synagent 0.0.1

Utility for reaction modeling using graph grammar

SynAgent

SynAgent is a proof-of-concept agent that orchestrates multiple Syn™ ecosystem packages: SynKit, SynRBL, SynTemp, SynCat, SynRFP, and SynRXN. It wraps each package into a standard tool interface and provides a simple agent core that sequences these tools for end-to-end reaction informatics workflows.

Features

• SynRBL: Rule- and MCS-based reaction rebalancing.
• SynKit: Reaction canonicalization and mechanistic transition graphs.
• SynTemp: High-accuracy reaction template extraction with consensus atom mapping.
• SynCat: Graph-based reaction classification via cross-attention models.
• SynRFP: Mapping-free, permutation-invariant reaction fingerprints.
• SynRXN: Reproducible reaction datasets and splits.

Structure

• synagent/: Core package providing the agent (agent.py), registry (registry.py) and tool wrappers.
  • tools/: Implementations of each tool wrapper and a base protocol.
• README.md: This document describing the package.

Usage

1. Register tools: Instantiate a :class:~synagent.registry.ToolRegistry and register imported tool instances from :mod:synagent.tools.
2. Create an agent: Instantiate :class:~synagent.agent.AgentCore with the registry.
3. Build a plan: Create a list of :class:~synagent.agent.PlanStep objects specifying tool names and their parameters.
4. Run the plan: Call agent.run(plan) to execute tool calls sequentially.

Example

```python
from synagent import ToolRegistry, AgentCore, PlanStep
from synagent.tools import synrbl_balance, synkit_canonicalize

# 1. Register tools
registry = ToolRegistry()
registry.register(synrbl_balance)
registry.register(synkit_canonicalize)

# 2. Initialize agent
agent = AgentCore(registry)

# 3. Build plan
plan = [
    PlanStep("synrbl.balance", {"reaction": "CC=O>>CC(=O)O"}),
    PlanStep("synkit.canonicalize", {"reaction": "CC=O>>CC(=O)O", "with_mt_graph": False}),
]

# 4. Run
result = agent.run(plan)
print(result)
```

Notes
-----

- The actual Syn™ packages must be installed in your environment for the
  wrappers to work.
- Each tool uses lazy imports to avoid unnecessary dependencies until
  invoked.
- Error handling is basic; real-world agents should implement more
  robust failure recovery and logging.

License
-------

This repository is released under the Apache 2.0 License, consistent
with the licensing of the underlying Syn packages.