xplorSimulation		index
xplorSimulation.py

simulation based on an XPLOR backend. 
 
constructor:
 
  XplorSimulation(clone=False):
 
      create a new xplor process and associated XplorSimulation object. If
   the optional clone argument is True, the current atomic coordinates and
   PSF information are mirrored in the new object. Otherwise, the object
   will have no atoms or PSF information.
 
Methods:
 
  This objects contains all of the methods of the simulation.Simulation 
class. In addition, it contains the following:
 
  potList() - return the potList.PotList of potential terms which are 
              evaluated when the SCRIpting XPLOR energy term is active.
 
 
  scriptingIndex() - index into XPLOR renr array corresponding to 
                     SCRIpting term.
 
  wrap()    - return the associated xplorWrap.XplorWrap object. This 
              member is not usually needed.
 
 
  
 The following routines synchronize simulation values to/from xplor. They
are not usually needed.  
 
  initFrom()          - initialize quantities from XPLOR
  syncFrom()
  syncAtomIDFrom()
  syncPosFrom()
  syncVelFrom()
  syncFricFrom()
  syncChargeFrom()
  syncMassFrom()
  syncTo()            - copy modified coordinates, etc. variables to xplor
 
 
 

 
Classes
       
__builtin__.object
Modified
ModifiedPtr
ModifiedBase
ModifiedBasePtr
Simulation
SimulationPtr
XplorSimulation
XplorSimulationPtr

 
class Modified(__builtin__.object)
     Methods defined here:
__call__(*args)
__del__(self, destroy=<built-in function delete_Modified>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
clear(*args)
set(*args)
update(*args)
value(*args)
Data and other attributes defined here:
MOD_SELF = 1
MOD_SIMULATION = 2
__dict__ = <dictproxy object at 0xef40c0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Modified' objects>
list of weak references to the object (if defined)

 
class ModifiedBase(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_ModifiedBase>)
__getattr__ lambda self, name
__init__(self)
__repr__(self)
__setattr__ lambda self, name, value
registerTo(*args)
unRegister(*args)
updateValues(*args)
Properties defined here:
modified
get = ModifiedBase_modified_get(...)
set = ModifiedBase_modified_set(...)
registeredSimulations
get = ModifiedBase_registeredSimulations_get(...)
set = ModifiedBase_registeredSimulations_set(...)
Data and other attributes defined here:
__dict__ = <dictproxy object at 0xee99f0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'modified': <built-in function ModifiedBase_modified_get>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_get>}
__swig_setmethods__ = {'modified': <built-in function ModifiedBase_modified_set>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'ModifiedBase' objects>
list of weak references to the object (if defined)

 
class ModifiedBasePtr(ModifiedBase)
    
Method resolution order:
ModifiedBasePtr
ModifiedBase
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from ModifiedBase:
__del__(self, destroy=<built-in function delete_ModifiedBase>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
registerTo(*args)
unRegister(*args)
updateValues(*args)
Properties inherited from ModifiedBase:
modified
get = ModifiedBase_modified_get(...)
set = ModifiedBase_modified_set(...)
registeredSimulations
get = ModifiedBase_registeredSimulations_get(...)
set = ModifiedBase_registeredSimulations_set(...)
Data and other attributes inherited from ModifiedBase:
__dict__ = <dictproxy object at 0xee97f8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'modified': <built-in function ModifiedBase_modified_get>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_get>}
__swig_setmethods__ = {'modified': <built-in function ModifiedBase_modified_set>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'ModifiedBase' objects>
list of weak references to the object (if defined)

 
class ModifiedPtr(Modified)
    
Method resolution order:
ModifiedPtr
Modified
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from Modified:
__call__(*args)
__del__(self, destroy=<built-in function delete_Modified>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
clear(*args)
set(*args)
update(*args)
value(*args)
Data and other attributes inherited from Modified:
MOD_SELF = 1
MOD_SIMULATION = 2
__dict__ = <dictproxy object at 0xee97f8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Modified' objects>
list of weak references to the object (if defined)

 
class Simulation(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_Simulation>)
__getattr__ lambda self, name
__init__(self)
__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(*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 0xef4050>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'currentSimulation': <function <lambda> at 0xadd8c0>, 'deleteSimulation': <function <lambda> at 0xaddb18>, 'getReference': <function <lambda> at 0xaddaa0>, 'makeCurrent': <function <lambda> at 0xadd938>, 'numSimulations': <function <lambda> at 0xadd9b0>, 'simulationByID': <function <lambda> at 0xadda28>}
__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>)
__getattr__ lambda self, name
__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(*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 0xee97f8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'currentSimulation': <function <lambda> at 0xadd8c0>, 'deleteSimulation': <function <lambda> at 0xaddb18>, 'getReference': <function <lambda> at 0xaddaa0>, 'makeCurrent': <function <lambda> at 0xadd938>, 'numSimulations': <function <lambda> at 0xadd9b0>, 'simulationByID': <function <lambda> at 0xadda28>}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Simulation' objects>
list of weak references to the object (if defined)

 
class XplorSimulation(Simulation)
    
Method resolution order:
XplorSimulation
Simulation
__builtin__.object
Methods defined here:
__del__(self)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
calcNonXplorEnergyAndDeriv(*args)
command(self, c, r=())
deleteAtoms(self, arg)
deleteAtoms_byIndex(*args)
disableOutput(self)
enableOutput(self, state)
fastCommand(self, c, r=())
call xplorWrap.XplorWrap.fastCommand
       
help(*args)
initFrom(*args)
potList(*args)
scriptingIndex(*args)
select(self, selString)
setAtomCharge(*args)
setAtomFric(*args)
setAtomMass(*args)
setAtomMassArr(*args)
setAtomName(*args)
setAtomPos(*args)
setAtomPosArr(*args)
setAtomVel(*args)
setAtomVelArr(*args)
setChemType(*args)
setModifiedProp(*args)
setResidueName(*args)
setResidueNum(*args)
setSegmentName(*args)
shell(self)
syncAtomIDFrom(*args)
syncChargeFrom(*args)
syncFricFrom(*args)
syncFrom(*args)
syncMassFrom(*args)
syncPosFrom(*args)
syncTo(*args)
syncVelFrom(*args)
type(*args)
wrap(*args)
xplorVars(*args)
Static methods defined here:
defaultSimulation = XplorSimulation_defaultSimulation(...)
deleteDefaultSimulation = XplorSimulation_deleteDefaultSimulation(...)
initSimulation = XplorSimulation_initSimulation(...)
resetDefaultSimulation = XplorSimulation_resetDefaultSimulation(...)
Data and other attributes defined here:
__swig_getmethods__ = {'currentSimulation': <function <lambda> at 0xadd8c0>, 'defaultSimulation': <function <lambda> at 0xadecf8>, 'deleteDefaultSimulation': <function <lambda> at 0xadede8>, 'deleteSimulation': <function <lambda> at 0xaddb18>, 'getReference': <function <lambda> at 0xaddaa0>, 'initSimulation': <function <lambda> at 0xadec80>, 'makeCurrent': <function <lambda> at 0xadd938>, 'numSimulations': <function <lambda> at 0xadd9b0>, 'resetDefaultSimulation': <function <lambda> at 0xaded70>, 'simulationByID': <function <lambda> at 0xadda28>}
__swig_setmethods__ = {}
Methods inherited from Simulation:
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)
id(*args)
kineticEnergy(*args)
markAsModified(*args)
modifiedID(*args)
name(*args)
numAtoms(*args)
numBonds(*args)
registerCallbacks(*args)
removeDependent(*args)
residueName(*args)
residueNum(*args)
segmentName(*args)
sync(*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 0xee9d00>
dictionary for instance variables (if defined)
__weakref__ = <attribute '__weakref__' of 'Simulation' objects>
list of weak references to the object (if defined)

 
class XplorSimulationPtr(XplorSimulation)
    
Method resolution order:
XplorSimulationPtr
XplorSimulation
Simulation
__builtin__.object
Methods defined here:
__init__(self, this)
Methods inherited from XplorSimulation:
__del__(self)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
calcNonXplorEnergyAndDeriv(*args)
command(self, c, r=())
deleteAtoms(self, arg)
deleteAtoms_byIndex(*args)
disableOutput(self)
enableOutput(self, state)
fastCommand(self, c, r=())
call xplorWrap.XplorWrap.fastCommand
       
help(*args)
initFrom(*args)
potList(*args)
scriptingIndex(*args)
select(self, selString)
setAtomCharge(*args)
setAtomFric(*args)
setAtomMass(*args)
setAtomMassArr(*args)
setAtomName(*args)
setAtomPos(*args)
setAtomPosArr(*args)
setAtomVel(*args)
setAtomVelArr(*args)
setChemType(*args)
setModifiedProp(*args)
setResidueName(*args)
setResidueNum(*args)
setSegmentName(*args)
shell(self)
syncAtomIDFrom(*args)
syncChargeFrom(*args)
syncFricFrom(*args)
syncFrom(*args)
syncMassFrom(*args)
syncPosFrom(*args)
syncTo(*args)
syncVelFrom(*args)
type(*args)
wrap(*args)
xplorVars(*args)
Static methods inherited from XplorSimulation:
defaultSimulation = XplorSimulation_defaultSimulation(...)
deleteDefaultSimulation = XplorSimulation_deleteDefaultSimulation(...)
initSimulation = XplorSimulation_initSimulation(...)
resetDefaultSimulation = XplorSimulation_resetDefaultSimulation(...)
Data and other attributes inherited from XplorSimulation:
__swig_getmethods__ = {'currentSimulation': <function <lambda> at 0xadd8c0>, 'defaultSimulation': <function <lambda> at 0xadecf8>, 'deleteDefaultSimulation': <function <lambda> at 0xadede8>, 'deleteSimulation': <function <lambda> at 0xaddb18>, 'getReference': <function <lambda> at 0xaddaa0>, 'initSimulation': <function <lambda> at 0xadec80>, 'makeCurrent': <function <lambda> at 0xadd938>, 'numSimulations': <function <lambda> at 0xadd9b0>, 'resetDefaultSimulation': <function <lambda> at 0xaded70>, 'simulationByID': <function <lambda> at 0xadda28>}
__swig_setmethods__ = {}
Methods inherited from Simulation:
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)
id(*args)
kineticEnergy(*args)
markAsModified(*args)
modifiedID(*args)
name(*args)
numAtoms(*args)
numBonds(*args)
registerCallbacks(*args)
removeDependent(*args)
residueName(*args)
residueNum(*args)
segmentName(*args)
sync(*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 0xee9da8>
dictionary for instance variables (if defined)
__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(...)
XplorSimulation_defaultSimulation(...)
XplorSimulation_deleteDefaultSimulation(...)
XplorSimulation_initSimulation(...)
XplorSimulation_resetDefaultSimulation(...)
currentSimulation(...)
fromSimulation(...)
getXplorSimulation(simulation=0)
 given a simulation, determine the associated XplorSimulation
    if simulation is None, use simulation.currentSimulation.
    
help(...)
makeCurrent(...)