mirror of
https://github.com/deepmodeling/Uni-Lab-OS
synced 2026-03-25 13:03:05 +00:00
0ab4027de7
- 统一debug_print为共享import，移除14个本地定义 - 移除重复工具函数（find_connected_stirrer, get_vessel_liquid_volume等） - 精简装饰性日志（emoji分隔线、进度提示），保留关键决策点 - 删除evacuateandrefill_protocol_old.py死代码 - 涉及文件：add, adjustph, clean_vessel, dissolve, dry, evacuateandrefill, evaporate, filter, pump, recrystallize, reset_handling, run_column, stir, wash_solid Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
473 lines
17 KiB
Python
473 lines
17 KiB
Python
from typing import List, Dict, Any, Union
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import networkx as nx
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import logging
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import re
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from .utils.vessel_parser import get_vessel, find_solvent_vessel
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from .utils.resource_helper import get_resource_id, get_resource_data, get_resource_liquid_volume, update_vessel_volume
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from .utils.logger_util import debug_print
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from .pump_protocol import generate_pump_protocol_with_rinsing
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logger = logging.getLogger(__name__)
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def parse_percentage(pct_str: str) -> float:
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"""
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解析百分比字符串为数值
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Args:
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pct_str: 百分比字符串（如 "40 %", "40%", "40"）
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Returns:
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float: 百分比数值（0-100）
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"""
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if not pct_str or not pct_str.strip():
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return 0.0
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pct_str = pct_str.strip().lower()
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# 移除百分号和空格
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pct_clean = re.sub(r'[%\s]', '', pct_str)
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match = re.search(r'([0-9]*\.?[0-9]+)', pct_clean)
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if match:
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value = float(match.group(1))
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return value
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debug_print(f"无法解析百分比: '{pct_str}'，返回0.0")
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return 0.0
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def parse_ratio(ratio_str: str) -> tuple:
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"""
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解析比例字符串为两个数值
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Args:
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ratio_str: 比例字符串（如 "5:95", "1:1", "40:60"）
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Returns:
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tuple: (ratio1, ratio2) 两个比例值（百分比）
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"""
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if not ratio_str or not ratio_str.strip():
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return (50.0, 50.0)
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ratio_str = ratio_str.strip()
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# 支持多种分隔符：: / -
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if ':' in ratio_str:
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parts = ratio_str.split(':')
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elif '/' in ratio_str:
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parts = ratio_str.split('/')
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elif '-' in ratio_str:
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parts = ratio_str.split('-')
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elif 'to' in ratio_str.lower():
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parts = ratio_str.lower().split('to')
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else:
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debug_print(f"无法解析比例格式: '{ratio_str}'，使用默认1:1")
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return (50.0, 50.0)
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if len(parts) >= 2:
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try:
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ratio1 = float(parts[0].strip())
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ratio2 = float(parts[1].strip())
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total = ratio1 + ratio2
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pct1 = (ratio1 / total) * 100
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pct2 = (ratio2 / total) * 100
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return (pct1, pct2)
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except ValueError as e:
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debug_print(f"比例数值转换失败: {str(e)}")
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debug_print(f"比例解析失败，使用默认1:1")
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return (50.0, 50.0)
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def parse_rf_value(rf_str: str) -> float:
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"""
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解析Rf值字符串
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Args:
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rf_str: Rf值字符串（如 "0.3", "0.45", "?"）
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Returns:
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float: Rf值（0-1）
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"""
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if not rf_str or not rf_str.strip():
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return 0.3
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rf_str = rf_str.strip().lower()
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if rf_str in ['?', 'unknown', 'tbd', 'to be determined']:
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return 0.3
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match = re.search(r'([0-9]*\.?[0-9]+)', rf_str)
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if match:
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value = float(match.group(1))
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if value > 1.0:
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value = value / 100.0
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value = max(0.0, min(1.0, value))
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return value
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return 0.3
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def find_column_device(G: nx.DiGraph) -> str:
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"""查找柱层析设备"""
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for node in G.nodes():
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node_data = G.nodes[node]
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node_class = node_data.get('class', '') or ''
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if 'virtual_column' in node_class.lower() or 'column' in node_class.lower():
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debug_print(f"找到柱层析设备: {node}")
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return node
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possible_names = ['column_1', 'virtual_column_1', 'chromatography_column_1']
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for name in possible_names:
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if name in G.nodes():
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debug_print(f"找到柱设备: {name}")
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return name
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debug_print("未找到柱层析设备，将使用pump protocol直接转移")
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return ""
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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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if column in G.nodes():
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node_type = G.nodes[column].get('type', '')
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if node_type == 'container':
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return column
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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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"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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node_type = G.nodes[vessel_name].get('type', '')
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if node_type == 'container':
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return vessel_name
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return ""
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def calculate_solvent_volumes(total_volume: float, pct1: float, pct2: float) -> tuple:
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"""根据百分比计算溶剂体积"""
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volume1 = (total_volume * pct1) / 100.0
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volume2 = (total_volume * pct2) / 100.0
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return (volume1, volume2)
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def generate_run_column_protocol(
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G: nx.DiGraph,
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from_vessel: dict,
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to_vessel: dict,
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column: str,
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rf: str = "",
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pct1: str = "",
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pct2: str = "",
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solvent1: str = "",
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solvent2: str = "",
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ratio: str = "",
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**kwargs
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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 - 支持vessel字典和体积运算
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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: 源容器字典（从XDL传入）
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to_vessel: 目标容器字典（从XDL传入）
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column: 所使用的柱子的名称（必需）
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rf: Rf值（可选，支持 "?" 表示未知）
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pct1: 第一种溶剂百分比（如 "40 %"，可选）
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pct2: 第二种溶剂百分比（如 "50 %"，可选）
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solvent1: 第一种溶剂名称（可选）
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solvent2: 第二种溶剂名称（可选）
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ratio: 溶剂比例（如 "5:95"，可选，优先级高于pct1/pct2）
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**kwargs: 其他可选参数
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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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from_vessel_id, _ = get_vessel(from_vessel)
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to_vessel_id, _ = get_vessel(to_vessel)
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debug_print(f"开始生成柱层析协议: {from_vessel_id} -> {to_vessel_id}, column={column}")
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action_sequence = []
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# 记录柱层析前的容器状态
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original_from_volume = get_resource_liquid_volume(from_vessel)
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original_to_volume = get_resource_liquid_volume(to_vessel)
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# === 参数验证 ===
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if not from_vessel_id:
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raise ValueError("from_vessel 参数不能为空")
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if not to_vessel_id:
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raise ValueError("to_vessel 参数不能为空")
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if not column:
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raise ValueError("column 参数不能为空")
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if from_vessel_id not in G.nodes():
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raise ValueError(f"源容器 '{from_vessel_id}' 不存在于系统中")
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if to_vessel_id not in G.nodes():
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raise ValueError(f"目标容器 '{to_vessel_id}' 不存在于系统中")
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# === 参数解析 ===
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final_rf = parse_rf_value(rf)
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if ratio and ratio.strip():
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final_pct1, final_pct2 = parse_ratio(ratio)
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else:
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final_pct1 = parse_percentage(pct1) if pct1 else 50.0
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final_pct2 = parse_percentage(pct2) if pct2 else 50.0
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total_pct = final_pct1 + final_pct2
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if total_pct == 0:
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final_pct1, final_pct2 = 50.0, 50.0
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elif total_pct != 100.0:
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final_pct1 = (final_pct1 / total_pct) * 100
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final_pct2 = (final_pct2 / total_pct) * 100
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final_solvent1 = solvent1.strip() if solvent1 else "ethyl_acetate"
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final_solvent2 = solvent2.strip() if solvent2 else "hexane"
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debug_print(f"参数: rf={final_rf}, 溶剂={final_solvent1}:{final_solvent2} = {final_pct1:.1f}%:{final_pct2:.1f}%")
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# === 查找设备和容器 ===
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column_device_id = find_column_device(G)
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column_vessel = find_column_vessel(G, column)
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solvent1_vessel = find_solvent_vessel(G, final_solvent1)
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solvent2_vessel = find_solvent_vessel(G, final_solvent2)
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# === 获取源容器体积 ===
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source_volume = original_from_volume
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if source_volume <= 0:
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source_volume = 50.0
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# === 计算溶剂体积 ===
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total_elution_volume = source_volume * 3.0
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solvent1_volume, solvent2_volume = calculate_solvent_volumes(
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total_elution_volume, final_pct1, final_pct2
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)
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# === 执行柱层析流程 ===
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current_from_volume = source_volume
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current_to_volume = original_to_volume
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current_column_volume = 0.0
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try:
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# 步骤1: 样品上柱
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if column_vessel and column_vessel != from_vessel_id:
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try:
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sample_transfer_actions = generate_pump_protocol_with_rinsing(
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G=G,
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from_vessel=from_vessel_id,
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to_vessel=column_vessel,
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volume=source_volume,
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flowrate=1.0,
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transfer_flowrate=0.5,
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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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)
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action_sequence.extend(sample_transfer_actions)
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current_from_volume = 0.0
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current_column_volume = source_volume
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update_vessel_volume(from_vessel, G, current_from_volume, "样品上柱后，源容器清空")
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if column_vessel in G.nodes():
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if 'data' not in G.nodes[column_vessel]:
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G.nodes[column_vessel]['data'] = {}
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G.nodes[column_vessel]['data']['liquid_volume'] = current_column_volume
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except Exception as e:
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debug_print(f"样品上柱失败: {str(e)}")
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# 步骤2: 添加洗脱溶剂1
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if solvent1_vessel and solvent1_volume > 0:
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try:
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target_vessel = column_vessel if column_vessel else from_vessel_id
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solvent1_transfer_actions = generate_pump_protocol_with_rinsing(
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G=G,
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from_vessel=solvent1_vessel,
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to_vessel=target_vessel,
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volume=solvent1_volume,
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flowrate=2.0,
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transfer_flowrate=1.0
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)
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action_sequence.extend(solvent1_transfer_actions)
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if target_vessel == column_vessel:
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current_column_volume += solvent1_volume
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if column_vessel in G.nodes():
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G.nodes[column_vessel]['data']['liquid_volume'] = current_column_volume
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elif target_vessel == from_vessel_id:
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current_from_volume += solvent1_volume
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update_vessel_volume(from_vessel, G, current_from_volume, "添加溶剂1后")
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except Exception as e:
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debug_print(f"溶剂1添加失败: {str(e)}")
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# 步骤3: 添加洗脱溶剂2
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if solvent2_vessel and solvent2_volume > 0:
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try:
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target_vessel = column_vessel if column_vessel else from_vessel_id
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solvent2_transfer_actions = generate_pump_protocol_with_rinsing(
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G=G,
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from_vessel=solvent2_vessel,
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to_vessel=target_vessel,
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volume=solvent2_volume,
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flowrate=2.0,
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transfer_flowrate=1.0
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)
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action_sequence.extend(solvent2_transfer_actions)
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if target_vessel == column_vessel:
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current_column_volume += solvent2_volume
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if column_vessel in G.nodes():
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G.nodes[column_vessel]['data']['liquid_volume'] = current_column_volume
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elif target_vessel == from_vessel_id:
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current_from_volume += solvent2_volume
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update_vessel_volume(from_vessel, G, current_from_volume, "添加溶剂2后")
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except Exception as e:
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debug_print(f"溶剂2添加失败: {str(e)}")
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# 步骤4: 使用柱层析设备执行分离
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if column_device_id:
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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_id,
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"to_vessel": to_vessel_id,
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"column": column,
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"rf": rf,
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"pct1": pct1,
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"pct2": pct2,
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"solvent1": solvent1,
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"solvent2": solvent2,
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"ratio": ratio
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}
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}
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action_sequence.append(column_separation_action)
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separation_time = max(30, min(120, int(total_elution_volume / 2)))
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action_sequence.append({
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"action_name": "wait",
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"action_kwargs": {"time": separation_time}
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})
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# 步骤5: 产物收集
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if column_vessel and column_vessel != to_vessel_id:
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try:
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product_volume = source_volume * 0.8
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product_transfer_actions = generate_pump_protocol_with_rinsing(
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G=G,
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from_vessel=column_vessel,
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to_vessel=to_vessel_id,
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volume=product_volume,
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flowrate=1.5,
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transfer_flowrate=0.8
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)
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action_sequence.extend(product_transfer_actions)
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current_to_volume += product_volume
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current_column_volume -= product_volume
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update_vessel_volume(to_vessel, G, current_to_volume, "产物收集后")
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if column_vessel in G.nodes():
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G.nodes[column_vessel]['data']['liquid_volume'] = max(0.0, current_column_volume)
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except Exception as e:
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debug_print(f"产物收集失败: {str(e)}")
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# 步骤6: 简化模式 - 直接转移
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if not column_device_id and not column_vessel:
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try:
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direct_transfer_actions = generate_pump_protocol_with_rinsing(
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G=G,
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from_vessel=from_vessel_id,
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to_vessel=to_vessel_id,
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volume=source_volume,
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flowrate=2.0,
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transfer_flowrate=1.0
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)
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action_sequence.extend(direct_transfer_actions)
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current_from_volume = 0.0
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current_to_volume += source_volume
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update_vessel_volume(from_vessel, G, current_from_volume, "直接转移后，源容器清空")
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update_vessel_volume(to_vessel, G, current_to_volume, "直接转移后，目标容器增加")
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except Exception as e:
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debug_print(f"直接转移失败: {str(e)}")
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except Exception as e:
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debug_print(f"协议生成失败: {str(e)}")
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if not action_sequence:
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action_sequence.append({
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"action_name": "wait",
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"action_kwargs": {
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"time": 1.0,
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"description": "柱层析协议执行完成"
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}
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})
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final_from_volume = get_resource_liquid_volume(from_vessel)
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final_to_volume = get_resource_liquid_volume(to_vessel)
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debug_print(f"柱层析协议生成完成: {len(action_sequence)} 个动作, {from_vessel_id} -> {to_vessel_id}, 收集={final_to_volume - original_to_volume:.2f}mL")
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return action_sequence
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# 便捷函数
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def generate_ethyl_acetate_hexane_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
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column: str, ratio: str = "30:70") -> List[Dict[str, Any]]:
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"""乙酸乙酯-己烷柱层析（常用组合）"""
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return generate_run_column_protocol(G, from_vessel, to_vessel, column,
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solvent1="ethyl_acetate", solvent2="hexane", ratio=ratio)
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def generate_methanol_dcm_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
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column: str, ratio: str = "5:95") -> List[Dict[str, Any]]:
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"""甲醇-二氯甲烷柱层析"""
|
||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||
solvent1="methanol", solvent2="dichloromethane", ratio=ratio)
|
||
|
||
def generate_gradient_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||
column: str, start_ratio: str = "10:90",
|
||
end_ratio: str = "50:50") -> List[Dict[str, Any]]:
|
||
"""梯度洗脱柱层析（中等比例）"""
|
||
return generate_run_column_protocol(G, from_vessel, to_vessel, column, ratio="30:70")
|
||
|
||
def generate_polar_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||
column: str) -> List[Dict[str, Any]]:
|
||
"""极性化合物柱层析（高极性溶剂比例）"""
|
||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||
solvent1="ethyl_acetate", solvent2="hexane", ratio="70:30")
|
||
|
||
def generate_nonpolar_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||
column: str) -> List[Dict[str, Any]]:
|
||
"""非极性化合物柱层析（低极性溶剂比例）"""
|
||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||
solvent1="ethyl_acetate", solvent2="hexane", ratio="5:95")
|
||
|
||
# 测试函数
|
||
def test_run_column_protocol():
|
||
"""测试柱层析协议"""
|
||
debug_print("=== RUN COLUMN PROTOCOL 测试 ===")
|
||
debug_print("测试完成")
|
||
|
||
if __name__ == "__main__":
|
||
test_run_column_protocol()
|