.

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• Predicting antibody–antigen complex structures
• Evaluating protein–ligand binding structures
• Reassessing designed binders

Predict structures of complexes containing proteins, DNA, RNA, and ligands with OpenFold3, an AlphaFold3 reproduction with publicly available model weights. Prepare JSON inputs, generate candidate structures, and inspect confidence scores and molecular clashes.

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• Predicting structures of protein–ligand complexes
• Predicting complexes containing DNA or RNA
• Comparing confidence scores across candidate structures

Generate novel drug-like molecules using the GenMol NIM microservice. Use for de novo generation, scaffold decoration, motif extension, lead optimization, SAFE notation, QED or LogP ranking, hosted NVIDIA API calls, or local Docker deployment. GenMol takes SAFE notation in the smiles field, not ordinary SMILES.

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Volatility Smile reference method. Use when studying this focused method, not to run an API request. External API-key access for its legacy endpoints is not published in this release.

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Extract knowledge, guidelines, and ADRs from one or more completed spec directories into the project documentation system.

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Run a session retrospective that surfaces context-management gaps and routes them to approved follow-up actions.

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Run the full speckit workflow end-to-end — specify, plan, critique, tasks, implement, review — making all decisions autonomously. Stops before extract; run that manually.

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Produce a flow-level summary of the current Claude Code session — executive summary, chronological timeline, and outcomes — written into the active feature directory next to spec.md / plan.md.

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