xplorSimulation
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/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 atomic coordinates and PSF
   information of the XplorSimulation associated with the 
   simulation.currentSimulation() 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:
 
  type() - returns the string "XplorSimulation"
 
  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.
 
  deleteAtoms(selection,
              noSync=False) - delete atoms specified by the given (string)
                              atom selection. Specify noSync=True for a 
                              performance improvement, but it requires the
                              caller to call the syncFrom() method before
                              manipulating any atom information on the C++
                              side.
 
  addAtom(atomName,residueNum,residueName,
          chemicalType="",
          segmentName="",
          mass=10.,
          pos=None,
          isPseudo=False) - add a single atom to this XplorSimulation with
                            the specified atomName, residueNum, residueName,
                            segmentName and mass. If pos is specified it is
                            also set. The isPeudo flag specifies whether or
                            not the atom will be selected with the PSEUdo atom
                            selection keyword. Do note that currently pseudo
                            atoms are identified by residue name, so that if
                            isPseudo=True is specified in this call, all atoms
                            with the given residueName will be identified as
                            PSEUDO. The created atom is returned as an
                            atom.Atom.
 
The following  method with this name from the underlying
                            xplorWrap.XplorWrap object.
  command(cmd, names) 
  fastCommand(cmd, names) 
  shell()                 
  disableOutput()
  enableOutpu()
 
 
 The following routines synchronize simulation values to/from xplor. They
are not usually needed.  
 
  initFrom()          - initialize quantities from XPLOR
  syncFrom()          - copy all information from XPLOR to C++ data structures
  syncAtomIDFrom()
  syncPosFrom()
  syncVelFrom()
  syncFricFrom()
  syncChargeFrom()
  syncMassFrom()
  syncTo()            - copy modified coordinates, etc. variables to xplor
 
 
 
 
 
# 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
simulation.Simulation(builtins.object)
XplorSimulation

 
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 XplorSimulation(simulation.Simulation)
    XplorSimulation(clone=False)
 

 
 
Method resolution order:
XplorSimulation
simulation.Simulation
builtins.object

Methods defined here:
__init__(self, clone=False)
Initialize self.  See help(type(self)) for accurate signature.
__oldinit__ = __init__(self, *args, **kwargs)
__repr__ = _swig_repr(self)
addAtom(self, atomName, residueNum, residueName, chemicalType='', segmentName='', mass=10.0, pos=None, isPseudo=False)
calcNonXplorEnergyAndDeriv(self, *args, **kwargs) -> 'float_type'
command(self, c, r=())
deleteAtoms(self, arg, noSync=False, force=False)
deleteAtoms_byIndex(self, *args, **kwargs) -> 'void'
disableOutput(self)
enableOutput(self, state)
fastCommand(self, c, r=())
call xplorWrap.XplorWrap.fastCommand
initFrom(self, *args, **kwargs) -> 'void'
potList(self, *args, **kwargs) -> 'PotList &'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rcWrap(self, *args, **kwargs) -> 'rc_XplorWrap'
scriptingIndex(self, *args, **kwargs) -> 'int'
select(self, selString)
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'
setModifiedProp(self, *args, **kwargs) -> 'void'
setResidueName(self, *args, **kwargs) -> 'void'
setResidueNum(self, *args, **kwargs) -> 'void'
setSegmentName(self, *args, **kwargs) -> 'void'
shell(self)
syncAtomIDFrom(self, *args, **kwargs) -> 'void'
syncChargeFrom(self, *args, **kwargs) -> 'void'
syncFricFrom(self, *args, **kwargs) -> 'void'
syncFrom(self, *args, **kwargs) -> 'void'
syncMassFrom(self, *args, **kwargs) -> 'void'
syncPosFrom(self, *args, **kwargs) -> 'void'
syncTo(self, *args, **kwargs) -> 'void'
syncVelFrom(self, *args, **kwargs) -> 'void'
type(self, *args, **kwargs) -> 'String const'
wrap(self, *args, **kwargs) -> 'XplorWrap *'
xplorVars(self, *args, **kwargs) -> 'XplorVars *'

Static methods defined here:
__swig_destroy__ = delete_XplorSimulation(...)
defaultSimulation(*args, **kwargs) -> 'XplorSimulation *'
deleteDefaultSimulation(*args, **kwargs) -> 'void'
initSimulation(*args, **kwargs) -> 'void'
resetDefaultSimulation(*args, **kwargs) -> 'void'

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'
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 >'
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'
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 >'
setForceUpdate(self, *args, **kwargs) -> 'void'
setNoFit(self, *args, **kwargs) -> 'void'
sync(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

 
Functions
       
XplorSimulation_defaultSimulation(*args) -> 'XplorSimulation *'
XplorSimulation_deleteDefaultSimulation(*args) -> 'void'
XplorSimulation_initSimulation(*args) -> 'void'
XplorSimulation_resetDefaultSimulation(*args) -> 'void'
currentSimulation(*args) -> 'Simulation *'
fromSimulation(*args, **kwargs) -> 'XplorSimulation *'
getXplorSimulation(simulation=0)
given a simulation, determine the associated XplorSimulation
if simulation is None, use simulation.currentSimulation.
makeCurrent(*args, **kwargs) -> 'void'
pyXplorHelp(*args) -> 'String'

 
Data
        orig_LD_LIBRARY_PATH = '/home/schwitrs/lib/Linux_x86_64:/home/schwitrs/l...s/lib/Linux_x86_64::/usr/local/lib:/usr/local/lib'
psfTemplate = '\nstructure\nPSF\n\n 1 !NTITLE\n REMARKS addD... 0 !NGRP\n 0 0 0\nend \n'