docs: add OpenBioMed platform module & interface analysis

[DREAM2084]

Motivation

• Provide a concise, repo-grounded mapping from the reference large-model platform architecture to the concrete OpenBioMed implementation to help architects and integrators understand which modules exist and how they connect.
• Capture the data-object I/O conventions and the tool/workflow execution arrows so downstream integrators can wire frontends, agents, and schedulers to the repo interfaces.
• Surface gaps and practical recommendations (task queue, scheduler, unified algorithm registry, evaluator) to guide next-stage platform engineering priorities.

Description

• Add docs/openbiomed_platform_module_analysis.md which documents module-to-file mappings, core data types (Molecule, Protein, Pocket, Text, Cell), create_tool_input conventions, and the Tool.run return contract.
• Document HTTP API ↔ TaskHandlers ↔ TOOLS pipeline flow, Agent/PlannerExecutor behavior, frontend-JSON → YAML workflow parsing, and the in-memory Workflow DAG execution arrows.
• Enumerate concrete tool capabilities (web request tools, visualizers, docking, generation, property predictors, P2Rank pocket prediction, etc.), three representative workflow examples, identified gaps versus the reference architecture, and suggested evolution steps.

Testing

• Run python -m py_compile on the core modules open_biomed/core/workflow.py, open_biomed/core/agent.py, open_biomed/core/pipeline.py, open_biomed/tools/tool_registry.py, open_biomed/scripts/run_server.py, and open_biomed/scripts/run_server_workflow.py, which completed successfully.
• Verified the new documentation file docs/openbiomed_platform_module_analysis.md is present and readable (static doc addition only, no runtime changes).

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Codex Task

[DREAM2084]

平台模块分析Codex