重构分子属性分析流程并更新目录结构

1. 目录结构调整：
   - 创建scripts目录统一存放分析脚本
   - 保持数据文件在原有目录结构中
   - 生成的CSV文件和PNG图表文件也放在scripts目录下

2. 功能改进：
   - 更新calculate_qed_values.py脚本，添加对参考分子SDF文件的处理
   - 修改analyze_qed_mw_distribution.py脚本，统一使用SDF文件stem名称作为参考分子标识符
   - 改进Vina得分提取逻辑，支持从SDF文件中提取所有构象的得分
   - 完善KDE分布图绘制，确保参考分子在所有图表中显示统一的名称

3. 文档更新：
   - 更新README.md中的目录结构说明
   - 更新命令行和API使用示例
   - 添加详细的使用说明和示例

4. 示例代码：
   - 更新example_api_usage.py以适应新的目录结构和API调用方式

scripts/example_api_usage.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+Example usage of the analyze_qed_mw_distribution API
+"""
+
+import sys
+import os
+# Add the scripts directory to the path
+sys.path.append(os.path.dirname(os.path.abspath(__file__)))
+
+from analyze_qed_mw_distribution import main_api
+
+print("Running analysis examples...")
+
+# Example 1: Basic usage
+print("\nExample 1: Basic usage")
+main_api(['qed_values_fgbar.csv', 'qed_values_trpe.csv'], ['fgbar', 'trpe'])
+
+# Example 2: With custom reference scores
+print("\nExample 2: With custom reference scores")
+main_api(['qed_values_fgbar.csv', 'qed_values_trpe.csv'], ['fgbar', 'trpe'], 
+         reference_scores={'fgbar': {'9NY': -5.268}, 'trpe': {'0GA': -6.531}})
+
+# Example 3: With specific conformation rank
+print("\nExample 3: With specific conformation rank")
+main_api(['qed_values_fgbar.csv', 'qed_values_trpe.csv'], ['fgbar', 'trpe'], rank=0)
+
+# Example 4: With both custom reference scores and specific conformation rank
+print("\nExample 4: With both custom reference scores and specific conformation rank")
+main_api(['qed_values_fgbar.csv', 'qed_values_trpe.csv'], ['fgbar', 'trpe'], 
+         reference_scores={'fgbar': {'9NY': -5.268}, 'trpe': {'0GA': -6.531}}, rank=0)
+
+print("\nAnalysis complete! Check the generated PNG files.")