simulationWorld
index
simulationWorld.py

common Xplor-NIH execution environment
 
there is one of SimulationWorld object, which can be obtained using the
SimulationWorld_world() function.
 
The SimulationWorld contains the following infrastructure items:
 
  timeFactor()        -returns the conversion from the internal time
                       representation to picoseconds.
  kBoltzmann()        -returns the Boltzmann constant in internal units.
  random              -a global instance of the RandomNum class
  setRandomSeed(seed) -method used to reset all random number seeds. 
                       This resets the seed in python's random module,
                       the global RandomNum seed, and the seed used in the
                       XPLOR interface.
  logLevel() / setLogLevel("none" | "normal" | "all" | "debug")
                      -get/set the current logging level. This functionality is
                       not currently utilized much.
  cpuTime()           - return the total CPU time since program start. This
                        time includes that of child processes which have
                        been properly terminated.
 
The units currently input to xplor-nih are
 
   length: Angstroms
   time: ps
   energy: Kcal/mol
   mass: atomic-mass-unit
   charge: electron-charge
 
 physical constants in SI units
 ------------------------------
     Kb = 1.380662 E-23 J/K
     Na = 6.022045 E23  1/mol
     e = 1.6021892 E-19 C
     eps = 8.85418782 E-12 F/m
 
     1 Kcal = 4184.0 J
     1 amu = 1.6605655 E-27 Kg
     1 A = 1.0 E-10 m
 
Internally, AKMA units are used:
 
timeFactor = SQRT ( ( 1A )**2 * 1amu * Na  / 1Kcal )
kBoltzmann = Na *Kb  / 1 Kcal)
 
 
 

 
Classes
       
__builtin__.object
RandomNum
RandomNumPtr
RandomSeeder
RandomSeederPtr
SimulationWorld
SimulationWorldPtr

 
class RandomNum(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_RandomNum>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
integerInRange(*args)
seed(*args)
setSeed(*args)
uniform(*args)

Data and other attributes defined here:
__dict__ = <dictproxy object at 0xee96e0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'RandomNum' objects>
list of weak references to the object (if defined)

 
class RandomNumPtr(RandomNum)
    
Method resolution order:
RandomNumPtr
RandomNum
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from RandomNum:
__del__(self, destroy=<built-in function delete_RandomNum>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
integerInRange(*args)
seed(*args)
setSeed(*args)
uniform(*args)

Data and other attributes inherited from RandomNum:
__dict__ = <dictproxy object at 0xee9e50>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'RandomNum' objects>
list of weak references to the object (if defined)

 
class RandomSeeder(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_RandomSeeder>)
__getattr__ lambda self, name
__init__(self)
__repr__(self)
__setattr__ lambda self, name, value
setSeed(*args)

Data and other attributes defined here:
__dict__ = <dictproxy object at 0xee96e0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'RandomSeeder' objects>
list of weak references to the object (if defined)

 
class RandomSeederPtr(RandomSeeder)
    
Method resolution order:
RandomSeederPtr
RandomSeeder
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from RandomSeeder:
__del__(self, destroy=<built-in function delete_RandomSeeder>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
setSeed(*args)

Data and other attributes inherited from RandomSeeder:
__dict__ = <dictproxy object at 0xee99f0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'RandomSeeder' objects>
list of weak references to the object (if defined)

 
class SimulationWorld(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_SimulationWorld>)
__getattr__ lambda self, name
__init__(self)
__repr__(self)
__setattr__ lambda self, name, value
cpuTime(*args)
kBoltzmann(*args)
logLevel(*args)
memoryUsed(*args)
registerRandomSeeder(*args)
setLogLevel(*args)
setRandomSeed(*args)
timeFactor(*args)

Static methods defined here:
addFinalizer = SimulationWorld_addFinalizer(...)
finalize = SimulationWorld_finalize(...)
init = SimulationWorld_init(...)
world = SimulationWorld_world(...)

Properties defined here:
random
get = SimulationWorld_random_get(...)
set = SimulationWorld_random_set(...)

Data and other attributes defined here:
LOG_ALL = 10
LOG_DEBUG = 15
LOG_NONE = 0
LOG_NORMAL = 5
__dict__ = <dictproxy object at 0xee9e50>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'addFinalizer': <function <lambda> at 0xc149b0>, 'finalize': <function <lambda> at 0xc14a28>, 'init': <function <lambda> at 0xc14938>, 'random': <built-in function SimulationWorld_random_get>, 'world': <function <lambda> at 0xc148c0>}
__swig_setmethods__ = {'random': <built-in function SimulationWorld_random_set>}
__weakref__ = <attribute '__weakref__' of 'SimulationWorld' objects>
list of weak references to the object (if defined)

 
class SimulationWorldPtr(SimulationWorld)
    
Method resolution order:
SimulationWorldPtr
SimulationWorld
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from SimulationWorld:
__del__(self, destroy=<built-in function delete_SimulationWorld>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
cpuTime(*args)
kBoltzmann(*args)
logLevel(*args)
memoryUsed(*args)
registerRandomSeeder(*args)
setLogLevel(*args)
setRandomSeed(*args)
timeFactor(*args)

Static methods inherited from SimulationWorld:
addFinalizer = SimulationWorld_addFinalizer(...)
finalize = SimulationWorld_finalize(...)
init = SimulationWorld_init(...)
world = SimulationWorld_world(...)

Properties inherited from SimulationWorld:
random
get = SimulationWorld_random_get(...)
set = SimulationWorld_random_set(...)

Data and other attributes inherited from SimulationWorld:
LOG_ALL = 10
LOG_DEBUG = 15
LOG_NONE = 0
LOG_NORMAL = 5
__dict__ = <dictproxy object at 0xee9980>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'addFinalizer': <function <lambda> at 0xc149b0>, 'finalize': <function <lambda> at 0xc14a28>, 'init': <function <lambda> at 0xc14938>, 'random': <built-in function SimulationWorld_random_get>, 'world': <function <lambda> at 0xc148c0>}
__swig_setmethods__ = {'random': <built-in function SimulationWorld_random_set>}
__weakref__ = <attribute '__weakref__' of 'SimulationWorld' objects>
list of weak references to the object (if defined)

 
Functions
       
SimulationWorld_addFinalizer(...)
SimulationWorld_finalize(...)
SimulationWorld_init(...)
SimulationWorld_world(...)
help(...)
world()