MolSys-AI

MolSys-AI is the AI subsystem specialized in understanding and operating MolSysSuite.

It is part of the MolSysSuite domain and is distinct from MOLI Agent, the scientific agent of the wider MOLI Platform.

MolSys-AI is a primary incubating specialist subsystem of MolSysSuite. This repository receives MolSysSuite governance through MOLSYSSUITE_GUIDE.md and governs its internal repositories through MOLSYS_AI_GUIDE.md.

This repository is the umbrella, governance, and architecture repository for MolSys-AI:

• molsys-ai-server — remote inference and reusable MolSysSuite Software Knowledge services, plus documentation assistants.
• molsys-ai-client — lightweight typed SDK for remote MolSys-AI services.
• molsys-ai-agent — local-first MolSysSuite specialist agent for planning, API inspection, tool execution, and recovery.

System view

                         MolSys-AI
                    umbrella / architecture
                             │
          ┌──────────────────┼──────────────────┐
          ▼                  ▼                  ▼
       Server              Client              Agent
 inference +             typed SDK       MolSysSuite specialist
 Software Knowledge          │             /      |      \
          ▲                  │            ▼       ▼       ▼
          └──────────────────┘       MolSysSuite Client  local/other

The documentation chatbot is the first operational MolSys-AI capability. Its grounded documentation-assistance capability should remain available while its internal implementation is free to evolve.

The server's Software Knowledge capability is reusable: the chatbot is its first consumer, not its architectural owner.

MolSys-AI Agent may be used directly by scientists or receive delegated modeling tasks from MOLI Agent. It may use Server through Client, but is not architecturally required to do so for every operation.

MolSys-AI knows how to use MolSysSuite. MOLI reasons about why, when, and what for.

Migration

The project predates the current four-repository structure. Existing material is retained as history and migration input. Legacy code should be migrated incrementally by responsibility, while preserving working capabilities rather than freezing legacy implementation details.

See devguide/ and the frozen MOLI Platform Architecture 1.0.

Governance

MOLI
  ↓
MolSysSuite
  ↓  MOLSYSSUITE_GUIDE.md
MolSys-AI
  ↓  MOLSYS_AI_GUIDE.md
├── Server
├── Client
└── Agent

The MolSys-AI umbrella is the MolSysSuite member. Server, Client, and Agent are internal subsystem repositories rather than independent MolSysSuite members. See molsys-ai.toml for the authoritative internal registry.