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312 lines
10 KiB
Python
312 lines
10 KiB
Python
from typing import List, Dict, Any
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import networkx as nx
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from .pump_protocol import generate_pump_protocol
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def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float:
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"""获取容器中的液体体积"""
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if vessel not in G.nodes():
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return 0.0
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vessel_data = G.nodes[vessel].get('data', {})
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liquids = vessel_data.get('liquid', [])
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total_volume = 0.0
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for liquid in liquids:
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if isinstance(liquid, dict):
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# 支持两种格式：新格式 (name, volume) 和旧格式 (liquid_type, liquid_volume)
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volume = liquid.get('volume') or liquid.get('liquid_volume', 0.0)
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total_volume += volume
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return total_volume
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def find_column_device(G: nx.DiGraph, column: str) -> str:
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"""查找柱层析设备"""
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# 首先检查是否有虚拟柱设备
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column_nodes = [node for node in G.nodes()
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if (G.nodes[node].get('class') or '') == 'virtual_column']
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if column_nodes:
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return column_nodes[0]
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# 如果没有虚拟柱设备，抛出异常
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raise ValueError(f"系统中未找到柱层析设备。请确保配置了 virtual_column 设备")
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def find_column_vessel(G: nx.DiGraph, column: str) -> str:
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"""查找柱容器"""
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# 直接使用 column 参数作为容器名称
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if column in G.nodes():
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return column
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# 尝试常见的柱容器命名规则
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possible_names = [
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f"column_{column}",
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f"{column}_column",
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f"vessel_{column}",
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f"{column}_vessel",
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"column_vessel",
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"chromatography_column",
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"silica_column",
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"preparative_column"
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]
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for vessel_name in possible_names:
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if vessel_name in G.nodes():
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return vessel_name
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raise ValueError(f"未找到柱容器 '{column}'。尝试了以下名称: {[column] + possible_names}")
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def find_eluting_solvent_vessel(G: nx.DiGraph, eluting_solvent: str) -> str:
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"""查找洗脱溶剂容器"""
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if not eluting_solvent:
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return ""
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# 按照命名规则查找溶剂瓶
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solvent_vessel_id = f"flask_{eluting_solvent}"
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if solvent_vessel_id in G.nodes():
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return solvent_vessel_id
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# 如果直接匹配失败，尝试模糊匹配
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for node in G.nodes():
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if node.startswith('flask_') and eluting_solvent.lower() in node.lower():
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return node
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# 如果还是找不到，列出所有可用的溶剂瓶
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available_flasks = [node for node in G.nodes()
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if node.startswith('flask_')
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and G.nodes[node].get('type') == 'container']
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raise ValueError(f"找不到洗脱溶剂 '{eluting_solvent}' 对应的溶剂瓶。可用溶剂瓶: {available_flasks}")
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def generate_run_column_protocol(
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G: nx.DiGraph,
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from_vessel: str,
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to_vessel: str,
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column: str
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) -> List[Dict[str, Any]]:
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"""
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生成柱层析分离的协议序列
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Args:
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G: 有向图，节点为设备和容器，边为流体管道
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from_vessel: 源容器的名称，即样品起始所在的容器
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to_vessel: 目标容器的名称，分离后的样品要到达的容器
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column: 所使用的柱子的名称
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Returns:
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List[Dict[str, Any]]: 柱层析分离操作的动作序列
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"""
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action_sequence = []
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print(f"RUN_COLUMN: 开始生成柱层析协议")
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print(f" - 源容器: {from_vessel}")
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print(f" - 目标容器: {to_vessel}")
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print(f" - 柱子: {column}")
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# 验证源容器和目标容器存在
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if from_vessel not in G.nodes():
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raise ValueError(f"源容器 '{from_vessel}' 不存在于系统中")
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if to_vessel not in G.nodes():
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raise ValueError(f"目标容器 '{to_vessel}' 不存在于系统中")
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# 查找柱层析设备
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column_device_id = None
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column_nodes = [node for node in G.nodes()
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if (G.nodes[node].get('class') or '') == 'virtual_column']
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if column_nodes:
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column_device_id = column_nodes[0]
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print(f"RUN_COLUMN: 找到柱层析设备: {column_device_id}")
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else:
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print(f"RUN_COLUMN: 警告 - 未找到柱层析设备")
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# 获取源容器中的液体体积
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source_volume = get_vessel_liquid_volume(G, from_vessel)
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print(f"RUN_COLUMN: 源容器 {from_vessel} 中有 {source_volume} mL 液体")
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# === 第一步：样品转移到柱子（如果柱子是容器） ===
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if column in G.nodes() and G.nodes[column].get('type') == 'container':
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print(f"RUN_COLUMN: 样品转移 - {source_volume} mL 从 {from_vessel} 到 {column}")
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try:
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sample_transfer_actions = generate_pump_protocol(
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G=G,
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from_vessel=from_vessel,
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to_vessel=column,
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volume=source_volume if source_volume > 0 else 100.0,
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flowrate=2.0
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)
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action_sequence.extend(sample_transfer_actions)
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except Exception as e:
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print(f"RUN_COLUMN: 样品转移失败: {str(e)}")
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# === 第二步：使用柱层析设备执行分离 ===
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if column_device_id:
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print(f"RUN_COLUMN: 使用柱层析设备执行分离")
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column_separation_action = {
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"device_id": column_device_id,
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"action_name": "run_column",
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"action_kwargs": {
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"from_vessel": from_vessel,
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"to_vessel": to_vessel,
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"column": column
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}
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}
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action_sequence.append(column_separation_action)
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# 等待柱层析设备完成分离
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action_sequence.append({
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"action_name": "wait",
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"action_kwargs": {"time": 60}
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})
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# === 第三步：从柱子转移到目标容器（如果需要） ===
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if column in G.nodes() and column != to_vessel:
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print(f"RUN_COLUMN: 产物转移 - 从 {column} 到 {to_vessel}")
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try:
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product_transfer_actions = generate_pump_protocol(
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G=G,
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from_vessel=column,
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to_vessel=to_vessel,
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volume=source_volume * 0.8 if source_volume > 0 else 80.0, # 假设有一些损失
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flowrate=1.5
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)
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action_sequence.extend(product_transfer_actions)
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except Exception as e:
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print(f"RUN_COLUMN: 产物转移失败: {str(e)}")
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print(f"RUN_COLUMN: 生成了 {len(action_sequence)} 个动作")
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return action_sequence
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# 便捷函数：常用柱层析方案
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def generate_flash_column_protocol(
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G: nx.DiGraph,
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from_vessel: str,
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to_vessel: str,
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column_material: str = "silica_gel",
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mobile_phase: str = "ethyl_acetate",
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mobile_phase_volume: float = 100.0
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) -> List[Dict[str, Any]]:
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"""快速柱层析：高流速分离"""
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return generate_run_column_protocol(
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G, from_vessel, to_vessel, column_material,
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mobile_phase, mobile_phase_volume, 1, "", 0.0, 3.0
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)
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def generate_preparative_column_protocol(
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G: nx.DiGraph,
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from_vessel: str,
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to_vessel: str,
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column_material: str = "silica_gel",
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equilibration_solvent: str = "hexane",
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eluting_solvent: str = "ethyl_acetate",
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eluting_volume: float = 50.0,
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eluting_repeats: int = 3
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) -> List[Dict[str, Any]]:
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"""制备柱层析：带平衡和多次洗脱"""
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return generate_run_column_protocol(
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G, from_vessel, to_vessel, column_material,
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eluting_solvent, eluting_volume, eluting_repeats,
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equilibration_solvent, 30.0, 1.5
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)
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def generate_gradient_column_protocol(
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G: nx.DiGraph,
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from_vessel: str,
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to_vessel: str,
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column_material: str = "silica_gel",
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gradient_solvents: List[str] = None,
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gradient_volumes: List[float] = None
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) -> List[Dict[str, Any]]:
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"""梯度洗脱柱层析：多种溶剂系统"""
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if gradient_solvents is None:
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gradient_solvents = ["hexane", "ethyl_acetate", "methanol"]
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if gradient_volumes is None:
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gradient_volumes = [50.0, 50.0, 30.0]
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action_sequence = []
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# 每种溶剂单独执行一次柱层析
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for i, (solvent, volume) in enumerate(zip(gradient_solvents, gradient_volumes)):
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print(f"RUN_COLUMN: 梯度洗脱第 {i+1}/{len(gradient_solvents)} 步: {volume} mL {solvent}")
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# 第一步使用源容器，后续步骤使用柱子作为源
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step_from_vessel = from_vessel if i == 0 else column_material
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# 最后一步使用目标容器，其他步骤使用柱子作为目标
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step_to_vessel = to_vessel if i == len(gradient_solvents) - 1 else column_material
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step_actions = generate_run_column_protocol(
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G, step_from_vessel, step_to_vessel, column_material,
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solvent, volume, 1, "", 0.0, 1.0
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)
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action_sequence.extend(step_actions)
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# 在梯度步骤之间加入等待时间
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if i < len(gradient_solvents) - 1:
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action_sequence.append({
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"action_name": "wait",
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"action_kwargs": {"time": 20}
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})
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return action_sequence
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def generate_reverse_phase_column_protocol(
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G: nx.DiGraph,
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from_vessel: str,
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to_vessel: str,
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column_material: str = "C18",
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aqueous_phase: str = "water",
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organic_phase: str = "methanol",
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gradient_ratio: float = 0.5
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) -> List[Dict[str, Any]]:
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"""反相柱层析：C18柱，水-有机相梯度"""
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# 先用水相平衡
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equilibration_volume = 20.0
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# 然后用有机相洗脱
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eluting_volume = 30.0 * gradient_ratio
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return generate_run_column_protocol(
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G, from_vessel, to_vessel, column_material,
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organic_phase, eluting_volume, 2,
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aqueous_phase, equilibration_volume, 0.8
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)
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def generate_ion_exchange_column_protocol(
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G: nx.DiGraph,
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from_vessel: str,
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to_vessel: str,
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column_material: str = "ion_exchange",
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buffer_solution: str = "buffer",
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salt_solution: str = "NaCl_solution",
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salt_volume: float = 40.0
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) -> List[Dict[str, Any]]:
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"""离子交换柱层析：缓冲液平衡，盐溶液洗脱"""
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return generate_run_column_protocol(
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G, from_vessel, to_vessel, column_material,
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salt_solution, salt_volume, 1,
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buffer_solution, 25.0, 0.5
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)
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# 测试函数
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def test_run_column_protocol():
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"""测试柱层析协议的示例"""
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print("=== RUN COLUMN PROTOCOL 测试 ===")
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print("测试完成")
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if __name__ == "__main__":
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test_run_column_protocol() |