def preprocess(self):
"""
Things to do before the main process runs
1. Change to the correct directory
2. Print out the reference for MR pipeline
"""
if self.verbose:
self.logger.debug('AutoMolRep::preprocess')
#change directory to the one specified in the incoming dict
self.working_dir = self.setup.get('work')
if os.path.exists(self.working_dir) == False:
os.makedirs(self.working_dir)
os.chdir(self.working_dir)
#Convert SCA to MTZ (if needed) and get unit cell and SG info and convert R3/H3
self.input_sg,self.cell,self.cell2,vol = Utils.getMTZInfo(self,False,True,True)
#Needed for running in different queues for more memory..
if Utils.calcResNumber(self,self.input_sg,False,vol) > 5000:
self.large_cell = True
#Check if input_pdb is pdb file or pdbID.
if self.input_pdb[-4:].upper() != '.PDB':
if len(self.input_pdb) == 4:
#self.input_pdb = Utils.downloadPDB(self,self.input_pdb)
self.input_pdb = Utils.getmmCIF(self,self.input_pdb)
else:
self.postprocess(True)
else:
#Have to copy into working_dir to limit path length in Phaser
try:
shutil.copy(self.input_pdb,os.getcwd())
except:
if self.verbose:
self.logger.debug('Cannot copy input pdb to working dir. Probably already there.')
self.input_pdb = os.path.join(os.getcwd(),os.path.basename(self.input_pdb))
#Check if pdb exists...
if self.input_pdb == False:
self.postprocess(True)
else:
self.dres = Utils.getRes(self)
self.pdb_info = Utils.getPDBInfo(self,self.input_pdb)
if self.pdb_info == False:
self.postprocess(True)
#If user requests to search for more mols, then allow.
if self.nmol:
if int(self.pdb_info['all'].get('NMol')) < int(self.nmol):
self.pdb_info['all']['NMol'] = self.nmol
if self.test:
self.logger.debug('TEST IS SET "ON"')
#print out recognition of the program being used
self.PrintInfo()
def preprocess(self):
"""
Things to do before the main process runs
1. Change to the correct directory
2. Print out the reference for Stat pipeline
"""
if self.verbose:
self.logger.debug('AutoStats::preprocess')
#Make the self.working_dir if it does not exist.
if os.path.exists(self.working_dir) == False:
os.makedirs(self.working_dir)
#change directory to the one specified in the incoming dict
os.chdir(self.working_dir)
#print out recognition of the program being used
self.PrintInfo()
#Check if input file is sca and convert to mtz.
if self.datafile:
self.input_sg,self.cell,self.cell2,vol = Utils.getMTZInfo(self,False,True,True)
#Change timer to allow more time for Ribosome structures.
if Utils.calcResNumber(self,self.input_sg,False,vol) > 5000:
self.stats_timer = 300
if self.test:
self.logger.debug('TEST IS SET "ON"')