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src/b/i/biskit-2.4/scripts/Dock/contacter.py   biskit(Download)
force = []
if options.has_key('f'):
    raw_force = t.toList( options['f'] )
 
    ## check that the key is valid
## remove excluded hosts
if 'e' in options:
    MU.removeFromList( cpus_all, t.toList( options['e'] ) )
 
host_number = int( options.get('h', len( cpus_all )) )

src/b/i/biskit-2.4/scripts/Dock/concat_complexLists.py   biskit(Download)
        syntax()
 
    fs = [ T.absfile( f ) for f in T.toList( options['i'] ) ]
 
    result = ComplexList()

src/b/i/biskit-2.4/scripts/Biskit/dope.py   biskit(Download)
 
if options.has_key('i'):
    inLst = T.toList( options['i'] )
    inLst = [ T.absfile( f ) for f in inLst ]
else:

src/b/i/biskit-2.4/scripts/Biskit/traj2ensemble.py   biskit(Download)
 
out = T.absfile( o['o'] )
inLst = T.toList( o['i'] )
start = int( o.get('s','0') )
end   = o.get( 'e', None )

src/b/i/biskit-2.4/scripts/Biskit/relocalize.py   biskit(Download)
 
 
files = tools.toList( options['i'] )
 
repl = []
if 'r' in options:
    relacements = tools.toList( options['r'] )

src/b/i/biskit-2.4/scripts/Biskit/averageASA.py   biskit(Download)
 
## mask to used to delete glycines
mask = [ int(i) for i in T.toList( options['mask'] )]
 
## create random prptides from template

src/b/i/biskit-2.4/scripts/Biskit/replace_wildcard_import.py   biskit(Download)
importas = options.get('as', module )
 
srcfiles = t.toList( options.get('i', None) )
 
exclude = t.toList( options['e'] )

src/b/i/biskit-2.4/Biskit/Dock/Docker.py   biskit(Download)
        """
        if ids:
            ids = t.toList( ids )
            cMap = m.chainMap()
 

src/b/i/biskit-2.4/Biskit/Mod/Aligner.py   biskit(Download)
        r = ''
 
        input = [ self.__add_type_code( i ) for i in T.toList(input) ]
 
        if input or method:
        if output:
            r += ' -output'
            for o in T.toList( output ):
                r += ' ' + o
 
            pdbFiles= [ T.relpath( cwd, f ) for f in pdbFiles ]
 
        r['pdbs'] = T.toList( pdbFiles )
        r['templates'] = fasta_templates or self.outFolder + TC.F_FASTA
        r['sequences'] = fasta_sequences or self.outFolder + SS.F_FASTA_NR

src/b/i/biskit-2.4/scripts/Dock/selectModels.py   biskit(Download)
    """
    if options['id']:
        id = T.toList( options['id'] )
        cMap = m.chainMap()
        for chain in range( m.lenChains() ):
    """
 
    allowedAtoms = T.toList( options.get('a',[]) )
    if allowedAtoms:
        mask = tc.traj.ref.mask( lambda a: a['name'] in allowedAtoms )
def cluster( tc, options ):
 
    n_cluster = int( options['n'] )
 
    allowedAtoms = T.toList( options.get('a',[]) )

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