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src/b/i/biskit-2.4/scripts/Biskit/1pdb2model.py   biskit(Download)
 
from Biskit.tools import *
from Biskit import PDBModel, PCRModel
 
def _use( o ):
        m = PCRModel( absfile(fpsf), absfile(fin), skipRes=skipRes )
    else:
        m = PDBModel( absfile(fin), skipRes=skipRes )
 
    if amber:

src/b/i/biskit-2.4/Biskit/Dock/XRefineComplex.py   biskit(Download)
 
from Biskit import Xplorer, XplorerError
from Biskit import PDBModel, PCRModel
import Biskit.tools as t
from Biskit.Dock.ComplexEvolving import ComplexEvolving
    def finish( self ):
 
        rec = self.cloneAtoms( self.com.rec(), PDBModel(source=self.rec_out) )
 
        lig = self.cloneAtoms( self.com.lig(), PDBModel(source=self.lig_out) )

src/b/i/biskit-2.4/Biskit/Hmmer.py   biskit(Download)
import Biskit.molTools as MT
import Biskit.molUtils as MU
from Biskit import Executor, TemplateError, PDBModel, StdLog, EHandler
 
 
    def prepare( self ):
        from Biskit import PDBModel
        import Biskit.tools as T
 
        if not self.M:
            if self.local: print "Loading PDB...",
            self.M = PDBModel( T.testRoot()+'/lig/1A19.pdb')

src/b/i/biskit-2.4/Biskit/atomCharger.py   biskit(Download)
import numpy as N
 
from Biskit import PDBModel, StdLog
from Biskit import AmberResidueLibrary
from Biskit import Reduce
    def test_reduce( self ):
        """AtomCharger test"""
        if self.local: self.log.add('\nLoading PDB...')
 
        self.m1 = PDBModel( T.testRoot( 'lig/1A19_dry.model' ) )
            self.log.add('\nNow test handling of atom miss-matches:\n')
 
        self.m3 = PDBModel(self.m1.clone())
        self.m3.remove( [0,3,100,101,102,200] )
        ac.charge( self.m3 )

src/b/i/biskit-2.4/Biskit/SurfaceRacer.py   biskit(Download)
    def test_SurfaceRacer(self):
        """SurfaceRacer test"""
 
        from Biskit import PDBModel
        import Biskit.mathUtils as MA
 
        if self.local: print 'Loading PDB...'
        f = T.testRoot()+'/lig/1A19.pdb'
        m = PDBModel(f)

src/b/i/biskit-2.4/Biskit/PDBModel.py   biskit(Download)
    def prepare(self):
        import tempfile
 
        ## loading output file from X-plor
        self.MODEL = _TestData.MODEL or B.PDBModel( T.testRoot()+'/com/1BGS.pdb')
    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 )
    def test_chainBreaks2(self):
        """PDBModel more complicated chain break detection"""
        self.m5 = B.PDBModel( T.testRoot()+'/pdbclean/foldx_citche.pdb')
        breaks = self.m5.chainBreaks()
        self.assertEqual( len(breaks), 2 )
 
        ## limitation of the method: same model but now with capping residues
        ## filling the gap
        self.m6 = B.PDBModel( T.testRoot()+'/pdbclean/citche_capped.pdb')
    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' )
 

src/b/i/biskit-2.4/Biskit/PDBDope.py   biskit(Download)
    def prepare(self):
        from Biskit import PDBModel
        self.f = T.testRoot() + '/com/1BGS.pdb'
 
        if not Test.M:
            if self.local: print "Loading PDB...",
            Test.M = PDBModel( self.f )
    def test_model(self):
        """PDBDope test final model"""
        from Biskit import PDBModel
 
        if self.local:
            print '\nChecking that models are unchanged by doping ...'
 
        m_ref = PDBModel( self.f )
        m_ref = m_ref.compress( m_ref.maskProtein() )
        for k in m_ref.atoms.keys():

src/b/i/biskit-2.4/Biskit/Dock/Intervor.py   biskit(Download)
    def prepare( self ):
        self.m = B.PDBModel( T.testRoot() + '/com/1BGS.pdb' )
 
    def test_Intervor( self ):
        """Intervor parsing test"""
    def prepare( self ):
        self.m = B.PDBModel( T.testRoot() + '/com/1BGS.pdb' )
 
    def test_IntervorDry(self):
        self.x = Intervor( self.m, [0], debug=self.DEBUG, verbose=self.local,

src/b/i/biskit-2.4/Biskit/WhatIf.py   biskit(Download)
    def test_Whatif(self):
        """Whatif test"""
 
        from Biskit import PDBModel
 
        ## Loading PDB...
 
        f = T.testRoot()+"/com/1BGS.pdb"
        m = PDBModel(f)
        if self.local:
            ## check that model hasn't changed
            m_ref = PDBModel(f)
            m_ref = m.compress( m.maskProtein() )
            for k in m_ref.atoms.keys():

src/b/i/biskit-2.4/Biskit/tmalign.py   biskit(Download)
    def test_tmalign( self ):
        """TMAlign test"""
        from Biskit import PDBModel
 
        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' ) )

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