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727
mw_tool/pubchem_tool.py
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727
mw_tool/pubchem_tool.py
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import streamlit as st
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import pubchempy as pcp
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import re
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from typing import Optional, Dict, List, cast
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from io import BytesIO
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import base64
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from PIL import Image
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import requests
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import pandas as pd
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import numpy as np
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class PubChemCompound:
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def __init__(self, compound: pcp.Compound, extra: Optional[Dict[str, Optional[List[str]]]] = None):
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self.cid = compound.cid
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self.name = compound.iupac_name
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self.formula = compound.molecular_formula
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self.smiles = compound.isomeric_smiles
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self.exact_mass = float(compound.exact_mass) if compound.exact_mass else None
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if extra:
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self.density = extra.get("density")
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self.melting_point = extra.get("melting_point")
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self.boiling_point = extra.get("boiling_point")
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else:
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self.density = None
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self.melting_point = None
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self.boiling_point = None
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def get_pubchem_properties(cid:str) -> Dict[str, Optional[List[str]]]:
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"""从PubChem获取密度、熔点、沸点信息"""
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try:
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# 初始化返回数据
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properties:Dict[str, Optional[List[str]]] = {
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'density': None,
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'melting_point': None,
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'boiling_point': None
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}
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# 尝试获取物理化学性质相关的记录
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try:
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url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON?heading=Experimental+Properties"
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data = requests.get(url, timeout=3).json()
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for section in data["Record"]["Section"]:
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if section["TOCHeading"] == "Chemical and Physical Properties":
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for sub in section["Section"]:
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if sub["TOCHeading"] == "Experimental Properties":
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for prop in sub["Section"]:
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prop_heading = prop["TOCHeading"]
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if prop_heading == "Density" and not properties['density']:
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# 可能有多条不同温度/浓度的记录，逐条返回
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properties['density'] = [
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info["Value"]["StringWithMarkup"][0]["String"]
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for info in prop["Information"]
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if "Value" in info and "StringWithMarkup" in info["Value"]
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]
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elif prop_heading == "Melting Point" and not properties['melting_point']:
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properties['melting_point'] = [
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info["Value"]["StringWithMarkup"][0]["String"]
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for info in prop["Information"]
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if "Value" in info and "StringWithMarkup" in info["Value"]
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]
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elif prop_heading == "Boiling Point" and not properties['boiling_point']:
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properties['boiling_point'] = [
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info["Value"]["StringWithMarkup"][0]["String"]
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for info in prop["Information"]
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if "Value" in info and "StringWithMarkup" in info["Value"]
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]
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return properties
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except Exception:
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return properties
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except Exception as e:
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# 静默处理异常，返回空的properties字典
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return {
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'density': None,
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'melting_point': None,
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'boiling_point': None
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}
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def search_compound(query: str, search_type: str = "name"):
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"""
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根据不同类型搜索化合物
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Args:
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query: 搜索词
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search_type: 搜索类型 ("name", "formula", "smiles")
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Returns:
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PubChem Compound对象或None
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"""
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try:
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if search_type == "name":
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compounds = pcp.get_compounds(query, 'name')
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elif search_type == "formula":
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compounds = pcp.get_compounds(query, 'formula')
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elif search_type == "smiles":
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compounds = pcp.get_compounds(query, 'smiles')
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else:
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return None
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if compounds is not None and len(compounds) > 0:
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return compounds[0] # 返回第一个匹配的化合物
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return None
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except Exception as e:
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st.error(f"搜索出错: {str(e)}")
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return None
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def get_structure_image(cid: int, width: int = 300, height: int = 300):
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"""
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获取化合物的2D结构图
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Args:
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cid: PubChem CID
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width: 图片宽度
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height: 图片高度
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Returns:
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url
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"""
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url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/PNG?record_type=2d&image_size={width}x{height}"
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return url
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def extract_density_value(density_text: str) -> Optional[float]:
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"""
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从密度文本中提取数值
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Args:
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density_text: 密度描述文本
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Returns:
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提取的密度数值或None
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"""
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# 使用正则表达式提取数字
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pattern = r'(\d*\.\d+|\d+\.\d*|\d+)'
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matches = re.findall(pattern, density_text)
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if matches:
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try:
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return float(matches[0])
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except ValueError:
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return None
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return None
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def calculate_properties(molecular_weight: float, amount_mmol: Optional[float] = None,
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mass_g: Optional[float] = None, volume_ml: Optional[float] = None,
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density: Optional[float] = None):
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"""
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计算用量、质量、体积之间的关系
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Args:
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molecular_weight: 分子量 (g/mol)
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amount_mmol: 用量 (mmol)
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mass_g: 质量 (g)
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volume_ml: 体积 (mL)
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density: 密度 (g/mL)
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Returns:
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计算结果字典
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"""
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result = {
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'amount_mmol': amount_mmol,
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'mass_g': mass_g,
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'volume_ml': volume_ml
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}
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# 如果有用量和分子量，计算质量
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if amount_mmol is not None and molecular_weight:
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result['mass_g'] = amount_mmol * molecular_weight / 1000
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# 如果有质量和分子量，计算用量
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if mass_g is not None and molecular_weight:
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result['amount_mmol'] = mass_g * 1000 / molecular_weight
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# 如果有质量和密度，计算体积
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if result['mass_g'] is not None and density is not None and density > 0:
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result['volume_ml'] = result['mass_g'] / density
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# 如果有体积和密度，计算质量
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if volume_ml is not None and density is not None and density > 0:
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result['mass_g'] = volume_ml * density
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result["amount_mmol"] = result['mass_g'] * 1000 / molecular_weight
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return result
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def reaction_table_page():
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"""反应表格页面"""
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st.header("⚗️ 反应表格")
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# 初始化数据
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if 'reaction_data' not in st.session_state:
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st.session_state.reaction_data = pd.DataFrame([[None,None,None,None,None,None,None,None]],columns=[
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"物质",
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"分子量",
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"当量",
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"用量(mmol)",
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"质量(g)",
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"密度(g/mL)",
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"体积(mL)",
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"备注"
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])
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st.write("### 反应物质表格")
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st.info("💡 当量为0时，该物质不参与当量计算。修改任意数值时会自动重新计算相关参数。")
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# 使用data_editor创建可编辑表格
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edited_data = st.data_editor(
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st.session_state.reaction_data,
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num_rows="dynamic",
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use_container_width=True,
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column_config={
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"物质": st.column_config.TextColumn("物质", width="medium"),
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"分子量": st.column_config.NumberColumn(
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"分子量",
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format="%.4f",
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min_value=0.0,
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step=0.0001
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),
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"当量": st.column_config.NumberColumn(
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"当量",
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format="%.2f",
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min_value=0.0,
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step=0.1,
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help="当量为0时不参与当量计算"
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),
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"用量(mmol)": st.column_config.NumberColumn(
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"用量(mmol)",
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format="%.3f",
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min_value=0.0,
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step=0.001
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),
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"质量(g)": st.column_config.NumberColumn(
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"质量(g)",
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format="%.6f",
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min_value=0.0,
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step=0.000001
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),
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"密度(g/mL)": st.column_config.NumberColumn(
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"密度(g/mL)",
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format="%.3f",
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min_value=0.0,
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step=0.001
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),
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"体积(mL)": st.column_config.NumberColumn(
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"体积(mL)",
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format="%.6f",
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min_value=0.0,
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step=0.000001
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),
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"备注": st.column_config.TextColumn("备注", width="medium")
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},
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key="reaction_table",
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on_change=recalculate_reaction_data
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)
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if st.session_state.get("reaction_table_refresh",0) == 2:
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st.warning("发生多个编辑，无法计算。")
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st.session_state.reaction_table_refresh = 0
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if st.session_state.get("reaction_table_refresh",0):
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st.session_state.reaction_data = edited_data
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st.session_state.reaction_table_refresh = 2
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st.rerun()
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# print(st.session_state.reaction_data)
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# 仅当返回的是 DataFrame 时再回写；如果是变更字典则由回调处理
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# if isinstance(edited_data, pd.DataFrame):
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# print("Edited DataFrame:", edited_data)
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# st.session_state.reaction_data = edited_data
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def recalculate_reaction_data():
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"""根据最近一次编辑的行及当量，推算其他未编辑行的用量，并更新质量/体积。"""
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try:
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edits = st.session_state.get("reaction_table")
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df = st.session_state.get("reaction_data")
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# 基本校验
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if df is None or not isinstance(df, pd.DataFrame):
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return
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# 仅当从 data_editor 拿到变更字典时才处理
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if not isinstance(edits, dict):
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return
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print(1,edits)
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# 处理新增/删除行（若有）
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for new_row in edits.get("added_rows", []) or []:
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# 对象列名对齐现有表头
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print(new_row)
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if isinstance(new_row, dict):
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to_add = {col: new_row.get(col, None) for col in df.columns}
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df = pd.concat([df, pd.DataFrame([to_add])], ignore_index=True)
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for del_idx in edits.get("deleted_rows", []) or []:
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try:
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df.drop(index=int(del_idx), inplace=True)
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except Exception:
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pass
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if (edits.get("deleted_rows") or []):
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df.reset_index(drop=True, inplace=True)
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edited_rows = edits.get("edited_rows", {}) or {}
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if not edited_rows:
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st.session_state.reaction_data = df
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print("No edited rows found, skipping recalculation.")
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return
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if len(edited_rows) > 1:
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st.session_state.reaction_table_refresh = 1
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return
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# 将编辑内容先写回到 DataFrame，记录“最后编辑的行”作为基准行
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edited_indices = []
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edited = {}
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for idx_str, changes in edited_rows.items():
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try:
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i = int(idx_str)
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except Exception:
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# 有些情况下索引就是 int
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i = idx_str
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edited_indices.append(i)
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for col, val in changes.items():
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if col in df.columns:
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edited[col] = val
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if col == "当量":
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df.loc[i, col] = val
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if val != 0:
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example = df[(df["当量"] > 0) & (df["用量(mmol)"] > 0)]
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if example.size > 0:
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j=0
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tmp = example.iloc[j]
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print(tmp.name)
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while tmp.name == i:
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j+=1
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tmp = example.iloc[j]
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sing = tmp['用量(mmol)']/tmp["当量"]
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edited["用量(mmol)"] = sing * edited["当量"]
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basis_idx = edited_indices[-1] # 以最后一条编辑为本次基准
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print(1,df)
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# 数值清洗工具
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def _to_float(x):
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try:
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if x is None:
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return None
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# 处理 NaN/空串
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try:
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import pandas as _pd
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if _pd.isna(x):
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return None
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except Exception:
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pass
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s = str(x).strip()
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if s == "":
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return None
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return float(s)
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except Exception:
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return None
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# 基准行的自洽计算（用量/质量/体积）
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assert edited
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brow = df.loc[basis_idx]
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b_mw = _to_float(brow.get("分子量"))
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b_density = _to_float(brow.get("密度(g/mL)"))
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b_amount = edited.get("用量(mmol)",None)
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b_mass = edited.get("质量(g)",None)
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b_volume = edited.get("体积(mL)",None)
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b_eq = edited.get("当量",_to_float(brow.get("当量")))
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props = calculate_properties(
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molecular_weight=b_mw if b_mw else 0,
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amount_mmol=b_amount,
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mass_g=b_mass,
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volume_ml=b_volume,
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density=b_density,
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)
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_v = props.get("amount_mmol")
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if isinstance(_v, (int, float)):
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df.at[basis_idx, "用量(mmol)"] = round(float(_v), 6)
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_v = props.get("mass_g")
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if isinstance(_v, (int, float)):
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df.at[basis_idx, "质量(g)"] = round(float(_v), 6)
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_v = props.get("volume_ml")
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if isinstance(_v, (int, float)):
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df.at[basis_idx, "体积(mL)"] = round(float(_v), 6)
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print(2,df)
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# 基准行当量为 0 或不可用，则不进行当量联动计算
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if not (b_eq and b_eq > 0):
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st.session_state.reaction_data = df
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return
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b_amount_final = _to_float(df.at[basis_idx, "用量(mmol)"])
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if b_amount_final is None:
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st.session_state.reaction_data = df
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return
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base_per_eq = b_amount_final / b_eq
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print(3,df)
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# 按当量推算其他“未编辑行”的用量，并据此计算质量/体积
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for j in range(len(df)):
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if j == basis_idx:
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continue
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if j in edited_indices:
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# 本次被用户直接修改的行不改动
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continue
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eq_j = _to_float(df.at[j, "当量"]) if "当量" in df.columns else None
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if not (eq_j and eq_j > 0):
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continue
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amt_j = base_per_eq * eq_j
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df.at[j, "用量(mmol)"] = round(amt_j, 6)
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mw_j = _to_float(df.at[j, "分子量"]) if "分子量" in df.columns else None
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if mw_j:
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mass_j = amt_j * mw_j / 1000.0 # mmol -> mol，再乘以 g/mol
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df.at[j, "质量(g)"] = round(mass_j, 6)
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dens_j = _to_float(df.at[j, "密度(g/mL)"]) if "密度(g/mL)" in df.columns else None
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if dens_j and dens_j > 0:
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vol_j = mass_j / dens_j
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df.at[j, "体积(mL)"] = round(vol_j, 6)
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print(4,df)
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# 持久化
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st.session_state.reaction_data = df
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except Exception as e:
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raise e
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print("recalculate_reaction_data error:", e)
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def add_compound_to_reaction(compound:PubChemCompound):
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"""将化合物添加到反应中"""
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d = {
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"物质":compound.formula,
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"分子量":compound.exact_mass,
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"当量":None,
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"用量(mmol)":None,
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"质量(g)":None,
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"密度(g/mL)":st.session_state.get("custom_density",None),
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"体积(mL)":None,
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"备注":compound.name
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}
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st.session_state.reaction_data = pd.concat([st.session_state.reaction_data, pd.DataFrame([d])], ignore_index=True)
|
||||
st.success("化合物已添加到反应中")
|
||||
|
||||
def compound_search_page():
|
||||
"""化合物搜索页面"""
|
||||
# 输入区域
|
||||
st.header("📝 输入查询条件")
|
||||
|
||||
col1, col2 = st.columns([1, 2])
|
||||
|
||||
with col1:
|
||||
# 选择搜索类型
|
||||
search_type = st.selectbox(
|
||||
"选择搜索类型",
|
||||
["name", "formula", "smiles"],
|
||||
format_func=lambda x: {"name": "名称", "formula": "化学式", "smiles": "SMILES"}[x]
|
||||
)
|
||||
|
||||
with col2:
|
||||
# 输入搜索词
|
||||
query = st.text_input(
|
||||
f"输入{'名称' if search_type == 'name' else '化学式' if search_type == 'formula' else 'SMILES'}",
|
||||
placeholder="例如: ethanol, C2H6O, CCO"
|
||||
)
|
||||
|
||||
search_button = st.button("🔍 搜索", type="primary")
|
||||
|
||||
# 主要内容区域
|
||||
if search_button and query:
|
||||
with st.spinner("正在搜索..."):
|
||||
_compound = search_compound(query, search_type)
|
||||
|
||||
if _compound is not None:
|
||||
st.info("找到匹配的化合物，正在获取详细信息...")
|
||||
# 在session_state中存储化合物信息
|
||||
additional_props = get_pubchem_properties(str(_compound.cid))
|
||||
st.session_state.compound = PubChemCompound(cast(pcp.Compound, _compound), additional_props)
|
||||
|
||||
else:
|
||||
st.error("未找到匹配的化合物，请检查输入并重试。")
|
||||
return
|
||||
|
||||
# 如果session_state中有化合物信息，显示结果
|
||||
if hasattr(st.session_state, 'compound') and st.session_state.compound:
|
||||
compound = st.session_state.compound
|
||||
st.button("添加到反应", on_click=add_compound_to_reaction, args=(compound,))
|
||||
|
||||
# 基本信息展示
|
||||
col1, col2 = st.columns(2)
|
||||
|
||||
with col1:
|
||||
st.header("📊 基本信息")
|
||||
|
||||
st.metric("物质名称", compound.name or "未知")
|
||||
st.metric("化学式", compound.formula or "未知")
|
||||
st.metric("分子量", f"{compound.exact_mass:.4f} g/mol" if compound.exact_mass else "未知")
|
||||
st.markdown(f"[**访问PubChem页面**](https://pubchem.ncbi.nlm.nih.gov/compound/{compound.cid})")
|
||||
# 创建信息表格
|
||||
info_data = {
|
||||
"属性": ["物质名称", "化学式", "分子量 (Exact Mass)", "CID"],
|
||||
"值": [
|
||||
compound.name or "未知",
|
||||
compound.formula or "未知",
|
||||
f"{compound.exact_mass:.4f} g/mol" if compound.exact_mass else "未知",
|
||||
str(compound.cid)
|
||||
]
|
||||
}
|
||||
|
||||
# st.table(info_data)
|
||||
|
||||
with col2:
|
||||
st.header("🖼️ 2D结构图")
|
||||
if hasattr(compound, 'cid') and compound.cid:
|
||||
structure_img = get_structure_image(compound.cid)
|
||||
if structure_img:
|
||||
st.image(structure_img, caption=f"CID: {compound.cid}")
|
||||
else:
|
||||
st.warning("无法获取结构图")
|
||||
else:
|
||||
st.warning("无CID信息，无法获取结构图")
|
||||
|
||||
# 扩展信息
|
||||
st.markdown("---")
|
||||
|
||||
# 密度信息
|
||||
with st.expander("📏 密度信息", expanded=False):
|
||||
if compound.density:
|
||||
st.subheader("可用密度数据:")
|
||||
|
||||
# 初始化session_state中的密度选择
|
||||
if 'selected_density_idx' not in st.session_state:
|
||||
st.session_state.selected_density_idx = 0
|
||||
if 'custom_density' not in st.session_state:
|
||||
st.session_state.custom_density = None
|
||||
|
||||
# 显示密度选项
|
||||
density_options = compound.density
|
||||
selected_idx = st.radio(
|
||||
"选择要使用的密度数据:",
|
||||
range(len(density_options)),
|
||||
format_func=lambda x: density_options[x],
|
||||
key="density_radio",
|
||||
index=st.session_state.selected_density_idx
|
||||
)
|
||||
|
||||
# 提取密度数值
|
||||
selected_density_text = density_options[selected_idx]
|
||||
extracted_density = extract_density_value(selected_density_text)
|
||||
|
||||
custom_density = st.number_input(
|
||||
"密度值 (g/mL):",
|
||||
value=extracted_density if extracted_density else 1.0,
|
||||
# min_value=0.001,
|
||||
# max_value=50.0,
|
||||
step=0.001,
|
||||
format="%.3f",
|
||||
key="custom_density_input"
|
||||
)
|
||||
st.session_state.custom_density = custom_density
|
||||
st.session_state.selected_density_idx = selected_idx
|
||||
else:
|
||||
st.warning("未找到密度数据")
|
||||
st.session_state.custom_density = None
|
||||
|
||||
# 熔沸点信息
|
||||
with st.expander("🌡️ 熔沸点信息", expanded=False):
|
||||
col1, col2 = st.columns(2)
|
||||
|
||||
with col1:
|
||||
st.subheader("熔点")
|
||||
if compound.melting_point:
|
||||
for mp in compound.melting_point:
|
||||
st.write(f"• {mp}")
|
||||
else:
|
||||
st.warning("未找到熔点数据")
|
||||
|
||||
with col2:
|
||||
st.subheader("沸点")
|
||||
if compound.boiling_point:
|
||||
for bp in compound.boiling_point:
|
||||
st.write(f"• {bp}")
|
||||
else:
|
||||
st.warning("未找到沸点数据")
|
||||
|
||||
# 计算器
|
||||
st.markdown("---")
|
||||
st.header("🧮 用量计算器")
|
||||
|
||||
if compound.exact_mass:
|
||||
# 初始化session_state中的计算器数值
|
||||
if 'calc_amount' not in st.session_state:
|
||||
st.session_state.calc_amount = None
|
||||
if 'calc_mass' not in st.session_state:
|
||||
st.session_state.calc_mass = None
|
||||
if 'calc_volume' not in st.session_state:
|
||||
st.session_state.calc_volume = None
|
||||
|
||||
col1, col2, col3 = st.columns(3)
|
||||
|
||||
with col1:
|
||||
amount_mmol = st.number_input(
|
||||
"用量 (mmol)",
|
||||
min_value=0.0,
|
||||
value=st.session_state.calc_amount if st.session_state.calc_amount else 0.0,
|
||||
step=0.1,
|
||||
format="%.3f",
|
||||
key="amount_input",
|
||||
)
|
||||
|
||||
with col2:
|
||||
mass_g = st.number_input(
|
||||
"质量 (g)",
|
||||
min_value=0.0,
|
||||
value=st.session_state.calc_mass if st.session_state.calc_mass else 0.0,
|
||||
step=0.001,
|
||||
format="%.6f",
|
||||
key="mass_input"
|
||||
)
|
||||
|
||||
with col3:
|
||||
# 只有在有密度数据时才显示体积输入
|
||||
if st.session_state.get('custom_density'):
|
||||
volume_ml = st.number_input(
|
||||
"体积 (mL)",
|
||||
min_value=0.0,
|
||||
value=st.session_state.calc_volume if st.session_state.calc_volume else 0.0,
|
||||
step=0.001,
|
||||
format="%.6f",
|
||||
key="volume_input"
|
||||
)
|
||||
else:
|
||||
volume_ml = None
|
||||
st.info("需要密度数据才能计算体积")
|
||||
|
||||
# 检测哪个值发生了变化并重新计算
|
||||
current_values = {
|
||||
'amount': amount_mmol if amount_mmol!=st.session_state.calc_amount else None,
|
||||
'mass': mass_g if mass_g != st.session_state.calc_mass else None,
|
||||
'volume': volume_ml if volume_ml and volume_ml != st.session_state.calc_volume else None
|
||||
}
|
||||
|
||||
# 执行计算
|
||||
if any(current_values.values()):
|
||||
density = st.session_state.get('custom_density')
|
||||
results = calculate_properties(
|
||||
molecular_weight=compound.exact_mass,
|
||||
amount_mmol=current_values['amount'],
|
||||
mass_g=current_values['mass'],
|
||||
volume_ml=current_values['volume'],
|
||||
density=density
|
||||
)
|
||||
|
||||
# 更新session_state
|
||||
st.session_state.calc_amount = results['amount_mmol']
|
||||
st.session_state.calc_mass = results['mass_g']
|
||||
st.session_state.calc_volume = results['volume_ml']
|
||||
print(f"计算结果: {results}")
|
||||
st.rerun()
|
||||
else:
|
||||
st.warning("无分子量数据，无法进行计算")
|
||||
|
||||
else:
|
||||
# 显示使用说明
|
||||
st.info("👈 请在左侧输入化合物信息开始查询")
|
||||
|
||||
st.markdown("""
|
||||
### 🔍 使用说明
|
||||
|
||||
1. **选择搜索类型**:
|
||||
- 名称: 输入化合物的常用名称或IUPAC名称
|
||||
- 化学式: 输入分子式 (如 C2H6O)
|
||||
- SMILES: 输入SMILES字符串 (如 CCO)
|
||||
|
||||
2. **输入查询条件**: 在输入框中输入相应的查询词
|
||||
|
||||
3. **点击搜索**: 系统将从PubChem数据库中查询匹配的化合物
|
||||
|
||||
4. **查看结果**:
|
||||
- 基本信息包括名称、化学式、分子量和2D结构图
|
||||
- 密度和熔沸点信息可在展开区域查看
|
||||
- 计算器可帮助您计算用量、质量和体积的关系
|
||||
|
||||
### 📝 示例查询
|
||||
- **名称**: ethanol, water, glucose
|
||||
- **化学式**: C2H6O, H2O, C6H12O6
|
||||
- **SMILES**: CCO, O, C(C1C(C(C(C(O1)O)O)O)O)O
|
||||
""")
|
||||
|
||||
|
||||
def main():
|
||||
st.set_page_config(
|
||||
page_title="PubChem化合物查询工具",
|
||||
page_icon="🧪",
|
||||
layout="wide"
|
||||
)
|
||||
|
||||
# 侧边栏导航
|
||||
with st.sidebar:
|
||||
st.title("🧪 化学工具")
|
||||
page = st.radio(
|
||||
"选择功能页面",
|
||||
["化合物查询", "反应表格"],
|
||||
index=0
|
||||
)
|
||||
|
||||
# 根据选择显示不同页面
|
||||
if page == "化合物查询":
|
||||
compound_search_page()
|
||||
elif page == "反应表格":
|
||||
reaction_table_page()
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
Reference in New Issue
Block a user