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src/b/i/biskit-2.4/Biskit/reduce.py   biskit(Download)
        lenchains = model.lenChains()
 
        Executor.__init__( self, 'reduce', 
                           args= '%s -BUILD -Nterm%i -DB %s %s' %\
                           (args, lenchains, self.f_db, self.f_pdbin),

src/b/i/biskit-2.4/Biskit/delphi.py   biskit(Download)
        kw['cwd']     = tempdir
 
        Executor.__init__( self, 'delphi', 
                           template=template,
                           f_in=f_in,

src/b/i/biskit-2.4/Biskit/Pymoler.py   biskit(Download)
            arg = '-qei %s'%self.foutName
 
        Executor.__init__( self, 'pymol', args=arg,
                           catch_err=1, catch_out=1, **kw )
 

src/b/i/biskit-2.4/Biskit/msms.py   biskit(Download)
            exe.bin = fmsms + '/gpdb_to_xyzrn'
 
        Executor.__init__( self, 'pdb2xyzrn', f_in=self.f_pdb,
                           cwd=fmsms, **kw )
 
        arg =' -surface ases -if %s  -af %s'%( self.f_xyzrn, self.f_surf )
 
        Executor.__init__( self, 'msms', args=arg, **kw )
 
        self.model = model.clone()

src/b/i/biskit-2.4/Biskit/DSSP.py   biskit(Download)
        self.f_out = tempfile.mktemp( '_dssp.out')
 
        Executor.__init__( self, 'dsspcmbi',
                           args='-na %s'%self.f_pdb,
                           catch_err=1, **kw )

src/b/i/biskit-2.4/Biskit/Mod/Aligner.py   biskit(Download)
        @type  host: str
        """
        Executor.__init__( self, 't_coffee', cmd, catch_out=1,
                           node=host, **kw )
 

src/b/i/biskit-2.4/Biskit/Hmmer.py   biskit(Download)
        @type  hmmdb: str
        """
        Executor.__init__( self, 'hmmindex', args='%s'%hmmdb, **kw )
 
        if not os.path.exists(hmmdb+'.ssi'):
        self.hmmdb = hmmdb
 
        Executor.__init__( self, 'hmmpfam', f_in= tempfile.mktemp('.fasta'),
                           catch_out=1, **kw )
 
        self.hmmName = hmmName
 
        Executor.__init__( self, 'hmmfetch',
                           args=' %s %s'%(hmmdb, hmmName), **kw )
 
               'input HMM file missing or empty'
 
        Executor.__init__( self, 'hmmalign',
                           args=' -q %s %s'%(hmmFile, fastaFile), **kw )
 

src/b/i/biskit-2.4/Biskit/Prosa2003.py   biskit(Download)
        self.pot_ub = 15.
 
        Executor.__init__( self, 'prosa2003', template=self.inp,
                           f_in=prosaInput, **kw )
 

src/b/i/biskit-2.4/Biskit/WhatIf.py   biskit(Download)
          log      - Biskit.LogFile, program log (None->STOUT) (default: None)
        """
        Executor.__init__( self, 'whatif', template=self.whatif_script,
                           f_out='/dev/null', **kw )
 

src/b/i/biskit-2.4/Biskit/Blast2Seq.py   biskit(Download)
                 %(self.inp1, self.inp2)
 
        Executor.__init__( self, 'bl2seq', blastcmd, catch_out=1, **kw )
 
 

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