def file_btn_click_event(self, clicked_btn):
name = self.info_table.item(0, 0)
if name is None:
QMessageBox.about(self, "Error", "There is no searching history")
return
# search information
searched_type = str(self.search_type_list.currentText())
searched_input = self.search_line.text()
selected_species = []
if self.species_all.isChecked():
selected_species.append('all')
else:
if self.species_btn1.isChecked():
selected_species.append('zebra fish')
if self.species_btn2.isChecked():
selected_species.append('fathead minnow')
if self.species_btn3.isChecked():
selected_species.append('medaka')
if self.species_btn4.isChecked():
selected_species.append('daphnia')
if self.species_others.isChecked():
selected_species.append('others')
selected_species = ', '.join(selected_species)
selected_ep = []
if self.ep_all.isChecked():
selected_ep.append('all')
else:
if self.ep_lc_btn.isChecked():
selected_ep.append('LC50')
if self.ep_ec_btn.isChecked():
selected_ep.append('EC50')
if self.ep_others.isChecked():
selected_ep.append('others')
selected_ep = ', '.join(selected_ep)
# chemical information
name = self.info_table.item(0, 0).text()
iupac_name = self.info_table.item(1, 0).text()
cas = self.info_table.item(2, 0).text()
smiles = self.info_table.item(3, 0).text()
# toxic information
poison_text = self.poison_text.toPlainText()
# mass spectrum
try:
self.msms_db[smiles]
fig, ax = utils.plot_mass(self.mz_array,
self.intensity_array,
save=True)
reference = self.reference_line.text()
except:
pass
# Make the entire text edit for save/print
entire_text = QTextEdit('')
entire_text.append('\n' + '=' * 10 + 'Search Information' + '=' * 10 +
'\n')
entire_text.append('Searched type: {}'.format(searched_type))
entire_text.append('Searched input: {}'.format(searched_input))
entire_text.append('Selected species: {}'.format(selected_species))
entire_text.append('Selected end point: {}'.format(selected_ep))
entire_text.append('\n' + '=' * 10 + 'Chemical Information' +
'=' * 10 + '\n')
entire_text.append('Name: {}'.format(name))
entire_text.append('IUPAC name: {}'.format(iupac_name))
entire_text.append('CAS number: {}'.format(cas))
entire_text.append('SMILES: {}'.format(smiles))
entire_text.append('\n' + '=' * 10 + 'Toxic Information' + '=' * 10 +
'\n')
entire_text.append(poison_text)
try:
self.msms_db[smiles]
entire_text.append('\n' + '=' * 10 + 'Mass Spectrum' + '=' * 10 +
'\n')
entire_text.append('reference: {}'.format(reference) + '\n')
cursor = entire_text.textCursor()
entire_text.moveCursor(QTextCursor.End)
cursor.insertImage('mass_fig.jpg')
except:
pass
if clicked_btn == 'save':
fn, _ = QFileDialog.getSaveFileName(
self, 'Export PDF', None, 'PDF files (.pdf);;All Files()')
if fn != '':
if QFileInfo(fn).suffix() == "": fn += '.pdf'
printer = QPrinter(QPrinter.HighResolution)
printer.setOutputFormat(QPrinter.PdfFormat)
printer.setOutputFileName(fn)
entire_text.document().print_(printer)
try:
os.remove('mass_fig.jpg')
except:
pass
elif clicked_btn == 'print':
printer = QPrinter(QPrinter.HighResolution)
dialog = QPrintDialog(printer, self)
if dialog.exec_() == QPrintDialog.Accepted:
entire_text.print_(printer)
try:
os.remove('mass_fig.jpg')
except:
pass
def search_btn_click_event(self):
### related to search grid ###
df = self.toxic_db
searched_type = str(self.search_type_list.currentText())
searched_input = self.search_line.text().replace(' ', '')
if searched_type == 'CAS':
try:
searched_cid = df[list(
map(lambda f: searched_input in f,
df['CAS']))]['cid'].item()
except:
QMessageBox.about(self, "Error",
"Please enter the correct CAS.")
return
elif searched_type == 'IUPAC':
try:
searched_cid = df[df['IUPAC'] == searched_input]['cid'].item()
except:
QMessageBox.about(self, "Error",
"Please enter the correct IUPAC_NAME.")
return
elif searched_type == 'SMILES':
try:
searched_cid = df[df['SMILES'] == searched_input]['cid'].item()
except:
QMessageBox.about(self, "Error",
"Please enter the correct SMILES.")
return
else:
QMessageBox.about(
self, "Error",
"Please select search type (CAS, IUPAC, or SMILES)")
return
### related to info grid ###
searched_data = self.toxic_db[self.toxic_db['cid'] == searched_cid]
cas = searched_data['CAS'].item()
iupac_name = searched_data['IUPAC'].item()
smiles = searched_data['SMILES'].item()
name, all_poison_list = utils.load_poison_info(searched_cid)
self.info_table.setItem(0, 0, QTableWidgetItem(name))
self.info_table.setItem(1, 0, QTableWidgetItem(iupac_name))
self.info_table.setItem(2, 0, QTableWidgetItem(', '.join(cas)))
self.info_table.setItem(3, 0, QTableWidgetItem(smiles))
self.info_table.resizeColumnsToContents()
### related to poison grid ###
if not self.species_all.isChecked() \
and not self.species_btn1.isChecked() \
and not self.species_btn2.isChecked() \
and not self.species_btn3.isChecked() \
and not self.species_btn4.isChecked() \
and not self.species_others.isChecked():
self.species_all.setChecked(True)
if not self.ep_all.isChecked() \
and not self.ep_lc_btn.isChecked() \
and not self.ep_ec_btn.isChecked() \
and not self.ep_others.isChecked():
self.ep_all.setChecked(True)
filtered_poison_list = []
if self.species_all.isChecked() and self.ep_all.isChecked():
filtered_poison_list = all_poison_list
elif self.species_all.isChecked() and not self.ep_all.isChecked():
if self.ep_lc_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
elif not self.species_all.isChecked() and self.ep_all.isChecked():
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
else:
ep_filtered_poison_list = []
if self.ep_lc_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in ep_filtered_poison_list
if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
poison_text = '\n\n'.join(filtered_poison_list)
self.poison_text.setText(poison_text)
### related to mass grid ###
try:
searched_msms_data = self.msms_db[smiles][0]['spectrum']
self.mz_array = [
float(d.split(':')[0]) for d in searched_msms_data.split(' ')
]
self.intensity_array = [
float(d.split(':')[1]) for d in searched_msms_data.split(' ')
]
fig, ax = utils.plot_mass(self.mz_array, self.intensity_array)
reference = self.msms_db[smiles][0]['library']['link']
self.mass_fig.clear()
self.mass_layout.removeWidget(self.mass_canvas)
self.mass_fig = fig
self.mass_canvas = FigureCanvas(self.mass_fig)
self.reference_line.setText(reference)
self.mass_canvas.draw()
self.mass_layout.addWidget(self.mass_canvas)
self.mass_layout.addWidget(self.reference_line)
self.mass_layout.addWidget(self.save_print_group)
self.mass_grid.setLayout(self.mass_layout)
self.mass_canvas.show()
except:
self.mass_fig.clear()
self.mass_layout.removeWidget(self.mass_canvas)
self.mass_canvas = FigureCanvas(self.mass_fig)
self.reference_line.setText('')
self.mass_canvas.draw()
self.mass_layout.addWidget(self.mass_canvas)
self.mass_layout.addWidget(self.reference_line)
self.mass_layout.addWidget(self.save_print_group)
QMessageBox.about(
self, "Error",
"There is no database corresponding to the {} in the mass spectrum DB"
.format(smiles))
return
def search_btn_click_event(self):
### related to search grid ###
df = self.toxic_db
searched_type = str(self.search_type_list.currentText())
searched_input = self.search_line.text().replace(' ', '')
if searched_type == 'CAS':
try:
searched_cid = df[list(
map(lambda f: searched_input in f,
df['CAS']))]['cid'].item()
except:
QMessageBox.about(
self, "No results found.",
"We do not have any datas for \"{}\"".format(
searched_input))
return
elif searched_type == 'IUPAC':
try:
searched_cid = df[df['IUPAC'] == searched_input]['cid'].item()
except:
QMessageBox.about(
self, "No results found.",
"We do not have any datas for \"{}\"".format(
searched_input))
return
elif searched_type == 'SMILES':
try:
searched_cid = df[df['SMILES'] == searched_input]['cid'].item()
except:
QMessageBox.about(
self, "No results found.",
"We do not have any datas for \"{}\"".format(
searched_input))
return
else:
QMessageBox.about(
self, "Error",
"Please select search type (CAS, IUPAC, or SMILES)")
return
### related to info grid ###
searched_data = df[df['cid'] == searched_cid]
cas = searched_data['CAS'].item()
iupac_name = searched_data['IUPAC'].item()
smiles = searched_data['SMILES'].item()
name, all_poison_list = utils.load_poison_info(searched_cid)
self.info_table.setItem(0, 0, QTableWidgetItem(name))
self.info_table.setItem(1, 0, QTableWidgetItem(iupac_name))
self.info_table.setItem(2, 0, QTableWidgetItem(', '.join(cas)))
self.info_table.setItem(3, 0, QTableWidgetItem(smiles))
self.info_table.resizeColumnsToContents()
### related to poison grid ###
if not self.species_all.isChecked() \
and not self.species_btn1.isChecked() \
and not self.species_btn2.isChecked() \
and not self.species_btn3.isChecked() \
and not self.species_btn4.isChecked() \
and not self.species_others.isChecked():
self.species_all.setChecked(True)
if not self.ep_all.isChecked() \
and not self.ep_lc_btn.isChecked() \
and not self.ep_ec_btn.isChecked() \
and not self.ep_others.isChecked():
self.ep_all.setChecked(True)
filtered_poison_list = []
if self.species_all.isChecked() and self.ep_all.isChecked():
filtered_poison_list = all_poison_list
elif self.species_all.isChecked() and not self.ep_all.isChecked():
if self.ep_lc_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
elif not self.species_all.isChecked() and self.ep_all.isChecked():
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
else:
ep_filtered_poison_list = []
if self.ep_lc_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in ep_filtered_poison_list
if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
filtered_poison_list = [' ● ' + f for f in filtered_poison_list]
poison_text = 'pubchem.{}'.format(searched_cid) + '\n\n' + '\n\n'.join(
filtered_poison_list)
self.poison_text.setText(poison_text)
### related to mass grid ###
try:
searched_msms_data = self.msms_db[smiles][0]['spectrum']
self.mz_array = [
float(d.split(':')[0]) for d in searched_msms_data.split(' ')
]
self.intensity_array = [
float(d.split(':')[1]) for d in searched_msms_data.split(' ')
]
self.mass_fig.clear()
ax = self.mass_fig.add_subplot(111)
ax = utils.plot_mass(ax, self.mz_array, self.intensity_array)
self.mass_canvas.draw()
reference = self.msms_db[smiles][0]['library']['link']
self.reference_line.setText(reference)
# +Added) Set Item and Lable of msinfo_table
idx_ms = 0
self.msinfo_table.setRowCount(
len(self.msms_db[smiles][0]['metaData']))
meta_n = []
meta_v = []
for ms_dict in self.msms_db[smiles][0]['metaData']:
self.header_list.append(ms_dict['name'])
meta_n.append(ms_dict['name'])
self.msinfo_table.setItem(
idx_ms, 0, QTableWidgetItem(str(ms_dict['value'])))
meta_v.append(ms_dict['value'])
idx_ms += 1
meta = str()
meta_all = str()
meta_all = "[MS spectrum metadata]\n\n"
for i in range(0, len(meta_n)):
meta = "►{} \n : {}".format(meta_n[i], meta_v[i])
meta_all += '{}\n'.format(meta)
print(meta_all)
self.meta_all.setText(meta_all)
print("up", meta_n)
print("up", meta_v)
self.msinfo_table.setVerticalHeaderLabels(self.header_list)
# self.msinfo_fig.clear()
# bx=self.msinfo_fig.add_subplot(111)
self.mass_canvas.draw()
self.mass_layout.addWidget(self.mass_canvas)
self.mass_layout.addWidget(self.reference_line)
self.mass_layout.addWidget(self.save_print_group)
self.mass_grid.setLayout(self.mass_layout)
self.mass_canvas.show()
#ADDED mass metadata png
# lis = []
# lis.append(utils.ms_name())
# print(utils.ms_name())
# print(lis)
# l10=[]
# for i in range (0,len(meta_n)):
# l1=(lis[0][0][i],lis[0][1][i])
# l10.append(l1)
# print(l10)
# fig = plt.figure()
# ax = fig.add_subplot(111)
# table_vals = l10
#Draw table
# the_table = plt.table(cellText=table_vals)
# the_table.auto_set_font_size(False)
# the_table.set_fontsize(24)
# the_table.scale(4, 4)
# plt.tick_params(axis='x', which='both', bottom=False, top=False, labelbottom=False)
# plt.tick_params(axis='y', which='both', right=False, left=False, labelleft=False)
# for pos in ['right','top','bottom','left']:
# plt.gca().spines[pos].set_visible(False)
# plt.savefig('msinfo.png', bbox_inches='tight', pad_inches=0.05)
# self.msinfo_table.setVerticalHeaderLabels(self.header_list)
# self.msinfo_fig.savefig('mass_info.png',
# bbox_inches='tight',
# dpi=150
# )
#ADDED MASS METADATA TABLE
#idx_ms2=0
#fig=plt.figure()
#ax=fig.add_subplot(111)
#for ms_dict in self.msms_db[smiles][0]['metaData']:
# rows=
except:
self.clear()
ax = self.mass_fig.add_subplot(111)
ax.set_yticks([0, 20, 40, 60, 80, 100])
ax.set_xlabel('m/z')
ax.set_ylabel('Intensity')
plt.tight_layout()
self.mass_canvas.draw()
self.reference_line.setText('')
QMessageBox.about(
self, "Error",
"There is no database corresponding to the {} in the mass spectrum DB"
.format(smiles))
# +Added) Clear Table
self.msinfo_table.clear()
self.msinfo_table.setRowCount(4)
self.msinfo_table.setVerticalHeaderLabels(
[" ", " ", " ", " "])
return
def search_btn_click_event(self):
### related to search grid ###
df = self.toxic_db
searched_type = str(self.search_type_list.currentText())
searched_input = self.search_line.text()
if searched_type == 'CAS':
try:
searched_input = searched_input.replace(' ', '')
searched_result = list(
map(lambda f: searched_input in f, df['CAS']))
# if there are more than one results , print first "True" cid number
searched_result = np.array(searched_result)
# print(searched_result)
if len(np.where(searched_result == True)[0]) != 1:
print("Searche results > 1")
# searched_cid = df.values[np.where(searched_result==True)[0][1]][0]
searched_cid = df.values[np.where(
searched_result == True)[0][0]][0]
else:
# searched_cid = df[list(map(lambda f: searched_input in f, df['CAS']))]['cid'].item()
searched_cid = df[searched_result]['cid'].item()
except:
QMessageBox.about(
self, "No results found.",
"We do not have any datas for \"{}\"".format(
searched_input))
return
elif searched_type == 'IUPAC':
try:
searched_input = searched_input.strip()
searched_result = df['IUPAC'] == searched_input
if len(np.where(searched_result == True)[0]) != 1:
print("Searche results > 1")
searched_cid = df.values[np.where(
searched_result == True)[0][0]][0]
else:
searched_cid = df[df['IUPAC'] ==
searched_input]['cid'].item()
# searched_cid = df[df['IUPAC']==searched_input]['cid'].item()
except:
QMessageBox.about(
self, "No results found.",
"We do not have any datas for \"{}\"".format(
searched_input))
return
elif searched_type == 'SMILES':
try:
searched_input = searched_input.replace(' ', '')
searched_result = df['SMILES'] == searched_input
if len(np.where(searched_result == True)[0]) != 1:
print("Searche results > 1")
searched_cid = df.values[np.where(
searched_result == True)[0][0]][0]
else:
searched_cid = df[df['SMILES'] ==
searched_input]['cid'].item()
# searched_cid = df[df['SMILES']==searched_input]['cid'].item()
except:
QMessageBox.about(
self, "No results found.",
"We do not have any datas for \"{}\"".format(
searched_input))
return
else:
QMessageBox.about(
self, "Error",
"Please select search type (CAS, IUPAC, or SMILES)")
return
### related to info grid ###
searched_data = df[df['cid'] == searched_cid]
cas = searched_data['CAS'].item()
iupac_name = searched_data['IUPAC'].item()
smiles = searched_data['SMILES'].item()
##########################set poison text module start###################################
DBid = 1
name, all_poison_list = utils.load_poison_info(searched_cid, DBid)
# self.info_table.horizontalScrollBar().setValue(0)
self.info_table.setItem(0, 0, QTableWidgetItem(name))
self.info_table.setItem(1, 0, QTableWidgetItem(iupac_name))
self.info_table.setItem(2, 0, QTableWidgetItem(', '.join(cas)))
self.info_table.setItem(3, 0, QTableWidgetItem(smiles))
self.info_table.resizeColumnsToContents()
# self.info_table.scrollToItem()
# self.info_table.setHorizontalScrollMode('mode : ScrollMode')
# self.info_table.horizontalScrollBar().setValue(0)
### related to poison grid ###
if not self.species_all.isChecked() \
and not self.species_btn1.isChecked() \
and not self.species_btn2.isChecked() \
and not self.species_btn3.isChecked() \
and not self.species_btn4.isChecked() \
and not self.species_others.isChecked():
self.species_all.setChecked(True)
if not self.ep_all.isChecked() \
and not self.ep_lc_btn.isChecked() \
and not self.ep_ec_btn.isChecked() \
and not self.ep_others.isChecked():
self.ep_all.setChecked(True)
filtered_poison_list = []
if self.species_all.isChecked() and self.ep_all.isChecked():
filtered_poison_list = all_poison_list
elif self.species_all.isChecked() and not self.ep_all.isChecked():
if self.ep_lc_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
elif not self.species_all.isChecked() and self.ep_all.isChecked():
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
else:
ep_filtered_poison_list = []
if self.ep_lc_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in ep_filtered_poison_list
if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
filtered_poison_list = [
' ▶︎ ' + f
for f in filtered_poison_list
]
poison_text = '<p style="font-size: 40px"><b>Ecotoxicity data form pubchem</b></p>' + '<br>' + '<br><br>'.join(
filtered_poison_list)
##########################set poison text module end###################################
##########################set poison text module start###################################
DBid = 2
all_poison_list = utils.load_poison_info(searched_cid, DBid)
### related to poison grid ###
if not self.species_all.isChecked() \
and not self.species_btn1.isChecked() \
and not self.species_btn2.isChecked() \
and not self.species_btn3.isChecked() \
and not self.species_btn4.isChecked() \
and not self.species_others.isChecked():
self.species_all.setChecked(True)
if not self.ep_all.isChecked() \
and not self.ep_lc_btn.isChecked() \
and not self.ep_ec_btn.isChecked() \
and not self.ep_others.isChecked():
self.ep_all.setChecked(True)
filtered_poison_list = []
if self.species_all.isChecked() and self.ep_all.isChecked():
filtered_poison_list = all_poison_list
elif self.species_all.isChecked() and not self.ep_all.isChecked():
if self.ep_lc_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
elif not self.species_all.isChecked() and self.ep_all.isChecked():
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
else:
ep_filtered_poison_list = []
if self.ep_lc_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in ep_filtered_poison_list
if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
filtered_poison_list = [
' ▶︎ ' + f
for f in filtered_poison_list
]
poison_text = poison_text + '<br><br>' + '<p style="font-size: 40px"><b>Ecotoxicity data of 생활화학제품 from various DBs</b></p>' + '<br>' + '<br><br>'.join(
filtered_poison_list)
##########################set poison text module end###################################
##########################set poison text module start###################################
DBid = 3
all_poison_list = utils.load_poison_info(searched_cid, DBid)
### related to poison grid ###
if not self.species_all.isChecked() \
and not self.species_btn1.isChecked() \
and not self.species_btn2.isChecked() \
and not self.species_btn3.isChecked() \
and not self.species_btn4.isChecked() \
and not self.species_others.isChecked():
self.species_all.setChecked(True)
if not self.ep_all.isChecked() \
and not self.ep_lc_btn.isChecked() \
and not self.ep_ec_btn.isChecked() \
and not self.ep_others.isChecked():
self.ep_all.setChecked(True)
filtered_poison_list = []
if self.species_all.isChecked() and self.ep_all.isChecked():
filtered_poison_list = all_poison_list
elif self.species_all.isChecked() and not self.ep_all.isChecked():
if self.ep_lc_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
elif not self.species_all.isChecked() and self.ep_all.isChecked():
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
else:
ep_filtered_poison_list = []
if self.ep_lc_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in ep_filtered_poison_list
if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
filtered_poison_list = [
' ▶︎ ' + f
for f in filtered_poison_list
]
poison_text = poison_text + '<br><br>' + '<p style="font-size: 40px"><b>Ecotoxicity data from experiments 안전성평가연구소 </b></p>' + '<br>' + '<br><br>'.join(
filtered_poison_list)
##########################set poison text module end###################################
self.poison_text.setText(poison_text)
### related to mass grid ###
try:
self.mass_fig.clear()
self.MS_data = utils.load_ms_info(smiles, self.msms_db)
searched_msms_data = self.MS_data[smiles][0]['spectrum']
self.mz_array = [
float(d.split(':')[0]) for d in searched_msms_data.split(' ')
]
self.intensity_array = [
float(d.split(':')[1]) for d in searched_msms_data.split(' ')
]
ax = self.mass_fig.add_subplot(111)
# ax = utils.plot_mass(ax, self.mz_array, self.intensity_array)
utils.plot_mass(ax, self.mz_array, self.intensity_array)
self.mass_canvas.draw()
reference = self.MS_data[smiles][0]['library']['link']
self.reference_line.setText(reference)
# (Added) Set Item and Label of msinfo_table
idx_ms = 0
self.msinfo_table.setRowCount(
len(self.MS_data[smiles][0]['metaData']))
meta_n = []
meta_v = []
for ms_dict in self.MS_data[smiles][0]['metaData']:
self.header_list.append(ms_dict['name'])
meta_n.append(ms_dict['name'])
self.msinfo_table.setItem(
idx_ms, 0, QTableWidgetItem(str(ms_dict['value'])))
meta_v.append(ms_dict['value'])
idx_ms += 1
# meta=str()
# meta_all=str()
meta_all = "[MS spectrum metadata]\n\n"
for i in range(0, len(meta_n)):
meta = "►{} \n : {}".format(meta_n[i], meta_v[i])
meta_all += '{}\n'.format(meta)
# print(meta_all)
self.meta_all.setText(meta_all)
# print("up", meta_n)
# print("up", meta_v)
self.msinfo_table.setVerticalHeaderLabels(self.header_list)
self.msinfo_table.setStyleSheet("Color : black")
self.msinfo_table.resizeColumnsToContents()
# self.mass_canvas.draw()
self.mass_layout.addWidget(self.mass_canvas)
self.mass_layout.addWidget(self.reference_line)
# self.mass_layout.addWidget(self.mass_info_group)
self.mass_grid.setLayout(self.mass_layout)
self.mass_canvas.show()
except:
self.mass_fig.clear()
ax = self.mass_fig.add_subplot(111)
ax.set_yticks([0, 20, 40, 60, 80, 100])
ax.set_xlabel('m/z')
ax.set_ylabel('Intensity')
plt.tight_layout()
self.mass_canvas.draw()
# (Added) Clear Table
self.msinfo_table.clear()
self.msinfo_table.setRowCount(20)
self.msinfo_table.setVerticalHeaderLabels([
" ", " ", " ", " ", " ",
" ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ",
" ", " ", " "
])
self.msinfo_table.setColumnWidth(0, 3000)
# self.msinfo_table.setVerticalHeaderLabels([" ", " ", " ", " "])
self.reference_line.setText('')
# self.mass_canvas = FigureCanvas(self.mass_fig)
# self.mass_canvas.draw()
self.mass_layout.addWidget(self.mass_canvas)
self.mass_layout.addWidget(self.reference_line)
# self.mass_layout.addWidget(self.save_print_group)
self.reference_line.setText('')
QMessageBox.about(
self, "Error",
"There is no database corresponding to the {} in the mass spectrum DB"
.format(smiles))
return
def search_btn_click_event(self):
### related to search grid ###
df = self.toxic_db
searched_type = str(self.search_type_list.currentText())
searched_input = self.search_line.text().replace(' ', '')
if searched_type == 'CAS':
try:
searched_cid = df[list(
map(lambda f: searched_input in f,
df['CAS']))]['cid'].item()
except:
QMessageBox.about(
self, "No results found.",
"We do not have any datas for \"{}\"".format(
searched_input))
return
elif searched_type == 'IUPAC':
try:
searched_cid = df[df['IUPAC'] == searched_input]['cid'].item()
except:
QMessageBox.about(
self, "No results found.",
"We do not have any datas for \"{}\"".format(
searched_input))
return
elif searched_type == 'SMILES':
try:
searched_cid = df[df['SMILES'] == searched_input]['cid'].item()
except:
QMessageBox.about(
self, "No results found.",
"We do not have any datas for \"{}\"".format(
searched_input))
return
else:
QMessageBox.about(
self, "Error",
"Please select search type (CAS, IUPAC, or SMILES)")
return
### related to info grid ###
searched_data = df[df['cid'] == searched_cid]
cas = searched_data['CAS'].item()
iupac_name = searched_data['IUPAC'].item()
smiles = searched_data['SMILES'].item()
name, all_poison_list = utils.load_poison_info(searched_cid)
self.info_table.setItem(0, 0, QTableWidgetItem(name))
self.info_table.setItem(1, 0, QTableWidgetItem(iupac_name))
self.info_table.setItem(2, 0, QTableWidgetItem(', '.join(cas)))
self.info_table.setItem(3, 0, QTableWidgetItem(smiles))
self.info_table.resizeColumnsToContents()
### related to poison grid ###
if not self.species_all.isChecked() \
and not self.species_btn1.isChecked() \
and not self.species_btn2.isChecked() \
and not self.species_btn3.isChecked() \
and not self.species_btn4.isChecked() \
and not self.species_others.isChecked():
self.species_all.setChecked(True)
if not self.ep_all.isChecked() \
and not self.ep_lc_btn.isChecked() \
and not self.ep_ec_btn.isChecked() \
and not self.ep_others.isChecked():
self.ep_all.setChecked(True)
filtered_poison_list = []
if self.species_all.isChecked() and self.ep_all.isChecked():
filtered_poison_list = all_poison_list
elif self.species_all.isChecked() and not self.ep_all.isChecked():
if self.ep_lc_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
elif not self.species_all.isChecked() and self.ep_all.isChecked():
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in all_poison_list if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in all_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
else:
ep_filtered_poison_list = []
if self.ep_lc_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'LC50' in p
]
if self.ep_ec_btn.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list if 'EC50' in p
]
if self.ep_others.isChecked():
ep_filtered_poison_list += [
p for p in all_poison_list
if not 'LC50' in p and not 'EC50' in p
]
if self.species_btn1.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' in p.lower() or \
'zebrafish' in p.lower() or \
'danio rerio' in p.lower()]
if self.species_btn2.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'fathead minnow' in p.lower() or \
'pimephales promelas' in p.lower()]
if self.species_btn3.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'medaka' in p.lower() or \
'oryzias latipes' in p.lower()]
if self.species_btn4.isChecked():
filtered_poison_list += [
p for p in ep_filtered_poison_list
if 'daphnia' in p.lower()
]
if self.species_others.isChecked():
filtered_poison_list += [p for p in ep_filtered_poison_list if 'zebra fish' not in p.lower() and \
'zebrafish' not in p.lower() and \
'danio rerio' not in p.lower() and \
'fathead minnow' not in p.lower() and \
'pimephales promelas' not in p.lower() and \
'medaka' not in p.lower() and \
'oryzias latipes' not in p.lower() and \
'daphnia' not in p.lower()]
filtered_poison_list = [' ● ' + f for f in filtered_poison_list]
poison_text = 'pubchem.{}'.format(searched_cid) + '\n\n' + '\n\n'.join(
filtered_poison_list)
self.poison_text.setText(poison_text)
### related to mass grid ###
try:
searched_msms_data = self.msms_db[smiles][0]['spectrum']
self.mz_array = [
float(d.split(':')[0]) for d in searched_msms_data.split(' ')
]
self.intensity_array = [
float(d.split(':')[1]) for d in searched_msms_data.split(' ')
]
self.mass_fig.clear()
ax = self.mass_fig.add_subplot(111)
ax = utils.plot_mass(ax, self.mz_array, self.intensity_array)
self.mass_canvas.draw()
reference = self.msms_db[smiles][0]['library']['link']
self.reference_line.setText(reference)
except:
self.mass_fig.clear()
ax = self.mass_fig.add_subplot(111)
ax.set_yticks([0, 20, 40, 60, 80, 100])
ax.set_xlabel('m/z')
ax.set_ylabel('Intensity')
plt.tight_layout()
self.mass_canvas.draw()
self.reference_line.setText('')
QMessageBox.about(
self, "Error",
"There is no database corresponding to the {} in the mass spectrum DB"
.format(smiles))
return