143 lines
5.0 KiB
Python
143 lines
5.0 KiB
Python
#!/usr/bin/env python
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# -*- encoding: utf-8 -*-
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'''
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@file :pymol_color_plugin.py
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@Description: :pymol配色方案
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@Date :2023/6/1 10:52:25
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@Author :hotwa
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@version :1.0
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'''
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from pymol import cmd
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from pathlib import Path
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class colorp():
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color1 = (('color1', '[186,182,217]'), 'purple')
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color2 = (('color2', '[233,195,153]'), 'yellow')
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color3 = (('color3', '[43,113,216]'), 'blue-N')
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color4 = (('color4', '[206,155,198]'), 'purple')
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color5 = (('color5', '[251,187,62]'), 'orange')
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color6 = (('color6', '[245,157,158]'), 'red')
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color7 = (('color7', '[133,188,135]'), 'green')
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color8 = (('color8', '[30,230,30]'),'green-CL') # Cl卤素配色
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color9 = (('color9', '[141,215,247]'),'blue-C') # C配色
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color10 = (('color10', '[0,132,55]'),'green-F') # F卤素配色
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grey1 = ('grey1','[224,224,224]')
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colors = (color1, color2, color3, color4, color5, color6, color7, color8, color9, color10)
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def __init__(self, path, id):
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self.id = id.lower()
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cmd.reinitialize()
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p = Path(path)
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if p.is_dir():
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file = p.joinpath(f"{id}.pdb")
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else:
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raise ValueError('path params error')
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cmd.load(file,id)
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def pretty(self):
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cmd.remove('solvent metals') # 移除金属离子和溶剂
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cmd.remove("resn SO4 or resn PO4 or resn NA,CL,GOL")
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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。
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cmd.pretty(selection=self.id)
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@staticmethod
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def defcolor():
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# 定义常用配色
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color_gennerate = map(lambda x:x[0],colorp.colors)
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list(map(lambda x:cmd.set_color(*x),color_gennerate))
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# 定义灰度配色
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cmd.set_color(*colorp.grey1)
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@staticmethod
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def grey(obj='sele',opt=True):
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colorp.defcolor()
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if opt: method.optimisation() # 优化
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# 对某个对象进行灰化
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cmd.color('grey1',f'{obj}')
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@staticmethod
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def color_mole(obj='hetatm'):
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# color blue,sele in name c*
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colorp.defcolor()
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cmd.color('color9',f'{obj} in name c*')
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cmd.color('color6',f'{obj} in name o*')
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cmd.color('color5',f'{obj} in name s*')
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cmd.color('color3',f'{obj} in name n*')
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cmd.color('color8',f'{obj} in name cl*')
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cmd.color('color10',f'{obj} in name f*')
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@staticmethod
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def pretty(obj = None):
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if not obj: obj = cmd.get_names()[0]
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cmd.remove('solvent metals') # 移除金属离子和溶剂
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cmd.pretty(selection=obj)
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class font():
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font_size = 28 # 单位就是正常的px。你也可以用负值，则单位是Å
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class mole():
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stick_radius=0.10
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class atom():
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size = 0.28
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class method():
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@staticmethod
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def optimisation(grey=True, selection='sele'):
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colorp.defcolor()
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if grey: cmd.set('cartoon_color','grey1', selection=selection)
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cmd.set('stick_transparency','0.1', selection=selection)
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cmd.set("ray_shadows","off", selection=selection)
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cmd.set('cartoon_highlight_color', selection=selection)
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cmd.set('cartoon_fancy_helices', selection=selection)
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cmd.set('cartoon_transparency','0.5', selection=selection)
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@staticmethod
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def remove():
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cmd.remove('resn SO4') # SO4 remove
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cmd.remove('solvent metals') # 移除金属离子和溶剂
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def get_resn(name:str = 'all'):
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resn_list = []
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cmd.iterate(selection=name, expression=lambda atom: resn_list.append(atom.resn))
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return tuple(set(resn_list))
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def protgrey():
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method.remove()
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method.optimisation()
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# 观察小分子
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# https://chatmol.org/qa/
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# protgrey()
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# colorp.color_mole('sele')
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# add label
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# label sele, "your label"
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# black background
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# set bg_rgb, [0, 0, 0]
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# define label
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# cmd.get_position("sele")
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# set label_position, [x,y,z]
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# cmd.h_add(pymol_obj) # add all hydrogens in this molecular
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# cmd.remove(f"{pymol_obj} & hydro & not nbr. (don.|acc.)") # remove no-polar-hydrogen
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# cmd.remove(f"sele & hydro") # 移除所有的H
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# cmd.set('cartoon_color','color8', 'obj')
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# cmd.hide("everything", "chain A and resn UHT and alt B") # 小分子隐藏B构象
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# cmd.label("chain A and resn UHT and alt A", "resn") # 添加标签
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#cmd.select('sele', f'resn {resn} and chain {chain}')
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#cmd.center('sele')
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#cmd.orient('sele')
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#obj_name = 'around_and_self'
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# cmd.create(obj_name, f'(resn {resn} and chain {chain}) around {distance}') # 不扩展残基
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# cmd.create(obj_name, f'byres (resn {resn} and chain {chain}) around {distance}') # 扩展残基
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# 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
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#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
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#cmd.hide('everything', 'all')
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#cmd.show('lines', obj_name)
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# cmd.remove('not polymer') #除非聚合物部分
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cmd.extend('colorp',colorp)
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cmd.extend('method',method) |