def __init__(self,panddas_directory,datasource,initial_model_directory,xce_logfile,update_datasource_only,which_models):
QtCore.QThread.__init__(self)
self.panddas_directory=panddas_directory
self.datasource=datasource
self.initial_model_directory=initial_model_directory
self.db=XChemDB.data_source(self.datasource)
self.db.create_missing_columns()
self.db_list=self.db.get_empty_db_dict()
self.external_software=XChemUtils.external_software(xce_logfile).check()
self.xce_logfile=xce_logfile
self.Logfile=XChemLog.updateLog(xce_logfile)
self.update_datasource_only=update_datasource_only
self.which_models=which_models
self.already_exported_models=[]
self.RefmacParams={ 'HKLIN': '', 'HKLOUT': '',
'XYZIN': '', 'XYZOUT': '',
'LIBIN': '', 'LIBOUT': '',
'TLSIN': '', 'TLSOUT': '',
'TLSADD': '',
'NCYCLES': '10',
'MATRIX_WEIGHT': 'AUTO',
'BREF': ' bref ISOT\n',
'TLS': '',
'NCS': '',
'TWIN': '' }
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 __init__(self):
###########################################################################################
# read in settings file from XChemExplorer to set the relevant paths
print 'current dir',os.getcwd()
self.settings = pickle.load(open(".xce_settings.pkl","rb"))
print 'setting',self.settings
# self.refine_model_directory=self.settings['refine_model_directory']
self.database_directory=self.settings['database_directory']
self.xce_logfile=self.settings['xce_logfile']
self.data_source=self.settings['data_source']
self.db=XChemDB.data_source(self.data_source)
# checking for external software packages
self.external_software=XChemUtils.external_software(self.xce_logfile).check()
self.selection_criteria = [ '0 - All Datasets',
'1 - Analysis Pending',
'2 - PANDDA model',
'3 - In Refinement',
'4 - CompChem ready',
'5 - Deposition ready',
'6 - Deposited' ]
self.experiment_stage = [ ['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0],
['In Refinement', '3 - In Refinement', 65000, 0, 0],
['Comp Chem Ready!', '4 - CompChem ready', 65000, 0, 0],
['Ready for Deposition!', '5 - Deposition ready', 65000, 0, 0] ]
self.ligand_confidence_category = [ '0 - no ligand present',
'1 - Low Confidence',
'2 - Correct ligand, weak density',
'3 - Clear density, unexpected ligand',
'4 - High Confidence' ]
self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot()
# this decides which samples will be looked at
self.selection_mode = ''
self.selected_site=''
# the Folder is kind of a legacy thing because my inital idea was to have separate folders
# for Data Processing and Refinement
self.project_directory = self.settings['initial_model_directory']
self.Serial=0
self.Refine=None
self.index = -1
self.Todo=[]
self.xtalID=''
self.compoundID=''
self.spider_plot=''
self.ligand_confidence=''
self.refinement_folder=''
# self.datasetOutcome=''
self.pdb_style='refine.pdb'
self.mtz_style='refine.mtz'
# stores imol of currently loaded molecules and maps
self.mol_dict = { 'protein': -1,
'ligand': -1,
'2fofc': -1,
'fofc': -1,
'event': -1 }
# two dictionaries which are flushed when a new crystal is loaded
# and which contain information to update the data source if necessary
self.db_dict_mainTable={}
self.db_dict_panddaTable={}
###########################################################################################
# some COOT settings
coot.set_map_radius(15)
coot.set_colour_map_rotation_for_map(0)
coot.set_colour_map_rotation_on_read_pdb_flag(0)
self.QualityIndicators = { 'RefinementRcryst': '-',
'RefinementRfree': '-',
'RefinementRfreeTraficLight': 'gray',
'RefinementResolution': '-',
'RefinementResolutionTL': 'gray',
'RefinementMolProbityScore': '-',
'RefinementMolProbityScoreTL': 'gray',
'RefinementRamachandranOutliers': '-',
'RefinementRamachandranOutliersTL': 'gray',
'RefinementRamachandranFavored': '-',
'RefinementRamachandranFavoredTL': 'gray',
'RefinementRmsdBonds': '-',
'RefinementRmsdBondsTL': 'gray',
'RefinementRmsdAngles': '-',
'RefinementRmsdAnglesTL': 'gray',
'RefinementMatrixWeight': '-' }
self.spider_plot_data = { 'PANDDA_site_ligand_id': '-',
'PANDDA_site_occupancy': '-',
'PANDDA_site_B_average': '-',
'PANDDA_site_B_ratio_residue_surroundings': '-',
'PANDDA_site_RSCC': '-',
'PANDDA_site_rmsd': '-',
'PANDDA_site_RSR': '-',
'PANDDA_site_RSZD': '-' }
# default refmac parameters
self.RefmacParams={ 'HKLIN': '', 'HKLOUT': '',
'XYZIN': '', 'XYZOUT': '',
'LIBIN': '', 'LIBOUT': '',
'TLSIN': '', 'TLSOUT': '',
'TLSADD': '',
'NCYCLES': '10',
'MATRIX_WEIGHT': 'AUTO',
'BREF': ' bref ISOT\n',
'TLS': '',
'NCS': '',
'TWIN': '' }
def __init__(self):
###########################################################################################
# read in settings file from XChemExplorer to set the relevant paths
self.settings = pickle.load(open(".xce_settings.pkl", "rb"))
remote_qsub_submission = self.settings['remote_qsub']
self.database_directory = self.settings['database_directory']
self.xce_logfile = self.settings['xce_logfile']
self.Logfile = XChemLog.updateLog(self.xce_logfile)
self.Logfile.insert('starting COOT gui for reference model refinement')
self.data_source = self.settings['data_source']
# checking for external software packages
self.external_software = XChemUtils.external_software(
self.xce_logfile).check()
self.external_software['qsub_remote'] = remote_qsub_submission
# the Folder is kind of a legacy thing because my inital idea was to have separate folders
# for Data Processing and Refinement
self.reference_directory = self.settings['reference_directory']
self.refinementDir = ''
self.Serial = 0
self.Refine = None
self.xtalID = ''
self.compoundID = ''
self.spider_plot = ''
self.refinement_folder = ''
self.pdbFile = ''
self.mtzFree = ''
self.pdb_style = 'refine.pdb'
self.mtz_style = 'refine.mtz'
# stores imol of currently loaded molecules and maps
self.mol_dict = {
'protein': -1,
'ligand': -1,
'2fofc': -1,
'fofc': -1,
'event': -1
}
self.ground_state_map_List = []
self.job_running = False
###########################################################################################
# some COOT settings
coot.set_map_radius(17)
coot.set_colour_map_rotation_for_map(0)
# coot.set_colour_map_rotation_on_read_pdb_flag(21)
self.QualityIndicators = {
'Rcryst': '-',
'Rfree': '-',
'RfreeTL': 'gray',
'ResolutionHigh': '-',
'ResolutionColor': 'gray',
'MolprobityScore': '-',
'MolprobityScoreColor': 'gray',
'RamachandranOutliers': '-',
'RamachandranOutliersColor': 'gray',
'RamachandranFavored': '-',
'RamachandranFavoredColor': 'gray',
'rmsdBonds': '-',
'rmsdBondsTL': 'gray',
'rmsdAngles': '-',
'rmsdAnglesTL': 'gray',
'MatrixWeight': '-'
}
# default refmac parameters
self.RefmacParams = {
'HKLIN': '',
'HKLOUT': '',
'XYZIN': '',
'XYZOUT': '',
'LIBIN': '',
'LIBOUT': '',
'TLSIN': '',
'TLSOUT': '',
'TLSADD': '',
'NCYCLES': '10',
'MATRIX_WEIGHT': 'AUTO',
'BREF': ' bref ISOT\n',
'TLS': '',
'NCS': '',
'TWIN': ''
}
