def save_para(self):
# 检查python
choose_python_path = self.choose_python_path_entry.textvariable.get()
if not Check.check_python(choose_python_path):
choose_python_path = ""
# 检查obabel
obabel_path = self.choose_obabel_path_entry.textvariable.get()
if not Check.check_obabel(obabel_path):
obabel_path = ""
self.config.para_dict["python_path"] = choose_python_path
self.config.para_dict["obabel_path"] = obabel_path
# 读取原始的配置文件
with open(para_file, "r") as f:
for line in f.readlines():
key = line.split("=")[0]
if key == "python_path" or key == "obabel_path":
continue
try:
value = line.split("=")[1]
except IndexError:
value = ""
self.config.para_dict[key] = value.strip()
self.config.save_para()
self.top.destroy()
def _vina_validate(self, event):
target_folder = self.input_path_entry.textvariable.get()
if not Check.check_obabel() and Check.check_python():
messagebox.showerror("错误！", "请检测obabel和mgltools的python设置！")
return
if not vina_validator.validate_folder(target_folder):
messagebox.showerror("错误！", "无法验证所选文件夹")
else:
messagebox.showinfo("验证成功！", "验证%s完成！" % target_folder)
def _gen_smi(self, event):
if not Check.check_obabel():
messagebox.showerror("错误！", "请检查obabel路径是否配置正确！")
return
smi = self.input_smi_entry.textvariable.get()
output_path = self.output_path_entry.textvariable.get()
if Check.check_path(output_path):
messagebox.showerror("错误", "输出路径不能为空或者包含空格！")
return
# 如果只有一个元素则表示没有[R]标签
if len(smi.split("[R]")) == 1:
messagebox.showerror("错误", "%s没有[R]标签！" % smi)
return
gen_smi_der(smi, output_path)
messagebox.showinfo("成功！", "成功生成衍生物！\n请检查后使用。")
def _start_convert(self, event):
if not Check.check_obabel():
return
if not Check.check_python():
return
input_files = self.choose_ligands_entry.textvariable.get()
# 判断输入内容不能包含空格
if Check.has_space(input_files):
messagebox.showerror("输入错误！", "输入路径不能包含空格！")
return
input_format = self.input_format.textvariable.get()
input_ligands = []
# 判断输入的内容
if input_files.endswith(";"):
if input_files.split(".")[-1][0:-1] != input_format:
messagebox.showerror("错误！", "选择的配体和输入的配体不符合！")
return
input_ligands.extend(input_files.split(";")[0:-1])
elif os.path.isdir(input_files):
list_file = os.listdir(input_files)
for file in list_file:
if file.endswith(input_format):
input_ligands.append(input_files + os.sep + file)
if len(input_ligands) == 0:
messagebox.showerror("错误！", "所选文件夹中不包含选择格式的配体！")
return
else:
messagebox.showerror("错误！", "请检查输入的配体！")
return
ph = self.ph.textvariable.get()
# ph不能为空
if ph == "":
messagebox.showerror("错误！", "请输入pH！")
return
gen3d = self.gen3d.variable.get()
is_minimize = self.is_minimize.variable.get()
minimize = self.minimize.textvariable.get()
output_format = self.output_format.textvariable.get()
output_path = self.choose_output_dir_entry.textvariable.get()
# 输出目录不能为空
if output_path == "" or output_path.count(" ") > 0:
messagebox.showerror("输入错误！", "输出路径不能包含空格！")
return
if not os.path.exists(output_path):
messagebox.showerror("输入错误！", "输出路径不存在！")
return
if input_format == output_format:
messagebox.showerror("错误！", "输入和输出格式不应相等！")
return
output_ligands = []
for ligand in input_ligands:
ligand_name = ligand.split(
os.sep)[-1].split(".")[0] + "." + output_format
output_ligands.append(output_path + os.sep + ligand_name)
self.progress["maximum"] = len(input_ligands)
# 进行格式转换
if input_format == "pdbqt": # pdbqt->other
# pdbqt->pdb
if output_format == "pdb":
i = 0
while i < len(input_ligands):
# 更改标签文字
label_text = "%i/%i" % (i + 1, len(input_ligands))
self.progress_label.label.configure(text=label_text)
self.progress_label.label.update()
# 更新进度条
self.progress["value"] = i + 1
self.progress.update()
pdbqt_2_pdb(input_ligands[i], output_ligands[i])
i += 1
messagebox.showinfo("转换完成！", "成功将pdbqt转换成pdb！")
self.progress["value"] = 0
self.progress_label.label.configure(text="没有任务")
return
# pdbqt->other
else:
# obabel转换成输出格式，先转成pdb
pdb_ligands = []
for ligand in input_ligands:
ligand_name = ligand.split(
os.sep)[-1].split(".")[0] + ".pdb"
pdb_ligands.append(output_path + os.sep + "tmp" + os.sep +
ligand_name)
self.progress["maximum"] = len(input_ligands) * 2
mk_output_dir(output_path + os.sep + "tmp") # 创建临时文件夹
i = 0
while i < len(input_ligands):
label_text = "%i/%i" % (i + 1, len(input_ligands))
self.progress_label.label.configure(text=label_text)
self.progress_label.label.update()
self.progress["value"] = i + 1
self.progress.update()
pdbqt_2_pdb(input_ligands[i], pdb_ligands[i])
i += 1
i = 0
while i < len(input_ligands):
# 更改标签文字
label_text = "%i/%i" % (i + 1, len(input_ligands))
self.progress_label.label.configure(text=label_text)
self.progress_label.label.update()
# 更新进度条
self.progress["value"] = i + 1 + len(input_ligands)
self.progress.update()
pdb_2_other(pdb_ligands[i], output_ligands[i])
i += 1
# 删除临时pdb文件
shutil.rmtree(output_path + os.sep + "tmp")
messagebox.showinfo("转换完成！", "成功将pdbqt转换%s！" % output_format)
self.progress["value"] = 0
self.progress_label.label.configure(text="没有任务")
return
# pdb/mol2->pdbqt
elif (input_format == "pdb"
or input_format == "mol2") and output_format == "pdbqt":
i = 0
while i < len(input_ligands):
# 更改标签文字
label_text = "%i/%i" % (i + 1, len(input_ligands))
self.progress_label.label.configure(text=label_text)
self.progress_label.label.update()
# 更新进度条
self.progress["value"] = i + 1 + len(input_ligands)
self.progress.update()
pdb_mol2_2_pdbqt(input_ligands[i], output_ligands[i])
i += 1
messagebox.showinfo("转换完成！", "成功将%s转换pdbqt！" % input_format)
self.progress["value"] = 0
self.progress_label.label.configure(text="没有任务")
return
else:
# mol/smi->pdbqt
if input_format == "mol" or input_format == "smi" and output_format == "pdbqt":
pdb_ligands = []
for ligand in input_ligands:
ligand_name = ligand.split(
os.sep)[-1].split(".")[0] + ".pdb"
pdb_ligands.append(output_path + os.sep + "tmp" + os.sep +
ligand_name)
self.progress["maximum"] = len(input_ligands) * 2
mk_output_dir(output_path + os.sep + "tmp") # 创建临时文件夹
i = 0
while i < len(input_ligands):
label_text = "%i/%i" % (i + 1, len(input_ligands))
self.progress_label.label.configure(text=label_text)
self.progress_label.label.update()
self.progress["value"] = i + 1
self.progress.update()
two_d_2_pdb(input_ligands[i], pdb_ligands[i], ph, minimize)
i += 1
i = 0
while i < len(input_ligands):
# 更改标签文字
label_text = "%i/%i" % (i + 1, len(input_ligands))
self.progress_label.label.configure(text=label_text)
self.progress_label.label.update()
# 更新进度条
self.progress["value"] = i + 1 + len(input_ligands)
self.progress.update()
pdb_mol2_2_pdbqt(pdb_ligands[i], output_ligands[i])
i += 1
# 删除临时pdb文件
shutil.rmtree(output_path + os.sep + "tmp")
messagebox.showinfo("转换完成！", "成功将%s转换pdbqt！" % input_format)
self.progress["value"] = 0
self.progress_label.label.configure(text="没有任务")
return
# sdf->pdbqt
elif (input_format == "sdf"
or input_format == "xyz") and output_format == "pdbqt":
# 先转pdb
pdb_ligands = []
for ligand in input_ligands:
ligand_name = ligand.split(
os.sep)[-1].split(".")[0] + ".pdb"
pdb_ligands.append(output_path + os.sep + "tmp" + os.sep +
ligand_name)
self.progress["maximum"] = len(input_ligands) * 2
mk_output_dir(output_path + os.sep + "tmp") # 创建临时文件夹
i = 0
while i < len(input_ligands):
label_text = "%i/%i" % (i + 1, len(input_ligands))
self.progress_label.label.configure(text=label_text)
self.progress_label.label.update()
self.progress["value"] = i + 1
self.progress.update()
three_d_2_pdb(input_ligands[i], pdb_ligands[i],
is_minimize, minimize)
i += 1
i = 0
while i < len(input_ligands):
# 更改标签文字
label_text = "%i/%i" % (i + 1, len(input_ligands))
self.progress_label.label.configure(text=label_text)
self.progress_label.label.update()
# 更新进度条
self.progress["value"] = i + 1 + len(input_ligands)
self.progress.update()
pdb_mol2_2_pdbqt(pdb_ligands[i], output_ligands[i])
i += 1
# 删除临时pdb文件
shutil.rmtree(output_path + os.sep + "tmp")
messagebox.showinfo("转换完成！", "成功将%s转换pdbqt！" % input_format)
self.progress["value"] = 0
self.progress_label.label.configure(text="没有任务")
return
# mol/smi/sdf/mol2/pdb/xyz->pdb/sdf/mol2/xyz
else:
if gen3d == "1":
# 3D并最小化
if is_minimize == "1":
i = 0
while i < len(input_ligands):
label_text = "%s/%s" % (i + 1, len(input_ligands))
self.progress_label.label.configure(
text=label_text)
self.progress_label.label.update()
self.progress["value"] = i + 1
self.progress.update()
ob_3d_min(input_ligands[i], output_ligands[i], ph,
minimize)
i += 1
messagebox.showinfo(
"成功！",
"成功将%s转换成%s！" % (input_format, output_format))
self.progress["value"] = 0
self.progress_label.label.configure(text="没有任务")
# 3D不最小化
else:
i = 0
while i < len(input_ligands):
label_text = "%s/%s" % (i + 1, len(input_ligands))
self.progress_label.label.configure(
text=label_text)
self.progress_label.label.update()
self.progress["value"] = i + 1
self.progress.update()
ob_3d(input_ligands[i], output_ligands[i], ph)
i += 1
messagebox.showinfo(
"成功！",
"成功将%s转换成%s！" % (input_format, output_format))
self.progress["value"] = 0
self.progress_label.label.configure(text="没有任务")
else:
# 不3D并最小化
if is_minimize == "1":
i = 0
while i < len(input_ligands):
label_text = "%s/%s" % (i + 1, len(input_ligands))
self.progress_label.label.configure(
text=label_text)
self.progress_label.label.update()
self.progress["value"] = i + 1
self.progress.update()
ob_min(input_ligands[i], output_ligands[i], ph,
minimize)
i += 1
messagebox.showinfo(
"成功！",
"成功将%s转换成%s！" % (input_format, output_format))
self.progress["value"] = 0
self.progress_label.label.configure(text="没有任务")
# 不3D也不最小化
else:
i = 0
while i < len(input_ligands):
label_text = "%s/%s" % (i + 1, len(input_ligands))
self.progress_label.label.configure(
text=label_text)
self.progress_label.label.update()
self.progress["value"] = i + 1
self.progress.update()
ob(input_ligands[i], output_ligands[i])
i += 1
messagebox.showinfo(
"成功！",
"成功将%s转换成%s！" % (input_format, output_format))
self.progress["value"] = 0
self.progress_label.label.configure(text="没有任务")
def _cal_rmsd(self, event):
single_ligand = self.single_ligand_entry.textvariable.get()
sec_ligands = self.sec_ligands_entry.textvariable.get()
rotate_method = self.rotate_method_box.textvariable.get()
reorder_method = self.reorder_method_box.textvariable.get()
if Check.check_path(single_ligand) or Check.check_path(sec_ligands):
messagebox.showerror("错误", "选择的文件或者路径不能为空或者包括空格！")
return
if not Check.check_obabel():
messagebox.showerror("错误！", "Obabel配置不正确!")
return
sec_ligands_path = []
# 如果选择的是一个文件
if os.path.isfile(sec_ligands):
sec_ligands_path.append(sec_ligands)
# 如果选的是多个文件
elif os.path.isdir(sec_ligands):
list_file = os.listdir(sec_ligands)
for file in list_file:
if file.endswith("xyz"):
sec_ligands_path.append(sec_ligands + os.sep + file)
if len(sec_ligands_path) == 0:
messagebox.showerror("错误！", "所选文件夹中不包含xyz的配体！")
return
else:
messagebox.showerror("错误！请检查输入的配体！")
return
rmsds = {}
for sec_ligand_path in sec_ligands_path:
rmsd = charnley_cal_rmsd(single_ligand, sec_ligand_path,
rotate_method, reorder_method)
if rmsd:
rmsds[os.path.split(sec_ligand_path)[-1][:-4]] = rmsd
else:
print("%s无法计算RMSD！" % sec_ligand_path)
continue
if len(rmsds) == 1:
top = SMultiTopLevel(self.windows,
win_x=400,
win_y=100,
title="RMSD结果").toplevel
for ligand in rmsds:
text = "%s vs %s" % (os.path.split(single_ligand)[-1]
[:-4], os.path.split(ligand)[-1])
SLabel(top, text=text, x=10, y=10)
text = rmsds[ligand]
SLabel(top, text=text, x=10, y=50)
elif len(rmsds) == 0:
messagebox.showerror("错误！", "没有得到RMSD值！")
return
else:
# 多个输出文件到目录中
output_filename = os.path.join(sec_ligands, "rmsd.txt")
with open(output_filename, "w") as f:
f.writelines("second_ligand\trmsd\n")
for ligand in rmsds:
f.write("%s\t%s\n" % (ligand, rmsds[ligand]))
messagebox.showinfo("成功！", "成功导出rmsd结果到%s" % output_filename)
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()