symSimulation
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/symSimulation.py

simulation.Simulation which contains copies of a subsimulation related 
by strict symmetry operations. A SymSimulation should not be manipulated 
directly by an IVM. Rather, energies can be evaluated for atoms in the
SymSimulation, but the underlying Simulation should instead by manipulated by 
the IVM. 
 
Constructor:
 
 
 SymSimulation(name,
               subSel,
               cloneFirst=True) 
 
   A SymSimulation with given name is created based on the specified subSel,
   which is an atomSel.AtomSel object. By default the atoms in
   subSel are inserted into the newly created SymSimulation as a first
   copy with an identity transformation. If cloneFirst is set to
   False, all copies must be added with addCopy().
 
   For SymSimulations, the simulation.Simulation noFit property of the
   subSel Simulation is set to True, as the absolute position of the protomer 
   is significant.
 
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 "SymSimulation"
 
  subSel() - returns the atomSel.AtomSel subSel specified during
             object construction.
 
  addCopy(rot,           - add a copy of the specified subSel atoms
          trans,           with the specified transformation parameters,
          centroidMult,    and one or more characters to use as a prefix, or 
          centroidProj,    suffix for the segment name (one of these must be 
          translateSel,    specified). Within a copy, the coordinates q_copy 
          translateMult,   are generated from those of subSel q via the      
          rotateSel,        transformation:
          rotateAmount,   
          segidPrefix,     
          segidSuffix)     
                           
     q_copy = rotMat * q + trans + centroidMult * centroidProj * q_centroid
              + translateMult * translatePos
 
    where q_centroid is the geometric center, centroidMult and translateMult 
    are floating point numbers, centroidProj can be used to specify that only a 
    subset of the centroid position is used for the translation calculation,
    and translateSel is an atomSel.AtomSel which specifies two atoms whose 
    difference defines a translation vector. rotMat is specified by the rot
    argument if it is fixed in space, or by the rotateSel and rotateAmount 
    arguments for a rotation matrix whose orientation is allowed to
    vary. In the later case, rotateSel should specify two atoms defining a
    rotation axis, and rotationAmount will specify the amount of rotation
    (in radians).
 
  numCopies()          - return the number of subSel copies are present. This
                         will be one more than the number of times addCopy
                         was called, as a single (identity) copy exists upon
                         object creation.
 
  symOp(copyID)        - return a SymSimulationOp object corresponding to the 
                         specified copy. copyID 0 corresponds to the initial 
                         identity copy.
 
The SymSimulationOp object has the following members:
 
  Mat3 rot
  Vec3 trans
  float_type centroidMult
  Mat3    centroidProj
  AtomSel transAtoms     
  float_type transMult
  String segidPrefix
  String segidSuffix
 
 
Functions:
 
  fromSimulation(sim)  - given a simulation.Simulation object, return (cast 
                         to) a SymSimulation. Will throw an exception if sim is
                         does not have SymSimulation 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
SymSimulation(simulation.Simulation, ModifiedBase)
SymSimulationOp
simulation.Simulation(builtins.object)
SymSimulation(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)
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 SymSimulation(simulation.Simulation, ModifiedBase)
    SymSimulation(*args, **kwargs)
 

 
 
Method resolution order:
SymSimulation
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 >'
chemType(self, *args, **kwargs) -> 'String'
chemTypeArr(self, *args, **kwargs) -> 'CDSVector< Simulation::char4 >'
deleteAtoms(self, *args, **kwargs) -> 'void'
genCoords(self, *args, **kwargs) -> 'void'
genCopy(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'
subSel(self, *args, **kwargs) -> 'AtomSel'
symOp(self, *args, **kwargs) -> 'SymSimulation::SymOp &'
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_SymSimulation(...)

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 SymSimulationOp(builtins.object)
    SymSimulationOp(*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_SymSimulationOp(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
centroidProj

 
rot

 
rotAmount

 
rotAtoms

 
segidPrefix

 
segidSuffix

 
thisown

 
The membership flag
trans

 
transAtoms

 
transMult

 

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