升级 NUPACK 4.1 并支持混合材料设计

docs/绘图自动分割.txt

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+                                在ununtu上使用该命令安装draw_rna
+pip install matplotlib numpy draw_rna --upgrade -i https://pypi.tuna.tsinghua.edu.cn/simple
+
+-------------------------------打开原本步骤中lab中的记事本--------------------------
+# 依赖导入
+from nupack import *
+from draw_rna.ipynb_draw import draw_struct
+import os
+import matplotlib.pyplot as plt
+
+# 开启显示（恢复正常绘图展示）
+plt.ion()
+
+# ======================================
+# 仅保留两个核心函数，完全用 draw_rna
+# ======================================
+def get_mfe_structure(complex_name: str, nupack_result, strands: list):
+    """获取复合物MFE结构，支持同源二聚体 Y1+Y1"""
+    strand_names = complex_name.strip('()').split('+')
+    strand_map = {s.name: s for s in strands}
+    strand_objs = [strand_map[name] for name in strand_names]
+    complex_obj = Complex(strand_objs)
+    return str(nupack_result[complex_obj].mfe[0].structure)
+
+def draw_complex(complex_name: str, nupack_result, strands: list, output_folder="./"):
+    """draw_rna绘图：无页面显示，直接保存图片到目标路径"""
+    os.makedirs(output_folder, exist_ok=True)
+
+    # 获取结构和序列（完全不变）
+    struct = get_mfe_structure(complex_name, nupack_result, strands)
+    strand_names = complex_name.strip('()').split('+')
+    strand_map = {s.name: s for s in strands}
+    seq = " ".join([str(strand_map[name]) for name in strand_names])   # 序列用空格分隔
+    draw_structure = struct.replace('+', ' ')                            # 结构用空格分隔
+    # 设置全局字体大小，可以根据需要调整数字 (例如 14, 18, 20)
+    plt.rcParams['font.size'] = 12
+    # ---------- 修正点：显式创建画布并传递给 draw_struct ----------
+    fig, ax = plt.subplots(figsize=(15, 15))   # 可调尺寸，保证图形清晰
+    draw_struct(seq, draw_structure, ax=ax)   # 在指定 ax 上绘图
+
+    # 保存并关闭
+    save_name = complex_name.strip('()').replace('+', '_') + '.png'
+    save_path = os.path.join(output_folder, save_name)
+    plt.savefig(save_path, dpi=300, bbox_inches='tight')
+
+    print(f"\n✅ 图片已保存至：{save_path}")
+    print(f"MFE 结构：{struct}")
+def draw_all_complexes(nupack_result, strands: list, output_folder="./"):
+    print("\n========== 开始批量绘制所有复合物 ==========")
+    
+    # 过滤出 Complex 对象
+    complex_objs = [obj for obj in nupack_result.keys() if not isinstance(obj, Tube)]
+    total = len(complex_objs)
+    success_count = 0
+    
+    for idx, complex_obj in enumerate(complex_objs, 1):
+        complex_name = complex_obj.name   # ✅ 修正点
+        try:
+            draw_complex(complex_name, nupack_result, strands, output_folder)
+            success_count += 1
+            print(f"进度：{idx}/{total} 完成")
+        except Exception as e:
+            print(f"❌ 绘制复合物 {complex_name} 失败: {e}")
+    
+    print("\n========== 所有复合物绘制完成 ==========")
+    print(f"✅ 批量绘制完成！成功：{success_count} / 总计：{total}")
+    print(f"📁 图片保存在：{os.path.abspath(output_folder)}")
+--------------------------------  nupack计算--------------------------------------
+
+model1 = Model(material='dna', celsius=37,sodium=0.1, magnesium=0.02)
+Y1 = Strand('CGTTAACGCAGTGAGGACGGTAGTTTGTCGTTCCATCGCACC', name='Y1')
+Y2 = Strand('CGTTAACGGGTGCGATGGAACGACTTTCGACAGGCCTGGTGTAATTTCACCCATGTTAGTCGA', name='Y2')
+Y3 = Strand('ATACGGAAAATGGAGATAGGAAGAGTACAATGTCAGCGATAAATTCCGTATACGACACCAGGCCTGTCGATTACTACCGTCCTCACTG', name='Y3')
+
+t1 = Tube({Y1: 1e-8, Y2: 1e-8, Y3:1e-8 },complexes=SetSpec(max_size=4), name='Tube 1')
+
+my_result = tube_analysis(tubes=[t1], model=model1,
+    compute=['pfunc', 'pairs', 'mfe', 'sample', 'subopt'],
+    options={'num_sample': 1, 'energy_gap': 0.5})
+print(my_result)
+
+--------------------------- --------------- 单复合物绘图------------------------------
+target = '(Y1+Y1+Y2+Y3)'   # 替换为你的目标复合物名称
+all_strands = [Y1, Y2, Y3]  # 所有链的列表
+
+# 1. 获取并打印MFE结构
+mfe_struct = get_mfe_structure(target, my_result, all_strands)
+#print("MFE结构：", mfe_struct)
+
+# 2. 绘制二级结构
+draw_complex(target, my_result, all_strands, output_folder="/home/zsy")
+--------------------------------------------批量绘图-----------------------------------
+strands_list = [Y1, Y2, Y3]
+draw_all_complexes(my_result, strands_list, output_folder="/home/zsy/jihe")