first version

script/pymol_color_plugin.py

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+#!/usr/bin/env python
+# -*- encoding: utf-8 -*-
+'''
+@file        :pymol_color_plugin.py
+@Description:       :pymol配色方案
+@Date     :2023/6/1 10:52:25
+@Author      :hotwa
+@version      :1.0
+'''
+
+
+from pymol import cmd
+from pathlib import Path
+
+class colorp():
+    color1 = (('color1', '[186,182,217]'), 'purple')
+    color2 = (('color2', '[233,195,153]'), 'yellow')
+    color3 = (('color3', '[43,113,216]'), 'blue-N')
+    color4 = (('color4', '[206,155,198]'), 'purple')
+    color5 = (('color5', '[251,187,62]'), 'orange')
+    color6 = (('color6', '[245,157,158]'), 'red')
+    color7 = (('color7', '[133,188,135]'), 'green')
+    color8 = (('color8', '[30,230,30]'),'green-CL') # Cl卤素配色
+    color9 = (('color9', '[141,215,247]'),'blue-C') # C配色
+    color10 = (('color10', '[0,132,55]'),'green-F') # F卤素配色
+    grey1 = ('grey1','[224,224,224]')
+    colors = (color1, color2, color3, color4, color5, color6, color7, color8, color9, color10)
+
+    def __init__(self, path, id):
+        self.id = id.lower()
+        cmd.reinitialize()
+        p = Path(path)
+        if p.is_dir():
+            file = p.joinpath(f"{id}.pdb")
+        else:
+            raise ValueError('path params error')
+        cmd.load(file,id)
+
+    def pretty(self):
+        cmd.remove('solvent metals') # 移除金属离子和溶剂
+        cmd.remove("resn SO4 or resn PO4 or resn NA,CL,GOL")
+        cmd.remove('not polymer') # 删除所有不是多聚物（通常指蛋白质或核酸链）的原子或分子。
+        cmd.pretty(selection=self.id)
+
+    @staticmethod
+    def defcolor():
+        # 定义常用配色
+        color_gennerate = map(lambda x:x[0],colorp.colors)
+        list(map(lambda x:cmd.set_color(*x),color_gennerate))
+        # 定义灰度配色
+        cmd.set_color(*colorp.grey1)
+
+    @staticmethod
+    def grey(obj='sele',opt=True):
+        colorp.defcolor()
+        if opt: method.optimisation() # 优化
+        # 对某个对象进行灰化
+        cmd.color('grey1',f'{obj}')
+
+    @staticmethod
+    def color_mole(obj='hetatm'):
+        # color blue,sele in name c*
+        colorp.defcolor()
+        cmd.color('color9',f'{obj} in name c*')
+        cmd.color('color6',f'{obj} in name o*')
+        cmd.color('color5',f'{obj} in name s*')
+        cmd.color('color3',f'{obj} in name n*')
+        cmd.color('color8',f'{obj} in name cl*')
+        cmd.color('color10',f'{obj} in name f*')
+    
+    @staticmethod
+    def pretty(obj = None):
+        if not obj: obj = cmd.get_names()[0] 
+        cmd.remove('solvent metals') # 移除金属离子和溶剂
+        cmd.pretty(selection=obj)
+        
+
+class font():
+    font_size = 28 # 单位就是正常的px。你也可以用负值，则单位是Å
+
+class mole():
+    stick_radius=0.10
+
+class atom():
+    size = 0.28
+
+class method():
+
+    @staticmethod
+    def optimisation(grey=True, selection='sele'):
+        colorp.defcolor()
+        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)
+
+    @staticmethod
+    def remove():
+        cmd.remove('resn SO4') # SO4 remove
+        cmd.remove('solvent metals') # 移除金属离子和溶剂
+      
+def get_resn(name:str = 'all'):
+    resn_list = []
+    cmd.iterate(selection=name, expression=lambda atom: resn_list.append(atom.resn))
+    return tuple(set(resn_list))      
+
+
+def protgrey():
+    method.remove()
+    method.optimisation()
+    
+# 观察小分子
+# https://chatmol.org/qa/
+# protgrey()
+# colorp.color_mole('sele')
+# add label
+# label sele, "your label"
+# black background
+# set bg_rgb, [0, 0, 0]
+# define label
+# cmd.get_position("sele")
+# set label_position, [x,y,z]
+# cmd.h_add(pymol_obj) # add all hydrogens in this molecular
+# cmd.remove(f"{pymol_obj} & hydro & not nbr. (don.|acc.)") # remove no-polar-hydrogen
+# cmd.remove(f"sele & hydro") # 移除所有的H
+# cmd.set('cartoon_color','color8', 'obj')
+# cmd.hide("everything", "chain A and resn UHT and alt B") # 小分子隐藏B构象
+# cmd.label("chain A and resn UHT and alt A", "resn") # 添加标签
+#cmd.select('sele', f'resn {resn} and chain {chain}')
+#cmd.center('sele')
+#cmd.orient('sele')
+#obj_name = 'around_and_self'
+# cmd.create(obj_name, f'(resn {resn} and chain {chain}) around {distance}') # 不扩展残基
+# cmd.create(obj_name, f'byres (resn {resn} and chain {chain}) around {distance}') # 扩展残基
+# cmd.create(obj_name, f'(resn {resn} and chain {chain}) around {distance} or (resn {resn} and chain {chain})') # 选择resn的对象和resn对象周围3A的原子
+#cmd.create(obj_name, f'byres (resn {resn} and chain {chain}) around {distance} or (resn {resn} and chain {chain})') # 选择resn的对象和resn对象周围3A的原子扩展至残基的原子
+#cmd.hide('everything', 'all')
+#cmd.show('lines', obj_name)
+# cmd.remove('not polymer') #除非聚合物部分
+cmd.extend('colorp',colorp)
+cmd.extend('method',method)