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src/b/i/biskit-2.4/scripts/Mod/modelling_example.py   biskit(Download)
#options = testOptions()
 
outFolder = tools.absfile( options['o'] )
f_target = tools.absfile( options['q'] )
f_target = f_target or outFolder + SequenceSearcher.F_FASTA_TARGET

src/b/i/biskit-2.4/Biskit/AmberEntropyMaster.py   biskit(Download)
        """
        ## normal and error output
        self.fout = T.absfile( out )
        self.ferror = os.path.dirname(self.fout) +'/AmberEntropy_errors.log'
        self.debug = debug
 
        self.log = StdLog()
 
        ## input files and variable option
        self.rec = T.absfile( rec, 0 )
        ## input files and variable option
        self.rec = T.absfile( rec, 0 )
        self.lig = T.absfile( lig, 0 )
        self.com = T.absfile( com, 0 )
        self.cr  = cr
 
        ## complex
        fname = T.stripSuffix( T.absfile( self.com, resolveLinks=0 ) )
        self.ref_com = fname + '_ref.complex'
        self.ref_blig= fname + '_blig.model'

src/b/i/biskit-2.4/Biskit/LocalPath.py   biskit(Download)
        """
        result = string.join( [ f[0] for f in self.fragments ], '' )
        result = T.absfile( result )
 
        if os.path.exists( result ):
                result += abs
 
        result = T.absfile( result )
 
        if existing and not os.path.exists( result ):
    def absfile( self, fname, resolveLinks=0 ):
        return T.absfile( fname, resolveLinks=resolveLinks )
 
 
    def set_path( self, fname, minLen=3, absolute=1, resolveLinks=0,
        if r:
            try:
                s = T.absfile( o )
                return 1
            except:

src/b/i/biskit-2.4/scripts/Biskit/dope.py   biskit(Download)
    print 'Updating ', f
 
    d = T.load( T.absfile( f ) )
 
    for m in d.values():
        m.update( updateMissing=1 )
 
    T.dump( d, T.absfile( f ) )
if options.has_key('i'):
    inLst = T.toList( options['i'] )
    inLst = [ T.absfile( f ) for f in inLst ]
else:
    inLst = []
 
sourceIn = T.absfile( options['s'] )
sourceOut = None
if options.has_key('so'):
    sourceOut = T.absfile( options['so'] )
 
prefix = options['o']

src/b/i/biskit-2.4/Biskit/Dock/Docker.py   biskit(Download)
        self.comPdb = None
        if comPdb:
            self.comPdb = t.absfile( comPdb )
 
        ## remember which HEX PDB was created for which model
            ## HEX PDB provided externally
            for k in self.recDic:
                self.recHexPdbs[ k ] = t.absfile( recPdb )
        else:
            ## HEX PDB has to be created
        if ligPdb:
            for k in self.ligDic:
                self.ligHexPdbs[ k ] = t.absfile( recPdb )
        else:
            self.ligHexPdbs = self.prepareHexPdbs( self.ligDic,
            datestr = "%02i%02i" % (localtime()[1], localtime()[2])
            fout = fout % ( datestr )
            if not os.path.exists( t.absfile( fout ) ):
                os.mkdir( t.absfile( fout ) )
 

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()
 
    rec_dic = T.load( T.absfile( options['rdic'] ) )
    lig_dic = T.load( T.absfile( options['ldic'] ) )
    T.flushPrint('done\n')
 
    save_changed_models( result, T.absfile( options['mo']) )
 
    T.flushPrint('Dumping result to %s' % T.absfile( options['o'] ) )

src/b/i/biskit-2.4/scripts/Biskit/traj2ensemble.py   biskit(Download)
def loadTraj( f, trajIndex, start=0, end=None, step=1 ):
    """Load traj from file, add frame names, extract portion if requested"""
 
    t = T.load( T.absfile( f ) )
    addFrameNames( t, trajIndex )
o = T.cmdDict( {'o':'traj_ensemble.dat'} )
 
out = T.absfile( o['o'] )
inLst = T.toList( o['i'] )
start = int( o.get('s','0') )
ref = o.get('ref',None)
if ref:
    ref = PDBModel( T.absfile( ref ) )
    if 'prot' in o:
        ref = ref.compress( ref.maskProtein() )
 
T.flushPrint( "Done\nDumping ensemble traj to " + o['o'] )
T.dump( result, T.absfile( o['o'] ) )
 

src/b/i/biskit-2.4/scripts/Dock/contacter.py   biskit(Download)
 
## load docking solutions
t.flushPrint( "\nLoading complex list %s ... " % t.absfile( options['i'] ) )
complex_lst = t.load( options['i'] )
t.flushPrint( "done\n" )
refComplex = None
if options.has_key('ref'):
    refComplex = t.load( t.absfile( options['ref'] ) )
 
## remove excluded hosts
 
except IOError, why:
    t.errWriteln("IOError while working on %s:" % t.absfile(options['i']) \
                 + str(why) )
    t.errWriteln( t.lastErrorTrace() )

src/b/i/biskit-2.4/Biskit/Mod/AlignerSlave.py   biskit(Download)
        @rtype: [str]
        """
        alpha_index = open(T.absfile('%s'%input_file,'a+'))
 
        string_lines = alpha_index.readlines()

src/b/i/biskit-2.4/scripts/Biskit/trajpool2ensemble.py   biskit(Download)
o = T.cmdDict( {'n':10} )
 
f_in  = T.absfile( o['i'] )
f_out = T.absfile( o.get('o', f_in) )
n = int( o['n'] )

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