simulation
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/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
 
  type() - returns the string "Simulation"
 
  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,ordered=False) - low level selector returns list of atom indices 
                              given string sel. Use atomSel.AtomSel 
                              object instead. See the atomSelLang 
                              documentation for the meaning of the optional
                              ordered argument.
 
  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,
              noSync=False,
              force=False) - delete the atoms corresponding selected by
                             the atom selection string, whose syntax is
                             described in atomSelLang. If this method is
                             called after potential terms are created
                             (associated with this simulation) then an
                             exception will be raised, unless the force
                             argument is set to True. Setting the noSync
                             argument to True will prevent synchronization
                             with associated sub-processes, and requires that
                             the sync() method be called before using
                             energy terms which depend on these subprocesses.
 
 sync(testResize=true) -  barrier and synchronize subprocess data. If the
                          argument is true, allow for changes in numAtoms,
                          numBonds.
 
 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
  atomMassArr      - a CDSVector of all atom masses
  noFit            - used by simulationTools.StructureLoop to set a
                     default value for which atoms to use in fitting.
 
 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
 
 
 
 
 
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

 
Classes
       
builtins.object
Simulation

 
class Simulation(builtins.object)
    Simulation(*args, **kwargs)
 

 
  Methods defined here:
__eq__(self, other)
Return self==value.
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__ne__(self, other)
Return self!=value.
__repr__ = _swig_repr(self)
addDependent(self, *args, **kwargs) -> 'void'
atomByID(self, *args, **kwargs) -> 'Atom'
atomCharge(self, *args, **kwargs) -> 'float_type const &'
atomFric(self, *args, **kwargs) -> 'float_type const &'
atomID(self, *args, **kwargs) -> 'int'
atomMass(self, *args, **kwargs) -> 'float_type const &'
atomMassArr(self, *args, **kwargs) -> 'CDSVector< float_type >'
atomName(self, *args, **kwargs) -> 'String'
atomNameArr(self, *args, **kwargs) -> 'CDSVector< Simulation::char4 >'
atomPos(self, *args, **kwargs) -> 'Vec3 const &'
atomPosArr(self, *args, **kwargs) -> 'CDSVector< Vec3 >'
atomString(self, *args, **kwargs) -> 'String'
atomVel(self, *args, **kwargs) -> 'Vec3 const &'
atomVelArr(self, *args, **kwargs) -> 'CDSVector< Vec3 >'
bondPairByID(self, *args, **kwargs) -> 'BondIDPair const &'
chemType(self, *args, **kwargs) -> 'String'
chemTypeArr(self, *args, **kwargs) -> 'CDSVector< Simulation::char4 >'
deleteAtoms(self, arg, noSync=False, force=False)
deleteAtoms_byIndex(self, *args, **kwargs) -> 'void'
forceUpdate(self, *args, **kwargs) -> 'int const'
kineticEnergy(self, *args, **kwargs) -> 'float_type'
lookupID(self, *args, **kwargs) -> 'int'
markAsModified(self, *args, **kwargs) -> 'void'
modifiedID(self, *args, **kwargs) -> 'Simulation const *'
name(self, *args, **kwargs) -> 'String const'
noFit(self, *args, **kwargs) -> 'bool const'
numAtoms(self, *args, **kwargs) -> 'int'
numBonds(self, *args, **kwargs) -> 'int'
numDependents(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rawID(self, *args, **kwargs) -> 'int'
registerCallbacks(self, *args, **kwargs) -> 'void'
removeDependent(self, *args, **kwargs) -> 'void'
residueName(self, *args, **kwargs) -> 'String'
residueNameArr(self, *args, **kwargs) -> 'CDSVector< Simulation::char4 >'
residueNum(self, *args, **kwargs) -> 'int'
residueNumArr(self, *args, **kwargs) -> 'CDSVector< int >'
segmentName(self, *args, **kwargs) -> 'String'
segmentNameArr(self, *args, **kwargs) -> 'CDSVector< Simulation::char4 >'
select(self, *args, **kwargs) -> 'CDSList< int >'
setAtomCharge(self, *args, **kwargs) -> 'void'
setAtomFric(self, *args, **kwargs) -> 'void'
setAtomMass(self, *args, **kwargs) -> 'void'
setAtomMassArr(self, *args, **kwargs) -> 'void'
setAtomName(self, *args, **kwargs) -> 'void'
setAtomPos(self, *args, **kwargs) -> 'void'
setAtomPosArr(self, *args, **kwargs) -> 'void'
setAtomVel(self, *args, **kwargs) -> 'void'
setAtomVelArr(self, *args, **kwargs) -> 'void'
setChemType(self, *args, **kwargs) -> 'void'
setForceUpdate(self, *args, **kwargs) -> 'void'
setNoFit(self, *args, **kwargs) -> 'void'
setResidueName(self, *args, **kwargs) -> 'void'
setResidueNum(self, *args, **kwargs) -> 'void'
setSegmentName(self, *args, **kwargs) -> 'void'
sync(self, *args, **kwargs) -> 'void'
type(self, *args, **kwargs) -> 'String const'

Static methods defined here:
__swig_destroy__ = delete_Simulation(...)
currentSimulation(*args, **kwargs) -> 'Simulation *'
deleteSimulation(*args, **kwargs) -> 'void'
getReference(*args, **kwargs) -> 'rc_Simulation &'
makeCurrent(*args, **kwargs) -> 'void'
numSimulations(*args, **kwargs) -> 'int'
simulationByID(*args, **kwargs) -> 'Simulation *'
syncAllSimulations(*args, **kwargs) -> 'void'
validSimulation(*args, **kwargs) -> 'bool'

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

Data and other attributes defined here:
__hash__ = None

 
Functions
       
Simulation_currentSimulation(*args) -> 'Simulation *'
Simulation_deleteSimulation(*args, **kwargs) -> 'void'
Simulation_getReference(*args, **kwargs) -> 'rc_Simulation &'
Simulation_makeCurrent(*args, **kwargs) -> 'void'
Simulation_numSimulations(*args) -> 'int'
Simulation_simulationByID(*args, **kwargs) -> 'Simulation *'
Simulation_syncAllSimulations(*args) -> 'void'
Simulation_validSimulation(*args, **kwargs) -> 'bool'
currentSimulation(*args) -> 'Simulation *'
makeCurrent(*args, **kwargs) -> 'void'
pyXplorHelp(*args) -> 'String'
syncAllSimulations = Simulation_syncAllSimulations(*args) -> 'void'
validSimulation = Simulation_validSimulation(*args, **kwargs) -> 'bool'