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src/b/i/biskit-2.4/Biskit/PDBModel.py   biskit(Download)
    def test_chainSingleResidues( self ):
        """PDBModel single residue chain test"""
        self.m5 = B.PDBModel( T.testRoot() + '/amber/1HPT_0.pdb' )
        self.assert_( self.m5.lenChains() < 10, 'single residue chains' )
 
        ## this should now trigger the reloading of fout2
        self.assertEqual( self._m2.atoms['name'], anames )
        self.assert_( N.all( self._m2.getXyz()[0] == xyz0) )
 
        ## after disconnection, slim() should not have any effect
        self._m2.disconnect()
        self._m2.slim()
        self.assert_( self._m2.atoms.profiles['name'] is not None )
        self.r = m1.concat( m2 )
        r = self.r
        self.assert_( r.lenChains() == m.lenChains() + 1 )
 
        r.mergeChains( 0 )
        self.r = r
        self.assert_( r.lenChains() == m.lenChains() )

src/b/i/biskit-2.4/Biskit/delphi.py   biskit(Download)
            self.assertAlmostEqual( expect[k], self.r[k], -1 )
 
        self.assert_(os.path.exists( self.fmap ), 'Potential map not found' )
        self.assert_(os.path.getsize( self.fmap) > 1000, 'empty potential map')
 
        self.dc.tofile( self.fcrg )
 
        self.assert_( os.path.exists( self.fcrg ) )
 
 

src/b/i/biskit-2.4/Biskit/atomCharger.py   biskit(Download)
        self.assertAlmostEqual( N.sum(self.m1['partial_charge']), -6, 2 )
        self.assertAlmostEqual( N.sum(self.m2['partial_charge']), -4, 2 )
        self.assert_(N.all(self.m1['partial_charge'] != 0),'unmatched atoms 1')
        self.assert_(N.all(self.m2['partial_charge'] != 0),'unmatched atoms 2')
 

src/b/i/biskit-2.4/Biskit/Statistics/ROCalyzer_2.py   biskit(Download)
 
        r =  p1 / p2
        self.assert_( (r<3.25) and (r>0.75),
                      'isnoise P should be about twice that of utest')
 
            plot( self.t_curve )
 
        self.assert_( max(self.t_curve[:,1]) > 0.4 )
 
 

src/b/i/biskit-2.4/Biskit/Dock/ContactMaster.py   biskit(Download)
                                     outFile = self.cl_out )
 
        self.assert_( len(self.hosts) > 0,
                      'master needs at least one pvm node for calculations' )
 

src/b/i/biskit-2.4/Biskit/Executor.py   biskit(Download)
            print 'Emacs was running for %.2f seconds'%self.e.runTime
 
        self.assert_( self.e.pid != None )
 
    def test_tempfiles(self):
                           debug=False )
        self.e.prepare()
        self.assert_( os.path.exists( self.e.tempdir ), 
                      'cannot find temp. folder' )
        self.e.cleanup()
        self.assert_( not os.path.exists( self.e.tempdir ),

src/b/i/biskit-2.4/Biskit/tmalign.py   biskit(Download)
            self.maligned.concat( ref ).plot()
 
        self.assert_( N.all( N.absolute(diff) < 1 ),
                      'superposition failed: \n%r' % diff)
 

src/b/i/biskit-2.4/Biskit/PDBCleaner.py   biskit(Download)
        self.c = PDBCleaner( self.model, log=self.log, verbose=self.local )       
        self.m2 = self.c.capTerminals( breaks=True )
        self.assert_( self.m2.atomNames() == self.model.atomNames() )
 
        self.m3 = self.model.clone()

src/b/i/biskit-2.4/Biskit/ProfileCollection.py   biskit(Download)
        self.p.update( self.p2, stickyChanged=1 )
 
        self.assert_( N.all( self.r['t1'] ==\
                      [0, 2, 4, 6, 8, 0, 2, 4, 6, 8, 0, 2, 4, 6, 8]))
 
        self.p4['letters'] = string.letters
 
        self.assert_( self.p4[0]['letters'] == 'a' )
        views = self.p4.toCrossViews()
 
        del self.p4
 
        self.assert_( views[0].alive is False ) 
 
    def test_plots(self):

src/b/i/biskit-2.4/Biskit/CommandLine.py   biskit(Download)
 
        pattern = self.o.REPORT_LAYOUT % ('cut', '', 'cutoff value for input')
        self.assert_( pattern in r )
 
 

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