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src/b/i/biskit-2.4/Biskit/Hmmer.py   biskit(Download)
import Biskit.molTools as MT
import Biskit.molUtils as MU
from Biskit import Executor, TemplateError, PDBModel, StdLog, EHandler
 
 
        self.hmmdb = hmmdb
        self.verbose = verbose
        self.log = log or StdLog()
        self.tempDir = settings.tempDirShared
        self.debug = debug

src/b/i/biskit-2.4/Biskit/Dock/delphiBindingEnergy.py   biskit(Download)
from Biskit import PDBModel
from Biskit import Delphi, DelphiError
from Biskit import StdLog
from Biskit import Reduce, AtomCharger
from Biskit.Dock import Complex
 
        self.verbose = verbose
        self.log = log or StdLog()
        self.debug = debug
        self.tempdir = tempdir

src/b/i/biskit-2.4/Biskit/Dock/Complex.py   biskit(Download)
"""
 
from Biskit import PCRModel, PDBModel, PDBDope, molUtils, mathUtils, StdLog, EHandler
## from Biskit import ProsaII
from Biskit.Prosa2003 import Prosa2003

src/b/i/biskit-2.4/Biskit/AmberEntropyMaster.py   biskit(Download)
from Biskit.PVM.TrackingJobMaster import TrackingJobMaster
from Biskit.PVM.hosts import cpus_all, nice_dic
from Biskit import PDBModel, PDBProfiles, EHandler, StdLog
 
from Biskit.Dock import Complex
        self.debug = debug
 
        self.log = StdLog()
 
        ## input files and variable option

src/b/i/biskit-2.4/Biskit/atomCharger.py   biskit(Download)
import numpy as N
 
from Biskit import PDBModel, StdLog
from Biskit import AmberResidueLibrary
from Biskit import Reduce
                                                        verbose=verbose)
        self.verbose = verbose
        self.log = log or StdLog()
 
 

src/b/i/biskit-2.4/Biskit/Mod/SequenceSearcher.py   biskit(Download)
import Biskit.tools as T
import Biskit.Errors as E
from Biskit import StdLog, EHandler
 
from Biskit.Mod import settings
 
        self.verbose = verbose
        self.log = log or StdLog()
 
        self.record_dic = None #: dict ID - Bio.Fasta.Record

src/b/i/biskit-2.4/Biskit/Mod/TemplateSearcher.py   biskit(Download)
import settings
import Biskit.tools as T
from Biskit import StdLog, EHandler
 
import re
        self.silent = silent
 
        self.log = log or StdLog()
 
        ## the maximal number of clusters to return
 
        self.l = LogFile( self.f_out, mode='w')
        if self.local:  self.l = StdLog()
 
        self.f_target = self.outfolder + '/target.fasta'

src/b/i/biskit-2.4/Biskit/amberResidueLibrary.py   biskit(Download)
 
from Biskit import PDBModel
from Biskit import AmberPrepParser, StdLog
import Biskit.tools as T
 
        self.topoindex = {} ## residue types indexed by topo and resname
 
        self.log = log or StdLog()
        self.verbose = verbose
 

src/b/i/biskit-2.4/Biskit/Mod/Aligner.py   biskit(Download)
    def prepare(self):
        import tempfile
        import shutil, stat
        from Biskit import LogFile, StdLog
 
            self.a_log = LogFile( self.outfolder + '/Aligner.log' )
        else:
            self.a_log = StdLog()
 
 

src/b/i/biskit-2.4/Biskit/Mod/TemplateFilter.py   biskit(Download)
import numpy as N
import Biskit.mathUtils as M
from Biskit import StdLog, EHandler
 
 
        @type  target_id: str
        """
        self.log = log or StdLog()
        self.verbose = verbose
 

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