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src/b/i/biskit-2.4/Biskit/Dock/Complex.py   biskit(Download)
"""
 
from Biskit import PCRModel, PDBModel, PDBDope, molUtils, mathUtils, StdLog, EHandler
## from Biskit import ProsaII
from Biskit.Prosa2003 import Prosa2003
        def getSurface( model, key ):
            if verbose:
                log.write("Calculating SurfaceRacer data for %s..."%key)
                d = PDBDope( model )
                d.addSurfaceRacer( probe=1.4 )
        ## add/update lig/rec fold-X energies if necessary
        if not 'foldX' in rec.info or rec.xyzChanged or force:
            d = PDBDope( rec )
            d.addFoldX()
 
        if not 'foldX' in lig.info or lig.xyzChanged or force:
            d = PDBDope( lig )
        m = self.model()
 
        d = PDBDope( m )
        d.addFoldX()
 

src/b/i/biskit-2.4/scripts/analysis/a_multiDock.py   biskit(Download)
from Biskit import mathUtils
from Biskit import Trajectory
from Biskit import PDBDope
from Biskit.Dock import Complex as ProteinComplex
 
## Add surface atom profile
flushPrint('Adding accessible surface profiles...\n')
rec_asa = PDBDope( traj_rec.getRef() )
rec_asa.addASA()
 
lig_asa = PDBDope( traj_lig.getRef() )   

src/b/i/biskit-2.4/scripts/Dock/hexInput.py   biskit(Download)
 
from Biskit.tools import *
from Biskit import PDBModel, PDBDope, molUtils
 
 
    if not rec.atoms.has_key('relASA'):
        flushPrint('\nCalculating receptor surface profile')
        rec_asa = PDBDope( rec )
        rec_asa.addASA()
    if not lig.atoms.has_key('relASA'):
        flushPrint('\nCalculating ligand surface profile')
        lig_asa = PDBDope( lig )

src/b/i/biskit-2.4/Biskit/Dock/hexTools.py   biskit(Download)
import Biskit.tools as t
import tempfile
from Biskit import PDBDope, molUtils
 
 
    if not recModel.atoms.has_key('relAS'):
        #t.flushPrint('\nCalculating receptor surface profile')
        rec_asa = PDBDope( recModel )
        rec_asa.addSurfaceRacer()
    if not ligModel.atoms.has_key('relAS'):
        #t.flushPrint('\nCalculating ligand surface profile')
        lig_asa = PDBDope( ligModel )

src/b/i/biskit-2.4/Biskit/Dock/PatchGeneratorFromOrbit.py   biskit(Download)
if __name__ == '__main__':
 
    from Biskit import PDBDope
    from Biskit.tools import *
    from Biskit.Dock import Complex
 
    ## add molecular surface to components
    doper = PDBDope( rec )
    doper.addSurfaceRacer( probe=1.4 )
    surf_rec = rec.profile2mask( 'MS', 0.0001, 101 )
 
    doper = PDBDope( lig )

src/b/i/biskit-2.4/Biskit/Dock/PatchGenerator.py   biskit(Download)
if __name__ == '__main__':
 
    from Biskit import PDBDope
    from Biskit.tools import *
    from Biskit.Dock import Complex
    m_com._resIndex = None   ## HACK, something wrong with legacy _resIndex
 
    doper = PDBDope( m_com )
    doper.addSurfaceRacer()
 

src/b/i/biskit-2.4/scripts/Biskit/trajFluct.py   biskit(Download)
 
from Biskit.tools import *
from Biskit import Trajectory, PDBDope
from Biskit.ProfileCollection import ProfileError
 
try:
 
    doper = PDBDope( ref )
 
    flushPrint('adding accessible surface profiles...')

src/b/i/biskit-2.4/Biskit/Dock/Docker.py   biskit(Download)
"""
 
from Biskit import PDBModel, PDBDope, molUtils
import Biskit.tools as t
 

src/b/i/biskit-2.4/scripts/analysis/a_multidock_contour.py   biskit(Download)
from Biskit import mathUtils
from Biskit import Trajectory
from Biskit import PDBDope
from Biskit import EHandler
from Biskit.Dock import Complex as ProteinComplex