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