PDBModel.PDBModel

from Biskit.Errors import BiskitError
from Biskit import EHandler
from PDBModel import PDBModel, PDBError
from ProfileCollection import ProfileCollection
 

 
        ## get Structure object for reference
        self.setRef( PDBModel( refpdb ) )
 
        ## Remove waters from ref (which will also remove it from each frame)

        @rtype: PDBModel
        """
        result = PDBModel( self.getRef(), noxyz=1 )
        result.setXyz( N.average( self.frames ) )
 

 
            ## Load
            m = PDBModel(f)
 
            ## compare atom order & content of first frame to reference pdb

        @rtype: PDBModel
        """
        s = PDBModel( self.ref, noxyz=1 )
        s.setXyz( self.frames[ index ] )
        return s

"""
 
from PDBModel import PDBModel
import tools as T
 

 
            try:
                m = PDBModel( pdbIn, skipRes=self.params['skipRes'] )
 
                if self.params['amber']:

import tools as T
from Trajectory import Trajectory
from PDBModel import PDBModel
from LogFile import StdLog
 

        self.crd  = T.gzopen( self.fcrd )
 
        self.ref  = PDBModel( T.absfile(fref), pdbCode=pdbCode )
        self.box  = box
 

"""
 
from PDBModel import PDBModel
from DictList import DictList
import numpy.oldnumeric as N

        xyz = self.reduceXyz( xyz )
 
        result = PDBModel()
 
        for k in self.atoms.keys():

    def test_ReduceCoordinates(self):
        """ReduceCoordinates test"""
 
        self.m = PDBModel( T.testRoot()+'/com/1BGS.pdb' )
        self.m = self.m.compress( N.logical_not( self.m.maskH2O() ) )

 
 
from PDBModel import PDBModel
import tools as T
import os

        """
        if self.struct == None:
            self.struct = PDBModel( self.fname )
            self.temporary = 1
 

        try:
            if self.struct == None:
                self.struct = PDBModel( self.fname )
                self.temporary = 1
 

"""
from DictList import DictList
from PDBModel import PDBModel
import Biskit.tools as T
 

            return file_or_model
 
        return PDBModel( file_or_model )
 
 

 
from AmberCrdParser import ParseError
from PDBModel import PDBModel
import tools as T
 

    def test_getModel(self):
        """AmberRstParser.getModel test"""
        self.ref = PDBModel( self.fref )
        self.model = self.p.getModel( self.ref )
        self.assertEqual( len(self.model), 11200 )

 
    from PCRModel import PCRModel
    from PDBModel import PDBModel, PDBProfiles, PDBError
 
    from ProfileCollection import ProfileCollection, ProfileError

 
import tools as t
from PDBModel import PDBModel
from LocalPath import LocalPath
 
 
class PCRModel( PDBModel ):