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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 ):
def go( fin, fout, fpsf=None, skipRes=None, amber=0, pdb=None ):
    if fpsf:
        m = PCRModel( absfile(fpsf), absfile(fin), skipRes=skipRes )

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 test_Complex(self):
        """Dock.Complex test"""
        lig = PCRModel( t.testRoot() + "/com/1BGS.psf",
                        t.testRoot() + "/com/lig.model")
        rec = PCRModel( t.testRoot() + "/com/1BGS.psf",

src/b/i/biskit-2.4/Biskit/Dock/ComplexRandomizer.py   biskit(Download)
import numpy.oldnumeric.random_array as ra
import numpy.oldnumeric as N
from Biskit import Xplorer, PCRModel
import tempfile
    def finish( self ):
        When done, write result to disc.
        self.rec = PCRModel( self.com.rec_model.getPsfFile(), self.rec_out )
        self.lig = PCRModel( self.com.lig_model.getPsfFile(), self.lig_out )
        lig_psf = t.testRoot() + '/lig/1A19.psf' 
        rec = PCRModel( rec_psf, rec_pdb )
        lig = PCRModel( lig_psf, lig_pdb )

src/b/i/biskit-2.4/scripts/Dock/selectModels.py   biskit(Download)
import Biskit.tools as T
import Biskit.mathUtils as MaU
from Biskit import TrajCluster, EnsembleTraj, PCRModel, molUtils
from Biskit.Dock import hexTools
from Biskit.EnsembleTraj import traj2ensemble
def dumpModel( m, options, fout ):
    if options.has_key('psf'):
        m = PCRModel( options['psf'], m )

src/b/i/biskit-2.4/scripts/Dock/PCR2hex.py   biskit(Download)
# last $Date: 2012-02-23 19:10:59 -0500 (Thu, 23 Feb 2012) $
from Biskit import PCRModel
from Biskit.tools import *
from Biskit.Dock.hexTools import *
        counter += 1
        model = PCRModel( absfile(psfName), absfile(f) )   
        # chain id removed by xplor, must be identical to ref complex

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

src/b/i/biskit-2.4/scripts/Biskit/relocalize.py   biskit(Download)
import Biskit.tools as tools
from Biskit import PDBModel, PCRModel, LocalPath
from Biskit.Dock import Complex

src/b/i/biskit-2.4/Biskit/Dock/HexParser.py   biskit(Download)
from Biskit.Dock import Complex, ComplexList
from Biskit import PCRModel
import Biskit.tools as t

src/b/i/biskit-2.4/scripts/Biskit/model2pdb.py   biskit(Download)
from Biskit.tools import *
from Biskit import PDBModel, PCRModel
import os.path as osp