def __init__(self, tab, config):
self.root = tab
self.config = config
# 需要保存的参数
self.input_format = None
self.choose_ligands_entry = None
self.output_format = None
self.gen3d = None
self.ph = None
self.is_minimize = None
self.choose_output_dir_entry = None
self._create_choose_ligand_frame()
self._create_output_ligand_frame()
# 开始转换
self._create_convert()
# 帮助按钮
help_button = HelpButton(root=self.root,
help_text=TAB3_HELP_TEXT,
x=410,
y=300,
width=80)
create_tooltip(help_button.help_button, "获取帮助")
def __init__(self, tab, config):
self.root = tab
self.config = config
# 需要保存的参数
self.choose_ligand_entry = None
self.choose_proteins_entry = None
self.choose_output_entry = None
self.times_entry = None
# 不需要保存的参数
self.docking_time_label = None
self._choose_ligand_frame()
self._choose_protein_frame()
self._choose_output_frame()
self._choose_docking_config()
self._start_docking()
# 帮助按钮
help_button = HelpButton(root=self.root,
help_text=TAB4_HELP_TEXT,
x=410,
y=300,
width=80)
create_tooltip(help_button.help_button, "获取帮助")
def __init__(self, tab, config):
self.root = tab
self.config = config
# 需要保存的参数
self.choose_ligand_entry = None
self.choose_receptor_entry = None
self.choose_pdbqt_dir_entry = None
self.choose_scores_entry = None
self.choose_output_entry = None
self.choose_extract_folder_entry = None
# 创建窗体
self.create_all_config()
self.create_move_pdbqt()
self.create_extract_scores()
self.extract_from_file()
# 帮助按钮
help_button = HelpButton(root=self.root,
help_text=TAB5_HELP_TEXT,
x=410,
y=300,
width=80)
create_tooltip(help_button.help_button, "获取帮助")
def _start_docking(self):
y = 250
docking_button = SButton(root=self.root, text="开始对接", x=10, y=y)
create_tooltip(docking_button.button, "使用Vina进行对接")
self.progress = Progressbar(self.root, mode="determinate")
self.progress.place(x=100, y=y + 2, width=400)
create_tooltip(self.progress, "对接进度")
self.progress_label = SLabel(self.root, text="没有任务", x=510, y=y)
docking_button.button.bind("<Button-1>", self._docking)
text_y = 276
current_protein_frame = Frame(self.root, width=200, height=40)
current_protein_frame.place(x=10, y=text_y)
self.current_protein = SLabel(root=current_protein_frame,
text="",
x=0,
y=0)
current_ligand_frame = Frame(self.root, width=200, height=50)
current_ligand_frame.place(x=220, y=text_y)
self.current_ligand = SLabel(root=current_ligand_frame,
text="",
x=0,
y=0)
current_time_frame = Frame(self.root, width=150, height=50)
current_time_frame.place(x=430, y=text_y)
self.current_time = SLabel(root=current_time_frame, text="", x=0, y=0)
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 _create_convert(self):
y = 230
convert_button = SButton(root=self.root, x=10, y=y, text="开始转换")
create_tooltip(convert_button.button, "开始转换")
self.progress = Progressbar(self.root, mode="determinate")
self.progress.place(x=100, y=y + 2, width=400)
create_tooltip(self.progress, "转换进度")
self.progress_label = SLabel(self.root, text="没有任务", x=510, y=y)
convert_button.button.bind("<Button-1>", self._start_convert)
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 choose_ligand(self):
self.ligand_list = Listbox(self.choose_ligand_tab, width=30, height=10)
self.ligand_list.place(x=10, y=10, width=255, height=150)
scroll = Scrollbar(self.ligand_list)
scroll.pack(side=RIGHT, fill=Y)
self.ligand_list.configure(yscrollcommand=scroll.set)
scroll.config(command=self.ligand_list.yview)
pre_button = SButton(self.choose_ligand_tab, "上一步", 10, 170)
pre_button.button.bind("<Button-1>", self.jump_chain)
next_button = SButton(self.choose_ligand_tab, "提取配体", 165, 170)
create_tooltip(next_button.button, "提取选中的配体为pdbqt格式")
next_button.button.bind("<Button-1>", self.save_ligand)
def create_download_receptor(self):
# frame创建
download_receptor_labelframe = LabelFrame(self.root, text="下载受体")
download_receptor_labelframe.place(x=LEFT_X,
y=LEFT_Y,
width=FULL_NOTEBOOK_WIDTH,
height=TAB1_LABEL_FRAME_HEIGHT)
# 第一排，输入pdbid
SLabel(download_receptor_labelframe, "PDBID：", x=LEFT_X, y=0)
self.pdb_id_entry = SEntry(download_receptor_labelframe,
textvariable=StringVar(),
text=Configer.get_para("pdbid"),
x=70,
y=0,
width=50)
create_tooltip(self.pdb_id_entry.entry, "请输入四位PDB的ID")
# 第二排，保存位置
pdb_save_path_button = SButton(download_receptor_labelframe,
text="选择保存的路径",
x=LEFT_X,
y=30)
create_tooltip(pdb_save_path_button.button, "选择下载受体要保存的位置")
self.pdb_save_path_entry = SEntry(download_receptor_labelframe,
textvariable=StringVar(),
text=Configer.get_para("pdb_path"),
x=110,
y=34,
width=440)
create_tooltip(self.pdb_save_path_entry.entry, "文件将要保存的目录，不存在将创建文件夹")
pdb_save_path_button.bind_open_dir(
entry_text=self.pdb_save_path_entry.textvariable, title="选择要保存的路径")
# 第三排，开始下载
download_pdb_button = SButton(download_receptor_labelframe,
text="开始下载",
x=LEFT_X,
y=60)
create_tooltip(download_pdb_button.button, "从Protein Data Bank下载受体")
download_pdb_button.button.bind("<Button-1>", self.download_pdb)
self.download_progressbar = Progressbar(download_receptor_labelframe,
mode="determinate")
self.download_progressbar.place(x=100, y=62, width=380)
create_tooltip(self.download_progressbar, "下载进度")
self.download_state_label = SLabel(download_receptor_labelframe,
text="没有下载",
x=490,
y=60)
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 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_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 __init__(self, root, help_text, x, y, width):
"""
:param root: 要放置到哪里
:param help_text: 弹出提示框显示的文字
:param x: 位置x
:param y: 位置y
:param width: 按钮宽度
"""
self.root = root
self.help_text = help_text
self.x = x
self.y = y
self.width = width
self.help_button = Button(self.root, text="帮助", command=self.show_help)
create_tooltip(self.help_button, "获取帮助")
self.help_button.place(x=self.x, y=self.y, width=self.width)
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 getinfo(self, event):
# 获取受体
receptor = self.choose_raw_receptor_entry.textvariable.get()
if not receptor.endswith(".pdb"):
messagebox.showerror("错误！", "只支持查看单个pdb格式的文件信息！")
return
if Check.check_path(receptor):
messagebox.showerror("错误", "受体路径不能包含空格！")
return
if not os.path.exists(receptor):
messagebox.showerror("错误", "所选文件或者文件夹不存在!")
return
structure = ReceptorProcessor.get_structure(receptor)
window = STopLevel(self.root, 500, 400, "PDB信息").toplevel
wrap_length = 480
s_name = structure.header["name"]
SLabel(window, "受体名称:\n" + s_name, 10,
10).label.configure(wraplength=wrap_length)
s_redate = structure.header["release_date"]
SLabel(window, "发布时间:\n" + s_redate, 10,
70).label.configure(wraplength=wrap_length)
s_method = structure.header["structure_method"]
SLabel(window, "方法:\n" + s_method, 10,
130).label.configure(wraplength=wrap_length)
s_resolution = str(structure.header["resolution"])
SLabel(window, "分辨率:\n" + s_resolution + "埃", 10,
190).label.configure(wraplength=wrap_length)
s_refe = structure.header["journal_reference"]
reference = SLabel(window, "参考文献:\n" + s_refe, 10, 250).label
reference.configure(wraplength=wrap_length)
doi_url = "http://www.doi.org/" + s_refe.strip().split(" ")[-1]
open_url_button = SButton(window, "打开文献网页", 75, 245)
open_url_button.button.configure(
command=lambda: webbrowser.open(doi_url))
create_tooltip(open_url_button.button, "使用默认浏览器打开文献链接")
def __init__(self, tab, config):
self.root = tab
self.config = config
# 需要保存的参数
self.input_format = None
self.complex_ligand_num_entry = None
self.remain_ligand = None
self.choose_ligands_entry = None
self.choose_output_entry = None
self.extract_output_entry = None
self._choose_ligand_frame()
self._choose_protein_frame()
self._choose_output_frame()
self._start_join()
# 帮助按钮
help_button = HelpButton(root=self.root, help_text=TAB6_HELP_TEXT, x=410, y=300, width=80)
create_tooltip(help_button.help_button, "获取帮助")
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_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 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 __init__(self, tab: Frame, config: Configer):
"""
创建一个选项卡,需要父窗口和用来保存配置的配置器
:param tab: 选项卡
:param config: 配置器
"""
# 变量
self.root = tab
self.config = config
# 需要保存的参数
self.center_x = None
self.center_y = None
self.center_z = None
self.size_x = None
self.size_y = None
self.size_z = None
self.exhaustiveness = None
self.num_modes = None
self.energy_range = None
self.read_config_entry = None
self.choose_raw_ligand_entry = None
self.output_config_entry = None
# 创建分块内容
self._create_main_frame()
self._create_option_frame()
self._create_tools_frame()
self._create_output_frame()
# 帮助按钮
help_button = HelpButton(root=self.root,
help_text=TAB2_HELP_TEXT,
x=410,
y=300,
width=BUTTON_WIDTH)
create_tooltip(help_button.help_button, "获取帮助")
def __init__(self, tab, config: Configer):
self.root = tab
self.config = config
self.windows = None
# 需要保存的参数
self.input_smi = ""
self.output_path = ""
self.single_ligand = ""
self.sec_ligands = ""
self.rotate_method = ""
self.reorder_method = ""
self.validate_folder = ""
# 需要保存的输入框
self.input_smi_entry = None
self.output_path_entry = None
self.single_ligand_entry = None
self.sec_ligands_entry = None
self.rotate_method_box = None
self.reorder_method_box = None
self.input_path_entry = None
# 创建按钮
self.create_buttons()
# 帮助按钮
help_button = HelpButton(root=self.root,
help_text=TAB8_HELP_TEXT,
x=410,
y=300,
width=80)
create_tooltip(help_button.help_button, "获取帮助")
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")
def _create_choose_ligand_frame(self):
choose_ligand_labelframe = LabelFrame(self.root, text="输入选项")
choose_ligand_labelframe.place(x=10, y=10, width=570, height=85)
# 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 = ("mol", "sdf", "mol2", "pdb", "pdbqt", "xyz")
self.input_format = SCombbox(
root=choose_ligand_labelframe,
textvariable=StringVar(),
values=input_format_text,
default_value=Configer.get_para("input_format"),
x=80,
y=0,
width=60)
create_tooltip(self.input_format.combobox, "导入配体的格式")
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_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")
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_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 create_buttons(self):
gen_smi_button = SButton(self.root, text="分子生成器", x=10, y=10)
create_tooltip(gen_smi_button.button, "根据smi生成不同取代基衍生物")
gen_smi_button.button.bind("<Button-1>", self.gen_smi)
cal_rmsd_button = SButton(self.root, text="计算小分子RMSD", x=110, y=10)
create_tooltip(cal_rmsd_button.button, "计算两个小分子之间的RMSD值。")
cal_rmsd_button.button.bind("<Button-1>", self.cal_rmsd)
vina_validate_button = SButton(self.root, text="Vina一键验证", x=230, y=10)
create_tooltip(vina_validate_button.button,
"一键验证某个含有配体的蛋白是否可以用于Vina对接。")
vina_validate_button.button.bind("<Button-1>", self.vina_validate)
