Example #1
0
 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()
Example #2
0
 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"')