first version

plugin/method.py

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+#!/usr/bin/env python
+# -*- encoding: utf-8 -*-
+'''
+@file               :method.py
+@Description:       :pymol中一些常用到的一些方法
+@Date               :2023/09/24 13:28:30
+@Author             :lyzeng
+@Email              :pylyzeng@gmail.com
+@version            :1.0
+'''
+import sys
+from pathlib import Path
+here = Path(__file__).absolute().parent
+sys.path.append(here.as_posix())
+from plugin.cmd_singleton import cmd
+from pymol.preset import ion_sele,lig_sele,solv_sele
+
+def color_mole(selection='hetatm'):
+    cmd.color('color9',f'{selection} in name c*')
+    cmd.color('color6',f'{selection} in name o*')
+    cmd.color('color5',f'{selection} in name s*')
+    cmd.color('color3',f'{selection} in name n*')
+    cmd.color('color8',f'{selection} in name cl*')
+    cmd.color('color10',f'{selection} in name f*')
+
+def focus_ligand(selection: str = 'sele'):
+    '''
+    watch ligand and protein structure
+    '''
+    cmd.remove(solv_sele) # 移除金属离子和溶剂
+    cmd.remove("resn SO4 or resn PO4 or resn CL")
+    cmd.pretty(selection)
+
+def grey(selection='sele',opt=True):
+    if opt: optimisation(selection) # 优化
+    cmd.color('grey1',f'{selection}')# 对某个对象进行灰化
+
+def optimisation(selection, grey=True):
+    if grey: cmd.set('cartoon_color','grey1', selection=selection)
+    cmd.set('stick_transparency','0.1', selection=selection)
+    cmd.set("ray_shadows","off", selection=selection)
+    cmd.set('cartoon_highlight_color', selection=selection)
+    cmd.set('cartoon_fancy_helices', selection=selection)
+    cmd.set('cartoon_transparency','0.5', selection=selection)