def create_extract_scores(self):
extract_scores_labelframe = Labelframe(self.root, text="提取分数")
extract_scores_labelframe.place(x=10, y=155, width=570, height=50)
choose_score = SButton(root=extract_scores_labelframe,
text="选择单个文件",
x=10,
y=0)
create_tooltip(choose_score.button, "选择单个打分结果pdbqt文件")
choose_scores_dir = SButton(root=extract_scores_labelframe,
text="选择文件夹",
x=100,
y=0)
create_tooltip(choose_scores_dir.button, "选择多个打分结果所在的文件夹")
self.choose_scores_entry = SEntry(
root=extract_scores_labelframe,
textvariable=StringVar(),
text=Configer.get_para("choose_score_file"),
x=190,
y=4,
width=260)
create_tooltip(self.choose_scores_entry.entry, "选择的文件/文件夹")
choose_score.bind_open_file(self.choose_scores_entry.textvariable,
title="选择对接结果pdbqt文件",
file_type="pdbqt")
choose_scores_dir.bind_open_dir(self.choose_scores_entry.textvariable,
title="选择含有对接结果的文件夹")
extract_button = SButton(extract_scores_labelframe,
text="提取分数",
x=460,
y=0,
width=90)
create_tooltip(extract_button.button, "提取分数结果。如果是单个文件直接显示窗口。"
"如果选择文件夹，则输出txt文件到选择的文件夹")
extract_button.button.bind("<Button-1>", self.extract_score)
def _choose_protein_frame(self):
choose_protein_labelframe = LabelFrame(self.root, text="选择受体")
choose_protein_labelframe.place(x=10, y=135, width=570, height=50)
choose_proteins = SButton(root=choose_protein_labelframe, text="选择受体", x=10, y=0)
create_tooltip(choose_proteins.button, "选择pdbqt格式的受体")
self.choose_proteins_entry = SEntry(root=choose_protein_labelframe, textvariable=StringVar(),
text=Configer.get_para("choose_complex_proteins"),
x=110, y=4, width=450)
create_tooltip(self.choose_proteins_entry.entry, "受体文件")
choose_proteins.bind_open_file(entry_text=self.choose_proteins_entry.textvariable,
title="选择蛋白受体", file_type="pdbqt")
def choose_obabel(self):
y = 50 # python路径
choose_obabel_path = SButton(self.top,
text="选择obabel.exe的路径",
x=10, y=y)
create_tooltip(choose_obabel_path.button, "选择obabel.exe文件")
self.choose_obabel_path_entry = SEntry(root=self.top,
textvariable=StringVar(),
text=Configer.get_para("obabel_path"),
x=150, y=y + 4, width=230)
create_tooltip(self.choose_obabel_path_entry.entry, "obabel.exe位置")
choose_obabel_path.bind_open_file(entry_text=self.choose_obabel_path_entry.textvariable,
title="选择obabel.exe",
file_type="exe", parent=self.top)
def choose_python(self):
y = 10
# python路径
choose_python_path = SButton(self.top,
text="选择ADT的python路径",
x=10, y=y)
create_tooltip(choose_python_path.button, "必须选择mgltools目录里面的python.exe文件！\n"
"比如：\nC:/mgltools/python.exe")
self.choose_python_path_entry = SEntry(root=self.top,
textvariable=StringVar(),
text=Configer.get_para("python_path"),
x=150, y=y + 4, width=230)
create_tooltip(self.choose_python_path_entry.entry, "ADT的python路径")
choose_python_path.bind_open_file(entry_text=self.choose_python_path_entry.textvariable,
title="选择ADT中的python.exe",
file_type="exe", parent=self.top)
def extract_from_file(self):
extract_from_file_labelframe = Labelframe(self.root, text="从文件提取配体")
extract_from_file_labelframe.place(x=10, y=210, width=570, height=85)
choose_file_button = SButton(extract_from_file_labelframe,
text="选择输入文件",
x=10,
y=0)
create_tooltip(choose_file_button.button, "选择输入的txt文件")
self.choose_output_entry = SEntry(extract_from_file_labelframe,
textvariable=StringVar(),
text=Configer.get_para("output_txt"),
x=100,
y=3,
width=450)
create_tooltip(self.choose_output_entry.entry, "选择的txt文件")
choose_file_button.bind_open_file(
entry_text=self.choose_output_entry.textvariable,
title="选择输入的txt文件",
file_type="txt")
choose_output_button = SButton(extract_from_file_labelframe,
text="选择提取目录",
x=10,
y=33)
create_tooltip(choose_output_button.button, "选择提取输出的目录")
self.choose_extract_folder_entry = SEntry(
extract_from_file_labelframe,
textvariable=StringVar(),
text=Configer.get_para("extract_folder"),
x=100,
y=33,
width=350)
create_tooltip(self.choose_extract_folder_entry.entry, "选择提取输出的目录")
choose_output_button.bind_open_dir(
entry_text=self.choose_extract_folder_entry.textvariable,
title="选择输出目录")
extract_button = SButton(extract_from_file_labelframe,
text="提取配体",
x=460,
y=30,
width=90)
create_tooltip(extract_button.button, "根据输入的文件提取配体")
extract_button.button.bind("<Button-1>", self.extract_file)
def _create_tools_frame(self):
tools_frame = LabelFrame(self.root, text="工具")
tools_frame.place(x=10, y=140, width=570, height=100)
# 读取配置文件
read_config_button = SButton(tools_frame, "读取配置文件", 10, 10)
create_tooltip(read_config_button.button, "必须选择config.txt文件！")
self.read_config_entry = SEntry(root=tools_frame,
textvariable=StringVar(),
text=Configer.get_para("read_config"),
x=100,
y=14,
width=360)
create_tooltip(self.read_config_entry.entry, "你选择的config.txt文件位置")
read_config_button.bind_open_file(
entry_text=self.read_config_entry.textvariable,
title="请选择config.txt文件",
file_type="txt")
read_button = SButton(tools_frame, "读取到参数", 470, 10)
create_tooltip(read_button.button, "读取到上方")
read_button.button.bind("<Button-1>", self.read_config)
# 自动生成盒子
choose_raw_ligand_button = SButton(tools_frame, "读取共晶配体", 10, 40)
create_tooltip(choose_raw_ligand_button.button, "必须选择共晶配体pdbqt文件！")
self.choose_raw_ligand_entry = SEntry(
root=tools_frame,
textvariable=StringVar(),
text=Configer.get_para("choose_raw_ligand"),
x=100,
y=44,
width=360)
choose_raw_ligand_button.bind_open_file(
entry_text=self.choose_raw_ligand_entry.textvariable,
title="请选择“共晶配体”PDBQT文件！",
file_type="pdbqt")
create_tooltip(self.choose_raw_ligand_entry.entry, "你选择的共晶配体pdbqt文件位置")
gen_box_button = SButton(tools_frame, "计算对接位点", 470, 40)
create_tooltip(gen_box_button.button, "自动计算对接位点，该对接位点为共晶配体的"
"最小外切正方体，结果仅供参考。")
gen_box_button.button.bind("<Button-1>", self.gen_box)
def create_all_config(self):
all_config_labelframe = LabelFrame(self.root, text="受体全局对接")
all_config_labelframe.place(x=10, y=10, width=570, height=85)
choose_ligand = SButton(all_config_labelframe, text="选择配体", x=10, y=0)
create_tooltip(choose_ligand.button, "选择参考配体pdbqt文件")
self.choose_ligand_entry = SEntry(
all_config_labelframe,
textvariable=StringVar(),
text=Configer.get_para("refer_ligand"),
x=100,
y=3,
width=450)
create_tooltip(self.choose_ligand_entry.entry, "选择的参考配体")
choose_ligand.bind_open_file(self.choose_ligand_entry.textvariable,
title="选择配体pdbqt文件",
file_type="pdbqt")
choose_receptor = SButton(all_config_labelframe,
text="选择受体",
x=10,
y=30)
create_tooltip(choose_receptor.button, "选择需要全局搜索的单/多个受体文件夹，具体请看帮助或者教程")
self.choose_receptor_entry = SEntry(
all_config_labelframe,
textvariable=StringVar(),
text=Configer.get_para("refer_receptor"),
x=100,
y=33,
width=350)
create_tooltip(self.choose_receptor_entry.entry, "选择的参考")
choose_receptor.bind_open_dir(
entry_text=self.choose_receptor_entry.textvariable,
title="选择单/多个受体所在文件夹")
generate_button = SButton(all_config_labelframe,
text="生成文件",
x=460,
y=30,
width=90)
create_tooltip(generate_button.button, "生成全局对接的多个config文件")
generate_button.button.bind("<Button-1>", self.generate_configs)
def create_prepared_receptor(self):
# 总框架
prepared_receptor_labelframe = LabelFrame(self.root, text="准备受体")
prepared_receptor_labelframe.place(x=LEFT_X,
y=130,
width=FULL_NOTEBOOK_WIDTH,
height=170)
# 第一排,选择受体
choose_raw_receptor_button = SButton(prepared_receptor_labelframe,
text="选择单个受体",
x=LEFT_X,
y=0)
create_tooltip(choose_raw_receptor_button.button, "选择要进行准备的单个pdb受体")
choose_raw_receptors_button = SButton(prepared_receptor_labelframe,
text="选择多个受体",
x=LEFT_X + 90,
y=0)
create_tooltip(choose_raw_receptors_button.button,
"选择要进行准备的包含多个pdb受体的文件夹")
self.choose_raw_receptor_entry = SEntry(
prepared_receptor_labelframe,
textvariable=StringVar(),
text=Configer.get_para("raw_receptor_path"),
x=190,
y=3,
width=270)
create_tooltip(self.choose_raw_receptor_entry.entry, "选择的受体")
# 绑定打开事件
choose_raw_receptor_button.bind_open_file(
entry_text=self.choose_raw_receptor_entry.textvariable,
title="选择受体pdb文件",
file_type="pdb")
choose_raw_receptors_button.bind_open_dir(
entry_text=self.choose_raw_receptor_entry.textvariable,
title="选择包含pdb受体文件的文件夹")
get_info_button = SButton(prepared_receptor_labelframe,
text="受体信息",
x=470,
y=0)
get_info_button.button.bind("<Button-1>", self.getinfo)
create_tooltip(get_info_button.button, "查看受体信息")
# 第二排，提取配体保存的路径
ligand_save_path_button = SButton(prepared_receptor_labelframe,
text="配体输出路径",
x=10,
y=30)
create_tooltip(ligand_save_path_button.button, "选择提取的配体要保存的位置")
self.ligand_save_path_entry = SEntry(
prepared_receptor_labelframe,
textvariable=StringVar(),
text=Configer.get_para("extract_ligand_path"),
x=100,
y=33,
width=360)
create_tooltip(self.ligand_save_path_entry.entry,
"提取的配体保存的目录，不存在将创建文件夹")
ligand_save_path_button.bind_open_dir(
entry_text=self.ligand_save_path_entry.textvariable,
title="选择要保存的路径")
save_ligand_button = SButton(prepared_receptor_labelframe,
text="提取配体",
x=470,
y=30)
save_ligand_button.button.bind("<Button-1>", self.extract_ligand)
create_tooltip(save_ligand_button.button, "提取受体中的配体")
# 第三排，准备受体
save_prepared_receptor_button = SButton(prepared_receptor_labelframe,
text="受体输出路径",
x=LEFT_X,
y=60)
create_tooltip(save_prepared_receptor_button.button, "选择准备后的受体保存路径")
self.choose_prepare_output_path = SEntry(
prepared_receptor_labelframe,
textvariable=StringVar(),
text=Configer.get_para("preped_path"),
x=100,
y=63,
width=360)
create_tooltip(self.choose_prepare_output_path.entry, "准备后的受体输出目录")
save_prepared_receptor_button.bind_open_dir(
self.choose_prepare_output_path.textvariable, title="选择输出目录")
prepare_receptor_button = SButton(prepared_receptor_labelframe,
text="准备受体",
x=470,
y=60)
prepare_receptor_button.button.bind("<Button-1>",
self.prepared_receptor)
create_tooltip(prepare_receptor_button.button, "开始准备受体")
# 第四排，准备选项
fourth_y = 90
SLabel(prepared_receptor_labelframe,
text="ADT参数",
x=LEFT_X,
y=fourth_y)
SLabel(prepared_receptor_labelframe, text="修复", x=100, y=fourth_y)
fix_text = ("bonds_hydrogens", "bonds", "hydrogens", "checkhydrogens",
"None")
self.fix_method = SCombbox(
root=prepared_receptor_labelframe,
textvariable=StringVar(),
values=fix_text,
default_value=Configer.get_para("fix_method"),
x=135,
y=fourth_y,
width=140)
create_tooltip(
self.fix_method.combobox, "使用ADT方法修复受体\n"
"bonds_hydrogens：修复键级和加氢\n"
"bonds：修复键级\n"
"hydrogens:加氢\n"
"checkhydrogens：没有氢的地方加氢\n"
"None:不进行修复")
self.preserve_charges = SCheckbutton(
prepared_receptor_labelframe,
text="保留电荷",
variable=StringVar(),
value=Configer.get_para("preserve_charges"),
x=290,
y=fourth_y)
create_tooltip(self.preserve_charges.checkbutton,
"勾选则保留输入电荷，不勾选添加gasteiger电荷")
SLabel(prepared_receptor_labelframe, text="|", x=380, y=fourth_y - 2)
self.is_fix_receptor = SCheckbutton(
prepared_receptor_labelframe,
text="Biopython功能",
variable=StringVar(),
value=Configer.get_para("fix_receptor"),
x=400,
y=fourth_y)
create_tooltip(
self.is_fix_receptor.checkbutton, "只针对单个受体。可以用来检测同源链，提取特定链，"
"修复受体(修复断链等)。"
"具体修复方法参见biopython官方文档")
# 第五排，清理格式
fifth_y = 120
SLabel(prepared_receptor_labelframe, text="受体处理", x=LEFT_X, y=fifth_y)
self.nphs = SCheckbutton(prepared_receptor_labelframe,
text="nphs",
variable=StringVar(),
value=Configer.get_para("nphs"),
x=LEFT_X + 90,
y=fifth_y)
create_tooltip(self.nphs.checkbutton, "合并非极性氢")
self.lps = SCheckbutton(prepared_receptor_labelframe,
text="lps",
variable=StringVar(),
value=Configer.get_para("lps"),
x=LEFT_X + 150,
y=fifth_y)
create_tooltip(self.lps.checkbutton, "合并电荷，去除孤对电子")
self.waters = self.waters = SCheckbutton(
prepared_receptor_labelframe,
text="waters",
variable=StringVar(),
value=Configer.get_para("waters"),
x=LEFT_X + 200,
y=fifth_y)
create_tooltip(self.waters.checkbutton, "去除水")
self.nonstdres = self.nonstdres = SCheckbutton(
prepared_receptor_labelframe,
text="nonstdres",
variable=StringVar(),
value=Configer.get_para("nonstdres"),
x=LEFT_X + 270,
y=fifth_y)
create_tooltip(self.nonstdres.checkbutton, "去除非标准氨基酸链(核酸等)")
def cal_rmsd(self, event):
self.windows = STopLevel(self.root,
win_x=570,
win_y=130,
title="计算RMSD").toplevel
# 参考配体
single_ligand_button = SButton(self.windows, text="选择参考配体", x=10, y=10)
create_tooltip(single_ligand_button.button, "选择一个参考配体，只支持xyz格式")
self.single_ligand_entry = SEntry(
self.windows,
textvariable=StringVar(),
text=Configer.get_para("single_ligand")
if self.single_ligand == "" else self.single_ligand,
x=100,
y=13,
width=450)
create_tooltip(self.single_ligand_entry.entry, "选择的参考配体")
single_ligand_button.bind_open_file(
entry_text=self.single_ligand_entry.textvariable,
title="选择参考配体",
file_type="xyz",
parent=self.windows)
# 比较配体
sec_ligand_button = SButton(self.windows, text="选择第二个配体", x=10, y=50)
create_tooltip(sec_ligand_button.button, "选择需要比较的单个配体")
sec_ligands_button = SButton(self.windows, text="选择文件夹", x=110, y=50)
create_tooltip(sec_ligands_button.button, "选择第二个配体所在的文件夹")
self.sec_ligands_entry = SEntry(
self.windows,
textvariable=StringVar(),
text=Configer.get_para("sec_ligands")
if self.sec_ligands == "" else self.sec_ligands,
x=200,
y=53,
width=350)
create_tooltip(self.sec_ligands_entry.entry, "选择需要比较的配体")
sec_ligand_button.bind_open_file(
entry_text=self.sec_ligands_entry.textvariable,
title="选择需要比较的配体",
file_type="xyz",
parent=self.windows)
sec_ligands_button.bind_open_dir(
entry_text=self.sec_ligands_entry.textvariable,
title="选择需要比较的配体所在的文件夹",
parent=self.windows)
SLabel(root=self.windows, text="旋转方法", x=10, y=90)
rotate_method_text = ("none", "kabsch", "quaternion")
self.rotate_method_box = SCombbox(
root=self.windows,
textvariable=StringVar(),
values=rotate_method_text,
default_value=Configer.get_para("rotate_method")
if self.rotate_method == "" else self.rotate_method,
x=70,
y=90,
width=85)
create_tooltip(self.rotate_method_box.combobox, "是否旋转原子和旋转方法")
SLabel(root=self.windows, text="原子对齐方法", x=170, y=90)
reorder_method_text = ("hungarian", "distance")
self.reorder_method_box = SCombbox(
root=self.windows,
textvariable=StringVar(),
values=reorder_method_text,
default_value=Configer.get_para("reorder_method")
if self.reorder_method == "" else self.reorder_method,
x=260,
y=90,
width=85)
create_tooltip(self.rotate_method_box.combobox, "是否旋转原子和旋转方法")
rmsd_button = SButton(self.windows, "计算RMSD", x=465, y=90)
create_tooltip(rmsd_button.button, "计算RMSD")
rmsd_button.button.bind("<Button-1>", self._cal_rmsd)
# 关闭窗口保存参数
self.windows.protocol(
"WM_DELETE_WINDOW", lambda: self.save_rmsd(
self.windows, self.single_ligand_entry.textvariable.get(),
self.sec_ligands_entry.textvariable.get(),
self.rotate_method_box.textvariable.get(),
self.reorder_method_box.textvariable.get()))
