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src/b/i/biskit-2.4/scripts/Mod/modelling_example.py   biskit(Download)
def testOptions():
    options = {}
    options['q'] = tools.testRoot()+ '/Mod/project/target.fasta'
    options['o'] = tools.testRoot()+ '/Mod/project'
    options['log'] = '1'

src/b/i/biskit-2.4/Biskit/delphi.py   biskit(Download)
    def test_delphi( self ):
        """Delphi test"""
        if self.local: print 'Loading PDB...'
 
        self.m1 = self.MODEL or PDBModel( T.testRoot( 'lig/1A19_dry.model' ) )
            T.errWrite( 'loading PDB...' )
 
        self.m1 = self.MODEL or PDBModel( T.testRoot( 'lig/1A19_dry.model' ) )
        Test.MODEL = self.m1
        if self.local:

src/b/i/biskit-2.4/Biskit/tmalign.py   biskit(Download)
        if self.local: print 'Loading PDB...'
 
        self.m1 = PDBModel( T.testRoot( 'tmalign/1huy_citrine.model' ) )
        self.m2 = PDBModel( T.testRoot('tmalign/1zgp_dsred_dimer.model' ) )
 
    def test_tmalignTransform( self ):
        """TMAlign.applyTransformation test"""
        m = T.load( T.testRoot( 'tmalign/1huy_citrine.model' ) )
        ref = T.load( T.testRoot( 'tmalign/1zgp_dsred_dimer.model' ) )
        ref = ref.takeChains( [0] )

src/b/i/biskit-2.4/Biskit/reduce.py   biskit(Download)
    def test_reduce( self ):
        """Reduce test"""
        if self.local: self.log.add('Loading PDB...')
 
        self.m1 = PDBModel( T.testRoot( 'lig/1A19_dry.model' ) )
        self.m2 = T.load( T.testRoot( 'com/ref.complex' ) )

src/b/i/biskit-2.4/Biskit/atomCharger.py   biskit(Download)
    def test_reduce( self ):
        """AtomCharger test"""
        if self.local: self.log.add('\nLoading PDB...')
 
        self.m1 = PDBModel( T.testRoot( 'lig/1A19_dry.model' ) )
        self.m2 = T.load( T.testRoot( 'com/ref.complex' ) )

src/b/i/biskit-2.4/Biskit/Dock/Docker.py   biskit(Download)
        import os.path
 
        ligDic = t.load( t.testRoot() + '/multidock/lig/1A19_models.dic' )
 
        ## in the test root the directories "multidock/rec" and
        ## "multidock/com" are symbolic links from "dock/rec" and
        ## "dock/com". If this is a fleshly checked out project
        ## they will not exist, so we will have to create them.
        rec_dir = t.testRoot() + '/dock/rec'
        com_dir = t.testRoot() + '/dock/com'
            if os.path.lexists( rec_dir ):
                os.unlink( rec_dir )
            os.symlink( t.testRoot() + '/dock/rec', rec_dir )
 
        if not os.path.exists( com_dir ):
            ## remove old invalid links
            if os.path.lexists( com_dir ):
                os.unlink( com_dir )
            os.symlink( t.testRoot() + '/dock/com', com_dir )

src/b/i/biskit-2.4/Biskit/Dock/Analyzer.py   biskit(Download)
 
        ## create a minimal 1-frame receptor trajectory from a pdb file
        self.t_rec = Trajectory( [t.testRoot()+'/rec/1A2P.pdb'],
                                 verbose=self.local)
        t.dump( self.t_rec, self.f_out )
 
        ## load a complex list
        cl = t.load( t.testRoot() + '/dock/hex/complexes.cl')
 
        self.a= Analyzer( rec = self.f_out,
                          lig = t.testRoot()+'/lig_pcr_00/traj.dat',
                          ref = t.testRoot()+'/com/ref.complex',
                          verbose = self.local)

src/b/i/biskit-2.4/Biskit/BioUnit.py   biskit(Download)
        self.p = B.PDBParseFile.PDBParseFile()
 
        self.m = self.p.parse2new( T.testRoot('biounit/2V4E.pdb') )
        if self.local:
            self.m.report()

src/b/i/biskit-2.4/Biskit/Mod/Analyse.py   biskit(Download)
 
            os.makedirs( self.outfolder +'/validation/%s/modeller'%v )
            shutil.copy( T.testRoot() +dir+'/%s/modeller/Modeller_Score.out'%v,
                         self.outfolder + '/validation/%s/modeller'%v)
 
            shutil.copy( T.testRoot() + dir + '/%s/identities_cov.out'%v,
            os.mkdir( self.outfolder +'/validation/%s/benchmark'%v )
            for f in [ 'rmsd_aa.out', 'rmsd_ca.out', 'PDBModels.list' ]:
                shutil.copy( T.testRoot() + dir + '/%s/benchmark/%s'%(v,f),
                             self.outfolder + '/validation/%s/benchmark'%v )
 
 
        ## data from main project
        os.mkdir( self.outfolder +'/modeller' )
        shutil.copy( T.testRoot() + '/Mod/project/modeller/PDBModels.list',
 
        os.mkdir( self.outfolder +'/t_coffee' )
        shutil.copy( T.testRoot() + '/Mod/project/t_coffee/final.pir_aln',
                     self.outfolder + '/t_coffee' )    
 

src/b/i/biskit-2.4/Biskit/Mod/Aligner.py   biskit(Download)
        os.mkdir( self.outfolder +'/sequences/' )
 
        shutil.copytree( T.testRoot() + '/Mod/project/templates/t_coffee',
                         self.outfolder + '/templates/t_coffee' )
 
        os.chmod( self.outfolder + '/templates/t_coffee', stat.S_IWRITE )
 
        shutil.copy( T.testRoot() + '/Mod/project/templates/templates.fasta',
                     self.outfolder + '/templates' )
 
        shutil.copy( T.testRoot() + '/Mod/project/sequences/nr.fasta',
                     self.outfolder + '/sequences/' )
 
        shutil.copy( T.testRoot() + '/Mod/project/target.fasta',

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