VMDInter Objects

  Objects in this module are used to communicate with the external VMD
program.  

Constructor:
  VMDInter(host,port) - arguments are optional. Default to the env variables
                        DP_HOST and DP_PORT. These correspond to the host and
                        port on which VMD is listening.

Methods:
  makeObj(name) - return a new VMDObject with given name.
  getObj(name)  - return an existing VMDObject with given name.

  deleteAll() - delete all VMD graphical objects associated with this
		xplor session.
  tclCommand(cmd) - execute TCL command in the VMD interpreter.
  setCenter(v)    - set the center of rotation to the 3-tuple v
  vmdLocal()      - return true true if VMD and XPLOR are running on
                    the same computer, else false.

  makeTop(name) - make object with given name VMD's ``top'' molecule.

  loadFiles(args) - load multiple structures at once. See help for this method.


VMDObject Objects

  are created by the appropriate VMDInter method

Methods:

    color(colorSpec) - set the color of the associated graphical object.
    delete() - delete the associated VMD graphical object
    labels(sel) - draw labels at the positions of the atoms specified by the
		  sel AtomSel. The format of the label is controlled
	 	  by the following boolean members:
            		labelSegID    - print segment ID
            		labelResName  - print residue name
            		labelResID    - print residue ID
            		labelAtomName - print atom name
    bonds(atomSel,
          style="lines"
          colorBy="Molecule") - draw molecular representation
		  including the atoms specified by atomSel. If the
		  second argument is omitted, lines are draw between
                  the atoms. Other styles include any of the VMD rendering
		  styles. colorBy corresponds to the VMD coloring method.
    append() - append the current coordinates to the graphical object
               and create a new VMD animation frame.

Example:

from vmdInter import VMDInter
vmd=VMDInter()
vobj=vmd.makeObj("struct")                  #creates a new VMD molecule
                                            # named ``struct''
vobj.bonds("name C or name N or name CA")   #draw backbone atoms

#ivm is an <m ivm>.IVM object
# the next line will cause a new animation frame to be appended to 
# the VMD trajectory for molecule named ``struct'' - every 100 steps
# of dynamics or minimization
ivm.setTrajectory( VMDTraj(vobj,saveInterval=100) )