添加pymol快速美化脚本
在pymolrc.pml,使用：run /path/to/setup_pymol.py
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setup_pymol.py
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169
setup_pymol.py
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# setup_pymol.py - PyMOL 自定义设置脚本
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from pymol import cmd
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def setup_rendering(bg_color='white', transparency=0.5, ray_shadow=False):
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"""设置 PyMOL 的背景、透明度和渲染优化"""
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cmd.bg_color(bg_color)
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if ray_shadow:
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cmd.set('ray_shadows', 'on')
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cmd.set('ray_shadow', 0.2)
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else:
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cmd.set('ray_shadows', 'off')
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cmd.set('ray_shadow', 0)
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cmd.set('transparency_mode', 2)
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cmd.set('transparency', transparency)
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cmd.set('surface_quality', 1)
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# 移除了 surface_color_by_atom，因为某些版本不支持
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# 使用 color 命令可以达到类似效果
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print(f"✓ 渲染设置完成: 背景={bg_color}, 透明度={transparency}, 阴影={'开' if ray_shadow else '关'}")
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def clean_structure(remove_water=True, remove_metals=True, remove_ions=True):
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"""
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清理结构中的水分子、金属离子和其他离子
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参数:
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remove_water (bool): 是否删除水分子，默认 True
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remove_metals (bool): 是否删除金属离子，默认 True
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remove_ions (bool): 是否删除其他常见离子，默认 True
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"""
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removed_items = []
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# 1. 删除水分子
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if remove_water:
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water_count = cmd.count_atoms('resn HOH+WAT+H2O+DOD+D2O')
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if water_count > 0:
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cmd.remove('resn HOH+WAT+H2O+DOD+D2O')
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removed_items.append(f'水分子 ({water_count} 个原子)')
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# 2. 删除常见金属离子
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if remove_metals:
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metals = [
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'NA', 'K', 'MG', 'CA', 'ZN', 'FE', 'MN', 'CU', 'NI', 'CO',
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'CD', 'HG', 'PB', 'AG', 'AU', 'PT', 'CR', 'MO', 'W', 'V'
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]
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metal_selection = '+'.join(metals)
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metal_count = cmd.count_atoms(f'resn {metal_selection}')
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if metal_count > 0:
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cmd.remove(f'resn {metal_selection}')
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removed_items.append(f'金属离子 ({metal_count} 个原子)')
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# 3. 删除其他常见离子（氯离子、硫酸根等）
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if remove_ions:
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ions = ['CL', 'BR', 'I', 'F', 'SO4', 'PO4', 'NO3', 'NH4']
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ion_selection = '+'.join(ions)
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ion_count = cmd.count_atoms(f'resn {ion_selection}')
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if ion_count > 0:
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cmd.remove(f'resn {ion_selection}')
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removed_items.append(f'其他离子 ({ion_count} 个原子)')
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if removed_items:
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print("✓ 结构清理完成:")
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for item in removed_items:
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print(f" - 已删除 {item}")
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else:
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print("✓ 未发现需要清理的分子")
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def create_colored_objects(protein_color='orange', nucleic_color='white', ligand_color='red'):
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"""创建蛋白质、核酸和小分子对象，并应用指定颜色"""
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if len(cmd.get_object_list()) == 0:
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print("⚠ 警告: 未检测到已加载的结构，请先加载 PDB 文件")
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return
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obj_created = []
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# 1. 创建蛋白质对象
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if cmd.count_atoms('polymer.protein') > 0:
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cmd.create('Protein_obj', 'polymer.protein')
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cmd.color(protein_color, 'Protein_obj')
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cmd.show('surface', 'Protein_obj')
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obj_created.append(f'Protein_obj ({protein_color}, {cmd.count_atoms("Protein_obj")} 原子)')
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# 2. 创建核酸对象
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if cmd.count_atoms('polymer.nucleic') > 0:
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cmd.create('Nucleic_obj', 'polymer.nucleic')
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cmd.color(nucleic_color, 'Nucleic_obj')
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cmd.show('surface', 'Nucleic_obj')
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obj_created.append(f'Nucleic_obj ({nucleic_color}, {cmd.count_atoms("Nucleic_obj")} 原子)')
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# 3. 创建小分子对象（排除水分子和离子）
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ligand_selection = 'organic and not (resn HOH+WAT+H2O+DOD+D2O)'
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if cmd.count_atoms(ligand_selection) > 0:
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cmd.create('Ligand_obj', ligand_selection)
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cmd.color(ligand_color, 'Ligand_obj')
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cmd.show('surface', 'Ligand_obj')
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obj_created.append(f'Ligand_obj ({ligand_color}, {cmd.count_atoms("Ligand_obj")} 原子)')
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# 缩放到所有对象
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cmd.zoom('all')
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if obj_created:
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print("✓ 对象创建完成:")
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for obj in obj_created:
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print(f" - {obj}")
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else:
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print("⚠ 未创建任何对象，请检查结构类型")
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def quick_setup(bg_color='white', transparency=0.5,
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protein_color='orange', nucleic_color='white', ligand_color='red',
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clean=True):
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"""
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一键完成所有设置：清理结构 + 渲染优化 + 对象创建与着色
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参数:
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bg_color (str): 背景颜色
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transparency (float): 透明度 (0-1)
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protein_color (str): 蛋白质颜色
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nucleic_color (str): 核酸颜色
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ligand_color (str): 小分子颜色
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clean (bool): 是否清理水分子和离子，默认 True
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使用示例:
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quick_setup() # 默认设置+清理
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quick_setup(clean=False) # 不清理
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quick_setup('black', 0.3, 'cyan', 'yellow', 'magenta')
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"""
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print("\n" + "="*60)
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print("开始 PyMOL 快速设置...")
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print("="*60)
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# 1. 清理结构（如果启用）
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if clean:
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clean_structure()
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# 2. 设置渲染
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setup_rendering(bg_color, transparency)
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# 3. 创建并着色对象
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create_colored_objects(protein_color, nucleic_color, ligand_color)
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print("\n" + "="*60)
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print("✓ PyMOL 快速设置完成！")
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print("="*60 + "\n")
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# 注册函数到 PyMOL 的全局命名空间
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cmd.extend('setup_rendering', setup_rendering)
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cmd.extend('clean_structure', clean_structure)
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cmd.extend('create_colored_objects', create_colored_objects)
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cmd.extend('quick_setup', quick_setup)
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print("\n" + "="*60)
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print("PyMOL 自定义函数已加载")
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print("\n可用命令:")
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print(" setup_rendering - 设置背景和渲染")
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print(" clean_structure - 清理水分子和离子")
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print(" create_colored_objects - 创建并着色对象")
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print(" quick_setup - 一键完成所有设置")
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print("\n使用示例:")
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print(" quick_setup() # 默认设置（包含清理）")
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print(" quick_setup(clean=False) # 不清理水和离子")
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print(" clean_structure() # 单独清理")
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print("="*60 + "\n")
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