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 _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 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 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_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 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)
def choose_chain(self):
self.chain_list = Listbox(self.choose_chain_tab, width=30, height=10)
self.chain_list.place(x=10, y=10, width=255, height=150)
scroll = Scrollbar(self.chain_list)
scroll.pack(side=RIGHT, fill=Y)
self.chain_list.configure(yscrollcommand=scroll.set)
scroll.config(command=self.chain_list.yview)
pre_button = SButton(self.choose_chain_tab, "上一步", 10, 170)
pre_button.button.bind("<Button-1>", self.jump_model)
next_button = SButton(self.choose_chain_tab, "下一步", 165, 170)
next_button.button.bind("<Button-1>", self.jump_ligand)
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 _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_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 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 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_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 _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 _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 _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_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 choose_model(self):
# 禁用后两个
self.notebook.tab(1, state="disable")
self.notebook.tab(2, state="disable")
self.model_list = Listbox(self.choose_model_tab, width=30, height=10)
model_ids = ReceptorProcessor.get_model_ids(self.structure)
Tab1.refresh_listbox(model_ids, self.model_list)
self.model_list.place(x=10, y=10, width=255, height=150)
scroll = Scrollbar(self.model_list)
scroll.pack(side=RIGHT, fill=Y)
self.model_list.configure(yscrollcommand=scroll.set)
scroll.config(command=self.model_list.yview)
next_button = SButton(self.choose_model_tab, "下一步", 165, 170)
next_button.button.bind("<Button-1>", self.jump_chain)
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 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 _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")
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 prepared_receptor(self, event):
input_file = self.choose_raw_receptor_entry.textvariable.get()
output_path = self.choose_prepare_output_path.textvariable.get()
fix_receptor = int(self.is_fix_receptor.variable.get())
fix_method = self.fix_method.textvariable.get()
preserve_charges = int(self.preserve_charges.variable.get())
nphs = int(self.nphs.variable.get())
lps = int(self.lps.variable.get())
waters = int(self.waters.variable.get())
nonstdres = int(self.nonstdres.variable.get())
if not Check.check_python():
return
if Check.check_path(input_file) or Check.check_path(output_path):
messagebox.showinfo("错误！", "输入输出文件不能包含空格")
return
if not os.path.exists(input_file):
messagebox.showerror("错误", "所选文件或者文件夹不存在!")
return
if os.path.isdir(input_file):
# 选择的是文件夹,批量准备受体
receptors = get_receptors(input_file)
input_dir = input_file
for receptor in receptors:
input_file = input_dir + os.sep + receptor
output_file = output_path + os.sep + receptor + "qt"
# 准备失败则继续
if not prepare_receptor(input_file, output_file, fix_method,
preserve_charges, nphs, lps, waters,
nonstdres):
continue
messagebox.showinfo("成功", "成功准备受体！\n注意：自动准备会删除DNA等非标准残基，结果仅供参考。")
elif input_file.endswith(".pdb"):
# 如果勾选biopython功能
if fix_receptor:
message = ChainExtractor.judge_homo(input_file)
# 包含同源链。选择同源链，保存到chains列表中。
if message:
warning = ""
for content in message:
warning += content + "\n"
if messagebox.askyesno("检测到同源链",
"是否保留只保留特定链？（可多选）\n" + warning):
structure = ReceptorProcessor.get_structure(input_file)
chains_ids = ReceptorProcessor.get_chain_ids(
structure[0])
top = STopLevel(self.root, 275, 205,
"选择要保存的链").toplevel
chains_list = Listbox(top,
width=30,
height=10,
selectmode=EXTENDED)
chains_list.place(x=10, y=10, width=255, height=150)
self.refresh_listbox(chains_ids, chains_list)
scroll = Scrollbar(chains_list)
scroll.pack(side=RIGHT, fill=Y)
chains_list.configure(yscrollcommand=scroll.set)
scroll.config(command=chains_list.yview)
def extract_chains():
Tab1.chains = []
selections = chains_list.curselection()
for select in selections:
Tab1.chains.append(chains_list.get(select))
top.destroy()
save_button = SButton(top, "提取链", 10, 170)
save_button.button.configure(command=extract_chains)
def cancel():
Tab1.chains = None
top.destroy()
cancel_button = SButton(top, "取消", 165, 170)
cancel_button.button.configure(command=cancel)
top.protocol("WM_DELETE_WINDOW", cancel)
self.root.wait_window(top)
else:
Tab1.chains = []
else:
messagebox.showinfo("没有检测到同源链", "尝试使用biopython进行修复……")
Tab1.chains = []
if Tab1.chains is None:
return
structure = ReceptorProcessor.get_structure(input_file)
output_file = output_path + os.sep + "bio_fix_" + os.path.split(
input_file)[-1]
ChainExtractor.extract_chain(structure, Tab1.chains,
output_file)
messagebox.showinfo("成功!", "成功保存到%s" % output_file)
else:
# 没有勾选，直接转换单个文件为pdbqt文件
output_file = output_path + os.sep + "preped.pdbqt"
if prepare_receptor(input_file, output_file, fix_method,
preserve_charges, nphs, lps, waters,
nonstdres):
messagebox.showinfo(
"成功", "成功准备受体！\n注意：自动准备会删除DNA等非标准残基，结果仅供参考。")
else:
messagebox.showerror("准备失败", "无法准备受体，请根据命令行查看原因。")
return
else:
messagebox.showinfo("错误!", "不支持输入内容，请确定是文件夹或者pdb文件")
return
def _create_output_ligand_frame(self):
choose_output_ligand_labelframe = LabelFrame(self.root, text="输出选项")
choose_output_ligand_labelframe.place(x=10,
y=100,
width=570,
height=115)
# 第一排
first_y = 0
SLabel(root=choose_output_ligand_labelframe,
text="输出格式：",
x=10,
y=first_y)
output_format_text = ("pdbqt", "pdb", "sdf", "xyz")
self.output_format = SCombbox(
root=choose_output_ligand_labelframe,
textvariable=StringVar(),
values=output_format_text,
default_value=Configer.get_para("output_format"),
x=80,
y=0,
width=60)
create_tooltip(self.output_format.combobox, "导出配体的格式")
# 第二排
second_y = 30
# 生成3d
SLabel(root=choose_output_ligand_labelframe,
text="选 项：",
x=10,
y=second_y)
self.gen3d = SCheckbutton(root=choose_output_ligand_labelframe,
text="3d",
variable=StringVar(),
value=Configer.get_para("gen3d"),
x=150,
y=second_y)
create_tooltip(self.gen3d.checkbutton, "是否生成三维坐标。\n"
"输入配体是平面结构时，请勾选。\n"
"输入配体时立体结构时，不建议勾选。")
# pH
SLabel(root=choose_output_ligand_labelframe,
text="pH",
x=80,
y=second_y)
self.ph = SEntry(root=choose_output_ligand_labelframe,
textvariable=StringVar(),
text=Configer.get_para("pH"),
x=110,
y=second_y + 2,
width=30)
create_tooltip(
self.ph.entry, "按照一定的规则在指定pH生成质子化状态。为obabel内置"
"方法，对某些氨基酸可能会发生变化，结果不一定可靠。")
# 能量最小化
self.is_minimize = SCheckbutton(choose_output_ligand_labelframe,
text="能量最小化",
variable=StringVar(),
value=Configer.get_para("is_minimize"),
x=200,
y=second_y)
create_tooltip(self.is_minimize.checkbutton, "是否对分子进行能量最小化")
self.is_minimize.checkbutton.bind("<Button-1>", self._disable_minimize)
SLabel(root=choose_output_ligand_labelframe,
text="力场",
x=290,
y=second_y)
minimize_value = ("MMFF94", "MMFF94s", "GAFF", "Chemical", "UFF")
self.minimize = SCombbox(root=choose_output_ligand_labelframe,
textvariable=StringVar(),
values=minimize_value,
default_value=Configer.get_para("minimize"),
x=325,
y=second_y,
width=100)
create_tooltip(self.minimize.combobox, "能量最小化使用的力场，推荐MMFF94")
# 默认
default_button = SButton(root=choose_output_ligand_labelframe,
text="默认",
x=450,
y=second_y - 2)
default_button.button.bind("<Button-1>", self._default)
create_tooltip(default_button.button, "恢复默认值")
# 初始化状态
if self.is_minimize.variable.get(
) == "0" or self.is_minimize.variable.get() == "":
self.minimize.combobox.configure(state="disable")
# 第三排
third_y = 60
choose_output_dir_button = SButton(choose_output_ligand_labelframe,
text="选择输出文件夹",
x=10,
y=third_y)
create_tooltip(choose_output_dir_button.button, "选择配体输出的文件夹")
self.choose_output_dir_entry = SEntry(
root=choose_output_ligand_labelframe,
textvariable=StringVar(),
text=Configer.get_para("ligand_output_dir"),
x=110,
y=third_y + 4,
width=450)
create_tooltip(self.choose_output_dir_entry.entry, "所选的输出目录")
choose_output_dir_button.bind_open_dir(
entry_text=self.choose_output_dir_entry.textvariable,
title="选择要输出配体的文件夹")
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()))