def __init__(self):
# 初始化
self.main_window = Tk()
# 参数保存工具
self.config = Configer()
self.tab1_configer = None
self.tab2_configer = None
self.tab3_configer = None
self.tab4_configer = None
self.tab5_configer = None
self.tab6_configer = None
self.tab7_configer = None
self.tab8_configer = None
# 如果第一次打开，创建参数文件
Configer.first_open()
# 窗口初始化
self.init_window()
# 创建切换卡
self.create_notebook()
# 三方程序配置
self.create_config_button()
# 退出按钮
self.create_exit_button()
# 点击x退出
self.main_window.protocol("WM_DELETE_WINDOW", self.save_para)
def _choose_ligand_frame(self):
choose_ligand_labelframe = LabelFrame(self.root, text="选择/提取配体")
choose_ligand_labelframe.place(x=10, y=10, width=570, height=120)
# 选择输入配体的格式
SLabel(root=choose_ligand_labelframe, text="输入格式：",
x=10, y=0)
input_format_text = ("pdbqt", "sdf", "pdb")
self.input_format = SCombbox(root=choose_ligand_labelframe, textvariable=StringVar(),
values=input_format_text,
default_value=Configer.get_para("complex_ligand_format"),
x=80, y=0, width=60)
create_tooltip(self.input_format.combobox, "导入配体的格式")
# 选择第几个配体
SLabel(root=choose_ligand_labelframe, text="选择第",
x=160, y=0)
self.complex_ligand_num_entry = SEntry(choose_ligand_labelframe, textvariable=StringVar(),
text=Configer.get_para("complex_ligand_num"),
x=205, y=2, width=20)
create_tooltip(self.complex_ligand_num_entry.entry, "只针对多构象pdbqt文件。输入"
"要进行复合或者提取的构象。"
"如果为0则全部提取/复合")
SLabel(root=choose_ligand_labelframe, text="个构象",
x=230, y=0)
# 选择配体
choose_ligands_button = SButton(choose_ligand_labelframe, text="选择单/多个配体", x=10, y=30)
create_tooltip(choose_ligands_button.button, "选择一个或者多个所选格式的配体")
choose_ligand_dir_button = SButton(choose_ligand_labelframe, text="选择文件夹", x=110, y=30)
create_tooltip(choose_ligand_dir_button.button, "选择包含配体的文件夹，匹配其中所选格式的文件")
self.choose_ligands_entry = SEntry(root=choose_ligand_labelframe, textvariable=StringVar(),
text=Configer.get_para("choose_complex_ligands"),
x=200, y=34, width=360)
create_tooltip(self.choose_ligands_entry.entry, "所选的配体或者包含配体的目录")
choose_ligands_button.bind_open_files(entry_text=self.choose_ligands_entry.textvariable,
title="选择单/多个配体",
file_type=self.input_format.textvariable)
choose_ligand_dir_button.bind_open_dir(entry_text=self.choose_ligands_entry.textvariable,
title="选择包含配体文件的文件夹")
# 选择单独输出配体文件夹
choose_output_button = SButton(choose_ligand_labelframe, text="提取配体输出路径", x=10, y=65)
create_tooltip(choose_output_button.button, "单独提取配体，选择要输出的文件夹。")
self.extract_output_entry = SEntry(choose_ligand_labelframe,
textvariable=StringVar(),
text=Configer.get_para("extract_pdbqt_dir"),
x=120, y=65 + 3, width=340)
create_tooltip(self.extract_output_entry.entry, "输出的文件夹")
choose_output_button.bind_open_dir(entry_text=self.extract_output_entry.textvariable,
title="选择提取配体输出的文件夹")
extract_button = SButton(choose_ligand_labelframe, text="提取选定的配体",
x=470, y=65)
extract_button.button.bind("<Button-1>", self.extract)
create_tooltip(extract_button.button, "提取配体")
def vina_validate(self, event):
self.windows = STopLevel(self.root,
win_x=570,
win_y=50,
title="计算RMSD").toplevel
# 选择目录
input_button = SButton(self.windows, text="选择验证目录", x=10, y=10)
create_tooltip(input_button.button, "选择要验证的目录。该目录必须包含配体和受体！")
self.input_path_entry = SEntry(
self.windows,
textvariable=StringVar(),
text=Configer.get_para("validate_folder")
if self.validate_folder == "" else self.validate_folder,
x=100,
y=13,
width=360)
create_tooltip(self.input_path_entry.entry, "选择的要验证的目录")
input_button.bind_open_dir(
entry_text=self.input_path_entry.textvariable,
title="选择要验证的目录",
parent=self.windows)
validate_button = SButton(self.windows, "开始验证", x=465, y=10)
create_tooltip(validate_button.button, "开始验证Vina方案")
validate_button.button.bind("<Button-1>", self._vina_validate)
# 关闭窗口保存参数
self.windows.protocol(
"WM_DELETE_WINDOW", lambda: self.save_validate(
self.windows, self.input_path_entry.textvariable.get()))
def _choose_ligand_frame(self):
choose_ligand_labelframe = LabelFrame(self.root, text="选择配体")
choose_ligand_labelframe.place(x=10, y=10, width=570, height=50)
choose_ligands = SButton(root=choose_ligand_labelframe,
text="选择单/多个配体",
x=10,
y=0)
create_tooltip(choose_ligands.button, "选择单/多个配体，配体格式必须是pdbqt！")
choose_ligand_dir = SButton(root=choose_ligand_labelframe,
text="选择文件夹",
x=110,
y=0)
create_tooltip(choose_ligand_dir.button, "选择包含pdbqt格式配体的文件夹。")
self.choose_ligand_entry = SEntry(
root=choose_ligand_labelframe,
textvariable=StringVar(),
text=Configer.get_para("choose_docking_ligands"),
x=200,
y=4,
width=360)
create_tooltip(self.choose_ligand_entry.entry, "选择的配体或者包含配体的文件夹")
choose_ligands.bind_open_files(
entry_text=self.choose_ligand_entry.textvariable,
title="选择单/多个配体",
file_type="pdbqt")
choose_ligand_dir.bind_open_dir(
entry_text=self.choose_ligand_entry.textvariable,
title="选择包含pdbqt配体的文件夹")
def create_move_pdbqt(self):
move_pdbqt_labelframe = Labelframe(self.root, text="移动受体文件")
move_pdbqt_labelframe.place(x=10, y=100, width=570, height=50)
choose_pdbqt_dir = SButton(move_pdbqt_labelframe,
text="选择文件",
x=10,
y=0)
create_tooltip(choose_pdbqt_dir.button, "选择包含pdbqt受体的文件夹")
self.choose_pdbqt_dir_entry = SEntry(
move_pdbqt_labelframe,
textvariable=StringVar(),
text=Configer.get_para("pdbqt_dir"),
x=100,
y=3,
width=350)
create_tooltip(self.choose_pdbqt_dir_entry.entry, "选择包含pdbqt受体的文件夹")
choose_pdbqt_dir.bind_open_dir(
self.choose_pdbqt_dir_entry.textvariable, title="选择有pdbqt受体的文件夹")
move_button = SButton(move_pdbqt_labelframe,
text="生成文件",
x=460,
y=0,
width=90)
create_tooltip(move_button.button, "开始移动pdbqt文件并重命名为preped.pdbqt")
move_button.button.bind("<Button-1>", self.move_file)
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 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_option_frame(self):
option_label_frame = LabelFrame(self.root, text="可选")
option_label_frame.place(x=340, y=10, width=240, height=120)
# exhaustiveness
SLabel(option_label_frame, text="exhaustiveness = ", x=10, y=5)
self.exhaustiveness = SEntry(option_label_frame,
textvariable=StringVar(),
text=Configer.get_para("exhaustiveness"),
x=140,
y=5,
width=20)
create_tooltip(self.exhaustiveness.entry, "搜索度，越大耗时越长，建议保持默认")
# num_modes
SLabel(option_label_frame, text="num_modes = ", x=10, y=35)
self.num_modes = SEntry(option_label_frame,
textvariable=StringVar(),
text=Configer.get_para("num_modes"),
x=140,
y=35,
width=20)
create_tooltip(self.num_modes.entry, "最多生成多少种结合模式")
# energy_range
SLabel(option_label_frame, text="energy_range = ", x=10, y=65)
self.energy_range = SEntry(option_label_frame,
textvariable=StringVar(),
text=Configer.get_para("energy_range"),
x=140,
y=65,
width=20)
create_tooltip(self.energy_range.entry, "最大最小结合模式能量差")
# 恢复默认值
default_button = SButton(option_label_frame,
text="默认",
x=170,
y=62,
width=60)
default_button.button.bind("<Button-1>", self._change_default)
create_tooltip(default_button.button, "恢复默认值")
def gen_smi(self, event):
self.windows = STopLevel(self.root,
win_x=570,
win_y=100,
title="分子生成器").toplevel
# 输入smi
SLabel(self.windows, text="输入smi", x=10, y=10)
self.input_smi_entry = SEntry(self.windows,
textvariable=StringVar(),
text=Configer.get_para("input_smi") if
self.input_smi == "" else self.input_smi,
x=80,
y=13,
width=470)
create_tooltip(self.input_smi_entry.entry, "输入含有[R]的smi文本")
# 输出目录
output_button = SButton(self.windows, text="选择输出目录", x=10, y=50)
create_tooltip(output_button.button, "选择衍生物输出的目录")
self.output_path_entry = SEntry(
self.windows,
textvariable=StringVar(),
text=Configer.get_para("mol_output_path")
if self.output_path == "" else self.output_path,
x=100,
y=53,
width=360)
create_tooltip(self.output_path_entry.entry, "选择衍生物mol的输出目录")
output_button.bind_open_dir(
entry_text=self.output_path_entry.textvariable,
title="选择衍生物输出目录",
parent=self.windows)
gen_button = SButton(self.windows, "生成衍生物", x=465, y=50)
create_tooltip(gen_button.button, "开始生成衍生物")
gen_button.button.bind("<Button-1>", self._gen_smi)
# 关闭窗口保存参数
self.windows.protocol(
"WM_DELETE_WINDOW", lambda: self.save_smi(
self.windows, self.input_smi_entry.textvariable.get(),
self.output_path_entry.textvariable.get()))
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_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 save_para(self):
if messagebox.askokcancel("退出", "保存参数并退出软件？"):
self.config.para_dict["python_path"] = Configer.get_para(
"python_path")
self.config.para_dict["obabel_path"] = Configer.get_para(
"obabel_path")
# 保存各个标签的参数
self.tab1_configer.save_para()
self.tab2_configer.save_para()
self.tab3_configer.save_para()
self.tab4_configer.save_para()
self.tab5_configer.save_para()
self.tab6_configer.save_para()
self.tab8_configer.save_para()
# 进行文件保存
self.config.save_para()
# 关闭窗口
self.main_window.destroy()
def _choose_output_frame(self):
choose_output_labelframe = LabelFrame(self.root, text="复合物输出")
choose_output_labelframe.place(x=10, y=190, width=570, height=50)
choose_output = SButton(root=choose_output_labelframe, text="选择输出文件夹", x=10, y=0)
create_tooltip(choose_output.button, "选择复合物输出目录")
self.choose_output_entry = SEntry(root=choose_output_labelframe, textvariable=StringVar(),
text=Configer.get_para("choose_complex_output"),
x=110, y=4, width=450)
create_tooltip(self.choose_output_entry.entry, "所选的复合物输出目录")
choose_output.bind_open_dir(entry_text=self.choose_output_entry.textvariable,
title="选择复合物输出的文件夹")
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 gen_config_file(output_name, x, y, z, size):
"""
根据x,y,z,size生成config文件
:param output_name: 输出路径文件名
:param x: x坐标
:param y: y坐标
:param z: z坐标
:param size: 盒子大小
"""
exhaustiveness = Configer.get_para(
"exhaustiveness") if Configer.get_para("exhaustiveness") != "" else 8
num_modes = Configer.get_para(
"num_modes") if Configer.get_para("num_modes") != "" else 9
energy_range = Configer.get_para(
"energy_range") if Configer.get_para("energy_range") != "" else 3
with open(output_name, "w") as f:
f.writelines("center_x = " + str(x) + "\n")
f.writelines("center_y = " + str(y) + "\n")
f.writelines("center_z = " + str(z) + "\n")
f.writelines("size_x = " + str(size) + "\n")
f.writelines("size_y = " + str(size) + "\n")
f.writelines("size_z = " + str(size) + "\n")
f.writelines("exhaustiveness = " + exhaustiveness + "\n")
f.writelines("num_modes = " + num_modes + "\n")
f.writelines("energy_range = " + energy_range + "\n")
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_docking_config(self):
choose_config_labelframe = LabelFrame(self.root, text="对接配置")
choose_config_labelframe.place(x=10, y=190, width=570, height=50)
self.docking_time_label = SLabel(root=choose_config_labelframe,
text="对接次数：",
x=10,
y=0)
self.times_entry = SEntry(root=choose_config_labelframe,
textvariable=StringVar(),
text=Configer.get_para("docking_times"),
x=80,
y=0,
width=20)
create_tooltip(self.times_entry.entry, "每个配体需要对接的次数")
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 check_obabel(obabel_path=""):
"""
检查obabel是否配置正确
:return: 正确返回True，不正确返回False
"""
if Configer.get_para("obabel_path") != "":
return True
if obabel_path.count(" ") > 0 or not obabel_path.endswith(
"obabel.exe"):
messagebox.showerror("输入错误！",
"obabel.exe选择不正确！请确保路径不包含空格并且是obabel.exe文件！")
return False
obabel_cmd = os.popen(obabel_path).read()
# print(obabel_cmd)
if "Usage:\nobabel" not in obabel_cmd:
messagebox.showerror("错误！", "obabel.exe不正确，请在“脚本配置”中选择！")
return False
messagebox.showinfo("obabel配置成功！", "obabel配置成功！")
return True
def check_python(choose_python_path=""):
"""
检查adt的python路径是否配置正确
:return: 正确返回True
"""
# 如果有内容，直接判断通过
if Configer.get_para("python_path") != "":
return True
if choose_python_path.count(
" ") > 0 or not choose_python_path.endswith("python.exe"):
messagebox.showerror(
"输入错误！", "adt的python.exe选择不正确，请确保路径不包含空格并且是python.exe文件！")
return False
check_cmd = "%s %s" % (choose_python_path, pdbqt_to_pdb_path)
state = os.system(check_cmd)
if state == 1:
messagebox.showerror("python路径错误！", "请确定选择的是安装adt软件的python.exe！")
return False
messagebox.showinfo("python配置成功！", "python配置成功！")
return True
def _create_output_frame(self):
output_frame = LabelFrame(self.root, text="输出配置文件")
output_frame.place(x=10, y=250, width=570, height=50)
# 输出配置文件
output_config_button = SButton(output_frame, "选择输出目录", 10, 0)
create_tooltip(output_config_button.button, "选择config.txt输出的目录")
self.output_config_entry = SEntry(
root=output_frame,
textvariable=StringVar(),
text=Configer.get_para("output_config"),
x=100,
y=4,
width=360)
create_tooltip(self.output_config_entry.entry, "输出config.txt文件的位置")
output_config_button.bind_open_dir(
self.output_config_entry.textvariable, title="选择输出目录")
gen_config_button = SButton(output_frame, "输出", 470, 0)
create_tooltip(gen_config_button.button, "开始输出")
gen_config_button.button.bind("<Button-1>", self.output_config)
def _start_join(self):
y = 250
join_button = SButton(root=self.root, text="结合", x=10, y=y)
create_tooltip(join_button.button, "将配体和受体结合成一个文件")
join_button.button.bind("<Button-1>", self._join)
self.progress = Progressbar(self.root, mode="determinate")
self.progress.place(x=100, y=y + 2, width=400)
create_tooltip(self.progress, "结合进度")
self.progress_label = SLabel(self.root, text="没有任务", x=510, y=y)
text_y = 286
current_ligand_frame = Frame(self.root, width=400, height=40)
current_ligand_frame.place(x=10, y=text_y)
self.current_ligand = SLabel(root=current_ligand_frame, text="", x=0, y=0)
# 是否保留提取配体
self.remain_ligand = SCheckbutton(self.root
, text="保留提取构象", variable=StringVar(),
value=Configer.get_para("remain_ligand"),
x=10, y=text_y + 20)
create_tooltip(self.remain_ligand.checkbutton, "保留提取或者转换的构象。")
def _choose_protein_frame(self):
choose_protein_labelframe = LabelFrame(self.root, text="选择受体")
choose_protein_labelframe.place(x=10, y=70, width=570, height=50)
choose_proteins = SButton(root=choose_protein_labelframe,
text="选择受体文件夹",
x=10,
y=0)
create_tooltip(
choose_proteins.button, "选择受体文件夹。受体必须命名为preped.pdbqt\n"
"单个受体请选择包含这个受体的文件夹\n"
"多个受体请选择包含多个受体文件夹的文件夹\n"
"详情见帮助及教程")
self.choose_proteins_entry = SEntry(
root=choose_protein_labelframe,
textvariable=StringVar(),
text=Configer.get_para("choose_docking_proteins"),
x=110,
y=4,
width=450)
create_tooltip(self.choose_proteins_entry.entry, "包含受体的文件夹")
choose_proteins.bind_open_dir(
entry_text=self.choose_proteins_entry.textvariable,
title="选择包含pdbqt受体的文件夹")
from tools.configer import Configer
from tools.file_path import *
obabel_path = Configer.get_para("obabel_path")
python_path = Configer.get_para("python_path")
def pdb_2_other(input_file, output_file):
"""
使用obabel将pdb文件转换为其他文件
:param input_file: 输入的pdb文件
:param output_file: 输出的其他格式文件
:return 执行结果
"""
cmd = "%s %s -O %s" % (obabel_path, input_file, output_file)
convert_result(cmd, output_file)
def pdbqt_2_pdb(input_file, output_file):
"""
使用adt将pdbqt文件转pdb文件
:param input_file: 输入的pdbqt文件
:param output_file: 输出的pdb文件
"""
cmd = "%s %s -f %s -o %s" % (python_path, pdbqt_to_pdb_path, input_file,
output_file)
convert_result(cmd, output_file)
def pdb_mol2_2_pdbqt(input_file, output_file):
"""
class MainWindows(object):
def __init__(self):
# 初始化
self.main_window = Tk()
# 参数保存工具
self.config = Configer()
self.tab1_configer = None
self.tab2_configer = None
self.tab3_configer = None
self.tab4_configer = None
self.tab5_configer = None
self.tab6_configer = None
self.tab7_configer = None
self.tab8_configer = None
# 如果第一次打开，创建参数文件
Configer.first_open()
# 窗口初始化
self.init_window()
# 创建切换卡
self.create_notebook()
# 三方程序配置
self.create_config_button()
# 退出按钮
self.create_exit_button()
# 点击x退出
self.main_window.protocol("WM_DELETE_WINDOW", self.save_para)
def create_config_button(self):
# 脚本配置
config_button = Button(self.main_window,
text="脚本配置",
command=self.set_config)
config_button.place(x=CONFIG_BUTTON_X,
y=CONFIG_BUTTON_Y,
width=BUTTON_WIDTH)
create_tooltip(config_button, "设置脚本所需路径")
def create_exit_button(self):
"""
创建退出按钮
"""
exit_button = Button(self.main_window,
text="退出",
command=self.save_para)
exit_button.place(x=EXIT_BUTTON_X, y=EXIT_BUTTON_Y, width=BUTTON_WIDTH)
create_tooltip(exit_button, "保存参数并退出软件")
def init_window(self):
"""
添加标题，禁用窗口缩放，显示居中。
"""
# 标题
self.main_window.title(WINDOWS_TITLE)
# 禁用窗口缩放
self.main_window.resizable(width=False, height=False)
# 窗口居中显示
screen_width = self.main_window.winfo_screenwidth()
screen_height = self.main_window.winfo_screenheight()
x = (screen_width / 2) - (MAIN_WINDOWS_WIDTH / 2)
y = (screen_height / 2) - (MAIN_WINDOWS_HEIGHT / 2)
self.main_window.geometry(
'%dx%d+%d+%d' % (MAIN_WINDOWS_WIDTH, MAIN_WINDOWS_HEIGHT, x, y))
def create_notebook(self):
# 大框架
notebook = Notebook()
# 准备受体
tab1 = Frame(notebook)
# 准备对接配置
tab2 = Frame(notebook)
# 准备配体
tab3 = Frame(notebook)
# 分子对接
tab4 = Frame(notebook)
# 工具
tab5 = Frame(notebook)
# 生成复合物
tab6 = Frame(notebook)
# 关于
tab7 = Frame(notebook)
# 其他工具
tab8 = Frame(notebook)
# 放置选项卡
notebook.add(tab1, text=TAB1_TEXT)
notebook.add(tab2, text=TAB2_TEXT)
notebook.add(tab3, text=TAB3_TEXT)
notebook.add(tab4, text=TAB4_TEXT)
notebook.add(tab5, text=TAB5_TEXT)
notebook.add(tab8, text=TAB8_TEXT)
notebook.add(tab6, text=TAB6_TEXT)
notebook.add(tab7, text=TAB7_TEXT)
# 默认显示卡
notebook.select(tab_id=DEFAULT_TAB)
# 禁用某一个选项卡
# self.notebook.tab(1, state="disable")
# 放置切换卡
notebook.place(x=NOTEBOOK_X,
y=NOTEBOOK_Y,
width=NOTEBOOK_WIDTH,
height=NOTEBOOK_HEIGHT)
# 选项卡内容
self.tab1_configer = Tab1(tab1, self.config)
self.tab2_configer = Tab2(tab2, self.config)
self.tab3_configer = Tab3(tab3, self.config)
self.tab4_configer = Tab4(tab4, self.config)
self.tab5_configer = Tab5(tab5, self.config)
self.tab6_configer = Tab6(tab6, self.config)
self.tab8_configer = AdditionToolsTab(tab8, self.config)
self.tab7_configer = Tab7(tab7)
def set_config(self):
SetConfig(self.main_window, self.config)
def save_para(self):
if messagebox.askokcancel("退出", "保存参数并退出软件？"):
self.config.para_dict["python_path"] = Configer.get_para(
"python_path")
self.config.para_dict["obabel_path"] = Configer.get_para(
"obabel_path")
# 保存各个标签的参数
self.tab1_configer.save_para()
self.tab2_configer.save_para()
self.tab3_configer.save_para()
self.tab4_configer.save_para()
self.tab5_configer.save_para()
self.tab6_configer.save_para()
self.tab8_configer.save_para()
# 进行文件保存
self.config.save_para()
# 关闭窗口
self.main_window.destroy()
def _join(self, event):
input_format = self.input_format.textvariable.get()
input_ligands_full = self.choose_ligands_entry.entry.get()
input_receptor = self.choose_proteins_entry.entry.get()
output_dir = self.choose_output_entry.entry.get()
choose_num = self.complex_ligand_num_entry.entry.get()
remain = self.remain_ligand.variable.get()
# 所有选择的路径和文件都不能为空。
if input_ligands_full == "" or input_receptor == "" or output_dir == "":
messagebox.showerror("错误！", "输入不能为空！")
return
# 不能包括空格
if Check.has_space(input_ligands_full):
messagebox.showerror("错误！", "配体路径不能包含空格！")
return
if Check.has_space(input_receptor):
messagebox.showerror("错误！", "受体路径不能包含空格！")
return
if Check.has_space(output_dir):
messagebox.showerror("错误！", "输出路径不能包含空格！")
return
# 选择构象要是数字
try:
num = int(choose_num)
except ValueError:
messagebox.showerror("错误！", "提取的构象必须是数字！")
return
if num < 0:
messagebox.showerror("错误！", "提取构象至少大于0！")
return
# 输出路径不存在则创建
if not os.path.exists(output_dir):
os.mkdir(output_dir)
# 受体格式必须是pdbqt
if not input_receptor.endswith(".pdbqt"):
messagebox.showerror("错误！", "输入的受体必须是pdbqt格式。")
return
input_ligands = []
# 输入的配体
if input_ligands_full.endswith(";"): # 如果是单个或者多个配体
if input_ligands_full.split(".")[-1][0:-1] != input_format: # 格式不匹配
messagebox.showerror("错误！", "配体格式不是所选格式！")
return
input_ligands.extend(input_ligands_full.split(";")[0:-1])
elif os.path.isdir(input_ligands_full): # 如果选择的是目录
list_file = os.listdir(input_ligands_full)
for file in list_file:
if file.endswith(input_format):
input_ligands.append(input_ligands_full + os.sep + file)
if len(input_ligands) == 0:
messagebox.showerror("错误！", "所选文件夹中不包含%s格式的配体！" % input_format)
return
else:
messagebox.showerror("错误！", "请检查输入的配体！")
return
# 检查路径是否正确
if not Check.check_python():
return
obabel_path = Configer.get_para("obabel_path")
if not Check.check_obabel():
return
self.progress_label.label.configure(text="准备受体")
self.progress_label.label.update()
# 将受体pdbqt转成pdb
input_pdb = output_dir + os.sep + input_receptor.split(".")[0].split(os.sep)[-1] + ".pdb"
pdbqt_2_pdb(input_receptor, input_pdb)
ligands = []
self.progress_label.label.configure(text="准备配体")
self.progress_label.label.update()
if input_format == "pdbqt":
for ligand in input_ligands:
# 是否是单个配体:
with open(ligand, "r") as f:
line = f.readline()
if "MODEL" not in line:
# 只有一个，直接转换成pdb
pdb_ligand = output_dir + os.sep + ligand.split(".")[0].split(os.sep)[-1] + ".pdb"
pdbqt_2_pdb(ligand, pdb_ligand)
ligands.append(pdb_ligand)
else:
output_pdbqts = extract_pdbqt(ligand, output_dir, num)
for output_pdbqt in output_pdbqts:
output_pdb = output_pdbqt[:-2]
pdbqt_2_pdb(output_pdbqt, output_pdb)
os.remove(output_pdbqt)
ligands.append(output_pdb)
else:
pdb_ligands = []
# 全部转换成pdb格式
for ligand in input_ligands:
output_ligand = output_dir + os.sep + ligand.split(".")[0].split(os.sep)[-1] + ".pdb"
ob(ligand, output_ligand)
pdb_ligands.append(output_ligand)
ligands = pdb_ligands
# 进行复合
self.progress["maximum"] = len(ligands)
for ligand in ligands:
# 更新进度条
label_text = str(ligands.index(ligand) + 1) + os.sep + str(len(ligands))
self.progress_label.label.configure(text=label_text)
self.progress_label.label.update()
self.progress["value"] = ligands.index(ligand) + 1
self.progress.update()
current_ligand = "当前配体：%s" % ligand.split(os.sep)[-1].split(".")[0]
self.current_ligand.label.configure(text=current_ligand)
self.current_ligand.label.update()
output_name = ligand.split(os.sep)[-1].split(".")[0] + "_" + input_receptor.split(os.sep)[-1].split(".")[
0] + ".pdb"
output = output_dir + os.sep + output_name
ob_join(ligand, input_pdb, output)
# 如果不保留提取配体，删除提取配体
if input_format == "pdbqt" and remain == "0":
for ligand in ligands:
os.remove(ligand)
# 删除受体
os.remove(input_pdb)
messagebox.showinfo("成功！", "生成复合物成功！")
self.progress_label.label.configure(text="没有任务")
self.progress_label.label.update()
self.progress["value"] = 0
self.progress.update()
self.current_ligand.label.configure(text="")
self.current_ligand.label.update()
def prepare_receptor(receptor: str, output_file: str, fix_method: str,
preserve_charges: int, nphs: int, lps: int, waters: int,
nonstdres: int):
"""
使用ADT的prepareReceptor4准备受体。
:param receptor: 受体路径。比如D:/test/a.pdb
:param output_file: 输出路径。比如D:/test
:param fix_method: 修复方法。"bonds_hydrogens", "bonds", "hydrogens", "checkhydrogens", "None"
:param preserve_charges: 保留电荷。1或者0
:param nphs:合并非极性氢。1或者0
:param lps:合并电荷。1或者0
:param waters:去水。1或者0
:param nonstdres:去除非标准氨基酸。1或者0
:return 准备成功返回真，失败返回假
"""
u_para_list = []
if nphs:
u_para_list.append("nphs")
if lps:
u_para_list.append("lps")
if waters:
u_para_list.append("waters")
if nonstdres:
u_para_list.append("nonstdres")
u_paras = ""
for u_para in u_para_list:
if u_para == u_para_list[-1]:
u_paras += u_para
break
u_paras += u_para + "_"
# print(u_paras)
if preserve_charges:
# 保留电荷,做处理
if u_paras != "":
cmd = "%s %s -r %s -o %s -A %s -C -U %s -e" % (
Configer.get_para("python_path"), prepare_receptor4_path,
receptor, output_file, fix_method, u_paras)
# 保留电荷，不做处理
else:
cmd = "%s %s -r %s -o %s -A %s -C -e" % (
Configer.get_para("python_path"), prepare_receptor4_path,
receptor, output_file, fix_method)
else:
# 不保留电荷,做处理
if u_paras != "":
cmd = "%s %s -r %s -o %s -A %s -U %s -e" % (
Configer.get_para("python_path"), prepare_receptor4_path,
receptor, output_file, fix_method, u_paras)
# 不保留电荷，不处理
else:
cmd = "%s %s -r %s -o %s -A %s -e" % (
Configer.get_para("python_path"), prepare_receptor4_path,
receptor, output_file, fix_method)
exit_code = os.system(cmd)
if exit_code == 0:
print("------------------------------------------------------------")
print("%s准备成功" % receptor)
print("------------------------------------------------------------")
return True
else:
print("------------------------------------------------------------")
print("%s准备失败，请尝试使用biopython进行修复。" % receptor)
print("------------------------------------------------------------")
return False
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()))
def _create_main_frame(self):
main_label_frame = LabelFrame(self.root, text="主要参数")
main_label_frame.place(x=10, y=10, width=320, height=120)
# center_x
SLabel(main_label_frame, text="center_x = ", x=10, y=5)
self.center_x = SEntry(main_label_frame,
textvariable=StringVar(),
text=Configer.get_para("center_x"),
x=95,
y=5,
width=60)
create_tooltip(self.center_x.entry, "对接位点的x坐标")
# center_y
SLabel(main_label_frame, text="center_y = ", x=10, y=35)
self.center_y = SEntry(main_label_frame,
textvariable=StringVar(),
text=Configer.get_para("center_y"),
x=95,
y=35,
width=60)
create_tooltip(self.center_y.entry, "对接位点的y坐标")
# center_z
SLabel(main_label_frame, text="center_z = ", x=10, y=65)
self.center_z = SEntry(main_label_frame,
textvariable=StringVar(),
text=Configer.get_para("center_z"),
x=95,
y=65,
width=60)
create_tooltip(self.center_z.entry, "对接位点的z坐标")
# size_x
SLabel(main_label_frame, text="size_x = ", x=175, y=5)
self.size_x = SEntry(main_label_frame,
textvariable=StringVar(),
text=Configer.get_para("size_x"),
x=245,
y=5,
width=60)
create_tooltip(self.size_x.entry, "对接位点的x方向大小")
# size_y
SLabel(main_label_frame, text="size_y = ", x=175, y=35)
self.size_y = SEntry(main_label_frame,
textvariable=StringVar(),
text=Configer.get_para("size_y"),
x=245,
y=35,
width=60)
create_tooltip(self.size_y.entry, "对接位点的y方向大小")
# size_z
SLabel(main_label_frame, text="size_z = ", x=175, y=65)
self.size_z = SEntry(main_label_frame,
textvariable=StringVar(),
text=Configer.get_para("size_z"),
x=245,
y=65,
width=60)
create_tooltip(self.size_z.entry, "对接位点的z方向大小")
