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src/b/i/biskit-2.4/scripts/Mod/modelling_example.py   biskit(Download)
 
import Biskit.Trajectory as Trajectory
import Biskit.Pymoler as Pymoler
import glob
import sys
 
    ## show backbone superimposed structures in pymol
    pm = Pymoler( )
    for t in traj:
        pm.addPdb( t )

src/b/i/biskit-2.4/Biskit/Dock/ComplexRandomizer.py   biskit(Download)
    def display(self, traj ):
        """Display random complexes as trajectory in Pymol.
        Only run in local interactive mode.
        """
        from Biskit import Pymoler
            print 'Wrote crd file to: %s' % self.f_crd
 
        self.pm = Pymoler( full=0 )
 
        mname = self.pm.addMovie( [ traj[i] for i in range(len(traj)) ] )

src/b/i/biskit-2.4/scripts/Biskit/pdb2xplor.py   biskit(Download)
from Biskit import Executor
from Biskit import settings
from Biskit import Pymoler
 
from numpy.oldnumeric import *
    if options.has_key('view'):
 
        pm = Pymoler( )
        mname = pm.addPdb( xplorer.outname + '.pdb' )
        pm.add('select xray-wat, segi 1XWW')

src/b/i/biskit-2.4/Biskit/Dock/Complex.py   biskit(Download)
 
        if self.local:           
            from Biskit import Pymoler
 
            self.pm = Pymoler()

src/b/i/biskit-2.4/Biskit/Dock/PatchGeneratorFromOrbit.py   biskit(Download)
def test( model, center2center, nAtoms=10, exclude=None ):
 
    from Biskit import Pymoler, PDBModel
 
    g = PatchGeneratorFromOrbit( model, center2center )
    profile = N.sum( N.array(r) )
 
    pm  = Pymoler()
    pm.addPdb( model, 'all' )
 

src/b/i/biskit-2.4/Biskit/Mod/Benchmark.py   biskit(Download)
    def test_Benchmark(self):
        """Mod.Benchmark test"""
        from Biskit import Pymoler
 
        self.b = Benchmark( self.outfolder )
 
        if self.local:
            pm = Pymoler()
            pm.addPdb( pdb, "m" )
            pm.addPdb( reference, "r" )

src/b/i/biskit-2.4/Biskit/Dock/Intervor.py   biskit(Download)
        @rtype: Pymoler
        """
        import Biskit.Pymoler as Pymoler
        model = self.model.clone()
 
            xwater = xwater.compress( N.greater( xwater['n_facets'], 0) )
 
        pm = Pymoler()
 
        pm.addPdb( model, 'com' )

src/b/i/biskit-2.4/Biskit/Dock/PatchGenerator.py   biskit(Download)
def test( model ):
 
    from Biskit import Pymoler
 
    g = PatchGenerator( model )
    r = g.randomPatches( 85, 50, max_overlap=25 )
 
    profile = N.sum( N.array(r) )
 
    pm  = Pymoler()

src/b/i/biskit-2.4/scripts/Mod/analyse.py   biskit(Download)
import Biskit.tools as T
import sys, os
import Biskit.Pymoler as Pymoler
 
def _use( o ):
    ## show result in PyMol
    if options.has_key('s'):
        p=Pymoler()
        p.addPdb( folders[0] + a.F_FINAL_PDB )
        p.add('color_b')