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pymol_anime.py

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+from loguru import logger
+from pymol import cmd
+import subprocess
+from pathlib import Path
+
+# 删除当前目录下的*.mp4和*.png文件
+for file_path in Path('.').glob('*.mp4'):
+    file_path.unlink()
+
+for file_path in Path('.').glob('*.png'):
+    file_path.unlink()
+
+# 设置日志文件
+logger.add("pymol_animation.log")
+cmd.log_open('pymol_animation_cmd.log')
+# 最高渲染质量
+cmd.util.performance(0)
+cmd.rebuild()
+# 初始化并加载4i24结构
+cmd.reinitialize('everything')
+cmd.fetch('4i24')
+cmd.copy('4i24_mutated', '4i24') # 复制4i24到4i24_mutated
+# 假设protgrey和colorp.color_mole是你自定义的函数
+protgrey('4i24')
+protgrey('4i24_mutated')
+colorp.color_mole(obj='hetatm')
+cmd.hide('everything', '4i24_mutated')
+i = '4i24_mutated' # object
+j = 'A' # chain
+k = '797' # site
+mutate_site = f"/{i}//{j}/{k}"
+mutation_type = 'GLY'
+# 对4i24_mutated进行突变
+cmd.select('mut_res', mutate_site)
+cmd.wizard("mutagenesis")
+cmd.refresh_wizard()
+cmd.get_wizard().set_mode(mutation_type)
+cmd.get_wizard().do_select(mutate_site)
+cmd.get_wizard().apply()
+cmd.set_wizard("done")
+cmd.show('sticks', mutate_site)
+cmd.hide('everything', '4i24_mutated')
+
+# 先打关键帧然后创建视频
+
+# 创建第一个关键帧
+selection1 = "/4i24//A/797"
+cmd.scene('scene1', 'store')
+cmd.orient(selection1)
+cmd.show('sticks', selection1)
+
+
+# 创建第二个关键帧
+selection2 = "/4i24//A/1C9"
+cmd.select("both_residues", f"{selection1} or {selection2}")
+cmd.orient("both_residues")
+cmd.scene('scene2', 'store')
+
+# 设置动画和mview
+cmd.mset("1 x900")  # 创建一个总共1200帧的动画框架，每秒120帧共计10秒
+# 第一个关键帧: 1帧
+cmd.mview(action='store', first=1, scene='scene1') 
+
+# 第二个关键帧: 300帧
+cmd.mview(action='store', first=300, scene='scene2') 
+
+# 插值以平滑过渡
+cmd.mview('interpolate', first=1, last=300)
+
+residue_to_show = "/4i24//A/797"  # 用你想显示的残基替换
+cmd.mdo(360, f"show lines, {residue_to_show}; label {residue_to_show}/n, f'res {residue_to_show}(CYS)'")
+
+# 隐藏4i24对象: 600帧
+cmd.mdo(600, "hide everything, 4i24")
+
+# 显示4i24_mutated对象: 610帧
+cmd.mdo(610, "show cartoon, 4i24_mutated")
+
+# 显示突变残基: 620帧
+cmd.mdo(620, "show sticks, /4i24_mutated//A/797")
+
+# 为残基添加标签: 630帧
+residue_to_show = "/4i24_mutated//A/797"
+cmd.mdo(630, f"show lines, {residue_to_show}; label {residue_to_show}/n, f'res {residue_to_show}(GLY)'")
+
+# 插值以平滑过渡
+cmd.mview('interpolate', first=300, last=900)
+
+# 设置viewport尺寸为1080P（1920x1080像素）
+cmd.viewport(1920, 1080)
+cmd.mplay() # 播放动画
+
+# 光线追踪和保存每一帧
+# for frame in range(1, 901):  
+#     cmd.frame(frame)
+#     logger.info(f"Rendering frame {frame}")  
+#     cmd.refresh()
+#     cmd.ray(width=1920, height=1080)
+#     cmd.png(f"frame_transition_{frame:04d}.png")
+
+# 使用ffmpeg合成视频
+# subprocess.run([
+#     'ffmpeg', 
+#     '-framerate', '120',  # 120帧/秒
+#     '-i', 'frame_transition_%04d.png', 
+#     '-c:v', 'libx264', 
+#     '-pix_fmt', 'yuv420p', 
+#     'transition_video.mp4'
+# ])
+
+
+# ffmpeg -framerate 120 -i frame_transition_%04d.png -c:v libx264 -pix_fmt yuv420p transition_video.mp4