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 append_dict_of_gda_barcodes(out_dict,files,xce_logfile):
# out_dict={}
# for files in glob.glob(os.path.join('/dls_sw',beamline,'logs','*')):
Logfile=XChemLog.updateLog(xce_logfile)
found_barcode_entry=False
gda_log= files[files.rfind('/')+1:]
if gda_log.startswith('gda_server.') and gda_log.endswith('.gz'):
with gzip.open(files,'r') as f:
for line in f:
if 'BART SampleChanger - getBarcode() returning' in line:
barcode=line.split()[len(line.split())-1]
found_barcode_entry=True
if found_barcode_entry:
if 'Snapshots will be saved' in line:
sampleID=line.split()[len(line.split())-1].split('/')[-1]
out_dict[sampleID]=barcode
Logfile.insert('found: sample=%s, barcode=%s, file=%s' %(sampleID,barcode,files))
found_barcode_entry=False
elif gda_log.startswith('gda_server') and gda_log.endswith('log'):
for line in open(files):
if 'BART SampleChanger - getBarcode() returning' in line:
barcode=line.split()[len(line.split())-1]
found_barcode_entry=True
if found_barcode_entry:
if 'Snapshots will be saved' in line:
sampleID=line.split()[len(line.split())-1].split('/')[-1]
out_dict[sampleID]=barcode
Logfile.insert('found: sample=%s, barcode=%s, file=%s' %(sampleID,barcode,files))
found_barcode_entry=False
return out_dict
def __init__(self,initial_model_directory,xce_logfile,datasource):
QtCore.QThread.__init__(self)
self.xce_logfile=xce_logfile
self.Logfile=XChemLog.updateLog(xce_logfile)
self.initial_model_directory=initial_model_directory
self.datasource=datasource
self.db=XChemDB.data_source(datasource)
def __init__(self, htmlDir, projectDir, database, xce_logfile):
self.htmlDir = htmlDir
self.projectDir = projectDir
self.Logfile = XChemLog.updateLog(xce_logfile)
self.db = XChemDB.data_source(database)
self.db_dict = None
self.pdb = None
def print_acedrg_status(xce_logfile,xtal_db_dict):
Logfile=XChemLog.updateLog(xce_logfile)
Logfile.insert('compound restraints summary:')
pending=0
started=0
running=0
missing_smiles=0
failed=0
success=0
unknown=0
for xtal in xtal_db_dict:
db_dict=xtal_db_dict[xtal]
status=db_dict['RefinementCIFStatus']
if 'pending' in status:
pending+=1
elif 'started' in status:
status+=1
elif 'running' in status:
running+=1
elif 'missing' in status:
missing_smiles+=1
elif 'failed' in status:
failed +=1
elif 'generated' in status:
success+=1
else:
unknown+=1
Logfile.insert('restraint generation pending: ...... %s' %str(pending))
Logfile.insert('restraint generation started: ...... %s' %str(started))
Logfile.insert('restraint generation running: ...... %s' %str(running))
Logfile.insert('missing smiles string: ............. %s' %str(missing_smiles))
Logfile.insert('restraint generation failed: ....... %s' %str(failed))
Logfile.insert('restraints successfully created: ... %s' %str(success))
Logfile.insert('unknown status: .................... %s' %str(unknown))
def __init__(self,initial_model_directory,pandda_params,xce_logfile,datasource,run_pandda_analyse):
QtCore.QThread.__init__(self)
self.panddas_directory=pandda_params['out_dir']
self.pdb_style=pandda_params['pdb_style']
self.mtz_style=pandda_params['mtz_style']
self.Logfile=XChemLog.updateLog(xce_logfile)
self.initial_model_directory=initial_model_directory
self.db=XChemDB.data_source(datasource)
self.run_pandda_analyse=run_pandda_analyse
def change_links_to_selected_data_collection_outcome(sample,data_collection_dict,data_collection_column_three_dict,dataset_outcome_dict,initial_model_directory,data_source_file,xce_logfile):
Logfile=XChemLog.updateLog(xce_logfile)
# find out which row was selected in respective data collection table
selected_processing_result='n/a'
indexes=data_collection_column_three_dict[sample][0].selectionModel().selectedRows()
if indexes != []: # i.e. logfile exists
for index in sorted(indexes):
selected_processing_result=index.row()
for n,entry in enumerate(data_collection_dict[sample]):
if entry[0]=='logfile':
if entry[7]==selected_processing_result:
visit=entry[1]
run=entry[2]
autoproc=entry[4]
db_dict=entry[6]
outcome=dataset_outcome_dict[sample]
path_to_logfile=db_dict['DataProcessingPathToLogfile']
path_to_mtzfile=db_dict['DataProcessingPathToMTZfile']
mtz_filename=db_dict['DataProcessingMTZfileName']
log_filename=db_dict['DataProcessingLOGfileName']
relative_path_to_mtzfile='./'+path_to_mtzfile.replace(initial_model_directory,'')
if relative_path_to_mtzfile.startswith('.//'):
relative_path_to_mtzfile=relative_path_to_mtzfile.replace('.//','./')
relative_path_to_logfile='./'+path_to_logfile.replace(initial_model_directory,'')
if relative_path_to_logfile.startswith('.//'):
relative_path_to_logfile=relative_path_to_logfile.replace('.//','./')
# first check if folders and files exist
# since user might do this before data are actually copied over
if os.path.isdir(os.path.join(initial_model_directory,sample,'autoprocessing',visit+'-'+run+autoproc)):
db_dict['DataProcessingAutoAssigned']='False'
Logfile.insert('changing directory to: '+os.path.join(initial_model_directory,sample))
os.chdir(os.path.join(initial_model_directory,sample))
# first remove old links
os.system('/bin/rm '+sample+'.mtz 2> /dev/null')
os.system('/bin/rm '+sample+'.log 2> /dev/null')
# make new links
# Logfile.insert('setting symlink: '+os.path.join(path_to_logfile,log_filename)+' -> '+sample+'.log')
# os.symlink(os.path.join(path_to_logfile,log_filename),sample+'.log')
# Logfile.insert('setting symlink: '+os.path.join(path_to_mtzfile,mtz_filename)+' -> '+sample+'.mtz')
# os.symlink(os.path.join(path_to_mtzfile,mtz_filename),sample+'.mtz')
Logfile.insert('setting relative symlink: '+os.path.join(relative_path_to_logfile,log_filename)+' -> '+sample+'.log')
os.symlink(os.path.join(relative_path_to_logfile,log_filename),sample+'.log')
Logfile.insert('setting relative symlink: '+os.path.join(relative_path_to_mtzfile,mtz_filename)+' -> '+sample+'.mtz')
os.symlink(os.path.join(relative_path_to_mtzfile,mtz_filename),sample+'.mtz')
# update data source
data_source=XChemDB.data_source(data_source_file)
data_source.update_insert_data_source(sample,db_dict)
else:
Logfile.insert('please copy data to PROJECT DIRECTORY first!')
def __init__(self,pandda_params,xce_logfile,datasource):
self.data_directory=pandda_params['data_dir']
self.panddas_directory=pandda_params['out_dir']
self.min_build_datasets=pandda_params['min_build_datasets']
self.pdb_style=pandda_params['pdb_style']
self.mtz_style=pandda_params['mtz_style']
self.input_dir_structure=pandda_params['pandda_dir_structure']
self.problem_found=False
self.error_code=-1
self.Logfile=XChemLog.updateLog(xce_logfile)
self.db=XChemDB.data_source(datasource)
def get_gda_barcodes(sampleList, gzipped_logs_parsed, gda_log_start_line,
beamline, xce_logfile):
Logfile = XChemLog.updateLog(xce_logfile)
Logfile.insert('checking GDA logfile in {0!s}'.format(
os.path.join('/dls_sw', beamline, 'logs')))
pinDict = {}
found_barcode_entry = False
for gdaLogFile in glob.glob(
os.path.join('/dls_sw', beamline, 'logs', 'gda-server*log*')):
Logfile.insert('parsing {0!s}'.format(gdaLogFile))
if gzipped_logs_parsed and gdaLogFile.endswith('.gz'):
Logfile.insert('{0!s} was already parsed during this visit'.format(
gdaLogFile))
continue
if gdaLogFile.endswith('.gz'):
with gzip.open(gdaLogFile, 'r') as f:
for line in f:
if 'BART SampleChanger - getBarcode() returning' in line:
barcode = line.split()[len(line.split()) - 1]
found_barcode_entry = True
if found_barcode_entry:
if 'Snapshots will be saved' in line:
sampleID = line.split()[len(line.split()) -
1].split('/')[-1]
if sampleID in sampleList:
pinDict[sampleID] = barcode
Logfile.insert(
'found: sample={0!s}, barcode={1!s}, file={2!s}'
.format(sampleID, barcode, gdaLogFile))
found_barcode_entry = False
else:
for n, line in enumerate(
open(gdaLogFile).readlines()[gda_log_start_line:]):
if 'BART SampleChanger - getBarcode() returning' in line:
barcode = line.split()[len(line.split()) - 1]
found_barcode_entry = True
if found_barcode_entry:
if 'Snapshots will be saved' in line:
sampleID = line.split()[len(line.split()) -
1].split('/')[-1]
if sampleID in sampleList:
pinDict[sampleID] = barcode
Logfile.insert(
'found: sample={0!s}, barcode={1!s}, file={2!s}'
.format(sampleID, barcode, gdaLogFile))
found_barcode_entry = False
gda_log_start_line = gda_log_start_line + n - 1
return pinDict, gda_log_start_line
def __init__(self,initial_model_directory,run_dict,protocol,spg,ref,reso_limit,cc_half,xce_logfile,external_software,ccp4_scratch_directory,max_queue_jobs,database):
QtCore.QThread.__init__(self)
self.initial_model_directory=initial_model_directory
self.run_dict=run_dict
self.protocol=protocol
self.spg=spg
self.ref=ref
self.reso_limit=reso_limit
self.cc_half=cc_half
self.xce_logfile=xce_logfile
self.Logfile=XChemLog.updateLog(xce_logfile)
self.external_software=external_software
self.ccp4_scratch_directory=ccp4_scratch_directory
self.max_queue_jobs=max_queue_jobs
self.database=database
self.db=XChemDB.data_source(database)
def __init__(self,initial_model_directory,run_dict,protocol,spg,ref,reso_limit,cc_half,xce_logfile,external_software,ccp4_scratch_directory,max_queue_jobs,database,overwrite):
QtCore.QThread.__init__(self)
self.initial_model_directory=initial_model_directory
self.run_dict=run_dict
self.protocol=protocol
self.spg=spg
self.ref=ref
self.reso_limit=reso_limit
self.cc_half=cc_half
self.xce_logfile=xce_logfile
self.Logfile=XChemLog.updateLog(xce_logfile)
self.external_software=external_software
self.ccp4_scratch_directory=ccp4_scratch_directory
self.max_queue_jobs=max_queue_jobs
self.database=database
self.db=XChemDB.data_source(database)
self.overwrite=overwrite
def __init__(self,project_directory,xtalID,event_map,ligand_pdb,xce_logfile,db_file,resolution):
self.Logfile=XChemLog.updateLog(xce_logfile)
self.event_map=event_map
if not os.path.isfile(self.event_map):
self.Logfile.insert('cannot find Event map: '+self.event_map)
self.Logfile.insert('cannot convert event_map to structure factors!')
return None
self.project_directory=project_directory
self.xtalID=xtalID
self.event_map=event_map
self.ligand_pdb=ligand_pdb
self.event=event_map[event_map.rfind('/')+1:].replace('.map','').replace('.ccp4','')
# self.resolution=resolution
self.db=XChemDB.data_source(db_file)
# self.db_file=db_file
self.resolution=resolution
def linkAutoProcessingResult(xtal, dbDict, projectDir, xce_logfile):
Logfile = XChemLog.updateLog(xce_logfile)
run = dbDict['DataCollectionRun']
visit = dbDict['DataCollectionVisit']
autoproc = dbDict['DataProcessingProgram']
mtzFileAbs = dbDict['DataProcessingPathToMTZfile']
mtzfile = mtzFileAbs[mtzFileAbs.rfind('/') + 1:]
logFileAbs = dbDict['DataProcessingPathToLogfile']
logfile = logFileAbs[logFileAbs.rfind('/') + 1:]
Logfile.insert('changing directory to ' + os.path.join(projectDir, xtal))
os.chdir(os.path.join(projectDir, xtal))
# MTZ file
Logfile.warning('removing %s.mtz' % xtal)
os.system('/bin/rm %s.mtz' % xtal)
print xtal, os.path.join('autoprocessing', visit + '-' + run + autoproc,
mtzfile)
if os.path.isfile(
os.path.join('autoprocessing', visit + '-' + run + autoproc,
mtzfile)):
os.symlink(
os.path.join('autoprocessing', visit + '-' + run + autoproc,
mtzfile), xtal + '.mtz')
Logfile.insert(
'linking MTZ file from different auto-processing pipeline:')
Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + '-' +
run + autoproc, mtzfile) + ' ' +
xtal + '.mtz')
# LOG file
Logfile.warning('removing %s.log' % xtal)
os.system('/bin/rm %s.log' % xtal)
if os.path.isfile(
os.path.join('autoprocessing', visit + '-' + run + autoproc,
logfile)):
os.symlink(
os.path.join('autoprocessing', visit + '-' + run + autoproc,
logfile), xtal + '.log')
Logfile.insert(
'linking LOG file from different auto-processing pipeline:')
Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + '-' +
run + autoproc, logfile) + ' ' +
xtal + '.log')
def print_cluster_status_message(program,cluster_dict,xce_logfile):
Logfile=XChemLog.updateLog(xce_logfile)
Logfile.insert('cluster status summary:')
Logfile.insert('%s %s jobs are running on the cluster' %(len(cluster_dict[program]),program))
if len(cluster_dict[program]) > 0:
cumulative_runtime=0
job_ids = []
for n,item in enumerate(cluster_dict[program]):
cumulative_runtime += item[2]
if not item[0] in job_ids:
job_ids.append(item[0])
average_runtime=round(float(cumulative_runtime)/float(n+1),0)
Logfile.insert('average run time '+str(average_runtime)+' minutes')
if job_ids != []:
Logfile.insert('you can kill them by pasting the following line into a new terminal window:')
out='qdel '
for job in job_ids:
out += str(job)+' '
Logfile.insert(out)
def get_names_of_current_clusters(xce_logfile,panddas_directory):
Logfile=XChemLog.updateLog(xce_logfile)
Logfile.insert('parsing %s/cluster_analysis' %panddas_directory)
os.chdir('%s/cluster_analysis' %panddas_directory)
cluster_dict={}
for out_dir in sorted(glob.glob('*')):
if os.path.isdir(out_dir):
cluster_dict[out_dir]=[]
found_first_pdb=False
for folder in glob.glob(os.path.join(out_dir,'pdbs','*')):
xtal=folder[folder.rfind('/')+1:]
if not found_first_pdb:
if os.path.isfile(os.path.join(panddas_directory,'cluster_analysis',out_dir,'pdbs',xtal,xtal+'.pdb') ):
cluster_dict[out_dir].append(os.path.join(panddas_directory,'cluster_analysis',out_dir,'pdbs',xtal,xtal+'.pdb'))
found_first_pdb=True
cluster_dict[out_dir].append(xtal)
# for key in cluster_dict:
# Logfile.insert('cluster %s: %s datasets' %(str(key),str(len(cluster_dict[key])-1)))
return cluster_dict
def print_acedrg_status(xce_logfile, xtal_db_dict):
Logfile = XChemLog.updateLog(xce_logfile)
Logfile.insert('compound restraints summary:')
pending = 0
started = 0
running = 0
missing_smiles = 0
failed = 0
success = 0
unknown = 0
for xtal in xtal_db_dict:
db_dict = xtal_db_dict[xtal]
status = db_dict['RefinementCIFStatus']
if 'pending' in status:
pending += 1
elif 'started' in status:
started += 1
elif 'running' in status:
running += 1
elif 'missing' in status:
missing_smiles += 1
elif 'failed' in status:
failed += 1
elif 'generated' in status:
success += 1
else:
unknown += 1
Logfile.insert('restraint generation pending: ...... {0!s}'.format(
str(pending)))
Logfile.insert('restraint generation started: ...... {0!s}'.format(
str(started)))
Logfile.insert('restraint generation running: ...... {0!s}'.format(
str(running)))
Logfile.insert('missing smiles string: ............. {0!s}'.format(
str(missing_smiles)))
Logfile.insert('restraint generation failed: ....... {0!s}'.format(
str(failed)))
Logfile.insert('restraints successfully created: ... {0!s}'.format(
str(success)))
Logfile.insert('unknown status: .................... {0!s}'.format(
str(unknown)))
def append_dict_of_gda_barcodes(out_dict, files, xce_logfile):
# out_dict={}
# for files in glob.glob(os.path.join('/dls_sw',beamline,'logs','*')):
Logfile = XChemLog.updateLog(xce_logfile)
found_barcode_entry = False
gda_log = files[files.rfind('/') + 1:]
if gda_log.startswith('gda_server.') or gda_log.startswith(
'gda-server.') and gda_log.endswith('.gz'):
with gzip.open(files, 'r') as f:
for line in f:
if 'BART SampleChanger - getBarcode() returning' in line:
barcode = line.split()[len(line.split()) - 1]
found_barcode_entry = True
if found_barcode_entry:
if 'Snapshots will be saved' in line:
sampleID = line.split()[len(line.split()) -
1].split('/')[-1]
out_dict[sampleID] = barcode
Logfile.insert(
'found: sample={0!s}, barcode={1!s}, file={2!s}'.
format(sampleID, barcode, files))
found_barcode_entry = False
elif gda_log.startswith('gda_server') or gda_log.startswith(
'gda-server') and gda_log.endswith('txt'):
for line in open(files):
if 'BART SampleChanger - getBarcode() returning' in line:
barcode = line.split()[len(line.split()) - 1]
found_barcode_entry = True
if found_barcode_entry:
if 'Snapshots will be saved' in line:
sampleID = line.split()[len(line.split()) -
1].split('/')[-1]
out_dict[sampleID] = barcode
Logfile.insert(
'found: sample={0!s}, barcode={1!s}, file={2!s}'.
format(sampleID, barcode, files))
found_barcode_entry = False
return out_dict
def print_cluster_status_message(program, cluster_dict, xce_logfile):
Logfile = XChemLog.updateLog(xce_logfile)
Logfile.insert('cluster status summary:')
Logfile.insert('{0!s} {1!s} jobs are running on the cluster'.format(
len(cluster_dict[program]), program))
if len(cluster_dict[program]) > 0:
cumulative_runtime = 0
job_ids = []
for n, item in enumerate(cluster_dict[program]):
cumulative_runtime += item[2]
if not item[0] in job_ids:
job_ids.append(item[0])
average_runtime = round(float(cumulative_runtime) / float(n + 1), 0)
Logfile.insert('average run time ' + str(average_runtime) + ' minutes')
if job_ids != []:
Logfile.insert(
'you can kill them by pasting the following line into a new terminal window:'
)
out = 'qdel '
for job in job_ids:
out += str(job) + ' '
Logfile.insert(out)
def __init__(self,pandda_params,xce_logfile,dataset_list,datasource):
QtCore.QThread.__init__(self)
self.data_directory=pandda_params['data_dir']
self.panddas_directory=pandda_params['out_dir']
self.submit_mode=pandda_params['submit_mode']
# if self.submit_mode == 'local machine':
# self.nproc=pandda_params['nproc']
# else:
# self.nproc='7'
self.nproc=pandda_params['nproc']
self.min_build_datasets=pandda_params['min_build_datasets']
self.pdb_style=pandda_params['pdb_style']
self.mtz_style=pandda_params['mtz_style']
self.sort_event=pandda_params['sort_event']
self.number_of_datasets=pandda_params['N_datasets']
self.max_new_datasets=pandda_params['max_new_datasets']
self.grid_spacing=pandda_params['grid_spacing']
self.filter_pdb=pandda_params['filter_pdb']
self.Logfile=XChemLog.updateLog(xce_logfile)
self.dataset_list=dataset_list
self.datasource=datasource
self.db=XChemDB.data_source(datasource)
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 set_xce_logfile(self, xce_object):
XChemLog.startLog(xce_object.xce_logfile).create_logfile(
xce_object.xce_version)
xce_object.update_log = XChemLog.updateLog(xce_object.xce_logfile)
def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile):
Logfile=XChemLog.updateLog(xce_logfile)
Serial=str(Serial)
# first check if refinement is ongoing and exit if yes
if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'REFINEMENT_IN_PROGRESS')):
# coot.info_dialog('*** REFINEMENT IN PROGRESS ***')
Logfile.insert('cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' %self.xtalID)
return None
#######################################################
# HKLIN & HKLOUT
if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz')):
RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz \\\n')
elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')):
RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n')
else:
Logfile.insert('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID)
return None
RefmacParams['HKLOUT']='HKLOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz \\\n')
#######################################################
# XYZIN & XYZOUT
RefmacParams['XYZIN']='XYZIN '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb \\\n')
RefmacParams['XYZOUT']='XYZOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb \\\n')
#######################################################
# LIBIN & LIBOUT
found_cif=False
if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')):
found_cif=True
# in cases where multiple liagnds are present (e.g. NOG, ATP) the user for now needs to put
# the respective dictionary into the xtalID folder
# need to think of a better mechanism in the future
additional_cif=False
additional_cif_file=''
for file in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')):
if file.endswith('.cif'):
if self.compoundID not in file:
additional_cif_file=file
# additional_cif=True <- should be true, but need to check this part of the code! 16/11/2016
additional_cif=False
if additional_cif:
Cmds = (
'#!'+os.getenv('SHELL')+'\n'
'\n'
'$CCP4/bin/libcheck << eof \n'
'_Y\n'
'_FILE_L '+os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')+'\n'
'_FILE_L2 '+additional_cif_file+'\n'
'_FILE_O '+os.path.join(self.ProjectPath,self.xtalID,'combined_cif')+'\n'
'_END\n'
'eof\n'
)
os.chdir(os.path.join(self.ProjectPath,self.xtalID))
print Cmds
os.system(Cmds)
RefmacParams['LIBIN']='LIBIN '+self.ProjectPath+'/'+self.xtalID+'/combined_cif.lib \\\n'
else:
RefmacParams['LIBIN']='LIBIN '+self.ProjectPath+'/'+self.xtalID+'/'+self.compoundID+'.cif \\\n'
RefmacParams['LIBOUT']='LIBOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n'
if not found_cif:
# this should actually not be necessary, but the following scenario can happen:
# if a new data source is created from a file system, but smiles and compoundID where not updated;
# so the ligand may still be in the structure, but since the compoundID is unknown to the datasource,
# its restraints won't be read in and refmac will fail
for file in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')):
if file.endswith('.cif'):
RefmacParams['LIBIN']='LIBIN '+file+' \\\n'
RefmacParams['LIBOUT']='LIBOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n'
break
#######################################################
# TLSIN & TLSOUT
findTLS='\n'
TLSphenix=''
if RefmacParams['TLS'].startswith('refi'):
if external_software['phenix.find_tls_groups']:
findTLS=os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','phenix_find_TLS_groups.py')+' in.pdb\n'
RefmacParams['TLSIN']='TLSIN '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refmac.tls \\\n'
RefmacParams['TLSOUT']='TLSOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine.tls \\\n'
TLSphenix=' phenix.tls '
else:
RefmacParams['TLS']='\n'
# #######################################################
# # create folder for new refinement cycle
# os.mkdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))
#
# #######################################################
# # write PDB file
# # now take protein pdb file and write it to newly create Refine_<serial> folder
# # note: the user has to make sure that the ligand file was merged into main file
# for item in coot_utils_XChem.molecule_number_list():
# if coot.molecule_name(item).endswith(self.prefix+'.pdb'):
# coot.write_pdb_file(item,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb'))
#######################################################
# PANDDAs stuff
# only use occupancy refinement if EVENT map is present
occupancy_refinement=''
if external_software['giant.create_occupancy_params']:
os.chdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))
cmd = ( '#!'+os.getenv('SHELL')+'\n'
'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n'
'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-sh')+'\n'
'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n'
"giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'\n" )
# os.system("giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'")
os.system(cmd)
# quick fix for the moment; need to talk to Nick since this should not be necessary
try:
params_file = fileinput.input('refmac_refine.params',inplace=True)
for line in params_file:
if 'incomplete' in line:
line=line.replace('incomplete','complete')
print line,
# elif 'occupancy refine' in line:
# line=line.replace('occupancy refine','occupancy refine ncycle 10\noccupancy refine')
# print line,
else:
print line,
params_file.close()
except OSError:
# this may happen in case giant.create_occupancy_params did not produce a params output file
pass
create_bound_conformation=''
if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac_refine.params')):
occupancy_refinement='@refmac_refine.params\n'
create_bound_conformation="/bin/rm *bound.pdb\ngiant.strip_conformations pdb=refine.pdb suffix='.bound.pdb'\n"
#######################################################
# we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refiment
os.chdir(os.path.join(self.ProjectPath,self.xtalID))
os.system('touch REFINEMENT_IN_PROGRESS')
#######################################################
# clean up!
# and remove all files which will be re-created by current refinement cycle
os.system('/bin/rm refine.pdb refine.mtz validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log')
if external_software['qsub']:
pbs_line='#PBS -joe -N XCE_refmac\n'
else:
pbs_line='\n'
#######################################################
# weight
if str(RefmacParams['MATRIX_WEIGHT']).lower() == 'auto':
weight='weight AUTO\n'
else:
weight='weight matrix '+str(RefmacParams['MATRIX_WEIGHT'])+'\n'
#######################################################
# PANDDA validation @ spider plot
spider_plot=''
if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb')):
if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')):
pdb_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb')
mtz_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')
pdb_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb')
mtz_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz')
spider_plot='giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' %(pdb_one,mtz_one,pdb_two,mtz_two)
#######################################################
# PHENIX stuff (if working at DLS)
module_load=''
if os.getcwd().startswith('/dls'):
module_load='module load phenix\n'
source =''
if 'bash' in os.getenv('SHELL'):
source = (
'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n'
'\n'
'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-sh')+'\n'
'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' )
elif 'csh' in os.getenv('SHELL'):
source = (
'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n'
'\n'
'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-csh')+'\n'
'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh')+'\n' )
refmacCmds = (
'#!'+os.getenv('SHELL')+'\n'
+pbs_line+
'\n'
+source+
'\n'
+module_load+
'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'\n'
'\n'
'$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(self.datasource,self.xtalID,'RefinementStatus','running') +
'\n'
+findTLS+
'refmac5 '
+RefmacParams['HKLIN']
+RefmacParams['HKLOUT']
+RefmacParams['XYZIN']
+RefmacParams['XYZOUT']
+RefmacParams['LIBIN']
+RefmacParams['LIBOUT']
+RefmacParams['TLSIN']
+RefmacParams['TLSOUT']+
' << EOF > refmac.log\n'
'make -\n'
' hydrogen ALL -\n'
' hout NO -\n'
' peptide NO -\n'
' cispeptide YES -\n'
' ssbridge YES -\n'
' symmetry YES -\n'
' sugar YES -\n'
' connectivity NO -\n'
' link NO\n'
+RefmacParams['NCS']+
'refi -\n'
' type REST -\n'
' resi MLKF -\n'
' meth CGMAT -\n'
+RefmacParams['BREF']
+RefmacParams['TLS']
+RefmacParams['TWIN']+
'ncyc '+RefmacParams['NCYCLES']+'\n'
'scal -\n'
' type SIMP -\n'
' LSSC -\n'
' ANISO -\n'
' EXPE\n'
+weight+
'solvent YES\n'
+occupancy_refinement+
'monitor MEDIUM -\n'
' torsion 10.0 -\n'
' distance 10.0 -\n'
' angle 10.0 -\n'
' plane 10.0 -\n'
' chiral 10.0 -\n'
' bfactor 10.0 -\n'
' bsphere 10.0 -\n'
' rbond 10.0 -\n'
' ncsr 10.0\n'
'labin FP=F SIGFP=SIGF FREE=FreeR_flag\n'
'labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM\n'
+RefmacParams['TLSADD']+'\n'
'DNAME '+self.xtalID+'\n'
'END\n'
'EOF\n'
'\n'
+spider_plot+
'\n'
'phenix.molprobity refine_%s.pdb refine_%s.mtz\n' %(Serial,Serial)+
'/bin/mv molprobity.out refine_molprobity.log\n'
'mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n' %(Serial,Serial)+
'cd '+self.ProjectPath+'/'+self.xtalID+'\n'
'#ln -s %s/%s/Refine_%s/refine_%s.pdb refine.pdb\n' %(self.ProjectPath,self.xtalID,Serial,Serial)+
'#ln -s %s/%s/Refine_%s/refine_%s.mtz refine.mtz\n' %(self.ProjectPath,self.xtalID,Serial,Serial)+
'ln -s ./Refine_%s/refine_%s.pdb refine.pdb\n' %(Serial,Serial)+
'ln -s ./Refine_%s/refine_%s.mtz refine.mtz\n' %(Serial,Serial)+
'\n'
+create_bound_conformation+
'\n'
'ln -s Refine_%s/validate_ligands.txt .\n' %Serial+
'ln -s Refine_%s/refine_molprobity.log .\n' %Serial+
'mmtbx.validation_summary refine.pdb > validation_summary.txt\n'
'\n'
'fft hklin refine.mtz mapout 2fofc.map << EOF\n'
'labin F1=FWT PHI=PHWT\n'
'EOF\n'
'\n'
'fft hklin refine.mtz mapout fofc.map << EOF\n'
'labin F1=DELFWT PHI=PHDELWT\n'
'EOF\n'
'\n'
'$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+
' %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))+
'\n'
'/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID)+
'\n'
)
Logfile.insert('writing refinement shell script to'+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac.csh'))
cmd = open(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac.csh'),'w')
cmd.write(refmacCmds)
cmd.close()
os.chdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))
# os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial))
Logfile.insert('changing directory to %s' %(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)))
if external_software['qsub']:
Logfile.insert('starting refinement on cluster')
os.system('qsub -P labxchem refmac.csh')
else:
os.system('chmod +x refmac.csh')
Logfile.insert('starting refinement on local machine')
os.system('./refmac.csh &')
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': ''
}
def change_links_to_selected_data_collection_outcome(
sample, data_collection_dict, data_collection_column_three_dict,
dataset_outcome_dict, initial_model_directory, data_source_file,
xce_logfile):
Logfile = XChemLog.updateLog(xce_logfile)
# find out which row was selected in respective data collection table
selected_processing_result = 'n/a'
indexes = data_collection_column_three_dict[sample][0].selectionModel(
).selectedRows()
if indexes != []: # i.e. logfile exists
for index in sorted(indexes):
selected_processing_result = index.row()
for n, entry in enumerate(data_collection_dict[sample]):
if entry[0] == 'logfile':
if entry[7] == selected_processing_result:
visit = entry[1]
run = entry[2]
autoproc = entry[4]
db_dict = entry[6]
outcome = dataset_outcome_dict[sample]
path_to_logfile = db_dict['DataProcessingPathToLogfile']
path_to_mtzfile = db_dict['DataProcessingPathToMTZfile']
mtz_filename = db_dict['DataProcessingMTZfileName']
log_filename = db_dict['DataProcessingLOGfileName']
# relative_path_to_mtzfile='./'+path_to_mtzfile.replace(initial_model_directory,'')
relative_path_to_mtzfile = './' + path_to_mtzfile.replace(
os.path.join(initial_model_directory, sample), '')
if relative_path_to_mtzfile.startswith('.//'):
relative_path_to_mtzfile = relative_path_to_mtzfile.replace(
'.//', './')
relative_path_to_logfile = './' + path_to_logfile.replace(
os.path.join(initial_model_directory, sample), '')
if relative_path_to_logfile.startswith('.//'):
relative_path_to_logfile = relative_path_to_logfile.replace(
'.//', './')
# first check if folders and files exist
# since user might do this before data are actually copied over
if os.path.isdir(
os.path.join(initial_model_directory, sample,
'autoprocessing',
visit + '-' + run + autoproc)):
db_dict['DataProcessingAutoAssigned'] = 'False'
Logfile.insert(
'changing directory to: ' +
os.path.join(initial_model_directory, sample))
os.chdir(os.path.join(initial_model_directory, sample))
# first remove old links
os.system('/bin/rm ' + sample + '.mtz 2> /dev/null')
os.system('/bin/rm ' + sample + '.log 2> /dev/null')
# make new links
# Logfile.insert('setting symlink: '+os.path.join(path_to_logfile,log_filename)+' -> '+sample+'.log')
# os.symlink(os.path.join(path_to_logfile,log_filename),sample+'.log')
# Logfile.insert('setting symlink: '+os.path.join(path_to_mtzfile,mtz_filename)+' -> '+sample+'.mtz')
# os.symlink(os.path.join(path_to_mtzfile,mtz_filename),sample+'.mtz')
Logfile.insert(
'setting relative symlink: ' +
os.path.join(relative_path_to_logfile, log_filename) +
' -> ' + sample + '.log')
os.symlink(
os.path.join(relative_path_to_logfile, log_filename),
sample + '.log')
Logfile.insert(
'setting relative symlink: ' +
os.path.join(relative_path_to_mtzfile, mtz_filename) +
' -> ' + sample + '.mtz')
os.symlink(
os.path.join(relative_path_to_mtzfile, mtz_filename),
sample + '.mtz')
# update data source
data_source = XChemDB.data_source(data_source_file)
data_source.update_insert_data_source(sample, db_dict)
else:
Logfile.insert(
'please copy data to PROJECT DIRECTORY first!')