tagSimulation
index

simulation.Simulation which contains copies of portions of a
subsimulation related, whereby the resulting coordinates correspond to
coordinates of the subsimulation translated and rotated
relative to those as previously added. A TagSimulation
should not be manipulated directly by an IVM. Rather, energies can be
evaluated for atoms in the TagSimulation, but the underlying
Simulation should instead by manipulated by the IVM.
 
Constructor:
 
 
 TagSimulation(name) 
 
   A TagSimulation with given name is created. Initially, this
   Simulation contains no atoms, and they must be added using addCopy().
 
   For TagSimulations, the simulation.Simulation noFit property of the
   subSel Simulation is set to False, specifying that the best fits
   can be made for atoms in the underlying Simulation. However, care
   must be taken in specifying which atoms are used, as specifying
   atoms in which the posSel is set in the addCopy() method will
   generally not give the desired results.
 
Methods:
 
  This objects contains all of the methods of the simulation.Simulation 
class, but some write operations may be disallowed. In addition, it contains 
the following: 
 
  type() - returns the string "TagSimulation"
 
  void addCopy(      AtomSel  sel,
                     AtomSel  posSel=AtomSel(),
                     AtomSel  rotateSel=AtomSel(),
               const int      resid=INT_MAX,
               const String&  segid="notUsed",
               const String&  segidPrefix="",
               const String&  segidSuffix="");
 
  addCopy(sel,           - sel specified atoms from a subsimulation to add.
          posSel         - atom (in a subsimulation) whose position to use
                           as the origin. Optional.
          rotateSel      - 3 atoms in a subsimulation used to generate a
                           rotation of those atoms in sel. As the atom order
                           is significant (see how rotMat is defined below),
                           this argument should be specified by an ordered
                           atomSel.AtomSel. Optional.
          resid          - residue number given to the copied atoms.
          segid          - segment name given to the copied atoms. The
                           special value "notUsed" specifies that this field
                           is not used, and this is the default.
          segidPrefix,   - prefix added to that of the copied atoms.
          segidSuffix)   - suffix given to that of the copied atoms.  
                           
    The coordinates of the copied selection are
 
      q_copy = rotMat * q + pos
 
    where rotMat is generated from rotateSel as
 
       rotMat = {X,Y,Z}
 
    where the column vectors X, Y, Z are:
 
       Z = unitVec(rotateSel[1].pos() - rotateSel[0].pos())
       Y = unitVec(V2 - dot(V2,Z)* Z)
       Z = cross( Y, Z )
 
    and V2 = rotateSel[2].pos() - rotateSel[0].pos(). If not specified,
    rotMat defaults to the unit matrix, and pos is the zero vector.
 
  numCopies()  - return the number of copies that are present. This
                 will be the number of times addCopy was called.
 
  copyOp(copyID) - return a TagSimulationOp object corresponding to the 
                   specified copy.
 
  baseAtom(tagAtom) - given an atom.Atom object in this TagSimulation,
                      return the atom corresponding to that in the the sel
                      argument given to addCopy.
 
The TagSimulationOp object has the following members:
 
  atomSel         - the first 7 values correspond to values passed to
  posSel            addCopy(), or their default values.
  rotSel
  resid
  segid
  segidPrefix
  segidSuffix
  offset          - contains an offset index placing atoms within the
                    TagSimulation.
 
 
Functions:
 
  fromSimulation(sim)  - given a simulation.Simulation object, return
                         (cast to) a TagSimulation. Will throw an exception
                         if sim is does not have TagSimulation type.
 
 
 
# 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
Modified
ModifiedBase
TagSimulation(simulation.Simulation, ModifiedBase)
TagSimulationOp
simulation.Simulation(builtins.object)
TagSimulation(simulation.Simulation, ModifiedBase)

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

 
  Methods defined here:
__call__(self, *args, **kwargs) -> 'int'
Call self as a function.
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
asString(self, *args, **kwargs) -> 'String'
clear(self, *args, **kwargs) -> 'void'
set(self, *args, **kwargs) -> 'void'
update(self, *args, **kwargs) -> 'void'
value(self, *args, **kwargs) -> 'int'

Static methods defined here:
__swig_destroy__ = delete_Modified(...)

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:
MOD_SELF = 1
MOD_SIMULATION = 2

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

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
registerTo(self, *args, **kwargs) -> 'void'
unRegister(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_ModifiedBase(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
registeredSimulations

 
thisown

 
The membership flag

 
class TagSimulation(simulation.Simulation, ModifiedBase)
    TagSimulation(*args, **kwargs)
 

 
 
Method resolution order:
TagSimulation
simulation.Simulation
ModifiedBase
builtins.object

Methods defined here:
__del__(self)
#somewhat fragile...
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addCopy(self, *args, **kwargs) -> 'void'
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 >'
atomVel(self, *args, **kwargs) -> 'Vec3 const &'
atomVelArr(self, *args, **kwargs) -> 'CDSVector< Vec3 >'
baseAtom(self, *args, **kwargs) -> 'Atom'
chemType(self, *args, **kwargs) -> 'String'
chemTypeArr(self, *args, **kwargs) -> 'CDSVector< Simulation::char4 >'
copyOp(self, *args, **kwargs) -> 'TagSimulation::CopyOp &'
deleteAtoms(self, *args, **kwargs) -> 'void'
genCoords(self, *args, **kwargs) -> 'void'
genVel(self, *args, **kwargs) -> 'void'
numCopies(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
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'
setResidueName(self, *args, **kwargs) -> 'void'
setResidueNum(self, *args, **kwargs) -> 'void'
setSegmentName(self, *args, **kwargs) -> 'void'
sync(self, *args, **kwargs) -> 'void'
syncDerivs(self, *args, **kwargs) -> 'void'
type(self, *args, **kwargs) -> 'String const'
updateValues(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_TagSimulation(...)

Data descriptors defined here:
thisown

 
The membership flag

Methods inherited from simulation.Simulation:
__eq__(self, other)
Return self==value.
__ne__(self, other)
Return self!=value.
addDependent(self, *args, **kwargs) -> 'void'
atomByID(self, *args, **kwargs) -> 'Atom'
atomString(self, *args, **kwargs) -> 'String'
bondPairByID(self, *args, **kwargs) -> 'BondIDPair const &'
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'
rawID(self, *args, **kwargs) -> 'int'
registerCallbacks(self, *args, **kwargs) -> 'void'
removeDependent(self, *args, **kwargs) -> 'void'
setForceUpdate(self, *args, **kwargs) -> 'void'
setNoFit(self, *args, **kwargs) -> 'void'

Static methods inherited from simulation.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 inherited from simulation.Simulation:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

Data and other attributes inherited from simulation.Simulation:
__hash__ = None

Methods inherited from ModifiedBase:
registerTo(self, *args, **kwargs) -> 'void'
unRegister(self, *args, **kwargs) -> 'void'

Data descriptors inherited from ModifiedBase:
modified

 
registeredSimulations

 

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

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)

Static methods defined here:
__swig_destroy__ = delete_TagSimulationOp(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
offset

 
posSel

 
resid

 
rotSel

 
segid

 
segidPrefix

 
segidSuffix

 
thisown

 
The membership flag

 
Functions
       
fromSimulation(*args, **kwargs) -> 'TagSimulation *'
pyXplorHelp(*args) -> 'String'