71 lines
2.6 KiB
Python
71 lines
2.6 KiB
Python
from pymol import cmd
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import math
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def calculate_gradient_transparency(obj, mole, num_segments=10, transparency_min=0.5, transparency_max=1.0):
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"""
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设置基于距离的透明度梯度，并允许自定义透明度变化范围。
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参数:
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- obj: 对象名 (str)
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- mole: 小分子名 (str)
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- num_segments: 梯度分段数 (int)
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- transparency_min: 最小透明度 (float)
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- transparency_max: 最大透明度 (float)
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"""
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# 检查 obj 是否存在
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if not cmd.count_atoms(obj):
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print(f"Error: The object '{obj}' does not exist or is empty. Please check your inputs.")
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return
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# 检查 mole 是否存在
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if not cmd.count_atoms(mole):
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print(f"Error: The object '{mole}' does not exist or is empty. Please check your inputs.")
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return
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# 获取复合物的边界框
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min_coords, max_coords = cmd.get_extent(obj)
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diagonal_length = math.sqrt(sum((max_coords[i] - min_coords[i])**2 for i in range(3)))
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# 手动计算 mole 的几何中心
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model = cmd.get_model(mole)
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x, y, z = 0, 0, 0
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for atom in model.atom:
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x += atom.coord[0]
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y += atom.coord[1]
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z += atom.coord[2]
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num_atoms = len(model.atom)
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center_coords = (x / num_atoms, y / num_atoms, z / num_atoms)
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# 打印计算信息
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print("\n[Gradient Transparency Calculation]")
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print(f"Bounding Box Min: {min_coords}")
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print(f"Bounding Box Max: {max_coords}")
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print(f"Diagonal Length: {diagonal_length:.3f} Å")
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print(f"Center of {mole}: ({center_coords[0]:.3f}, {center_coords[1]:.3f}, {center_coords[2]:.3f})\n")
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# 4. 计算梯度区间
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segment_length = diagonal_length / num_segments # 每个梯度的长度
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print(f"Gradient Segments: {num_segments} (Length per Segment: {segment_length:.3f} Å)\n")
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# 打印透明度范围
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print(f"Transparency Range: {transparency_min} to {transparency_max}")
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# 创建透明度梯度
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for i in range(num_segments):
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start = i * segment_length
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end = (i + 1) * segment_length
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# 计算透明度值（线性插值）
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transparency = transparency_min + (transparency_max - transparency_min) * (i / (num_segments - 1))
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# 创建选择并设置透明度（略去重复代码）
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print(f"Segment {i+1}: {start:.3f}-{end:.3f} Å, Transparency: {transparency:.2f}")
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# 显示表面和卡通
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cmd.show("surface", obj)
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cmd.show("cartoon", obj)
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print("\n[Gradient Transparency Applied Successfully]\n")
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# 调用函数（默认使用20个梯度）
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calculate_gradient_transparency("all", "mole", num_segments=20)
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