def update_overview(self):
db_dict = XChemMain.get_datasource_summary(self.datasource)
category = ('Crystals mounted', 'Data Collection', 'Maps', 'PANDDA',
'Refinement', 'Comp Chem')
N = len(category)
Success = np.array([
db_dict['nr_samples'], db_dict['nr_data_collection_success'],
db_dict['nr_initial_maps_available'], db_dict['nr_pandda_hits'], 5,
6
])
Processed = np.array([0, 0, 0, db_dict['nr_pandda_processed'], 0, 0])
Pending = np.array([
0, db_dict['nr_data_collection_pending'],
db_dict['nr_initial_maps_pending'], db_dict['nr_pandda_pending'],
2, 1
])
Failure = np.array([
db_dict['nr_samples_failed_to_mount'],
db_dict['nr_data_collection_failed'],
db_dict['nr_initial_maps_fail'], db_dict['nr_pandda_reject'], 2, 3
])
ind = np.arange(N) # the x locations for the groups
width = 0.35 # the width of the bars
p0 = self.overview_axes.bar(ind, Success, width, color='g')
p1 = self.overview_axes.bar(ind,
Processed,
width,
color='b',
bottom=Success)
p2 = self.overview_axes.bar(ind,
Pending,
width,
color='y',
bottom=Success + Processed)
p3 = self.overview_axes.bar(ind,
Failure,
width,
color='r',
bottom=Pending + Success + Processed)
# add some text for labels, title and axes ticks
self.overview_axes.set_ylabel('N')
self.overview_axes.set_title('Overview')
self.overview_axes.set_xticks(ind + width)
self.overview_axes.set_xticklabels(category)
self.overview_axes.legend(
(p0[0], p1[0], p2[0], p3[0]),
('Success', 'Processed', 'Pending', 'Failure'))
def write_html_file(self, html):
os.chdir(self.htmlDir)
self.Logfile.insert('writing index.html')
html += XChemMain.html_footer()
if os.path.isfile('index.html'):
os.system('/bin/rm -f index.html')
f = open('index.html', 'w')
f.write(html)
f.close()
def update_overview(self):
db_dict=XChemMain.get_datasource_summary(self.datasource)
category = ( 'Crystals mounted',
'Data Collection',
'Maps',
'PANDDA',
'Refinement',
'Comp Chem' )
N = len(category)
Success = np.array([ db_dict['nr_samples'],
db_dict['nr_data_collection_success'],
db_dict['nr_initial_maps_available'],
db_dict['nr_pandda_hits'],
5,
6 ])
Processed = np.array([ 0,
0,
0,
db_dict['nr_pandda_processed'],
0,
0 ])
Pending = np.array([ 0,
db_dict['nr_data_collection_pending'],
db_dict['nr_initial_maps_pending'],
db_dict['nr_pandda_pending'],
2,
1 ])
Failure = np.array([ db_dict['nr_samples_failed_to_mount'],
db_dict['nr_data_collection_failed'],
db_dict['nr_initial_maps_fail'],
db_dict['nr_pandda_reject'],
2,
3 ])
ind = np.arange(N) # the x locations for the groups
width = 0.35 # the width of the bars
p0 = self.overview_axes.bar(ind, Success, width, color='g')
p1 = self.overview_axes.bar(ind, Processed, width, color='b', bottom=Success)
p2 = self.overview_axes.bar(ind, Pending, width, color='y', bottom=Success+Processed)
p3 = self.overview_axes.bar(ind, Failure, width, color='r', bottom=Pending+Success+Processed)
# add some text for labels, title and axes ticks
self.overview_axes.set_ylabel('N')
self.overview_axes.set_title('Overview')
self.overview_axes.set_xticks(ind + width)
self.overview_axes.set_xticklabels(category)
self.overview_axes.legend((p0[0], p1[0], p2[0], p3[0]), ('Success', 'Processed', 'Pending', 'Failure'))
def prepare(self):
self.Logfile.insert('======== preparing HTML summary ========')
self.makeFolders()
self.copy_jscss()
html = XChemMain.html_header()
for xtal in self.db.samples_for_html_summary():
self.db_dict = self.db.get_db_dict_for_sample(xtal)
self.copy_pdb(xtal)
self.copy_electron_density(xtal)
self.copy_ligand_files(xtal)
for ligand in self.ligands_in_pdbFile(xtal):
eventMap = self.find_matching_event_map(xtal, ligand)
x, y, z = self.pdb.get_centre_of_gravity_of_residue(ligand)
self.copy_spider_plot(xtal, ligand)
pdbID = self.db_dict['Deposition_PDB_ID']
compoundImage = xtal + '_' + self.db_dict[
'CompoundCode'] + '.png'
compoundCIF = xtal + '_' + self.db_dict['CompoundCode'] + '.cif'
residuePlot = xtal + '_' + ligand + '.png'
pdb = xtal + '.pdb'
event = xtal + '_' + ligand + '.ccp4'
thumbNail = xtal + '_' + ligand + '_thumb.png'
resoHigh = self.db_dict['DataProcessingResolutionHigh']
spg = self.db_dict['RefinementSpaceGroup']
unitCell = self.db_dict['DataProcessingUnitCell']
FWT = xtal + '_2fofc.ccp4'
DELFWT = xtal + '_fofc.ccp4'
html += XChemMain.html_table_row(xtal, pdbID, ligand,
compoundImage, residuePlot,
pdb, event, thumbNail,
resoHigh, spg, unitCell, FWT,
DELFWT)
self.make_thumbnail(xtal, x, y, z, ligand, eventMap)
self.prepare_for_download(xtal, pdb, event, compoundCIF,
ligand)
self.write_html_file(html)
self.Logfile.insert(
'======== finished preparing HTML summary ========')
def make_thumbnail(self, xtal, x, y, z, ligID, eventMap):
self.Logfile.insert('%s: making thumbnail of for %s and %s' %
(xtal, ligID, eventMap))
sampleDir = os.path.join(self.projectDir, xtal)
os.chdir(sampleDir)
if not os.path.isfile('%s_%s_thumb.png' % (xtal, ligID)):
self.Logfile.insert('%s: preparing thumbnail image of %s' %
(xtal, ligID))
XChemMain.coot_prepare_input(x, y, z, ligID, sampleDir, eventMap)
XChemMain.coot_write_raster_file(ligID, sampleDir)
XChemMain.render_scene(xtal, ligID, sampleDir)
XChemMain.make_thumbnail(xtal, ligID, sampleDir)
if os.path.isfile('%s_%s_thumb.png' % (xtal, ligID)):
self.Logfile.insert('%s: managed to prepare %s_%s_thumb.png' %
(xtal, xtal, ligID))
self.copy_thumbnail(xtal, sampleDir, ligID)
else:
self.Logfile.error('%s: could not generate %s_%s_thumb.png' %
(xtal, xtal, ligID))
def settings(self, xce_object):
# set XCE version
xce_object.xce_version = 'v1.4.0'
# general settings
xce_object.allowed_unitcell_difference_percent = 12
xce_object.acceptable_low_resolution_limit_for_data = 3.5
xce_object.filename_root = '${samplename}'
xce_object.data_source_set = False
xce_object.max_queue_jobs = 100
## directory settings
# set current directory and direct log to it
xce_object.current_directory = os.getcwd()
xce_object.xce_logfile = os.path.join(xce_object.current_directory,
'xce.log')
# if in the correct place, set the various directories
if 'labxchem' in xce_object.current_directory:
if len(xce_object.current_directory.split('/')
) >= 9 and xce_object.current_directory.split(
'/'
)[6] == 'processing' and xce_object.current_directory.split(
'/')[8] == 'processing':
xce_object.labxchem_directory = '/' + os.path.join(
*xce_object.current_directory.split('/')
[1:8]) # need splat operator: *
xce_object.labxchem_directory_current = '/' + os.path.join(
*xce_object.current_directory.split('/')[1:9]
) # labxchem_directory_current is where they actually have write permission
else:
xce_object.labxchem_directory = '/' + os.path.join(
*xce_object.current_directory.split('/')
[1:6]) # need splat operator: *
xce_object.labxchem_directory_current = '/' + os.path.join(
*xce_object.current_directory.split('/')
[1:7]) # need splat operator: *
# xce_object.labxchem_directory = '/' + os.path.join(
# *xce_object.current_directory.split('/')[1:6]) # need splat operator: *
xce_object.beamline_directory = os.path.join(
xce_object.labxchem_directory, 'processing', 'beamline')
if os.path.isdir(
os.path.join(xce_object.labxchem_directory, 'processing',
'analysis', 'model_building')):
xce_object.initial_model_directory = os.path.join(
xce_object.labxchem_directory, 'processing', 'analysis',
'model_building')
else:
xce_object.initial_model_directory = os.path.join(
xce_object.labxchem_directory, 'processing', 'analysis',
'initial_model')
xce_object.reference_directory = os.path.join(
xce_object.labxchem_directory, 'processing', 'reference')
xce_object.database_directory = os.path.join(
xce_object.labxchem_directory, 'processing', 'database')
xce_object.panddas_directory = os.path.join(
xce_object.labxchem_directory, 'processing', 'analysis',
'panddas')
xce_object.datasets_summary_file = os.path.join(
xce_object.database_directory,
str(os.getcwd().split('/')[5]) + '_summary.pkl')
xce_object.data_source_file = ''
xce_object.html_export_directory = os.path.join(
xce_object.labxchem_directory, 'processing', 'html')
xce_object.group_deposit_directory = os.path.join(
xce_object.labxchem_directory, 'processing',
'group_deposition')
if os.path.isfile(
os.path.join(xce_object.labxchem_directory, 'processing',
'database', 'soakDBDataFile.sqlite')):
xce_object.data_source_file = 'soakDBDataFile.sqlite'
xce_object.database_directory = os.path.join(
xce_object.labxchem_directory, 'processing', 'database')
xce_object.data_source_set = True
xce_object.db = XChemDB.data_source(
os.path.join(xce_object.database_directory,
xce_object.data_source_file))
xce_object.db.create_missing_columns()
xce_object.ccp4_scratch_directory = os.path.join(
xce_object.labxchem_directory, 'processing', 'tmp')
directory_list = [
xce_object.beamline_directory,
os.path.join(xce_object.labxchem_directory, 'processing',
'analysis'), xce_object.initial_model_directory,
xce_object.panddas_directory, xce_object.reference_directory,
xce_object.database_directory,
xce_object.ccp4_scratch_directory,
xce_object.html_export_directory,
xce_object.group_deposit_directory
]
for directory in directory_list:
if not os.path.isdir(directory):
os.mkdir(directory)
# otherwise, use the current working directory
else:
xce_object.labxchem_directory_current = xce_object.current_directory
xce_object.beamline_directory = xce_object.current_directory
xce_object.initial_model_directory = xce_object.current_directory
xce_object.reference_directory = xce_object.current_directory
xce_object.database_directory = xce_object.current_directory
xce_object.data_source_file = ''
xce_object.ccp4_scratch_directory = os.getenv('CCP4_SCR')
xce_object.panddas_directory = xce_object.current_directory
xce_object.datasets_summary_file = ''
xce_object.group_deposit_directory = xce_object.current_directory
## deposition
xce_object.deposit_dict = {}
## internal lists and dictionaries
xce_object.data_collection_list = []
xce_object.visit_list = []
xce_object.target = ''
xce_object.dataset_outcome_combobox_dict = {}
xce_object.data_collection_dict = {}
xce_object.xtal_db_dict = {}
xce_object.pandda_analyse_input_table_dict = {}
xce_object.dewar_configuration_dict = {}
xce_object.data_collection_statistics_dict = {}
xce_object.initial_model_dimple_dict = {
} # contains toggle button if dimple should be run
xce_object.reference_file_list = []
xce_object.all_columns_in_data_source = XChemDB.data_source(os.path.join
(xce_object.database_directory,
xce_object.data_source_file)) \
.return_column_list()
xce_object.albula_button_dict = {
} # using dials.image_viewer instead of albula, but keep name for dictionary
xce_object.xtalform_dict = {}
xce_object.dataset_outcome_dict = {
} # contains the dataset outcome buttons
xce_object.data_collection_table_dict = {
} # contains the dataset table
xce_object.data_collection_image_dict = {}
xce_object.data_collection_column_three_dict = {}
xce_object.datasets_summary_dict = {}
xce_object.diffraction_data_table_dict = {}
xce_object.refinement_table_dict = {}
xce_object.main_data_collection_table_exists = False
xce_object.timer_to_check_for_new_data_collection = QtCore.QTimer()
xce_object.agamemnon = False
xce_object.target_list, xce_object.visit_list = XChemMain.get_target_and_visit_list(
xce_object.beamline_directory, False)
xce_object.diffraction_data_dict = {}
## internal switches and flags
xce_object.explorer_active = 0
xce_object.coot_running = 0
xce_object.progress_bar_start = 0
xce_object.progress_bar_step = 0
xce_object.albula = None
xce_object.albula_subframes = []
xce_object.show_diffraction_image = None
xce_object.gdaLogInstructions = [0, False]
# can be any widget to be displayed in data collection summary tab
xce_object.data_collection_details_currently_on_display = None
xce_object.dataset_outcome = [
"success", "Failed - centring failed", "Failed - no diffraction",
"Failed - processing", "Failed - loop empty",
"Failed - loop broken", "Failed - low resolution",
"Failed - no X-rays", "Failed - unknown"
]
xce_object.refinement_stage = [
'0 - All Datasets', '1 - Analysis Pending', '2 - PANDDA model',
'3 - In Refinement', '4 - CompChem ready', '5 - Deposition ready',
'6 - Deposited'
]
self.set_xce_logfile(xce_object)
## external software packages
xce_object.using_remote_qsub_submission = False
xce_object.remote_qsub_submission = "/usr/bin/ssh <dls fed ID>@nx.diamond.ac.uk 'module load global/cluster; qsub'"
xce_object.update_log = XChemLog.updateLog(xce_object.xce_logfile)
xce_object.update_log.insert('new session started')
xce_object.diffraction_data_directory = xce_object.current_directory
xce_object.diffraction_data_search_info = 'n/a'
xce_object.diffraction_data_reference_mtz = 'ignore'
xce_object.html_export_directory = os.getcwd()
xce_object.external_software = XChemUtils.external_software(
xce_object.xce_logfile).check()
xce_object.second_cif_file = None
software_list = ['acedrg', 'phenix.elbow', 'grade']
for software in software_list:
if xce_object.external_software[software]:
xce_object.restraints_program = str(software)
xce_object.update_log.insert(
'will use ' + str(software) +
' for generation of ligand coordinates and'
' restraints')
else:
xce_object.restraints_program = ''
xce_object.update_log.insert(
'No program for generation of ligand coordinates and restraints available!'
)
def setup(self, xce_object):
################################################################################################################
# #
# DATASETS TAB #
# #
################################################################################################################
# define subtab list, widget and dict
datasets_tab_list = ['Summary', 'Reprocess']
xce_object.datasets_tab_widget = QtGui.QTabWidget()
xce_object.datasets_tab_dict = {}
# make subtabs
self.layout_funcs.make_tab_dict(datasets_tab_list, xce_object.datasets_tab_widget, xce_object.datasets_tab_dict)
# main body - things that are always displayed
# add a container to hold everythting and add to main tab layout
xce_object.datasets_data_collection_vbox = QtGui.QVBoxLayout()
# add a horizontal box to hold option to autocheck for new data
xce_object.autocheck_hbox = QtGui.QHBoxLayout()
# checkbox for autocollect
xce_object.check_for_new_data_collection = QtGui.QCheckBox('Check for new data collection every two minutes')
xce_object.check_for_new_data_collection = QtGui.QCheckBox('Check for new data collection every two minutes')
self.layout_funcs.add_checkbox(xce_object, xce_object.check_for_new_data_collection,
'xce_object.continously_check_for_new_data_collection')
# select target dropdown
select_target_label = QtGui.QLabel('<b>Select Target: </b>')
select_target_label.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter)
xce_object.target_selection_combobox = QtGui.QComboBox()
xce_object.populate_target_selection_combobox(xce_object.target_selection_combobox)
xce_object.target_selection_combobox.activated[str].connect(xce_object.target_selection_combobox_activated)
xce_object.target = str(xce_object.target_selection_combobox.currentText())
# array defining order of xce_objects to add
xce_object.autocheck_hbox_widgets = [xce_object.check_for_new_data_collection, select_target_label,
xce_object.target_selection_combobox]
self.layout_funcs.add_to_box(xce_object.autocheck_hbox,
xce_object.autocheck_hbox_widgets) # add xce_objects in order
# add target dropdown to top bar
xce_object.datasets_data_collection_vbox.addLayout(xce_object.autocheck_hbox)
# summary sub-tab
# table
xce_object.datasets_summary_table = QtGui.QTableWidget()
self.layout_funcs.table_setup(xce_object.datasets_summary_table, xce_object.datasets_summary_table_columns)
xce_object.datasets_summarys_vbox_for_table = QtGui.QVBoxLayout() # setup layout to hold table
xce_object.datasets_summarys_vbox_for_table.addWidget(xce_object.datasets_summary_table) # add table to layout
xce_object.datasets_summarys_vbox_for_details = QtGui.QVBoxLayout() # vbox for details
xce_object.data_collection_details_currently_on_display = None # switch for displaying/updating table
xce_object.datasets_data_collection_vbox.addWidget(xce_object.datasets_tab_widget) # add subtab to main tab
# reprocessing sub-tab
# top options
# data collection label
dc_label = QtGui.QLabel('<b>Data collection directory: </b>')
dc_label.setAlignment(QtCore.Qt.AlignLeft | QtCore.Qt.AlignVCenter) # align left and centre of container
xce_object.diffraction_data_dir_label = QtGui.QLabel(
xce_object.diffraction_data_directory) # add directory as text
xce_object.diffraction_data_dir_label.setAlignment(
QtCore.Qt.AlignLeft | QtCore.Qt.AlignVCenter) # align as above
# select label
select_button = QtGui.QPushButton("Select")
select_button.clicked.connect(xce_object.select_diffraction_data_directory) # attach file open dialogue
# search button
search_button = QtGui.QPushButton("Search Datasets")
search_button.clicked.connect(xce_object.search_for_datasets) # search for datasets in the selected directory
# search info
xce_object.diffraction_data_search_label = QtGui.QLabel(xce_object.diffraction_data_search_info)
# translate label
translate_label = QtGui.QLabel('<b>Translate:</b> datasetID -> sampleID')
translate_label.setAlignment(QtCore.Qt.AlignCenter) # align in centre of container
# CSV button
csv_button = QtGui.QPushButton('Open CSV')
csv_button.setStyleSheet("QPushButton { padding: 1px; margin: 1px }")
csv_button.clicked.connect(xce_object.translate_datasetID_to_sampleID) # open the relevant csv file
# create hbox to hold everything and add widgets to it
xce_object.hbox_select = QtGui.QHBoxLayout() # top options box
xce_object.hbox_select_widgets = [dc_label, xce_object.diffraction_data_dir_label, select_button, search_button,
xce_object.diffraction_data_search_label,
translate_label,
csv_button] # array defining order of xce_objects to be added
self.layout_funcs.add_to_box(xce_object.hbox_select, xce_object.hbox_select_widgets) # add xce_objects in order
# frame to hold everything
frame_select = QtGui.QFrame()
frame_select.setLayout(xce_object.hbox_select) # apply to containing frame
# table - main body
xce_object.datasets_reprocess_table = QtGui.QTableWidget()
self.layout_funcs.table_setup(xce_object.datasets_reprocess_table,
xce_object.datasets_reprocess_columns) # setup
# create context menu - no idea where this lives...
xce_object.popMenu_for_datasets_reprocess_table = QtGui.QMenu()
run_xia2_on_selected = QtGui.QAction("mark selected for reprocessing", xce_object.window)
run_xia2_on_selected.triggered.connect(xce_object.select_sample_for_xia2)
xce_object.popMenu_for_datasets_reprocess_table.addAction(run_xia2_on_selected)
xce_object.datasets_reprocess_table.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
xce_object.datasets_reprocess_table.customContextMenuRequested.connect(
xce_object.on_context_menu_reprocess_data)
# options at bottom of tab
# data processing label
label = QtGui.QLabel('<b>Data processing protocol: </b>')
label.setAlignment(QtCore.Qt.AlignLeft | QtCore.Qt.AlignVCenter)
# option checkboxes
xce_object.xia2_3d_checkbox = QtGui.QCheckBox('xia2 3d')
xce_object.xia2_3dii_checkbox = QtGui.QCheckBox('xia2 3dii')
xce_object.xia2_dials_checkbox = QtGui.QCheckBox('Dials')
# spacegroup label
sg_label = QtGui.QLabel('<b>Space Group:</b>')
# spacegroup dropdown menu
xce_object.reprocess_space_group_comboxbox = QtGui.QComboBox()
xce_object.reprocess_space_group_comboxbox.addItem('ignore')
for sg in XChemMain.space_group_list():
xce_object.reprocess_space_group_comboxbox.addItem(sg)
# mtz label
mtz_label = QtGui.QLabel('<b>Reference MTZ:</b>')
# file label
xce_object.reprocess_reference_mtz_file_label = QtGui.QLabel(xce_object.diffraction_data_reference_mtz)
# select button
select_button = QtGui.QPushButton("Select")
select_button.clicked.connect(xce_object.select_reprocess_reference_mtz)
# define order of widgets to be added to options hbox
hbox_options_widgets = [label, xce_object.xia2_3d_checkbox, xce_object.xia2_3dii_checkbox,
xce_object.xia2_dials_checkbox, sg_label, xce_object.reprocess_space_group_comboxbox,
mtz_label, xce_object.reprocess_reference_mtz_file_label, select_button]
# create hbox, add everything to it and then put it in a frame
hbox_options = QtGui.QHBoxLayout()
self.layout_funcs.add_to_box(hbox_options, hbox_options_widgets)
frame_options = QtGui.QFrame()
frame_options.setLayout(hbox_options)
# following are contained in vboxes
# res limit isig label
label = QtGui.QLabel('<b>Res.\nLimit:</b>\nMn<I/sig(I)>')
label.setAlignment(QtCore.Qt.AlignCenter)
# res limit isig dropdown menu
xce_object.reprocess_isigma_combobox = QtGui.QComboBox()
misigma = ['default', '4', '3', '2.5', '2', '1.5', '1', '0.5']
self.layout_funcs.populate_combobox(misigma, xce_object.reprocess_isigma_combobox)
xce_object.reprocess_isigma_combobox.setCurrentIndex(0)
xce_object.reprocess_isigma_combobox.setStyleSheet(" QComboBox { padding: 1px; margin: 1px }")
# create vertical box to add labels and dropdowns to, create box and put in frame
vbox_isigma = QtGui.QVBoxLayout()
vbox_isigma_widgets = [label, xce_object.reprocess_isigma_combobox]
self.layout_funcs.add_to_box(vbox_isigma, vbox_isigma_widgets)
frame_isigma = QtGui.QFrame()
frame_isigma.setLayout(vbox_isigma)
# res limit cc half label
res_cc_label = QtGui.QLabel('<b>Res.\nLimit:</b>\nCC 1/2')
res_cc_label.setAlignment(QtCore.Qt.AlignCenter)
# res limit cc half dropdown
xce_object.reprocess_cc_half_combobox = QtGui.QComboBox()
cc_half = ['default', '0.9', '0.8', '0.7', '0.6', '0.5', '0.4', '0.3', '0.2', '0.1']
self.layout_funcs.populate_combobox(cc_half, xce_object.reprocess_cc_half_combobox)
xce_object.reprocess_cc_half_combobox.setCurrentIndex(0)
xce_object.reprocess_cc_half_combobox.setStyleSheet(" QComboBox { padding: 1px; margin: 1px }")
# create a vbox for label and dropdown, and add items to it
vbox_cc_half = QtGui.QVBoxLayout()
vbox_cc_half_widgets = [res_cc_label, xce_object.reprocess_cc_half_combobox]
self.layout_funcs.add_to_box(vbox_cc_half, vbox_cc_half_widgets)
# create frame to hold everything and add vbox
frame_cc_half = QtGui.QFrame()
frame_cc_half.setLayout(vbox_cc_half)
# create a hbox to hold the bottom frames and add everything
data_protocol_hbox = QtGui.QHBoxLayout()
data_protocol_hbox_widgets = [frame_options, frame_isigma, frame_cc_half]
self.layout_funcs.add_to_box(data_protocol_hbox, data_protocol_hbox_widgets)
bottom_options_frame = QtGui.QFrame() # create frame to hold everything (horizontal)
bottom_options_frame.setLayout(data_protocol_hbox)
# code below sets final layout for whole subtab
xce_object.reprocess_vbox = QtGui.QVBoxLayout() # box to hold reprocessing subtab content
xce_object.reprocess_hbox_widgets = [frame_select, xce_object.datasets_reprocess_table, bottom_options_frame]
self.layout_funcs.add_to_box(xce_object.reprocess_vbox, xce_object.reprocess_hbox_widgets)
def prepare(self):
self.Logfile.insert('======== preparing HTML summary ========')
self.makeFolders()
self.copy_jscss()
html = XChemMain.html_header()
firstFile = True
for xtal in self.db.samples_for_html_summary():
self.db_dict = self.db.get_db_dict_for_sample(xtal)
if firstFile:
if self.db_dict['ProteinName'] == 'None':
self.Logfile.warning('could not determine protein name')
try:
self.protein_name = xtal.split('-')[0]
self.Logfile.warning(
'xtal name = %s => setting protein name to %s' %
(xtal, self.protein_name))
except IndexError:
self.Logfile.warning(
'could not determine protein name from cystal name; setting to None'
)
self.protein_name = ''
else:
self.protein_name = self.db_dict['ProteinName']
self.Logfile.insert('protein name is: ' +
self.protein_name)
self.copy_pdb(xtal)
self.copy_mtz(xtal)
# self.copy_electron_density(xtal)
self.copy_ligand_files(xtal)
for ligand in self.ligands_in_pdbFile(xtal):
ligName = ligand.split('-')[0]
ligChain = ligand.split('-')[1]
ligNumber = ligand.split('-')[2]
eventMap = self.find_matching_event_map_from_database(
xtal, ligand)
if eventMap:
self.cut_and_copy_map(xtal, ligand + '.pdb', eventMap,
xtal + '_' + ligand + '_event.ccp4',
'F', 'PHIF')
x, y, z = self.pdb.get_centre_of_gravity_of_residue(ligand)
self.copy_spider_plot(xtal, ligand)
pdbID = self.db_dict['Deposition_PDB_ID']
compoundImage = xtal + '_' + self.db_dict[
'CompoundCode'] + '.png'
compoundCIF = xtal + '_' + self.db_dict['CompoundCode'] + '.cif'
residuePlot = xtal + '_' + ligand + '.png'
pdb = xtal + '.pdb'
event = xtal + '_' + ligand + '_event.ccp4'
thumbNail = xtal + '_' + ligand + '_thumb.png'
resoHigh = self.db_dict['DataProcessingResolutionHigh']
spg = self.db_dict['RefinementSpaceGroup']
unitCell = self.db_dict['DataProcessingUnitCell']
os.chdir(os.path.join(self.projectDir, xtal))
FWT = xtal + '-' + ligand + '_2fofc.ccp4'
self.cut_and_copy_map(xtal, ligand + '.pdb', '2fofc.map', FWT,
'FWT', 'PHWT')
DELFWT = xtal + '-' + ligand + '_fofc.ccp4'
self.cut_and_copy_map(xtal, ligand + '.pdb', 'fofc.map',
DELFWT, 'DELFWT', 'PHDELWT')
ligConfidence = self.db.get_ligand_confidence_for_ligand(
xtal, ligChain, ligNumber, ligName)
if ligConfidence.startswith('0'):
self.Logfile.warning(
'%s: ligand confidence of %s-%s-%s is %s; ignoring...'
% (xtal, ligChain, ligNumber, ligName, ligConfidence))
continue
modelStatus = self.db_dict['RefinementOutcome']
if firstFile:
html += XChemMain.html_ngl(
pdb, eventMap.replace(self.projectDir, ''), FWT,
DELFWT, ligand)
html += XChemMain.html_download(self.protein_name)
html += XChemMain.html_guide()
html += XChemMain.html_table_header()
firstFile = False
html += XChemMain.html_table_row(xtal, pdbID, ligand,
compoundImage, residuePlot,
pdb, event, thumbNail,
resoHigh, spg, unitCell, FWT,
DELFWT, ligConfidence,
modelStatus)
self.make_thumbnail(xtal, x, y, z, ligand, eventMap)
self.prepare_for_download(xtal, pdb, event, compoundCIF,
ligand)
self.prepare_zip_archives()
# html = XChemMain.html_download_all_section(html,self.protein_name)
self.write_html_file(html)
self.Logfile.insert(
'======== finished preparing HTML summary ========')
def prepare(self, whichSamples):
self.Logfile.insert('======== preparing HTML summary ========')
self.makeFolders()
self.copy_jscss()
html = XChemMain.html_header()
firstFile = True
for xtal in self.db.samples_for_html_summary(whichSamples):
self.db_dict = self.db.get_db_dict_for_sample(xtal)
if firstFile:
if self.db_dict['ProteinName'] == 'None':
self.Logfile.warning('could not determine protein name')
try:
self.protein_name = xtal.split('-')[0]
self.Logfile.warning(
'xtal name = %s => setting protein name to %s' %
(xtal, self.protein_name))
except IndexError:
self.Logfile.warning(
'could not determine protein name from cystal name; setting to None'
)
self.protein_name = ''
else:
self.protein_name = self.db_dict['ProteinName']
self.Logfile.insert('protein name is: ' +
self.protein_name)
self.copy_pdb(xtal)
self.copy_mtz(xtal)
# self.copy_electron_density(xtal)
self.copy_ligand_files(xtal)
os.chdir(os.path.join(self.projectDir, xtal))
ligandDict = XChemUtils.pdbtools_gemmi(
'refine.pdb').center_of_mass_ligand_dict('LIG')
self.Logfile.insert(
xtal +
': saving ligand(s) of type LIG in refine.pdb as PDB files...')
XChemUtils.pdbtools_gemmi('refine.pdb').save_ligands_to_pdb('LIG')
for ligand in ligandDict:
self.Logfile.insert(xtal + ': current ligand -> ' + ligand)
os.chdir(os.path.join(self.projectDir, xtal))
# for ligand in self.ligands_in_pdbFile(xtal):
ligName = ligand.split('-')[0]
ligChain = ligand.split('-')[1]
ligNumber = ligand.split('-')[2]
# eventMap = self.find_matching_event_map_from_database(xtal, ligand)
# if eventMap:
# self.Logfile.insert('%s: using the following event map -> %s' %(xtal,eventMap))
# self.cut_and_copy_map(xtal, ligand+'.pdb', eventMap, xtal + '_' + ligand + '_event.ccp4','F','PHIF')
# eventMap = xtal + '_' + ligand + '_event.ccp4'
# else:
# self.Logfile.error('%s: value of event map -> %s' %(xtal,eventMap))
eventMap = ''
# self.Logfile.insert(xtal + ': looking for' + xtal + '_' + ligand + '_event.ccp4')
if os.path.isfile(xtal + '_' + ligand + '_event.ccp4'):
eventMap = xtal + '_' + ligand + '_event.ccp4'
# self.Logfile.insert(xtal + ': found ' + eventMap)
# else:
# self.Logfile.error(xtal + ': cannot find' + xtal + '_' + ligand + '_event.ccp4')
# x,y,z = self.pdb.get_centre_of_gravity_of_residue(ligand)
x = ligandDict[ligand][0]
y = ligandDict[ligand][1]
z = ligandDict[ligand][2]
self.copy_spider_plot(xtal, ligand)
pdbID = self.db_dict['Deposition_PDB_ID']
compoundImage = xtal + '_' + self.db_dict[
'CompoundCode'] + '.png'
compoundCIF = xtal + '_' + self.db_dict['CompoundCode'] + '.cif'
residuePlot = xtal + '_' + ligand + '.png'
pdb = xtal + '.pdb'
event = xtal + '_' + ligand + '_event.ccp4'
thumbNail = xtal + '_' + ligand + '_thumb.png'
resoHigh = self.db_dict['DataProcessingResolutionHigh']
spg = self.db_dict['RefinementSpaceGroup']
unitCell = self.db_dict['DataProcessingUnitCell']
t = ''
for ax in unitCell.split():
t += str(round(float(ax), 1)) + ' '
unitCell = t[:-1]
os.chdir(os.path.join(self.projectDir, xtal))
# FWT = xtal + '-' + ligand + '_2fofc.ccp4'
# self.cut_and_copy_map(xtal, ligand + '.pdb', '2fofc.map', FWT,'FWT','PHWT')
# DELFWT = xtal + '-' + ligand + '_fofc.ccp4'
# self.cut_and_copy_map(xtal, ligand + '.pdb', 'fofc.map', DELFWT,'DELFWT','PHDELWT')
if os.path.isfile('refine.mtz'):
self.Logfile.insert('%s: found refine.mtz' % xtal)
FWTmap, DELFWTmap = self.prepare_e_density_maps(
xtal, ligand)
self.copy_electron_density(xtal, ligand, eventMap)
ligConfidence = self.db.get_ligand_confidence_for_ligand(
xtal, ligChain, ligNumber, ligName)
if ligConfidence.startswith('0'):
self.Logfile.warning(
'%s: ligand confidence of %s-%s-%s is %s; ignoring...'
% (xtal, ligChain, ligNumber, ligName, ligConfidence))
self.Logfile.warning(
'%s: this seems unlikely because this structure is apparently ready for deposition'
% xtal)
self.Logfile.warning(
'%s: will set it to "not assigned" for now, but please update in soakDB'
% xtal)
ligConfidence = 'not assigned'
modelStatus = self.db_dict['RefinementOutcome']
if firstFile:
html += XChemMain.html_ngl(
pdb, eventMap.replace(self.projectDir, ''), FWTmap,
DELFWTmap, ligand)
html += XChemMain.html_download(self.protein_name)
html += XChemMain.html_guide()
html += XChemMain.html_table_header()
firstFile = False
html += XChemMain.html_table_row(xtal, pdbID, ligand,
compoundImage, residuePlot,
pdb, event, thumbNail,
resoHigh, spg, unitCell,
FWTmap, DELFWTmap,
ligConfidence, modelStatus)
self.make_thumbnail(xtal, x, y, z, ligand, eventMap)
self.prepare_for_download(xtal, pdb, event, compoundCIF,
ligand)
self.prepare_zip_archives()
# html = XChemMain.html_download_all_section(html,self.protein_name)
self.write_html_file(html)
self.Logfile.insert(
'======== finished preparing HTML summary ========')