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src/b/i/biskit-2.4/Biskit/TrajFlexSlave.py   biskit(Download)
import Biskit.rmsFit as rmsFit
import numpy.oldnumeric as N
from Biskit.LogFile import ErrLog, LogFile
 
import os, time
            self.errorLog = ErrLog()
        else:
            self.errorLog = LogFile( self.ferror, mode='a' )
 
        self.frame_cache = {}

src/b/i/biskit-2.4/Biskit/Mod/TemplateSearcher.py   biskit(Download)
    def prepare(self):
        import tempfile
        import shutil
        from Biskit.LogFile import LogFile
 
        self.f_out = self.outfolder + '/TemplateSearcher.log'
 
        self.l = LogFile( self.f_out, mode='w')
        if self.local:  self.l = StdLog()
 

src/b/i/biskit-2.4/Biskit/Mod/TemplateCleaner.py   biskit(Download)
    def prepare(self):
        import tempfile
        import shutil
        from Biskit.LogFile import LogFile
 
        self.l = None
        if not self.local:
            self.l = LogFile( self.f_out, mode='w')
 
        shutil.copytree( T.testRoot() + '/Mod/project/templates/nr',

src/b/i/biskit-2.4/Biskit/Dock/ContactSlave.py   biskit(Download)
import Biskit.tools as T
from Biskit import mathUtils as MU
from Biskit.LogFile import StdLog, LogFile
import numpy.oldnumeric as N
from Complex import Complex
        self.log    = StdLog()
        if params['log']:        ## log to same file as master
            self.log = LogFile( self.flog )
        self.verbose = params['verbose']
 

src/b/i/biskit-2.4/Biskit/TrajFlexMaster.py   biskit(Download)
import Biskit.mathUtils as mathUtils
from Biskit.Errors import BiskitError
from Biskit.LogFile import ErrLog, LogFile
from Biskit.EnsembleTraj import EnsembleTraj, traj2ensemble
 
 
        self.log      = log or ErrLog()
        self.slaveLog = slaveLog or LogFile('TrajFlexSlave_errors.log')
        self.verbose  = verbose
        self.hosts    = hosts

src/b/i/biskit-2.4/Biskit/ErrorHandler.py   biskit(Download)
    def test_ErrorHandler( self ):
        """ErrorHandler test"""
        from Biskit.LogFile import LogFile
 
        self.err_log = LogFile( self.f_out )

src/b/i/biskit-2.4/Biskit/AmberParmBuilder.py   biskit(Download)
import Biskit.settings as s
import Biskit.mathUtils as MU
from Biskit.LogFile import LogFile, StdLog
from Biskit.PDBModel import PDBModel
from Biskit.Errors import BiskitError

src/b/i/biskit-2.4/Biskit/PDBCleaner.py   biskit(Download)
    def prepare(self):
        from Biskit.LogFile import LogFile
        import tempfile
 
 

src/b/i/biskit-2.4/Biskit/Mod/SequenceSearcher.py   biskit(Download)
        import tempfile
        import shutil
        from Biskit.LogFile import LogFile
 
        self.outfolder = tempfile.mkdtemp( '_test_SequenceSearcher_%s'%ident )