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src/b/i/biskit-2.4/Biskit/Dock/HexParser.py   biskit(Download)
import re
import numpy.oldnumeric as Numeric  ## array
from Biskit.Dock import Complex, ComplexList
 
from Biskit import PCRModel
 
        ## Create new complex taking PCR models from dictionary
        c = Complex( self.rec_models[ i['model1'] ],
                     self.lig_models[ i['model2'] ],  matrix, i )
        return c

src/b/i/biskit-2.4/doc/tutorial1/meganuclease.py   biskit(Download)
 
## Contact analysis with Complex
from Biskit.Dock import Complex
 
com = Complex( prot, dna )

src/b/i/biskit-2.4/Biskit/Dock/PatchGeneratorFromOrbit.py   biskit(Download)
    from Biskit import PDBDope
    from Biskit.tools import *
    from Biskit.Dock import Complex
 
    print "Loading"
    lig = lig.compress( surf_lig )
 
    com = Complex( rec, lig )
 
    ## get interface patch

src/b/i/biskit-2.4/Biskit/Dock/PatchGenerator.py   biskit(Download)
    from Biskit import PDBDope
    from Biskit.tools import *
    from Biskit.Dock import Complex
 
    print "Loading"
 
    ## show real interface patch
    com = Complex( m_com.takeChains([0]), m_com.takeChains([1]))
    cont = com.atomContacts()
    rec_i = N.flatnonzero( N.sum( cont, 1 ) )

src/b/i/biskit-2.4/scripts/Dock/delphiBinding.py   biskit(Download)
 
import Biskit.tools as T
from Biskit.Dock import DelphiBindingEnergy, Complex
from Biskit import PDBModel
 
 
    ## create Protein complex
    com = Complex( rec, lig )
    return com
 

src/b/i/biskit-2.4/Biskit/Dock/delphiBindingEnergy.py   biskit(Download)
from Biskit import StdLog
from Biskit import Reduce, AtomCharger
from Biskit.Dock import Complex
 
import Biskit.tools as T
        mlig = m.takeChains( range( mrec.lenChains(), m.lenChains() ) )
 
        self.delphicom = Complex( mrec, mlig )
 
 
        rec = self.m.takeChains( [0,1] )
        lig = self.m.takeChains( [2] )
        self.com = Complex( rec, lig )
 
        self.dG = DelphiBindingEnergy( self.com, log = self.log, scale=0.5,

src/b/i/biskit-2.4/scripts/Dock/pdb2complex.py   biskit(Download)
import Biskit.tools as T
from Biskit import PDBModel
from Biskit.Dock import Complex as ProteinComplex
 
def _use( options ):
 
## create Protein complex
com = ProteinComplex( ref_rec, ref_lig )
 
print "Saving..."

src/b/i/biskit-2.4/scripts/analysis/a_multiDock.py   biskit(Download)
from Biskit import Trajectory
from Biskit import PDBDope
from Biskit.Dock import Complex as ProteinComplex
 
def _use():
traj_lig, traj_lig_ref = castTraj( traj_lig, traj_lig_ref )
 
refCom = ProteinComplex( traj_rec_ref.ref, traj_lig_ref.ref )
 
traj_rec = traj_rec_ref.concat( traj_rec )

src/b/i/biskit-2.4/Biskit/AmberEntropyMaster.py   biskit(Download)
from Biskit import PDBModel, PDBProfiles, EHandler, StdLog
 
from Biskit.Dock import Complex
 
slave_path = T.projectRoot()+"/Biskit/AmberEntropySlave.py"
 
        del t
        self.dumpMissing( Complex( rec, lig ), self.ref_com )
        self.dumpMissing( rec, self.ref_brec )
        self.dumpMissing( lig, self.ref_blig )

src/b/i/biskit-2.4/scripts/Biskit/replacePath.py   biskit(Download)
#!/usr/bin/env python
import sys
from Biskit import LocalPath, PDBModel, Trajectory
from Biskit.Dock import Complex, ComplexList
from Biskit.tools import load, dump, absfile

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