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src/b/i/biskit-2.4/Biskit/PDBModel.py   biskit(Download)
        self._m = self.m.clone()
        self._m.removeRes(['TIP3', 'HOH'])
        self.assertEqual( len(self._m), 1968)
        self.assertAlmostEqual( self._m.mass(), 21325.90004, 3 )
        if self.local: print "removeRes: ", time.clock() - t
                print self._m.sequence( chainMask )
 
        self.assertEqual( self._m.lenChains(), 4)
 
 
    def test_chainBreaks(self):
        """PDBModel chain break handling and writing test"""
        self.m4 = B.PDBModel( T.testRoot()+'/com/1BGS_original.pdb')
        self.assertEqual( self.m4.lenChains(), 9 )
        self.assertEqual( self.m4.lenChains( breaks=1 ), 9 )
        self.assertEqual( self.m4.lenChains( breaks=1, singleRes=1, solvent=1), 

src/b/i/biskit-2.4/Biskit/CommandLine.py   biskit(Download)
            print '\n\toutput dictionary: ', self.o
 
        self.assertEqual( o['i'], [0,0] )
        self.assertEqual( o['cut'], 25 )
        self.assertEqual( o['v'], '1.2')
        self.assertEqual( o['out'], 'out.txt' )
        self.assertEqual( o['a'], True )

src/b/i/biskit-2.4/Biskit/PDBCleaner.py   biskit(Download)
        self.c = PDBCleaner( self.m3, log=self.log, verbose=self.local )
        self.m3 = self.c.capTerminals( breaks=True, capC=[0], capN=[0,1])
        self.assertEqual( self.m3.takeChains([0]).sequence()[:18], 
                          'XVINTFDGVADXXKLPDN' )
 
        self.c = PDBCleaner( self.m4, log=self.log, verbose=self.local )
        self.m4 = self.c.capTerminals( auto=True )
        self.assertEqual( self.m4.takeChains([0]).sequence()[:18], 
                          'XVINTFDGVADXXKLPDN' )
 
            self.log.add('OK: CappingError has been raised indicating clash.' )
 
        self.assertEqual( len(self.m2.takeChains([1]).chainBreaks()), 1 )
 
 

src/b/i/biskit-2.4/Biskit/DictList.py   biskit(Download)
            self.l1 += [ d ]
 
        self.assertEqual( len(self.l1), 10, '%r != 10' % len(self.l1) )
 
 

src/b/i/biskit-2.4/Biskit/AmberLeap.py   biskit(Download)
            self.log.add( '\ntarget leaprc: %s' % target )
 
        self.assertEqual( self.x.findLeaprc('ff10'), target )
        self.assertEqual( self.x.findLeaprc('leaprc.ff10'), target )
        self.assertEqual( self.x.findLeaprc('dat/leap/cmd/leaprc.ff10'),target)
        self.assertEqual( self.x.findLeaprc( target ), target )

src/b/i/biskit-2.4/Biskit/ProfileCollection.py   biskit(Download)
        double = self.p3.concat( self.p3 )
        self.p5 = empty.concat( self.p3 )
        self.assertEqual( self.p3['letters'], self.p5['letters'] )
 
        self.p5 = self.p3.concat( empty, empty, self.p3 )
        self.assertEqual( double['letters'], self.p5['letters'] )
 
        letters = ''.join( [ v['letters'] for v in views ] )
        self.assertEqual( letters, string.letters )
 
        del self.p4

src/b/i/biskit-2.4/Biskit/AmberEntropist.py   biskit(Download)
                                 log=self.log)
        self.r = self.a.run()
        self.assertEqual( int(self.r['S_total']), 398 )
        self.assertAlmostEqual( self.r['mass'], 3254, 0 )
        self.assertAlmostEqual( self.r['S_vibes'], 298, 0 )
        self.assertEqual( int(self.r['S_rot']), 50 )
        self.assertEqual( int(self.r['nframes']), 44 )

src/b/i/biskit-2.4/Biskit/delphi.py   biskit(Download)
        self.dc.prepare()
 
        self.assertEqual( len(self.dc.resmap['LYS']), 2 )  # normal and N'
        self.assertEqual( len(self.dc.resmap['SER']), 2 )  # normal and C'
 

src/b/i/biskit-2.4/Biskit/residue.py   biskit(Download)
        r = Residue( m, 0 )
 
        self.assertEqual( len( r.atom_index ), 15 )
 
        m.mergeResidues( 0 )
        r.reset()
 
        self.assertEqual( len( r.atom_index ), 28 )

src/b/i/biskit-2.4/Biskit/Mod/SequenceSearcher.py   biskit(Download)
 
        self.assert_( len(self.searcher.clusters) > 0 )
        self.assertEqual( len(self.searcher.clusters),
                          len(self.searcher.bestOfCluster) )
 

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