def reduceToModel( self, xyz=None, reduce_profiles=1 ):
"""
Create a reduced PDBModel from coordinates. Atom profiles the source
PDBModel are reduced by averaging over the grouped atoms.
@param xyz: coordinte array (N_atoms x 3) or
None (->use reference coordinates)
@type xyz: array OR None
@return: PDBModel with reduced atom set and profile 'mass'
@rtype: PDBModel
"""
mass = self.m.atoms.get('mass')
if xyz is None: xyz = self.m.getXyz()
mProf = [ N0.sum( N0.take( mass, group ) ) for group in self.groups ]
xyz = self.reduceXyz( xyz )
result = PDBModel()
for k in self.atoms.keys():
result.atoms.set( k, self.atoms.valuesOf(k) )
## result.setAtoms( self.atoms )
result.setXyz( xyz )
result.atoms.set( 'mass', mProf )
if reduce_profiles:
self.reduceAtomProfiles( self.m, result )
result.residues = self.m.residues
return result
def getPDBModel( self, index ):
"""
Get PDBModel object for a particular frame of the trajectory.
:param index: frame index
:type index: int
:return: model
:rtype: PDBModel
"""
s = PDBModel( self.ref, noxyz=1 )
s.setXyz( self.frames[ index ] )
return s
def avgModel( self ):
"""
Returna a PDBModel with coordinates that are the average of
all frames.
:return: PDBModel with average structure of trajectory (no fitting!)
this trajectory's ref is the source of result model
:rtype: PDBModel
"""
result = PDBModel( self.getRef(), noxyz=1 )
result.setXyz( N0.average( self.frames ) )
return result
