MoleculeRep

The MoleculeRep class, defined in the Molecule module, is designed to make it easy to keep track of the reps in a molecule and to update reps in many molecules simultaneously. The way it works is to create a MoleculeRep instance, then add it to as many molecules as you want using the Molecule.addRep() method. The only operations on MoleculeRep objects is to change their properties; when this occurs, all molecules to which the rep has been added will be updated. Deleting a MoleculeRep instance has no effect. A list of MoleculeRep instances for a given molecule can be gotten from the Molecule.reps() method.

The MoleculeRep class provides the following methods:

• __init__(style=defStyle, color=defColor, selection=defSelection, material=defMaterial): Initialize the Rep object with optional style, color, selection and material properties. MoleculeRep objects also have attributes with the same names as the above keywords; these can be used to query the state of the rep. Don't set these attributes directly; use the change* methods below instead.
• changeStyle(style):
• changeColor(color):
• changeSelection(selection):
• changeMaterial(material): Set the draw style, color, atom selection and material for this rep. If the rep is assigned to any molecules, the molecule rep will be updated accordingly. style must be a valid draw style; see the *Style functions below.

In the following example, we load a molecule, add a new transparent VDW rep to the molecule, then change the atom selection for the rep to "name CA":

>>> from VMD import *
>>> from Molecule import *
>>> bR=Molecule()
>>> bR.load('../proteins/brH.pdb')
      <snip>
>>> reps=bR.reps()
>>> reps[0].style
'Lines'
>>> vdw=MoleculeRep(style='VDW', material='Transparent')
>>> bR.addRep(vdw)     
>>> vdw.changeSelection('name CA')