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https://github.com/dptech-corp/Uni-Lab-OS.git
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添加了run column和filter through的protocol，亲测能跑
This commit is contained in:
KCFeng425
@@ -1,5 +1,72 @@
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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) and 'liquid_volume' in liquid:
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total_volume += liquid['liquid_volume']
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return total_volume
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def find_filter_through_vessel(G: nx.DiGraph, filter_through: str) -> str:
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"""查找过滤介质容器"""
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# 直接使用 filter_through 参数作为容器名称
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if filter_through in G.nodes():
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return filter_through
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# 尝试常见的过滤介质容器命名
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possible_names = [
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f"filter_{filter_through}",
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f"{filter_through}_filter",
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f"column_{filter_through}",
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f"{filter_through}_column",
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"filter_through_vessel",
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"column_vessel",
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"chromatography_column",
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"filter_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"未找到过滤介质容器 '{filter_through}'。尝试了以下名称: {[filter_through] + 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_filter_through_protocol(
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G: nx.DiGraph,
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@@ -12,10 +79,15 @@ def generate_filter_through_protocol(
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residence_time: float = 0.0
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) -> List[Dict[str, Any]]:
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"""
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生成通过过滤介质过滤的协议序列
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生成通过过滤介质过滤的协议序列，复用 pump_protocol 的成熟算法
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过滤流程：
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1. 液体转移：将样品从源容器转移到过滤介质
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2. 重力过滤：液体通过过滤介质自动流到目标容器
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3. 洗脱操作：将洗脱溶剂通过过滤介质洗脱目标物质
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Args:
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G: 有向图，节点为设备和容器
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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，即物质起始所在的容器
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to_vessel: 目标容器的名称，物质过滤后要到达的容器
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filter_through: 过滤时所通过的介质，如滤纸、柱子等
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@@ -28,123 +100,288 @@ def generate_filter_through_protocol(
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List[Dict[str, Any]]: 过滤操作的动作序列
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Raises:
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ValueError: 当找不到必要的设备时抛出异常
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ValueError: 当找不到必要的设备或容器时
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Examples:
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filter_through_protocol = generate_filter_through_protocol(
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G, "reactor", "collection_flask", "celite", "ethanol", 50.0, 2, 60.0
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filter_through_actions = generate_filter_through_protocol(
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G, "reaction_mixture", "collection_bottle_1", "celite", "ethanol", 20.0, 2, 30.0
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)
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"""
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action_sequence = []
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# 验证容器是否存在
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print(f"FILTER_THROUGH: 开始生成通过过滤协议")
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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" - 过滤介质: {filter_through}")
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print(f" - 洗脱溶剂: {eluting_solvent}")
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print(f" - 洗脱体积: {eluting_volume} mL" if eluting_volume > 0 else " - 洗脱体积: 无")
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print(f" - 洗脱重复次数: {eluting_repeats}")
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print(f" - 停留时间: {residence_time}s" if residence_time > 0 else " - 停留时间: 无")
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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} 不存在于图中")
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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} 不存在于图中")
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raise ValueError(f"目标容器 '{to_vessel}' 不存在于系统中")
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# 查找转移泵设备（用于液体转移）
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pump_nodes = [node for node in G.nodes()
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if G.nodes[node].get('class') == 'virtual_transfer_pump']
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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"FILTER_THROUGH: 源容器 {from_vessel} 中有 {source_volume} mL 液体")
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if not pump_nodes:
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raise ValueError("没有找到可用的转移泵设备")
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# 查找过滤介质容器
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try:
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filter_through_vessel = find_filter_through_vessel(G, filter_through)
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print(f"FILTER_THROUGH: 找到过滤介质容器: {filter_through_vessel}")
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except ValueError as e:
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raise ValueError(f"无法找到过滤介质容器: {str(e)}")
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pump_id = pump_nodes[0]
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# 查找洗脱溶剂容器（如果需要）
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eluting_vessel = ""
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if eluting_solvent and eluting_volume > 0 and eluting_repeats > 0:
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try:
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eluting_vessel = find_eluting_solvent_vessel(G, eluting_solvent)
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print(f"FILTER_THROUGH: 找到洗脱溶剂容器: {eluting_vessel}")
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except ValueError as e:
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raise ValueError(f"无法找到洗脱溶剂容器: {str(e)}")
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# 查找过滤设备（可选，如果有专门的过滤设备）
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filter_nodes = [node for node in G.nodes()
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if G.nodes[node].get('class') == 'virtual_filter']
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# === 第一步：将样品从源容器转移到过滤介质 ===
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transfer_volume = source_volume if source_volume > 0 else 100.0 # 默认100mL
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print(f"FILTER_THROUGH: 将 {transfer_volume} mL 样品从 {from_vessel} 转移到 {filter_through_vessel}")
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filter_id = filter_nodes[0] if filter_nodes else None
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try:
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# 使用成熟的 pump_protocol 算法进行液体转移
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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=filter_through_vessel,
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volume=transfer_volume,
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flowrate=0.8, # 较慢的流速，避免冲击过滤介质
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transfer_flowrate=1.2
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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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raise ValueError(f"无法将样品转移到过滤介质: {str(e)}")
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# 查找洗脱溶剂容器（如果需要洗脱）
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eluting_vessel = None
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if eluting_solvent and eluting_volume > 0:
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eluting_vessel = f"flask_{eluting_solvent}"
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if eluting_vessel not in G.nodes():
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# 查找可用的溶剂容器
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available_vessels = [node for node in G.nodes()
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if node.startswith('flask_') and
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G.nodes[node].get('type') == 'container']
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if available_vessels:
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eluting_vessel = available_vessels[0]
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else:
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raise ValueError(f"没有找到洗脱溶剂容器 {eluting_solvent}")
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# 步骤1：将样品从源容器转移到过滤装置（模拟通过过滤介质）
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# 这里我们将过滤过程分解为多个转移步骤来模拟通过介质的过程
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# 首先转移样品（模拟样品通过过滤介质）
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action_sequence.append({
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"device_id": pump_id,
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"action_name": "transfer",
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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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"volume": 0.0, # 转移所有液体，体积由系统确定
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"amount": f"通过 {filter_through} 过滤",
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"time": residence_time if residence_time > 0 else 0.0,
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"viscous": False,
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"rinsing_solvent": "",
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"rinsing_volume": 0.0,
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"rinsing_repeats": 0,
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"solid": True # 通过过滤介质可能涉及固体分离
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}
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})
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# 步骤2：如果有专门的过滤设备，使用过滤设备处理
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if filter_id:
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# === 第二步：等待样品通过过滤介质（停留时间） ===
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if residence_time > 0:
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print(f"FILTER_THROUGH: 等待样品在过滤介质中停留 {residence_time}s")
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action_sequence.append({
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"device_id": filter_id,
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"action_name": "filter_sample",
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"action_kwargs": {
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"vessel": to_vessel,
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"filtrate_vessel": to_vessel,
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"stir": False,
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"stir_speed": 0.0,
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"temp": 25.0,
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"continue_heatchill": False,
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"volume": 0.0
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}
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"action_name": "wait",
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"action_kwargs": {"time": residence_time}
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})
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else:
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# 即使没有指定停留时间，也等待一段时间让液体通过
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default_wait_time = max(10, transfer_volume / 10) # 根据体积估算等待时间
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print(f"FILTER_THROUGH: 等待样品通过过滤介质 {default_wait_time}s")
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action_sequence.append({
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"action_name": "wait",
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"action_kwargs": {"time": default_wait_time}
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})
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# 步骤3：洗脱操作（如果指定了洗脱溶剂和重复次数）
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# === 第三步：洗脱操作（如果指定了洗脱参数） ===
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if eluting_solvent and eluting_volume > 0 and eluting_repeats > 0 and eluting_vessel:
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for repeat in range(eluting_repeats):
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# 添加洗脱溶剂
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print(f"FILTER_THROUGH: 开始洗脱操作 - {eluting_repeats} 次，每次 {eluting_volume} mL {eluting_solvent}")
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for repeat_idx in range(eluting_repeats):
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print(f"FILTER_THROUGH: 第 {repeat_idx + 1}/{eluting_repeats} 次洗脱")
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try:
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# 将洗脱溶剂转移到过滤介质
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eluting_transfer_actions = generate_pump_protocol(
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G=G,
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from_vessel=eluting_vessel,
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to_vessel=filter_through_vessel,
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volume=eluting_volume,
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flowrate=0.6, # 洗脱用更慢的流速
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transfer_flowrate=1.0
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)
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action_sequence.extend(eluting_transfer_actions)
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except Exception as e:
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raise ValueError(f"第 {repeat_idx + 1} 次洗脱转移失败: {str(e)}")
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# 等待洗脱溶剂通过过滤介质
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eluting_wait_time = max(30, eluting_volume / 5) # 根据洗脱体积估算等待时间
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print(f"FILTER_THROUGH: 等待第 {repeat_idx + 1} 次洗脱液通过 {eluting_wait_time}s")
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action_sequence.append({
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"device_id": pump_id,
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"action_name": "transfer",
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"action_kwargs": {
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"from_vessel": eluting_vessel,
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"to_vessel": to_vessel,
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"volume": eluting_volume,
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"amount": f"洗脱溶剂 {eluting_solvent} - 第 {repeat + 1} 次",
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"time": 0.0,
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"viscous": False,
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"rinsing_solvent": "",
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"rinsing_volume": 0.0,
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"rinsing_repeats": 0,
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"solid": False
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}
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"action_name": "wait",
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"action_kwargs": {"time": eluting_wait_time}
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})
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# 如果有过滤设备，再次过滤洗脱液
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if filter_id:
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# 洗脱间隔等待
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if repeat_idx < eluting_repeats - 1: # 不是最后一次洗脱
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action_sequence.append({
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"device_id": filter_id,
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"action_name": "filter_sample",
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"action_kwargs": {
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"vessel": to_vessel,
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"filtrate_vessel": to_vessel,
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"stir": False,
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"stir_speed": 0.0,
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"temp": 25.0,
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"continue_heatchill": False,
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"volume": eluting_volume
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}
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"action_name": "wait",
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"action_kwargs": {"time": 10}
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})
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return action_sequence
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# === 第四步：最终等待，确保所有液体完全通过 ===
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print(f"FILTER_THROUGH: 最终等待，确保所有液体完全通过过滤介质")
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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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print(f"FILTER_THROUGH: 生成了 {len(action_sequence)} 个动作")
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print(f"FILTER_THROUGH: 通过过滤协议生成完成")
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print(f"FILTER_THROUGH: 样品从 {from_vessel} 通过 {filter_through} 到达 {to_vessel}")
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if eluting_repeats > 0:
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total_eluting_volume = eluting_volume * eluting_repeats
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print(f"FILTER_THROUGH: 总洗脱体积: {total_eluting_volume} mL {eluting_solvent}")
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return action_sequence
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# 便捷函数：常用过滤方案
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def generate_gravity_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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) -> List[Dict[str, Any]]:
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"""重力柱层析：简单重力过滤，无洗脱"""
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return generate_filter_through_protocol(G, from_vessel, to_vessel, column_material, "", 0.0, 0, 0.0)
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def generate_celite_filter_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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wash_solvent: str = "ethanol",
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wash_volume: float = 20.0
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) -> List[Dict[str, Any]]:
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"""硅藻土过滤：用于去除固体杂质"""
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return generate_filter_through_protocol(G, from_vessel, to_vessel, "celite", wash_solvent, wash_volume, 1, 30.0)
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def generate_column_chromatography_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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eluting_solvent: str = "ethyl_acetate",
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eluting_volume: float = 30.0,
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eluting_repeats: int = 3
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) -> List[Dict[str, Any]]:
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"""柱层析：多次洗脱分离"""
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return generate_filter_through_protocol(
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G, from_vessel, to_vessel, column_material, eluting_solvent, eluting_volume, eluting_repeats, 60.0
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)
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def generate_solid_phase_extraction_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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spe_cartridge: str = "C18",
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eluting_solvent: str = "methanol",
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eluting_volume: float = 15.0,
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eluting_repeats: int = 2
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) -> List[Dict[str, Any]]:
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"""固相萃取：C18柱或其他SPE柱"""
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return generate_filter_through_protocol(
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G, from_vessel, to_vessel, spe_cartridge, eluting_solvent, eluting_volume, eluting_repeats, 120.0
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)
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|
||||
def generate_resin_filter_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
resin_type: str = "ion_exchange",
|
||||
regeneration_solvent: str = "NaCl_solution",
|
||||
regeneration_volume: float = 25.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""树脂过滤：离子交换树脂或其他功能树脂"""
|
||||
return generate_filter_through_protocol(
|
||||
G, from_vessel, to_vessel, resin_type, regeneration_solvent, regeneration_volume, 1, 180.0
|
||||
)
|
||||
|
||||
|
||||
def generate_multi_step_purification_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
filter_steps: List[Dict[str, Any]]
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
多步骤纯化：连续多个过滤介质
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
from_vessel: 源容器
|
||||
to_vessel: 最终目标容器
|
||||
filter_steps: 过滤步骤列表，每个元素包含过滤参数
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 完整的动作序列
|
||||
|
||||
Example:
|
||||
filter_steps = [
|
||||
{
|
||||
"to_vessel": "intermediate_vessel_1",
|
||||
"filter_through": "celite",
|
||||
"eluting_solvent": "",
|
||||
"eluting_volume": 0.0,
|
||||
"eluting_repeats": 0,
|
||||
"residence_time": 30.0
|
||||
},
|
||||
{
|
||||
"from_vessel": "intermediate_vessel_1",
|
||||
"to_vessel": "final_vessel",
|
||||
"filter_through": "silica_gel",
|
||||
"eluting_solvent": "ethyl_acetate",
|
||||
"eluting_volume": 20.0,
|
||||
"eluting_repeats": 2,
|
||||
"residence_time": 60.0
|
||||
}
|
||||
]
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
current_from_vessel = from_vessel
|
||||
|
||||
for i, step in enumerate(filter_steps):
|
||||
print(f"FILTER_THROUGH: 处理第 {i+1}/{len(filter_steps)} 个过滤步骤")
|
||||
|
||||
# 使用步骤中指定的参数，或使用默认值
|
||||
step_from_vessel = step.get('from_vessel', current_from_vessel)
|
||||
step_to_vessel = step.get('to_vessel', to_vessel if i == len(filter_steps) - 1 else f"intermediate_vessel_{i+1}")
|
||||
|
||||
# 生成单个过滤步骤的协议
|
||||
step_actions = generate_filter_through_protocol(
|
||||
G=G,
|
||||
from_vessel=step_from_vessel,
|
||||
to_vessel=step_to_vessel,
|
||||
filter_through=step.get('filter_through', 'silica_gel'),
|
||||
eluting_solvent=step.get('eluting_solvent', ''),
|
||||
eluting_volume=step.get('eluting_volume', 0.0),
|
||||
eluting_repeats=step.get('eluting_repeats', 0),
|
||||
residence_time=step.get('residence_time', 0.0)
|
||||
)
|
||||
|
||||
action_sequence.extend(step_actions)
|
||||
|
||||
# 更新下一步的源容器
|
||||
current_from_vessel = step_to_vessel
|
||||
|
||||
# 在步骤之间加入等待时间
|
||||
if i < len(filter_steps) - 1: # 不是最后一个步骤
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 15}
|
||||
})
|
||||
|
||||
print(f"FILTER_THROUGH: 多步骤纯化协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_filter_through_protocol():
|
||||
"""测试通过过滤协议的示例"""
|
||||
print("=== FILTER THROUGH PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_filter_through_protocol()
|
||||
@@ -8,7 +8,8 @@ def is_integrated_pump(node_name):
|
||||
|
||||
def find_connected_pump(G, valve_node):
|
||||
for neighbor in G.neighbors(valve_node):
|
||||
if "pump" in G.nodes[neighbor]["class"]:
|
||||
node_class = G.nodes[neighbor].get("class") or "" # 防止 None
|
||||
if "pump" in node_class:
|
||||
return neighbor
|
||||
raise ValueError(f"未找到与阀 {valve_node} 唯一相连的泵节点")
|
||||
|
||||
|
||||
@@ -1,5 +1,87 @@
|
||||
from typing import List, Dict, Any
|
||||
import networkx as nx
|
||||
from .pump_protocol import generate_pump_protocol
|
||||
|
||||
|
||||
def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float:
|
||||
"""获取容器中的液体体积"""
|
||||
if vessel not in G.nodes():
|
||||
return 0.0
|
||||
|
||||
vessel_data = G.nodes[vessel].get('data', {})
|
||||
liquids = vessel_data.get('liquid', [])
|
||||
|
||||
total_volume = 0.0
|
||||
for liquid in liquids:
|
||||
if isinstance(liquid, dict):
|
||||
# 支持两种格式：新格式 (name, volume) 和旧格式 (liquid_type, liquid_volume)
|
||||
volume = liquid.get('volume') or liquid.get('liquid_volume', 0.0)
|
||||
total_volume += volume
|
||||
|
||||
return total_volume
|
||||
|
||||
|
||||
def find_column_device(G: nx.DiGraph, column: str) -> str:
|
||||
"""查找柱层析设备"""
|
||||
# 首先检查是否有虚拟柱设备
|
||||
column_nodes = [node for node in G.nodes()
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_column']
|
||||
|
||||
if column_nodes:
|
||||
return column_nodes[0]
|
||||
|
||||
# 如果没有虚拟柱设备，抛出异常
|
||||
raise ValueError(f"系统中未找到柱层析设备。请确保配置了 virtual_column 设备")
|
||||
|
||||
|
||||
def find_column_vessel(G: nx.DiGraph, column: str) -> str:
|
||||
"""查找柱容器"""
|
||||
# 直接使用 column 参数作为容器名称
|
||||
if column in G.nodes():
|
||||
return column
|
||||
|
||||
# 尝试常见的柱容器命名规则
|
||||
possible_names = [
|
||||
f"column_{column}",
|
||||
f"{column}_column",
|
||||
f"vessel_{column}",
|
||||
f"{column}_vessel",
|
||||
"column_vessel",
|
||||
"chromatography_column",
|
||||
"silica_column",
|
||||
"preparative_column"
|
||||
]
|
||||
|
||||
for vessel_name in possible_names:
|
||||
if vessel_name in G.nodes():
|
||||
return vessel_name
|
||||
|
||||
raise ValueError(f"未找到柱容器 '{column}'。尝试了以下名称: {[column] + possible_names}")
|
||||
|
||||
|
||||
def find_eluting_solvent_vessel(G: nx.DiGraph, eluting_solvent: str) -> str:
|
||||
"""查找洗脱溶剂容器"""
|
||||
if not eluting_solvent:
|
||||
return ""
|
||||
|
||||
# 按照命名规则查找溶剂瓶
|
||||
solvent_vessel_id = f"flask_{eluting_solvent}"
|
||||
|
||||
if solvent_vessel_id in G.nodes():
|
||||
return solvent_vessel_id
|
||||
|
||||
# 如果直接匹配失败，尝试模糊匹配
|
||||
for node in G.nodes():
|
||||
if node.startswith('flask_') and eluting_solvent.lower() in node.lower():
|
||||
return node
|
||||
|
||||
# 如果还是找不到，列出所有可用的溶剂瓶
|
||||
available_flasks = [node for node in G.nodes()
|
||||
if node.startswith('flask_')
|
||||
and G.nodes[node].get('type') == 'container']
|
||||
|
||||
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}")
|
||||
|
||||
|
||||
def generate_run_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
@@ -11,92 +93,220 @@ def generate_run_column_protocol(
|
||||
生成柱层析分离的协议序列
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为设备和容器
|
||||
G: 有向图，节点为设备和容器，边为流体管道
|
||||
from_vessel: 源容器的名称，即样品起始所在的容器
|
||||
to_vessel: 目标容器的名称，分离后的样品要到达的容器
|
||||
column: 所使用的柱子的名称
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 柱层析分离操作的动作序列
|
||||
|
||||
Raises:
|
||||
ValueError: 当找不到必要的设备时抛出异常
|
||||
|
||||
Examples:
|
||||
run_column_protocol = generate_run_column_protocol(G, "reactor", "collection_flask", "silica_column")
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 验证容器是否存在
|
||||
print(f"RUN_COLUMN: 开始生成柱层析协议")
|
||||
print(f" - 源容器: {from_vessel}")
|
||||
print(f" - 目标容器: {to_vessel}")
|
||||
print(f" - 柱子: {column}")
|
||||
|
||||
# 验证源容器和目标容器存在
|
||||
if from_vessel not in G.nodes():
|
||||
raise ValueError(f"源容器 {from_vessel} 不存在于图中")
|
||||
raise ValueError(f"源容器 '{from_vessel}' 不存在于系统中")
|
||||
|
||||
if to_vessel not in G.nodes():
|
||||
raise ValueError(f"目标容器 {to_vessel} 不存在于图中")
|
||||
|
||||
# 查找转移泵设备（用于样品转移）
|
||||
pump_nodes = [node for node in G.nodes()
|
||||
if G.nodes[node].get('class') == 'virtual_transfer_pump']
|
||||
|
||||
if not pump_nodes:
|
||||
raise ValueError("没有找到可用的转移泵设备")
|
||||
|
||||
pump_id = pump_nodes[0]
|
||||
raise ValueError(f"目标容器 '{to_vessel}' 不存在于系统中")
|
||||
|
||||
# 查找柱层析设备
|
||||
column_device_id = None
|
||||
column_nodes = [node for node in G.nodes()
|
||||
if G.nodes[node].get('class') == 'virtual_column']
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_column']
|
||||
|
||||
if not column_nodes:
|
||||
raise ValueError("没有找到可用的柱层析设备")
|
||||
if column_nodes:
|
||||
column_device_id = column_nodes[0]
|
||||
print(f"RUN_COLUMN: 找到柱层析设备: {column_device_id}")
|
||||
else:
|
||||
print(f"RUN_COLUMN: 警告 - 未找到柱层析设备")
|
||||
|
||||
column_id = column_nodes[0]
|
||||
# 获取源容器中的液体体积
|
||||
source_volume = get_vessel_liquid_volume(G, from_vessel)
|
||||
print(f"RUN_COLUMN: 源容器 {from_vessel} 中有 {source_volume} mL 液体")
|
||||
|
||||
# 步骤1：将样品从源容器转移到柱子上
|
||||
action_sequence.append({
|
||||
"device_id": pump_id,
|
||||
"action_name": "transfer",
|
||||
"action_kwargs": {
|
||||
"from_vessel": from_vessel,
|
||||
"to_vessel": column_id, # 将样品转移到柱子设备
|
||||
"volume": 0.0, # 转移所有液体，体积由系统确定
|
||||
"amount": f"样品上柱 - 使用 {column}",
|
||||
"time": 0.0,
|
||||
"viscous": False,
|
||||
"rinsing_solvent": "",
|
||||
"rinsing_volume": 0.0,
|
||||
"rinsing_repeats": 0,
|
||||
"solid": False
|
||||
# === 第一步：样品转移到柱子（如果柱子是容器） ===
|
||||
if column in G.nodes() and G.nodes[column].get('type') == 'container':
|
||||
print(f"RUN_COLUMN: 样品转移 - {source_volume} mL 从 {from_vessel} 到 {column}")
|
||||
|
||||
try:
|
||||
sample_transfer_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=from_vessel,
|
||||
to_vessel=column,
|
||||
volume=source_volume if source_volume > 0 else 100.0,
|
||||
flowrate=2.0
|
||||
)
|
||||
action_sequence.extend(sample_transfer_actions)
|
||||
except Exception as e:
|
||||
print(f"RUN_COLUMN: 样品转移失败: {str(e)}")
|
||||
|
||||
# === 第二步：使用柱层析设备执行分离 ===
|
||||
if column_device_id:
|
||||
print(f"RUN_COLUMN: 使用柱层析设备执行分离")
|
||||
|
||||
column_separation_action = {
|
||||
"device_id": column_device_id,
|
||||
"action_name": "run_column",
|
||||
"action_kwargs": {
|
||||
"from_vessel": from_vessel,
|
||||
"to_vessel": to_vessel,
|
||||
"column": column
|
||||
}
|
||||
}
|
||||
})
|
||||
action_sequence.append(column_separation_action)
|
||||
|
||||
# 等待柱层析设备完成分离
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 60}
|
||||
})
|
||||
|
||||
# 步骤2：运行柱层析分离
|
||||
action_sequence.append({
|
||||
"device_id": column_id,
|
||||
"action_name": "run_column",
|
||||
"action_kwargs": {
|
||||
"from_vessel": from_vessel,
|
||||
"to_vessel": to_vessel,
|
||||
"column": column
|
||||
}
|
||||
})
|
||||
# === 第三步：从柱子转移到目标容器（如果需要） ===
|
||||
if column in G.nodes() and column != to_vessel:
|
||||
print(f"RUN_COLUMN: 产物转移 - 从 {column} 到 {to_vessel}")
|
||||
|
||||
try:
|
||||
product_transfer_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=column,
|
||||
to_vessel=to_vessel,
|
||||
volume=source_volume * 0.8 if source_volume > 0 else 80.0, # 假设有一些损失
|
||||
flowrate=1.5
|
||||
)
|
||||
action_sequence.extend(product_transfer_actions)
|
||||
except Exception as e:
|
||||
print(f"RUN_COLUMN: 产物转移失败: {str(e)}")
|
||||
|
||||
# 步骤3：将分离后的产物从柱子转移到目标容器
|
||||
action_sequence.append({
|
||||
"device_id": pump_id,
|
||||
"action_name": "transfer",
|
||||
"action_kwargs": {
|
||||
"from_vessel": column_id, # 从柱子设备转移
|
||||
"to_vessel": to_vessel,
|
||||
"volume": 0.0, # 转移所有液体，体积由系统确定
|
||||
"amount": f"收集分离产物 - 来自 {column}",
|
||||
"time": 0.0,
|
||||
"viscous": False,
|
||||
"rinsing_solvent": "",
|
||||
"rinsing_volume": 0.0,
|
||||
"rinsing_repeats": 0,
|
||||
"solid": False
|
||||
}
|
||||
})
|
||||
print(f"RUN_COLUMN: 生成了 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 便捷函数：常用柱层析方案
|
||||
def generate_flash_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "silica_gel",
|
||||
mobile_phase: str = "ethyl_acetate",
|
||||
mobile_phase_volume: float = 100.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""快速柱层析：高流速分离"""
|
||||
return generate_run_column_protocol(
|
||||
G, from_vessel, to_vessel, column_material,
|
||||
mobile_phase, mobile_phase_volume, 1, "", 0.0, 3.0
|
||||
)
|
||||
|
||||
|
||||
def generate_preparative_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "silica_gel",
|
||||
equilibration_solvent: str = "hexane",
|
||||
eluting_solvent: str = "ethyl_acetate",
|
||||
eluting_volume: float = 50.0,
|
||||
eluting_repeats: int = 3
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""制备柱层析：带平衡和多次洗脱"""
|
||||
return generate_run_column_protocol(
|
||||
G, from_vessel, to_vessel, column_material,
|
||||
eluting_solvent, eluting_volume, eluting_repeats,
|
||||
equilibration_solvent, 30.0, 1.5
|
||||
)
|
||||
|
||||
|
||||
def generate_gradient_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "silica_gel",
|
||||
gradient_solvents: List[str] = None,
|
||||
gradient_volumes: List[float] = None
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""梯度洗脱柱层析：多种溶剂系统"""
|
||||
if gradient_solvents is None:
|
||||
gradient_solvents = ["hexane", "ethyl_acetate", "methanol"]
|
||||
if gradient_volumes is None:
|
||||
gradient_volumes = [50.0, 50.0, 30.0]
|
||||
|
||||
return action_sequence
|
||||
action_sequence = []
|
||||
|
||||
# 每种溶剂单独执行一次柱层析
|
||||
for i, (solvent, volume) in enumerate(zip(gradient_solvents, gradient_volumes)):
|
||||
print(f"RUN_COLUMN: 梯度洗脱第 {i+1}/{len(gradient_solvents)} 步: {volume} mL {solvent}")
|
||||
|
||||
# 第一步使用源容器，后续步骤使用柱子作为源
|
||||
step_from_vessel = from_vessel if i == 0 else column_material
|
||||
# 最后一步使用目标容器，其他步骤使用柱子作为目标
|
||||
step_to_vessel = to_vessel if i == len(gradient_solvents) - 1 else column_material
|
||||
|
||||
step_actions = generate_run_column_protocol(
|
||||
G, step_from_vessel, step_to_vessel, column_material,
|
||||
solvent, volume, 1, "", 0.0, 1.0
|
||||
)
|
||||
action_sequence.extend(step_actions)
|
||||
|
||||
# 在梯度步骤之间加入等待时间
|
||||
if i < len(gradient_solvents) - 1:
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 20}
|
||||
})
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
def generate_reverse_phase_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "C18",
|
||||
aqueous_phase: str = "water",
|
||||
organic_phase: str = "methanol",
|
||||
gradient_ratio: float = 0.5
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""反相柱层析：C18柱，水-有机相梯度"""
|
||||
# 先用水相平衡
|
||||
equilibration_volume = 20.0
|
||||
# 然后用有机相洗脱
|
||||
eluting_volume = 30.0 * gradient_ratio
|
||||
|
||||
return generate_run_column_protocol(
|
||||
G, from_vessel, to_vessel, column_material,
|
||||
organic_phase, eluting_volume, 2,
|
||||
aqueous_phase, equilibration_volume, 0.8
|
||||
)
|
||||
|
||||
|
||||
def generate_ion_exchange_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "ion_exchange",
|
||||
buffer_solution: str = "buffer",
|
||||
salt_solution: str = "NaCl_solution",
|
||||
salt_volume: float = 40.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""离子交换柱层析：缓冲液平衡，盐溶液洗脱"""
|
||||
return generate_run_column_protocol(
|
||||
G, from_vessel, to_vessel, column_material,
|
||||
salt_solution, salt_volume, 1,
|
||||
buffer_solution, 25.0, 0.5
|
||||
)
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_run_column_protocol():
|
||||
"""测试柱层析协议的示例"""
|
||||
print("=== RUN COLUMN PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_run_column_protocol()
|
||||
Reference in New Issue
Block a user