simulation		index
simulation.py

structure information for a simulation
 
 
Simulations provide structure information, including atom information
and connectivity. It is generally easier to get and set this
information using the higher level atom.Atom interface accessed
through the atomSel.AtomSel class.
 
The following functions are provided:
  currentSimulation() 
    return the current Simulation
 
  makeCurrent(sim)
    make the specified Simulation current.
 
  numSimulations()
    return the current number of Simulations.
 
 
The following methods for the Simulation class are available
 
  currentSimulation() - static method returning the current active Simulation
 
  name() - Simulation name
 
  numAtoms() - number of atoms in Simulation
  numBonds() - number of bonds in Simulation
 
  atomByID(index)     - return an atom.Atom object by its index
  bondPairByID(index) - return a pair of atom indices for bond indexed by index
 
  select(sel) - low level selector returns list of atom indices 
                given string sel. Use atomSel.AtomSel object instead.
 
  kineticEnergy() - calculate kinetic energy associated with the current
                    masses, velocities.
 
  atomString(index) - a 19 character string unique identifier of an atom, 
                      given an atom index.
 
  deleteAtoms(string) - delete the atoms corresponding selected by select().
                        If this method is called after potential terms are
                        created (associated with this simulation) then an
                        exception will be raised.
 
 The quantities below may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value)
 
  atomPosArr       - a CDSVector of all atom positions
  atomVelArr       - a CDSVector of all atom velocities
 
 The quantities below may be retrieved using the member function form
 quantity(index), while they are set using the form setQuantity(index,value), 
 where index is an atom index.
 
  atomPos
  atomVel
  atomMass
  atomFric
  atomCharge
  segmentName
  residueName
  residueNum
  atomName
  fullName
 
 
 

 
Classes
       
__builtin__.object
Simulation
SimulationPtr

 
class Simulation(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_Simulation>)
__eq__(self, other)
__getattr__ lambda self, name
__init__(self)
__ne__(self, other)
__repr__(self)
__setattr__ lambda self, name, value
addDependent(*args)
atomByID(*args)
atomCharge(*args)
atomFric(*args)
atomMass(*args)
atomMassArr(*args)
atomName(*args)
atomPos(*args)
atomPosArr(*args)
atomString(*args)
atomVel(*args)
atomVelArr(*args)
bondPairByID(*args)
chemType(*args)
deleteAtoms(self, arg)
deleteAtoms_byIndex(*args)
help(*args)
id(*args)
kineticEnergy(*args)
markAsModified(*args)
modifiedID(*args)
name(*args)
numAtoms(*args)
numBonds(*args)
registerCallbacks(*args)
removeDependent(*args)
residueName(*args)
residueNum(*args)
segmentName(*args)
select(*args)
setAtomCharge(*args)
setAtomFric(*args)
setAtomMass(*args)
setAtomMassArr(*args)
setAtomName(*args)
setAtomPos(*args)
setAtomPosArr(*args)
setAtomVel(*args)
setAtomVelArr(*args)
setChemType(*args)
setResidueName(*args)
setResidueNum(*args)
setSegmentName(*args)
sync(*args)
type(*args)
Static methods defined here:
currentSimulation = Simulation_currentSimulation(...)
deleteSimulation = Simulation_deleteSimulation(...)
getReference = Simulation_getReference(...)
makeCurrent = Simulation_makeCurrent(...)
numSimulations = Simulation_numSimulations(...)
simulationByID = Simulation_simulationByID(...)
Data and other attributes defined here:
__dict__ = <dictproxy object at 0xee2130>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'currentSimulation': <function <lambda> at 0xac5050>, 'deleteSimulation': <function <lambda> at 0xac52a8>, 'getReference': <function <lambda> at 0xac5230>, 'makeCurrent': <function <lambda> at 0xac50c8>, 'numSimulations': <function <lambda> at 0xac5140>, 'simulationByID': <function <lambda> at 0xac51b8>}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Simulation' objects>
list of weak references to the object (if defined)

 
class SimulationPtr(Simulation)
    
Method resolution order:
SimulationPtr
Simulation
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from Simulation:
__del__(self, destroy=<built-in function delete_Simulation>)
__eq__(self, other)
__getattr__ lambda self, name
__ne__(self, other)
__repr__(self)
__setattr__ lambda self, name, value
addDependent(*args)
atomByID(*args)
atomCharge(*args)
atomFric(*args)
atomMass(*args)
atomMassArr(*args)
atomName(*args)
atomPos(*args)
atomPosArr(*args)
atomString(*args)
atomVel(*args)
atomVelArr(*args)
bondPairByID(*args)
chemType(*args)
deleteAtoms(self, arg)
deleteAtoms_byIndex(*args)
help(*args)
id(*args)
kineticEnergy(*args)
markAsModified(*args)
modifiedID(*args)
name(*args)
numAtoms(*args)
numBonds(*args)
registerCallbacks(*args)
removeDependent(*args)
residueName(*args)
residueNum(*args)
segmentName(*args)
select(*args)
setAtomCharge(*args)
setAtomFric(*args)
setAtomMass(*args)
setAtomMassArr(*args)
setAtomName(*args)
setAtomPos(*args)
setAtomPosArr(*args)
setAtomVel(*args)
setAtomVelArr(*args)
setChemType(*args)
setResidueName(*args)
setResidueNum(*args)
setSegmentName(*args)
sync(*args)
type(*args)
Static methods inherited from Simulation:
currentSimulation = Simulation_currentSimulation(...)
deleteSimulation = Simulation_deleteSimulation(...)
getReference = Simulation_getReference(...)
makeCurrent = Simulation_makeCurrent(...)
numSimulations = Simulation_numSimulations(...)
simulationByID = Simulation_simulationByID(...)
Data and other attributes inherited from Simulation:
__dict__ = <dictproxy object at 0xed9fd8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'currentSimulation': <function <lambda> at 0xac5050>, 'deleteSimulation': <function <lambda> at 0xac52a8>, 'getReference': <function <lambda> at 0xac5230>, 'makeCurrent': <function <lambda> at 0xac50c8>, 'numSimulations': <function <lambda> at 0xac5140>, 'simulationByID': <function <lambda> at 0xac51b8>}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Simulation' objects>
list of weak references to the object (if defined)

 
Functions
       
Simulation_currentSimulation(...)
Simulation_deleteSimulation(...)
Simulation_getReference(...)
Simulation_makeCurrent(...)
Simulation_numSimulations(...)
Simulation_simulationByID(...)
currentSimulation(...)
help(...)
makeCurrent(...)