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XChemExplorer.py
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XChemExplorer.py
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########################################################################################################################
# DEVELOPER README: #
# This is the main script, where the GUI is initialised from. All of the main layout objects live in their own scripts #
# under ./gui_scripts (i.e. the tab content). The settings and preferences script sets up all of the directory paths #
# and contains dictionaries defining the top menu, push buttons and the tables held in the main tabs. The layout #
# script contains functions for performing simple layout tasks, such as adding a combobox, and contains init. #
# functions for all of the main layout functions. #
# #
# In the future, the functions associated with buttons and frames etc. should be moved into the relevant script, but #
# this is a bit more complicated. For now, they are separated out into sections within this script. The only GUI stuff #
# going on in here is calling the initialisation functions. To change the layout of a tab, edit it in it's own script, #
# and add any new functions in this script, in the relevant section. (If there is one yet) #
# #
# There's still a lot of cleaning up to be done in the future... #
########################################################################################################################
# solve gtk startup error
import gtk
gtk.set_interactive(False)
import base64
import getpass
import glob
import math
import multiprocessing
import pickle
import subprocess
import sys, os
import webbrowser
from datetime import datetime
from PyQt4 import QtGui, QtCore, QtWebKit
sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib'))
sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'web'))
sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts'))
from settings_preferences import *
from layout import *
from stylesheet import set_stylesheet
from XChemUtils import parse
import XChemThread
import XChemDB
import XChemPANDDA
import XChemToolTips
import XChemMain
import XChemPlots
import XChemLog
import XChemProcess
import XChemDeposit
import XChemWeb
import matplotlib.pyplot as plt
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
class XChemExplorer(QtGui.QApplication):
def __init__(self, args):
# init a QApplication object to hold XCE
QtGui.QApplication.__init__(self, args)
# start GUI
self.start_GUI()
# set stylesheet - how the gui looks
set_stylesheet(self)
self.exec_()
def start_GUI(self):
# check http://doc.qt.io/qt-4.8/stylesheet-customizing.html#the-box-model
# This needs moving somewhere more appropriate...
self.headlineLabelfont = QtGui.QFont("Arial", 20, QtGui.QFont.Bold)
setup().settings(self)
setup().preferences(self)
setup().tables(self)
self.layout_funcs = LayoutFuncs()
# GUI setup
self.window = QtGui.QWidget()
self.window.setWindowTitle("XChemExplorer")
self.screen = QtGui.QDesktopWidget().screenGeometry()
LayoutObjects(self).workflow(self)
LayoutObjects(self).main_layout(self)
LayoutFuncs().add_widgets_layouts(self)
# function to update datasource
def datasource_menu_reload_samples(self):
self.update_log.insert(
'reading samples from data source: ' + os.path.join(self.database_directory, self.data_source_file))
self.update_status_bar(
'reading samples from data source: ' + os.path.join(self.database_directory, self.data_source_file))
self.update_header_and_data_from_datasource()
self.update_all_tables()
self.overview_datasource_table.resizeColumnsToContents()
# function to create new datasource
def create_new_data_source(self):
file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'Save file', self.database_directory))
# make sure that the file always has .sqlite extension
if file_name.rfind('.') != -1:
file_name = file_name[:file_name.rfind('.')] + '.sqlite'
else:
file_name = file_name + '.sqlite'
self.db = XChemDB.data_source(file_name)
print('==> XCE: creating new data source')
self.db.create_empty_data_source_file()
self.db.create_missing_columns()
self.database_directory = file_name[:file_name.rfind('/')]
self.data_source_file = file_name[file_name.rfind('/') + 1:]
self.data_source_file_label.setText(os.path.join(self.database_directory, self.data_source_file))
self.settings['database_directory'] = self.database_directory
self.settings['data_source'] = self.data_source_file
self.data_source_set = True
self.datasource_menu_reload_samples()
####################################################################################################################
# #
# DATASETS TAB #
# #
####################################################################################################################
def continously_check_for_new_data_collection(self, state):
self.timer_to_check_for_new_data_collection.timeout.connect(
lambda: self.check_for_new_autoprocessing_or_rescore(False))
if state == QtCore.Qt.Checked:
print('==> XCE: checking automatically every 120s for new data collection')
self.timer_to_check_for_new_data_collection.start(120000)
else:
print('==> XCE: stopped checking for new data collections')
self.timer_to_check_for_new_data_collection.stop()
def target_selection_combobox_activated(self, text):
self.target = str(text)
def select_diffraction_data_directory(self):
self.diffraction_data_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory"))
self.diffraction_data_dir_label.setText(self.diffraction_data_directory)
self.settings['diffraction_data_directory'] = self.diffraction_data_directory
self.update_log.insert('setting diffraction data directory to ' + self.diffraction_data_directory)
def search_for_datasets(self):
self.update_log.insert('search diffraction data directory for datasets...')
print('will search ' + str(self.diffraction_data_directory))
self.work_thread = XChemMain.find_diffraction_image_directory_fast(self.diffraction_data_directory)
self.explorer_active = 1
self.connect(self.work_thread, QtCore.SIGNAL("update_datasets_reprocess_table"),
self.update_datasets_reprocess_table)
self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar)
self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.work_thread.start()
#self.work_thread = self.update_datasets_reprocess_table(self.diffraction_data_directory)
def translate_datasetID_to_sampleID(self):
translate = QtGui.QMessageBox()
translateLayout = translate.layout()
self.translate_datasetID_to_sampleID_file = '-'
vbox = QtGui.QVBoxLayout()
button = QtGui.QPushButton('Open CSV')
button.clicked.connect(self.open_csv_file_translate_datasetID_to_sampleID)
vbox.addWidget(button)
self.translate_datasetID_to_sampleID_csv_label = QtGui.QLabel(self.translate_datasetID_to_sampleID_file)
vbox.addWidget(self.translate_datasetID_to_sampleID_csv_label)
translateLayout.addLayout(vbox, 0, 0)
translate.addButton(QtGui.QPushButton('OK'), QtGui.QMessageBox.YesRole)
translate.addButton(QtGui.QPushButton('Cancel'), QtGui.QMessageBox.RejectRole)
reply = translate.exec_();
if reply == 0:
if os.path.isfile(self.translate_datasetID_to_sampleID_file):
trans_dict = {}
for line in open(self.translate_datasetID_to_sampleID_file):
if len(line.split(',')) == 2:
dataset = line.split(',')[0]
new_sample_id = line.split(',')[1]
trans_dict[dataset] = new_sample_id
if len(trans_dict) >= 1:
allRows = self.datasets_reprocess_table.rowCount()
for row in xrange(0, allRows):
dataset_id = str(self.datasets_reprocess_table.item(row, 0).text())
sample_id = str(self.datasets_reprocess_table.item(row, 1).text())
if dataset_id in trans_dict:
cell_text = QtGui.QTableWidgetItem()
cell_text.setText(trans_dict[dataset_id])
cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter)
self.datasets_reprocess_table.setItem(row, 1, cell_text)
self.update_log.insert(
'dataset: {0!s} -> changing sampleID to: {1!s}'.format(dataset_id,
trans_dict[dataset_id]))
def select_sample_for_xia2(self):
indexes = self.datasets_reprocess_table.selectionModel().selectedRows()
for index in sorted(indexes):
xtal = str(self.datasets_reprocess_table.item(index.row(), 1).text())
print(xtal, self.diffraction_data_table_dict[xtal][0])
self.update_log.insert('{0!s} marked for reprocessing'.format(index.row()))
self.diffraction_data_table_dict[xtal][0].setChecked(True)
def select_reprocess_reference_mtz(self):
self.update_log.insert('trying to set new reference mtz file for reprocessing with xia2')
file_name = str(QtGui.QFileDialog.getOpenFileName(self.window, 'Select file', self.database_directory))
if os.path.isfile(file_name):
if file_name.endswith('.mtz'):
self.diffraction_data_reference_mtz = file_name
self.update_log.insert(
'new reference file for data processing with xia2: ' + self.diffraction_data_reference_mtz)
self.reprocess_reference_mtz_file_label.setText(self.diffraction_data_reference_mtz)
else:
self.update_log.insert('this does not seem to be a mtz file: ' + file_name)
def check_for_new_autoprocessing_or_rescore(self, rescore_only):
self.update_log.insert('checking for new data collection')
start_thread = False
if rescore_only:
# first pop up a warning message as this will overwrite all user selections
msgBox = QtGui.QMessageBox()
msgBox.setText("*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?")
msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole)
msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole)
reply = msgBox.exec_();
if reply == 0:
start_thread = True
else:
start_thread = False
else:
start_thread = True
if start_thread:
if self.target == '=== SELECT TARGET ===':
msgBox = QtGui.QMessageBox()
warning = ('*** WARNING ***\n'
'Please select a target or\n'
'select "=== project directory ===" if you want to read reprocessed results\n'
'In case target list is empty, make sure that you have selected the actual\n'
'data collection visit (e.g. /dls/i04-1/data/2018/lb18145-70)' )
msgBox.setText(warning)
start_thread = False
# msgBox.setText(warning)
# msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole)
# msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole)
# reply = msgBox.exec_();
# if reply == 0:
# start_thread = True
# else:
# start_thread = False
# else:
# start_thread = True
if start_thread:
self.work_thread = XChemThread.read_autoprocessing_results_from_disc(self.visit_list,
self.target,
self.reference_file_list,
self.database_directory,
self.data_collection_dict,
self.preferences,
self.datasets_summary_file,
self.initial_model_directory,
rescore_only,
self.acceptable_low_resolution_limit_for_data,
os.path.join(self.database_directory,
self.data_source_file),
self.xce_logfile)
self.explorer_active = 1
self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar)
self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.connect(self.work_thread, QtCore.SIGNAL("create_widgets_for_autoprocessing_results_only"),
self.create_widgets_for_autoprocessing_results_only)
self.work_thread.start()
#################################################################################################################
#
#
#
# => for new module from hell
# > start
def update_gdaLog_parsing_instructions_and_score(self, gdaLogInstructions):
self.gdaLogInstructions = gdaLogInstructions
self.select_best_autoprocessing_result()
def read_pinIDs_from_gda_logs(self):
self.update_log.insert('reading pinIDs from gda logfiles...')
visit, beamline = XChemMain.getVisitAndBeamline(self.beamline_directory)
self.work_thread = XChemThread.read_pinIDs_from_gda_logs(beamline,
visit,
os.path.join(
self.database_directory,
self.data_source_file),
self.gdaLogInstructions,
self.xce_logfile)
self.explorer_active = 1
self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar)
self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.connect(self.work_thread, QtCore.SIGNAL("update_gdaLog_parsing_instructions_and_score"),
self.update_gdaLog_parsing_instructions_and_score)
self.work_thread.start()
def check_for_new_autoprocessing_results(self):
self.update_log.insert('checking for new data collection')
if self.target == '=== SELECT TARGET ===':
self.update_log.error('NO TARGET SELECTED, PLEASE SELECT A TARGET AND TRY AGAIN!')
start_thread = False
elif self.target == '=== project directory ===':
processedDir = self.initial_model_directory
start_thread = True
else:
processedDir = os.path.join(self.beamline_directory, 'processed', self.target)
start_thread = True
if start_thread:
# processedDir=os.path.join(self.beamline_directory,'processed',self.target)
self.work_thread = XChemThread.read_write_autoprocessing_results_from_to_disc(processedDir,
os.path.join(
self.database_directory,
self.data_source_file),
self.initial_model_directory,
self.xce_logfile,
self.target )
self.explorer_active = 1
self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar)
self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.connect(self.work_thread, QtCore.SIGNAL("read_pinIDs_from_gda_logs"),
self.read_pinIDs_from_gda_logs)
self.work_thread.start()
def select_best_autoprocessing_result(self):
if self.rescore:
# first pop up a warning message as this will overwrite all user selections
msgBox = QtGui.QMessageBox()
msgBox.setText("*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?")
msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole)
msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole)
reply = msgBox.exec_();
if reply != 0:
start_thread = False
else:
start_thread = True
else:
start_thread = True
if start_thread:
self.update_log.insert('selecting best autoprocessing result')
self.update_log.insert('samples where user made manual changes will be ignored!')
if self.target == '=== project directory ===':
processedDir = self.initial_model_directory
else:
processedDir = os.path.join(self.beamline_directory, 'processed', self.target)
visit,beamline = XChemMain.getVisitAndBeamline(processedDir)
self.work_thread = XChemThread.choose_autoprocessing_outcome(os.path.join(self.database_directory,
self.data_source_file),
visit,
self.reference_file_list,
self.preferences,
self.initial_model_directory,
self.rescore,
self.xce_logfile)
self.explorer_active = 1
self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar)
self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.connect(self.work_thread, QtCore.SIGNAL("populate_datasets_summary_table_NEW"),
self.populate_datasets_summary_table_NEW)
self.work_thread.start()
# < end
###################################################################################################################
####################################################################################################################
# #
# MAPS TAB #
# #
####################################################################################################################
def set_new_reference_if_applicable(self):
print('hallo')
reference_root = str(self.reference_file_selection_combobox.currentText())
pg_ref = ''
ucVol_ref = 0.0
for reference in self.reference_file_list:
print(reference[0], reference_root)
if reference[0] == reference_root:
pg_ref = reference[5]
ucVol_ref = reference[4]
break
if ucVol_ref == 0.0:
self.update_log.insert('cannot set reference file since unit cell volume of reference pdb is 0!')
return
for xtal in self.initial_model_dimple_dict:
reference_file_selection_combobox = self.initial_model_dimple_dict[xtal][1]
self.populate_reference_combobox(reference_file_selection_combobox)
db_dict = self.xtal_db_dict[xtal]
pg_xtal = db_dict['DataProcessingPointGroup']
ucVol_xtal = db_dict['DataProcessingUnitCellVolume']
try:
difference = math.fabs(1 - (float(ucVol_xtal) / float(ucVol_ref))) * 100
except ValueError:
self.update_log.insert(xtal + ' -> cannot calculate unit cell volume difference')
continue
if pg_xtal == pg_ref and difference < self.allowed_unitcell_difference_percent:
print(xtal, pg_xtal, ucVol_xtal)
index = reference_file_selection_combobox.findText(reference_root, QtCore.Qt.MatchFixedString)
reference_file_selection_combobox.setCurrentIndex(index)
self.update_log.insert(xtal + ' -> setting ' + reference_root + ' as input PDB file for DIMPLE')
def refresh_reference_file_list(self):
self.reference_file_list = self.get_reference_file_list(' ')
self.populate_reference_combobox(self.reference_file_selection_combobox)
def on_context_menu_initial_model(self, point):
# show context menu
self.popMenu_for_maps_table.exec_(self.sender().mapToGlobal(point))
####################################################################################################################
# #
# PANDDA TAB #
# #
####################################################################################################################
def select_pandda_input_template(self):
mtzin = ''
filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select Example PDB or MTZ File',
self.initial_model_directory, '*.pdb;;*.mtz')
filepath = str(tuple(filepath_temp)[0])
pdbin = filepath.split('/')[-1]
if filepath.endswith('.pdb'):
pdbin = filepath.split('/')[-1]
mtzin_temp = pdbin.replace('.pdb', '.mtz')
if os.path.isfile(filepath.replace(pdbin, mtzin_temp)):
mtzin = mtzin_temp
else:
mtzin = ''
if filepath.endswith('.mtz'):
mtzin = filepath.split('/')[-1]
pdbin_temp = pdbin.replace('.mtz', '.pdb')
if os.path.isfile(filepath.replace(mtzin, pdbin_temp)):
pdbin = pdbin_temp
else:
pdbin = ''
try:
self.pandda_input_data_dir_entry.setText(
'/'+os.path.join(*filepath.split('/')[0:len(filepath.split('/'))-2]))
except TypeError:
self.update_log.error('directory selection invalid')
# if len(filepath.split('/')) - len(self.initial_model_directory.split('/')) == 2:
# self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*'))
# elif len(filepath.split('/')) - len(self.initial_model_directory.split('/')) > 2:
# subdir = os.path.join(
# *filepath.split('/')[len(self.initial_model_directory.split('/')) + 1:len(filepath.split('/')) - 1])
# self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*', subdir))
# else:
# pass
self.pandda_pdb_style_entry.setText(pdbin)
self.pandda_mtz_style_entry.setText(mtzin)
def change_pandda_spg_label(self):
combo_text = str(self.pandda_reference_file_selection_combobox.currentText())
for file in self.reference_file_list:
if file[0] == combo_text:
self.pandda_reference_file_spg_label.setText(file[1])
break
def on_context_menu_pandda(self, point):
# show context menu
self.popMenu_for_pandda_table.exec_(self.sender().mapToGlobal(point))
####################################################################################################################
# #
# DEPO TAB #
# #
####################################################################################################################
def export_to_html(self):
XChemWeb.export_to_html(self.html_export_directory,
self.initial_model_directory,
os.path.join(self.database_directory, self.data_source_file),
self.xce_logfile).prepare()
# self.update_log.insert('exporting contents of SQLite database into ' + self.html_export_directory)
# os.system(
# 'ccp4-python ' + os.getenv('XChemExplorer_DIR') + '/web/process_sqlite.py -t Summary -s ' + os.path.join(
# self.database_directory, self.data_source_file) + ' -d ' + self.html_export_directory)
# XChemWeb.create_ICM_input_file(self.html_export_directory,
# os.path.join(self.database_directory, self.data_source_file))
# self.update_log.insert('open ICMpro:')
# self.update_log.insert('/dls/science/groups/i04-1/software/icm-3.8-5/icm64 -g')
# self.update_log.insert('open file browser and navigate to ' + self.html_export_directory)
# self.update_log.insert('drag and drop dsEvent_sqlite.icm into the main window')
# self.update_log.insert('the script will appear in the Workspace Panel')
# self.update_log.insert('right click on the script and select RUN')
# self.update_log.insert('be patient, this may take a while, depending on the number of events')
# self.status_bar.showMessage('please check terminal window for further information')
def select_ground_state_pdb(self):
p = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(),'*.pdb')
pdb = str(tuple(p)[0])
self.ground_state_pdb_button_label.setText(pdb)
def select_ground_state_mtz(self):
m = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(),'*.mtz')
mtz = str(tuple(m)[0])
self.ground_state_mtz_button_label.setText(mtz)
def add_ground_state_db(self):
db_dict = {'DimplePANDDApath': self.panddas_directory,
'PDB_file': str(self.ground_state_pdb_button_label.text()),
'MTZ_file': str(self.ground_state_mtz_button_label.text())}
self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, 'ground_state', 'ground_state',
db_dict)
def prepare_ground_state_mmcif(self):
self.update_log.insert('preparing mmcif file for apo structure deposition')
self.prepare_models_for_deposition_ligand_bound('ground-state')
def open_icm(self):
self.update_log.insert('starting ICM...')
self.work_thread = XChemThread.start_ICM(self.html_export_directory)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.work_thread.start()
def prepare_files_for_zenodo_upload(self):
self.update_log.insert('preparing files for ZENODO upload...')
os.system('ccp4-python ' + os.getenv(
'XChemExplorer_DIR') + '/helpers/prepare_for_zenodo_upload.py ' + self.html_export_directory)
def update_html_for_zenodo_upload(self):
try:
uploadID = int(self.zenodo_upload_id_entry.text())
self.update_log.insert('updating html files for ZENODO upload,...')
self.update_log.insert('ZENODO upload = ' + str(uploadID))
os.system('ccp4-python ' + os.getenv(
'XChemExplorer_DIR') + '/helpers/prepare_for_zenodo_upload.py {0!s} {1!s}'.format(
self.html_export_directory, uploadID))
except ValueError:
self.update_log.insert('zenodo upload ID must be an integer!')
####################################################################################################################
# #
# SETTINGS TAB #
# #
####################################################################################################################
def settings_button_clicked(self):
if self.sender().text() == 'Select Project Directory':
self.initial_model_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory"))
self.initial_model_directory_label.setText(self.initial_model_directory)
self.pandda_input_data_dir_entry.setText(self.initial_model_directory)
self.settings['initial_model_directory'] = self.initial_model_directory
if self.sender().text() == 'Select Reference Structure Directory':
reference_directory_temp = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory"))
if reference_directory_temp != self.reference_directory:
self.reference_directory = reference_directory_temp
self.update_reference_files(' ')
self.reference_directory_label.setText(self.reference_directory)
self.settings['reference_directory'] = self.reference_directory
if self.sender().text() == 'Select Data Source File':
filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File',
self.database_directory, '*.sqlite')
filepath = str(tuple(filepath_temp)[0])
self.data_source_file = filepath.split('/')[-1]
self.database_directory = filepath[:filepath.rfind('/')]
self.settings['database_directory'] = self.database_directory
self.settings['data_source'] = os.path.join(self.database_directory, self.data_source_file)
write_enabled = self.check_write_permissions_of_data_source()
if not write_enabled:
self.data_source_set = False
else:
self.data_source_set = True
self.data_source_file_label.setText(os.path.join(self.database_directory, self.data_source_file))
self.db = XChemDB.data_source(os.path.join(self.database_directory, self.data_source_file))
self.db.create_missing_columns()
self.datasource_menu_reload_samples()
if self.sender().text() == 'Select Data Collection Directory':
dir_name = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory"))
if dir_name != self.beamline_directory:
self.beamline_directory = dir_name
self.target_list, self.visit_list = XChemMain.get_target_and_visit_list(self.beamline_directory)
self.populate_target_selection_combobox(self.target_selection_combobox)
self.beamline_directory_label.setText(self.beamline_directory)
self.settings['beamline_directory'] = self.beamline_directory
if self.sender().text() == 'Select Existing\nCollection Summary File':
if self.datasets_summary_file != '':
filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File',
self.datasets_summary_file[
:self.datasets_summary_file.rfind(
'/')], '*.pkl')
else:
filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(),
'*.pkl')
filepath = str(tuple(filepath_temp)[0])
self.datasets_summary_file = filepath
self.datasets_summary_file_label.setText(self.datasets_summary_file)
self.settings['datasets_summary'] = self.datasets_summary_file
if self.sender().text() == 'Assign New\nCollection Summary File':
if self.datasets_summary_file != '':
file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'New file',
self.datasets_summary_file[
:self.datasets_summary_file.rfind('/')]))
else:
file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'New file', self.current_directory))
# make sure that the file always has .pkl extension
if str(file_name).rfind('.') != -1:
file_name = file_name[:file_name.rfind('.')] + '.pkl'
else:
file_name = file_name + '.pkl'
self.datasets_summary_file = file_name
self.datasets_summary_file_label.setText(self.datasets_summary_file)
self.settings['datasets_summary'] = self.datasets_summary_file
if self.sender().text() == 'Select CCP4_SCR Directory':
self.ccp4_scratch_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory"))
self.ccp4_scratch_directory_label.setText(self.ccp4_scratch_directory)
self.settings['ccp4_scratch'] = self.ccp4_scratch_directory
if self.sender().text() == 'Select PanDDA Directory':
self.panddas_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory"))
self.panddas_directory_label.setText(self.panddas_directory)
self.pandda_output_data_dir_entry.setText(self.panddas_directory)
print('PANDDA', self.panddas_directory)
self.settings['panddas_directory'] = self.panddas_directory
self.layout_funcs.pandda_html(self)
if self.sender().text() == 'Select HTML Export Directory':
self.html_export_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory"))
self.html_export_directory_label.setText(self.html_export_directory)
self.settings['html_export_directory'] = self.html_export_directory
if self.sender().text() == 'Select Group deposition Directory':
self.group_deposit_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory"))
self.group_deposition_directory_label.setText(self.group_deposit_directory)
self.settings['group_deposit_directory'] = self.group_deposit_directory
#self.datasource_menu_reload_samples()
######################################### sort stuff below here ####################################################
def select_sample_for_dimple(self):
indexes = self.maps_table.selectionModel().selectedRows()
for index in sorted(indexes):
xtal = str(self.maps_table.item(index.row(), 0).text())
self.update_log.insert('{0!s} is marked for DIMPLE'.format(index.row()))
self.initial_model_dimple_dict[xtal][0].setChecked(True)
def update_summary_plot(self):
if self.data_source_set:
XChemPlots.summary_plot(os.path.join(self.database_directory, self.data_source_file),
self.overview_axes).update_overview()
self.overview_canvas.draw()
def show_preferences(self):
preferences = QtGui.QMessageBox()
preferencesLayout = preferences.layout()
vbox = QtGui.QVBoxLayout()
settings_hbox_filename_root = QtGui.QHBoxLayout()
filename_root_label = QtGui.QLabel('filename root:')
settings_hbox_filename_root.addWidget(filename_root_label)
filename_root_input = QtGui.QLineEdit()
filename_root_input.setFixedWidth(400)
filename_root_input.setText(str(self.filename_root))
filename_root_input.textChanged[str].connect(self.change_filename_root)
settings_hbox_filename_root.addWidget(filename_root_input)
vbox.addLayout(settings_hbox_filename_root)
settings_hbox_adjust_allowed_unit_cell_difference = QtGui.QHBoxLayout()
adjust_allowed_unit_cell_difference_label = QtGui.QLabel(
'Max. Allowed Unit Cell Difference between Reference and Target (%):')
settings_hbox_adjust_allowed_unit_cell_difference.addWidget(adjust_allowed_unit_cell_difference_label)
adjust_allowed_unit_cell_difference = QtGui.QLineEdit()
adjust_allowed_unit_cell_difference.setFixedWidth(200)
adjust_allowed_unit_cell_difference.setText(str(self.allowed_unitcell_difference_percent))
adjust_allowed_unit_cell_difference.textChanged[str].connect(self.change_allowed_unitcell_difference_percent)
settings_hbox_adjust_allowed_unit_cell_difference.addWidget(adjust_allowed_unit_cell_difference)
vbox.addLayout(settings_hbox_adjust_allowed_unit_cell_difference)
settings_hbox_acceptable_low_resolution_limit = QtGui.QHBoxLayout()
adjust_acceptable_low_resolution_limit_label = QtGui.QLabel(
'Acceptable low resolution limit for datasets (in Angstrom):')
settings_hbox_acceptable_low_resolution_limit.addWidget(adjust_acceptable_low_resolution_limit_label)
adjust_acceptable_low_resolution_limit = QtGui.QLineEdit()
adjust_acceptable_low_resolution_limit.setFixedWidth(200)
adjust_acceptable_low_resolution_limit.setText(str(self.acceptable_low_resolution_limit_for_data))
adjust_acceptable_low_resolution_limit.textChanged[str].connect(self.change_acceptable_low_resolution_limit)
settings_hbox_acceptable_low_resolution_limit.addWidget(adjust_acceptable_low_resolution_limit)
vbox.addLayout(settings_hbox_acceptable_low_resolution_limit)
vbox_data = QtGui.QVBoxLayout()
vbox_data.addWidget(
QtGui.QLabel('Select amount of processed data you wish to copy to initial_model directory:'))
self.preferences_data_to_copy_combobox = QtGui.QComboBox()
for item in self.preferences_data_to_copy:
self.preferences_data_to_copy_combobox.addItem(item[0])
self.preferences_data_to_copy_combobox.currentIndexChanged.connect(
self.preferences_data_to_copy_combobox_changed)
vbox_data.addWidget(self.preferences_data_to_copy_combobox)
vbox.addLayout(vbox_data)
vbox_select = QtGui.QVBoxLayout()
vbox_select.addWidget(QtGui.QLabel('Dataset Selection Mechanism:'))
self.preferences_selection_mechanism_combobox = QtGui.QComboBox()
for item in self.preferences_selection_mechanism:
self.preferences_selection_mechanism_combobox.addItem(item)
self.preferences_selection_mechanism_combobox.currentIndexChanged.connect(
self.preferences_selection_mechanism_combobox_changed)
vbox_select.addWidget(self.preferences_selection_mechanism_combobox)
vbox.addLayout(vbox_select)
vbox_restraints = QtGui.QVBoxLayout()
vbox_restraints.addWidget(QtGui.QLabel('Restraints generation program:'))
self.preferences_restraints_generation_combobox = QtGui.QComboBox()
program_list = []
if self.external_software['acedrg']:
program_list.append('acedrg')
self.restraints_program = 'acedrg'
if self.external_software['phenix.elbow']: program_list.append('phenix.elbow')
if self.external_software['grade']: program_list.append('grade')
for item in program_list:
self.preferences_restraints_generation_combobox.addItem(item)
self.preferences_restraints_generation_combobox.currentIndexChanged.connect(
self.preferences_restraints_generation_combobox_changed)
index = self.preferences_restraints_generation_combobox.findText(self.restraints_program,
QtCore.Qt.MatchFixedString)
self.preferences_restraints_generation_combobox.setCurrentIndex(index)
vbox_restraints.addWidget(self.preferences_restraints_generation_combobox)
vbox.addLayout(vbox_restraints)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(QtGui.QLabel('XCE logfile:'))
self.xce_logfile_label = QtGui.QLabel(self.xce_logfile)
hbox.addWidget(self.xce_logfile_label)
button = QtGui.QPushButton("Change")
button.clicked.connect(self.set_xce_logfile)
hbox.addWidget(button)
vbox.addLayout(hbox)
settings_hbox_max_queue_jobs = QtGui.QHBoxLayout()
adjust_max_queue_jobs_label = QtGui.QLabel('Max. number of jobs running at once on DLS cluster:')
settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs_label)
adjust_max_queue_jobs = QtGui.QLineEdit()
adjust_max_queue_jobs.setFixedWidth(200)
adjust_max_queue_jobs.setText(str(self.max_queue_jobs))
adjust_max_queue_jobs.textChanged[str].connect(self.change_max_queue_jobs)
settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs)
vbox.addLayout(settings_hbox_max_queue_jobs)
settings_hbox_remote_qsub = QtGui.QHBoxLayout()
remote_qsub_label = QtGui.QLabel('remote qsub:')
settings_hbox_remote_qsub.addWidget(remote_qsub_label)
self.remote_qsub_checkbox = QtGui.QCheckBox('use')
#self.remote_qsub_checkbox.toggled.connect(self.run_qsub_remotely)
settings_hbox_dimple_twin_mode = QtGui.QHBoxLayout()
self.dimple_twin_mode_label_checkbox = QtGui.QCheckBox('run DIMPLE in TWIN mode')
if self.preferences['dimple_twin_mode']:
self.dimple_twin_mode_label_checkbox.setChecked(True)
self.dimple_twin_mode_label_checkbox.toggled.connect(self.dimple_change_twin_mode)
settings_hbox_dimple_twin_mode.addWidget(self.dimple_twin_mode_label_checkbox)
vbox.addLayout(settings_hbox_dimple_twin_mode)
if self.using_remote_qsub_submission:
self.remote_qsub_checkbox.setChecked(True)
settings_hbox_remote_qsub.addWidget(self.remote_qsub_checkbox)
self.remote_qsub_command = QtGui.QLineEdit()
self.remote_qsub_command.setFixedWidth(550)
self.remote_qsub_command.setText(self.remote_qsub_submission)
settings_hbox_remote_qsub.addWidget(self.remote_qsub_command)
vbox.addLayout(settings_hbox_remote_qsub)
apply_button = QtGui.QPushButton('Apply')
apply_button.clicked.connect(self.run_qsub_remotely)
settings_hbox_remote_qsub.addWidget(apply_button)
preferencesLayout.addLayout(vbox, 0, 0)
preferences.exec_();
def dimple_change_twin_mode(self):
if self.preferences['dimple_twin_mode']:
self.update_log.insert('changing preferences: turning off DIMPLE in TWIN mode')
self.preferences['dimple_twin_mode'] = False
else:
self.update_log.insert('changing preferences: changing DIMPLE to TWIN mode')
self.preferences['dimple_twin_mode'] = True
def run_qsub_remotely(self):
self.remote_qsub_submission = str(self.remote_qsub_command.text())
print(str(self.remote_qsub_submission))
if self.remote_qsub_checkbox.isChecked():
self.update_log.insert('submitting jobs to remote machine with: %s' % self.remote_qsub_submission)
self.external_software['qsub_remote'] = self.remote_qsub_submission
self.using_remote_qsub_submission = True
self.settings['remote_qsub'] = self.remote_qsub_submission
else:
self.update_log.insert('switching off remote job submission')
self.external_software['qsub_remote'] = ''
self.settings['remote_qsub'] = ''
self.using_remote_qsub_submission = False
def enter_pdb_codes(self):
pdbID_entry = QtGui.QMessageBox()
pdbID_entryLayout = pdbID_entry.layout()
vbox = QtGui.QVBoxLayout()
frame = QtGui.QFrame()
frame.setFrameShape(QtGui.QFrame.StyledPanel)
grid = QtGui.QGridLayout()
grid.addWidget(QtGui.QLabel('Text from PDB email'), 0, 0)
self.pdb_code_entry = QtGui.QTextEdit()
self.pdb_code_entry.setText('')
self.pdb_code_entry.setFixedWidth(500)
grid.addWidget(self.pdb_code_entry, 1, 0, 20, 1)
frame.setLayout(grid)
vbox.addWidget(frame)
hbox = QtGui.QHBoxLayout()
button = QtGui.QPushButton('Update Database')
button.clicked.connect(self.update_database_with_pdb_codes)
hbox.addWidget(button)
vbox.addLayout(hbox)
pdbID_entryLayout.addLayout(vbox, 0, 0)
pdbID_entry.exec_();
def create_missing_apo_records_in_depositTable(self):
self.db.create_missing_apo_records_for_all_structures_in_depositTable(self.initial_model_directory,
self.xce_logfile)
# def update_file_information_of_apo_records(self):
# XChemDeposit.update_file_locations_of_apo_structuresin_DB(
# os.path.join(self.database_directory, self.data_source_file), self.initial_model_directory,
# self.xce_logfile)
def prepare_models_for_deposition_ligand_bound(self,structureType):
if structureType == 'ground-state':
ground_state = [ str(self.ground_state_pdb_button_label.text()),
str(self.ground_state_mtz_button_label.text()),
self.panddas_directory ]
else:
ground_state = []
# structureType = "ligand_bound"
overwrite_existing_mmcif = True
self.work_thread = XChemDeposit.prepare_mmcif_files_for_deposition(
os.path.join(self.database_directory, self.data_source_file),
self.xce_logfile,
overwrite_existing_mmcif,
self.initial_model_directory,
ground_state)
self.explorer_active = 1
self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar)
self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.work_thread.start()
def prepare_models_for_deposition_apo(self):
structureType = "apo"
overwrite_existing_mmcif = True
self.work_thread = XChemDeposit.prepare_mmcif_files_for_deposition(
os.path.join(self.database_directory, self.data_source_file),
self.xce_logfile,
overwrite_existing_mmcif,
self.initial_model_directory,
structureType)
self.explorer_active = 1
self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar)
self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.work_thread.start()
def prepare_for_group_deposition_upload_ligand_bound(self):
self.work_thread = XChemDeposit.prepare_for_group_deposition_upload(
os.path.join(self.database_directory, self.data_source_file),
self.xce_logfile,
self.group_deposit_directory,self.initial_model_directory,'ligand_bound')
self.explorer_active = 1
self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar)
self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.work_thread.start()
def prepare_for_group_deposition_upload_ground_state(self):
self.work_thread = XChemDeposit.prepare_for_group_deposition_upload(
os.path.join(self.database_directory, self.data_source_file),
self.xce_logfile,
self.group_deposit_directory,self.initial_model_directory,'ground_state')
self.explorer_active = 1
self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar)
self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.work_thread.start()
def check_smiles_in_db_and_pdb(self):
self.work_thread = XChemDeposit.compare_smiles_in_db_with_ligand_in_pdb(self.initial_model_directory,
os.path.join(self.database_directory,
self.data_source_file),
self.xce_logfile)
self.explorer_active = 1
self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar)
self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar)
self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished)
self.connect(self.work_thread, QtCore.SIGNAL("show_error_dict"), self.show_error_dict)
self.work_thread.start()
def deposition_data(self):
depositData = QtGui.QMessageBox()
depositDataLayout = depositData.layout()
vbox = QtGui.QVBoxLayout()
deposit_tab_widget = QtGui.QTabWidget()
deposit_tab_list = ['Contact',
'General',
'Authors',
'Citation',
'Molecule',
'Misc',
'Methods',
'Software']
deposit_tab_dict = {}
for page in deposit_tab_list:
tab = QtGui.QWidget()
vb = QtGui.QVBoxLayout(tab)
deposit_tab_widget.addTab(tab, page)
deposit_tab_dict[page] = [tab, vb]
## PI and scientist info
vb = QtGui.QVBoxLayout()
hbox = QtGui.QHBoxLayout()
frame = QtGui.QFrame()
frame.setFrameShape(QtGui.QFrame.StyledPanel)
grid = QtGui.QGridLayout()
grid.addWidget(QtGui.QLabel('Principal Investigator'), 0, 0)
grid.addWidget(QtGui.QLabel('Salutation'), 1, 0)
self.contact_author_PI_salutation = QtGui.QLineEdit()
self.contact_author_PI_salutation.setText('Dr.')
self.contact_author_PI_salutation.setFixedWidth(200)
grid.addWidget(self.contact_author_PI_salutation, 1, 1)
grid.addWidget(QtGui.QLabel('First name'), 2, 0)
self.contact_author_PI_first_name = QtGui.QLineEdit()
self.contact_author_PI_first_name.setText('')
self.contact_author_PI_first_name.setFixedWidth(200)
grid.addWidget(self.contact_author_PI_first_name, 2, 1)
grid.addWidget(QtGui.QLabel('Last name'), 3, 0)
self.contact_author_PI_last_name = QtGui.QLineEdit()
self.contact_author_PI_last_name.setText('')
self.contact_author_PI_last_name.setFixedWidth(200)
grid.addWidget(self.contact_author_PI_last_name, 3, 1)
grid.addWidget(QtGui.QLabel('Middle name'), 4, 0)
self.contact_author_PI_middle_name = QtGui.QLineEdit()
self.contact_author_PI_middle_name.setText('')
self.contact_author_PI_middle_name.setFixedWidth(200)
self.contact_author_PI_middle_name.setStyleSheet("background-color: rgb(192, 192, 192);")
grid.addWidget(self.contact_author_PI_middle_name, 4, 1)
grid.addWidget(QtGui.QLabel('PI role'), 5, 0)
self.contact_author_PI_role = QtGui.QComboBox()