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src/b/i/biskit-2.4/scripts/Mod/modelling_example.py   biskit(Download)
##                  /nr.fasta                 (input for Aligner)
 
tools.flushPrint('Searching for homologues ...')
 
try:
    searcher.writeFastaClustered()
 
    tools.flushPrint('Done.\n')
 
except:
##                     /*.pdb              (  "    "         "       )
 
tools.flushPrint('Searching for templates ...')
 
try:
    fn = searcher.saveClustered()
 
    tools.flushPrint('Done.\n')
 
except:
##         templates/modeller/*.pdb      (input for Modeller)
 
tools.flushPrint('Cleaning template structures...')
 
try:

src/b/i/biskit-2.4/Biskit/PVM/ExampleSlave.py   biskit(Download)
        d = {}
 
        T.flushPrint( self.params['progress_str'] )
        for id, val in dict.items():
 
                f = 1.0 * i / 1200232112312.11
 
            T.flushPrint( str(id) + ' ' )
            time.sleep(0.5)
 

src/b/i/biskit-2.4/scripts/Dock/concat_complexLists.py   biskit(Download)
        for j in range( i+1, len( models) ):
 
            T.flushPrint('.')
 
            m1 = models[i]
    """
    if len( cl ) != len(cl.models.recModels()) * len(cl.models.ligModels()) * 512:
        T.flushPrint('\nRemoving HEX solutions greater than 512.\n')
        len_old = len( cl )
        cl = cl.filter('soln', (0,512) )
        T.flushPrint('%i solutions removed.\n' % (len_old - len(cl) ) )
        T.flushPrint('%i solutions remain.\n' % len( cl ) )
    for f in fs:
 
        T.flushPrint('Loading %s ...' % f )
 
        cl = T.load( f )

src/b/i/biskit-2.4/scripts/Dock/contacter.py   biskit(Download)
        return cl
 
    t.flushPrint('\nRemoving HEX solutions greater than 512.\n')
    r = cl.filter('soln', (0,512) )
    t.flushPrint('%i solutions removed.\n' % (len( cl ) - len( r ) ) )
    t.flushPrint('%i solutions remain.\n' % len( r ) )
    if len( todo ) > 0:
        msg = "\n%i out of %i complexes are to be updated\n\n"
        t.flushPrint( msg%(len(todo), len(cl) ) )
        return cl
    else:
        t.flushPrint( "\nList contains no data that can be updated\n" )

src/b/i/biskit-2.4/scripts/Biskit/trajpool2ensemble.py   biskit(Download)
n = int( o['n'] )
 
T.flushPrint("Loading...")
t = T.load( f_in )
 
T.flushPrint("Converting %i frames..." % len(t) )
 
if isinstance(t, EnsembleTraj ):
    T.flushPrint( "Nothing to be done!\n")
    os.rename( f_in, f_in + '_backup')
 
T.flushPrint("Saving...")
T.dump( t, f_out )
 
T.flushPrint("Done.\n")

src/b/i/biskit-2.4/scripts/Biskit/traj2ensemble.py   biskit(Download)
result_ref = None
 
T.flushPrint("Loading and appending trajectories...")
for i in range( len( inLst ) ):
 
        result_frameNames.append( fname )
 
    T.flushPrint('#')
 
print " Done"
## result = trajLst[0].concat( *trajLst[1:] )
 
T.flushPrint("Converting to EnsembleTraj...")
result = traj2ensemble( result, len(inLst))
 
T.flushPrint( "Done\nDumping ensemble traj to " + o['o'] )

src/b/i/biskit-2.4/scripts/Biskit/redump.py   biskit(Download)
    """
    try:
        T.flushPrint( "Loading " + str(f) + '\n' )
 
        return T.load( T.absfile( f ) )
            o.forcePickle = 1
 
        T.flushPrint('Dumping %s\n' % f )
        T.dump( o, T.absfile( f ) )
 

src/b/i/biskit-2.4/Biskit/Dock/Analyzer.py   biskit(Download)
        self.options = options
 
        if verbose: t.flushPrint("\nLoading...")
        self.t_lig = t.load( options['lig'] )
        self.t_rec = t.load( options['rec'] )
 
        ## equalize atom content of free (trajectory) and bound models
        if verbose: t.flushPrint('\nCasting...')
 
        bnd_rec = self.com.rec()
        @type  com_lst: ComplexList
        """
        t.flushPrint('adding hex-generated complexes')
 
        self.hexContacts = []
 
            com = com_lst[i]
            t.flushPrint('#')
 
            try:

src/b/i/biskit-2.4/scripts/Mod/setup_validation.py   biskit(Download)
        _use( options )
 
    T.flushPrint( "Creating folders and links...\n" )
 
    for f in folders:
        sv = VS(outFolder=f)
        sv.go(f)
 
    T.flushPrint( "done\n" )

src/b/i/biskit-2.4/scripts/Biskit/restartPVM.py   biskit(Download)
cmd = T.cmdDict()
 
T.flushPrint('Loading restart data...')
rst = T.load( cmd['i'] )
 
master = restart( rst, hosts=hosts )
 
T.flushPrint('Master initialized for restart.')
 
master.start()

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