#!/usr/bin/env python
# -*- encoding: utf-8 -*-
'''
@file        :pymol_color_plugin.py
@Description:       :pymol配色方案
@Date     :2023/8/29 10:52:25
@Author      :hotwa
@version      :1.0
'''


from pymol import cmd
from pathlib import Path
from dataclasses import dataclass
from json import dumps
from Bio.Data import IUPACData
from Bio.SeqUtils import seq3
from collections import defaultdict

STANDARD_AMINO_ACIDS_1 = set(IUPACData.protein_letters)
STANDARD_AMINO_ACIDS_3 = set([seq3(i).upper() for i in STANDARD_AMINO_ACIDS_1])


def bejson(d:dict(help='need to beauty json')) -> dict:
    return dumps(d,indent=4,ensure_ascii=False)

@dataclass
class pymolbase():
    file: Path

    def __post_init__(self):
        cmd.reinitialize('everything')
        cmd.load(filename=self.file.as_posix())
        PDBs = cmd.get_names()
        if len(PDBs) == 1:
            PDB = PDBs[0]
        else:
            raise ValueError(f'this pdb have more than one object! PDBs:{PDBs}')
        self.CAindex = cmd.identify(f"{PDB} and name CA") # get CA index
        self.pdbstrList = [cmd.get_pdbstr("%s and id %s" % (PDB, CAid)).splitlines() for CAid in CAindex]
        self.ProtChainResiList = [[PDB, i[0][21], i[0][22:26].strip()] for i in pdbstrList] # get pdb chain line string
        resn_hetatm = self.get_resn('hetatm')

    def mutate(self, site:str, chain:str, mutation_type: str):
        '''
        mutation_type:ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL
        '''
        for i, j, k in self.ProtChainResiList:
            if int(k) == int(site) and j == str(chain):
                cmd.wizard("mutagenesis")
                cmd.refresh_wizard()
                cmd.get_wizard().set_mode(mutation_type)
                selection = f"/{i}//{j}/{k}"
                cmd.get_wizard().do_select(selection)
                cmd.get_wizard().apply()
            cmd.set_wizard("done")

    def add_polar_hydrogen(self, pymol_obj='sele'):
        '''
        add polar hydrogen
        '''
        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

    def save(self, file_name: Path, selection: str):
        cmd.save(file_name.as_posix(), f"{selection}")

    # def get_resn(self, name:str = 'all'):
    #     resn_list = []
    #     if name == 'protein':
    #         cmd.iterate(f"all and not hetatm", expression=lambda atom: resn_list.append(atom.resn))
    #         return tuple(set(resn_list))
    #     else:
    #         cmd.iterate(selection=name, expression=lambda atom: resn_list.append(atom.resn))
    #     return tuple(set(resn_list))   

    def get_resn(self, name:str = 'all'): # ! not test
        resn_dict = defaultdict(set)
        
        def collect_resn(atom):
            category = 'protein' if atom.chain and not atom.hetatm else 'small_molecule'
            resn_dict[category].add(atom.resn)

        cmd.iterate(name, expression=collect_resn)
        
        protein_resns = resn_dict.get('protein', set())
        small_mol_resns = resn_dict.get('small_molecule', set())
        
        standard_aa = protein_resns.intersection(STANDARD_AMINO_ACIDS_3)
        non_standard_aa = protein_resns - STANDARD_AMINO_ACIDS_3

        return {
            'small_molecules': list(small_mol_resns),
            'protein_resns': list(protein_resns),
            'standard_aa': list(standard_aa),
            'non_standard_aa': list(non_standard_aa)
        }

class colorp(pymolbase):
    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 CL")
        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(selection, grey=True):
        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(selection='all'):
    method.remove()
    method.optimisation(selection)
    
# 观察小分子
# 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)
# 选择所有核酸（DNA 或 RNA）
# select nucleic_acids, polymer.nucleic
# # 选择所有蛋白质
# select proteins, polymer.protein
# # 锁定到链
# select chainA_protein, polymer.protein and chain A 
## pymol 编辑模式
#选择mouse，3 botton edit 模式，需要在3 botton view 模式下先选择对象。
#按住shift + 左键进行旋转
#按住shift + 中键进行平移
cmd.extend('colorp',colorp)
cmd.extend('method',method)

if __name__ == '__main__':
    PDB = '4i24'
    cmd.reinitialize('everything')
    cmd.fetch('4i24')
    protgrey('4i24')
    colorp.color_mole(obj='hetatm')
    # 设置动画帧数
    # cmd.mset("1 x60 61 x60")  # 60帧展示初始结构，第61帧用于突变，再60帧展示突变后结构

    # 保存第1帧
    cmd.scene('frame1', 'store')
    cmd.mview('store', state=1, scene='frame1')

    # 执行残基突变。这里以将位于链A和编号为797的残基突变为ALA为例。
    selection1 = "/4i24//A/797"
    selection2 = "/4i24//A/1C9"
    cmd.select("both_residues", f"{selection1} or {selection2}")
    cmd.orient("both_residues")
    cmd.show('sticks', selection1)
    # 保存第2帧
    cmd.scene('frame60', 'store')
    cmd.mview('store', state=60, scene='frame60')
    # 关闭电影模式
    cmd.mstop()  # 停止电影播放
    cmd.mdelete()  # 删除所有电影帧
    cmd.wizard("mutagenesis")
    cmd.refresh_wizard()
    cmd.get_wizard().set_mode("GLY")
    cmd.get_wizard().do_select(selection1)
    # 保存第3帧
    cmd.scene('frame120', 'store')
    cmd.mview('store', state=120, scene='frame120')
    cmd.get_wizard().apply()
    cmd.set_wizard()
    # 保存第4帧
    cmd.scene('frame180', 'store')
    cmd.mview('store', state=180, scene='frame180')

    cmd.mpng('frame_prefix_', 1, 4)