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src/b/i/biskit-2.4/scripts/Mod/modelling_example.py   biskit(Download)
from Biskit import LogFile
 
import Biskit.Trajectory as Trajectory
import Biskit.Pymoler as Pymoler
import glob
 
## create a Trajectory object with the models
traj = Trajectory( pdbs=models )
 
## fit the models against the average structure iteratively

src/b/i/biskit-2.4/Biskit/Dock/ComplexTraj.py   biskit(Download)
"""
 
from Biskit import Trajectory, TrajError, EnsembleTraj, hist
from Complex import Complex as ProteinComplex
 
        ## to create a fake trajectory with a complex
        f =  [ T.testRoot()+ '/com/1BGS.pdb' ] * 5
        t = Trajectory( f, verbose=self.local )
 
        t = ComplexTraj( t, recChains=[0] )

src/b/i/biskit-2.4/Biskit/Dock/Analyzer.py   biskit(Download)
 
import Biskit.tools as t
from Biskit import Trajectory, mathUtils,  molUtils
 
 
    def test_Analyzer( self):
        """Dock.Analyzer test """
        from Biskit import Trajectory
        from Biskit.Dock import ComplexList
 
        ## create a minimal 1-frame receptor trajectory from a pdb file
        self.t_rec = Trajectory( [t.testRoot()+'/rec/1A2P.pdb'],

src/b/i/biskit-2.4/Biskit/Dock/ComplexRandomizer.py   biskit(Download)
    def test_ComplexRandomizer(self):
        """Dock.ComplexRandomizer test"""
        from Biskit import Trajectory
 
        if self.local:
        cs = [ self.cr.random_complex() for i in range(3) ]
 
        self.traj = Trajectory( [ c.model() for c in cs ] )
 
        if self.local:

src/b/i/biskit-2.4/scripts/analysis/a_multiDock.py   biskit(Download)
from Biskit.tools import *
from Biskit import mathUtils
from Biskit import Trajectory
from Biskit import PDBDope
from Biskit.Dock import Complex as ProteinComplex
 
## Load Trajectories - read and sort bound ligand and recepror trajectories
traj_rec = Trajectory( rec_pdbs )
traj_lig = Trajectory( lig_pdbs )
 
 
## Load Trajectories - read and sort bound ligand and recepror trajectories
traj_rec_ref = Trajectory( [ ref_rec_file ] )
traj_lig_ref = Trajectory( [ ref_lig_file ] )
 

src/b/i/biskit-2.4/scripts/analysis/random_grouping.py   biskit(Download)
from Biskit.Dock import ContactMaster, ComplexGroups
 
from Biskit import Trajectory
from Biskit.PVM.hosts import nice_dic, cpus_own
 
flushPrint('\nPreparing trajectory...')
 
t = Trajectory( [ c.model() for c in nr_cl ] )
t.ref.addChainId()
t.ref.writePdb( fout+'nr_traj_ref.pdb', ter=2 )

src/b/i/biskit-2.4/scripts/analysis/random_complexes.py   biskit(Download)
from Biskit.tools import *
from Biskit.Dock import ComplexRandomizer, ComplexList
from Biskit import Trajectory
 
default_options = {'o':'random_complexes.cl', 'n':'25',
if traj:
    flushPrint('\nWriting trajectory...')
    t = Trajectory( [ c.model() for c in result ] )
    t.ref.writePdb( traj + '.pdb' )
    t.writeCrd( traj + '.crd' )

src/b/i/biskit-2.4/scripts/analysis/a_multidock_contour.py   biskit(Download)
from Biskit.tools import *
from Biskit import mathUtils
from Biskit import Trajectory
from Biskit import PDBDope
from Biskit import EHandler

src/b/i/biskit-2.4/scripts/Biskit/traj2ensemble.py   biskit(Download)
 
import Biskit.tools as T
from Biskit import Trajectory
from Biskit import EnsembleTraj
from Biskit.EnsembleTraj import traj2ensemble
print " Done"
 
result = Trajectory()
 
result.ref = result_ref

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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