distSymmPot		index
distSymmPot.py


 
Potential term restraining distances expected to be symmetric. This is
approximately the same functionality as that of the XPLOR NOE SYMMetry
routine. The primary difference is that this term will correctly treat
<n ensembleSimulation>.EnsembleSimulation averaging.
 
 
Constructor:
 
  It is suggested that this potential term be created using the helper 
  function distSymmTools.create_DistSymmPot().
 
 
  DistSymmPot(instanceName,   - creates a potential term with the given name. 
              simulation  )     The simulation argument is optional- it omitted
                                simulation.defaultSimulation() will be used.
 
  
Methods:
 
  addRestraint(listOfTuples) - list of two-membered tuples of atom
                                selections, each of which specifies a
                                distance which should be
                                restrained. E.g. for a dimer, the list
                                should contain two sets of dimers.
 
  rms()                      - returns a measure of RMSD of distance
                               symmetry violation (see below).
 
  violations()               - returns number of violated distance
                               symmetry restraints
 
  numRestraints()            - return the number of restraints
 
  info()                    - current info about the state of this instance
  showViolations()          - return string containing pretty-printed info
                              on all violated restraints.
 
  restraints()              - return a list of restraints. See the description 
                              of the Restraint class below.
 
  ensWeigth(index) - return the ensemble weight associated with the
                     specified member.
  setEnsWeights(vals) - use the specified ensemble weights instead of those
                        in the underlying EnsembleSimulation.
 
 Read-Write accessors:
  scale             - scale factor (force constant) for the potential term.
  ensembleAveType   - "none" or "average" - controls whether to enforce
                      symmetry restraints on each ensemble member- or to
                      enforce only overall ensemble symmetry (see below).
  threshold         - amount of violation of restraint greater than which 
                      the restraint is considered violated [0.2 angstrom]
  showAllRestraints - boolean which changes the behavior of showViolations. If 
                      this parameter is set to True, the behavior of
                      showViolations is modified such that all restraints are
                      printed. Violated restraints are indicated by an
                      asterisk in the first column. [False]
  useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
                    or to use those of the underlying EnsembleSimulation.
  
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
 
class DistSymmPot_Restraint:
 
methods:
    
public:
  energy() - return current energy
  name()   - restraint name (String)
 
raw members:
 
  tol      - error tolerance for this restraint
 
  distAtom1 - list of lists of atoms. These contain atoms specified by
  distAtom2   addRestraints.
 
  
  contrib    - array containing the contribution to energy from each ensemble 
               member
 
  aveDistIntra - ave. dist. within an ensemble member
  deltaIntra     
  aveDistInter -  distance between atom1 in different ensemble members
  deltaInter1
  aveDistInter2 - distance between atom2 in different ensemble members
  deltaInter2
 
The potential term is defined as
 
  E = scale() * sum_r E_r
 
with
 
  E_r being the contribution from each restraint.
 
For averageType="none", each restraint's energy is a sum over
contributions from each ensemble member i:
 
   E_r = sum_i w_i ( ca_i + sum_i' w_i' (cr1_ii' + cr2_ii') ),
 
with w_i being the ensemble member's weight,
 
  ca_i = < d_i^2 >_j - < d_i >_j^2        (averaged over all distances)
 
   with  d_ij = |q1_ij - q2_ij|
   and q1_ij, the position of the atom corresponding to the first
   selection of the jth entry in the restraint's distAtom1 in ensemble
   member i.
 
  cr1_ii' = < dr1_ii'^2 >_j - < dr1_ii' >_j^2 
  cr2_ii' = < dr2_ii'^2 >_j - < dr2_ii' >_j^2 
 
    with dr1_ii'j = |q1_ij - q2_i'j|
 
The RMSD is calculated as
 
   sqrt( sum_r E_r / N_r )
 
  where N_r is the number of restraints.
 
 
 
# This file was created automatically by SWIG.
# Don't modify this file, modify the SWIG interface instead.
# This file is compatible with both classic and new-style classes.

 
Classes
       
__builtin__.object
CDSList_CDSList_Atom
CDSList_CDSList_AtomPtr
CDSList_DistSymmPot_Restraint
CDSList_DistSymmPot_RestraintPtr
DistSymmPot
DistSymmPotPtr
DistSymmPot_LetterClass
DistSymmPot_LetterClassPtr
Modified
ModifiedPtr
ModifiedBase
ModifiedBasePtr
Restraint_DistSymmPot
DistSymmPot_Restraint
DistSymmPot_RestraintPtr
Restraint_DistSymmPotPtr
rc_ptr_DistSymmPot_Restraint
rc_ptr_DistSymmPot_RestraintPtr

 
class CDSList_CDSList_Atom(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_CDSList_Atom>)

 
__delitem__(*args)

 
__getattr__ lambda self, name

 
__getitem__(*args)

 
__getslice__(*args)

 
__init__(self, *args)

 
__len__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
__setitem__(*args)

 
help(*args)

 
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x2a66e18>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_CDSList_Atom' objects>

 
list of weak references to the object (if defined)

 
class CDSList_CDSList_AtomPtr(CDSList_CDSList_Atom)
   
 

 
 
Method resolution order:
CDSList_CDSList_AtomPtr
CDSList_CDSList_Atom
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from CDSList_CDSList_Atom:
__del__(self, destroy=<built-in function delete_CDSList_CDSList_Atom>)

 
__delitem__(*args)

 
__getattr__ lambda self, name

 
__getitem__(*args)

 
__getslice__(*args)

 
__len__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
__setitem__(*args)

 
help(*args)

 
Data and other attributes inherited from CDSList_CDSList_Atom:
__dict__ = <dictproxy object at 0x2a66e88>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_CDSList_Atom' objects>

 
list of weak references to the object (if defined)

 
class CDSList_DistSymmPot_Restraint(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_DistSymmPot_Restraint>)

 
__delitem__(*args)

 
__getattr__ lambda self, name

 
__getitem__(*args)

 
__getslice__(*args)

 
__init__(self, *args)

 
__len__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
__setitem__(*args)

 
help(*args)

 
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x2a66cc8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_DistSymmPot_Restraint' objects>

 
list of weak references to the object (if defined)

 
class CDSList_DistSymmPot_RestraintPtr(CDSList_DistSymmPot_Restraint)
   
 

 
 
Method resolution order:
CDSList_DistSymmPot_RestraintPtr
CDSList_DistSymmPot_Restraint
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from CDSList_DistSymmPot_Restraint:
__del__(self, destroy=<built-in function delete_CDSList_DistSymmPot_Restraint>)

 
__delitem__(*args)

 
__getattr__ lambda self, name

 
__getitem__(*args)

 
__getslice__(*args)

 
__len__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
__setitem__(*args)

 
help(*args)

 
Data and other attributes inherited from CDSList_DistSymmPot_Restraint:
__dict__ = <dictproxy object at 0x2a66e18>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_DistSymmPot_Restraint' objects>

 
list of weak references to the object (if defined)

 
class DistSymmPot(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_DistSymmPot>)

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__mul__(*args)

 
__oldinit__ = __init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
addRestraint(*args)

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
decrRefCount(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
ensWeight(*args)

 
ensembleAveType(*args)

 
help(*args)

 
incrRefCount(*args)

 
info(*args)

 
instanceData(*args)

 
instanceName(*args)

 
numRestraints(*args)

 
pointer(*args)

 
potName(*args)

 
registerInstanceData(*args)

 
registerTo(*args)

 
resetPotName(*args)

 
restraints(*args)

 
rms(*args)

 
scale(*args)

 
setEnsWeights(*args)

 
setEnsembleAveType(*args)

 
setScale(*args)

 
setShowAllRestraints(*args)

 
setThreshold(*args)

 
setUseSimEnsWeights(*args)

 
setVerbose(*args)

 
showAllRestraints(*args)

 
showViolations(*args)

 
simulation(*args)

 
simulation2(*args)

 
threshold(*args)

 
unRegister(*args)

 
updateDelta(*args)

 
updateValues(*args)

 
useSimEnsWeights(*args)

 
verbose(*args)

 
violations(*args)

 
Properties defined here:
instanceData_

 
get = DistSymmPot_instanceData__get(...)

 
set = DistSymmPot_instanceData__set(...)

 
modified

 
get = DistSymmPot_modified_get(...)

 
set = DistSymmPot_modified_set(...)

 
registeredSimulations

 
get = DistSymmPot_registeredSimulations_get(...)

 
set = DistSymmPot_registeredSimulations_set(...)

 
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x2a66cc8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function DistSymmPot_instanceData__get>, 'modified': <built-in function DistSymmPot_modified_get>, 'registeredSimulations': <built-in function DistSymmPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function DistSymmPot_instanceData__set>, 'modified': <built-in function DistSymmPot_modified_set>, 'registeredSimulations': <built-in function DistSymmPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'DistSymmPot' objects>

 
list of weak references to the object (if defined)

 
class DistSymmPotPtr(DistSymmPot)
   
 

 
 
Method resolution order:
DistSymmPotPtr
DistSymmPot
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from DistSymmPot:
__del__(self, destroy=<built-in function delete_DistSymmPot>)

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__mul__(*args)

 
__oldinit__ = __init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
addRestraint(*args)

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
decrRefCount(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
ensWeight(*args)

 
ensembleAveType(*args)

 
help(*args)

 
incrRefCount(*args)

 
info(*args)

 
instanceData(*args)

 
instanceName(*args)

 
numRestraints(*args)

 
pointer(*args)

 
potName(*args)

 
registerInstanceData(*args)

 
registerTo(*args)

 
resetPotName(*args)

 
restraints(*args)

 
rms(*args)

 
scale(*args)

 
setEnsWeights(*args)

 
setEnsembleAveType(*args)

 
setScale(*args)

 
setShowAllRestraints(*args)

 
setThreshold(*args)

 
setUseSimEnsWeights(*args)

 
setVerbose(*args)

 
showAllRestraints(*args)

 
showViolations(*args)

 
simulation(*args)

 
simulation2(*args)

 
threshold(*args)

 
unRegister(*args)

 
updateDelta(*args)

 
updateValues(*args)

 
useSimEnsWeights(*args)

 
verbose(*args)

 
violations(*args)

 
Properties inherited from DistSymmPot:
instanceData_

 
get = DistSymmPot_instanceData__get(...)

 
set = DistSymmPot_instanceData__set(...)

 
modified

 
get = DistSymmPot_modified_get(...)

 
set = DistSymmPot_modified_set(...)

 
registeredSimulations

 
get = DistSymmPot_registeredSimulations_get(...)

 
set = DistSymmPot_registeredSimulations_set(...)

 
Data and other attributes inherited from DistSymmPot:
__dict__ = <dictproxy object at 0x2a66e88>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function DistSymmPot_instanceData__get>, 'modified': <built-in function DistSymmPot_modified_get>, 'registeredSimulations': <built-in function DistSymmPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function DistSymmPot_instanceData__set>, 'modified': <built-in function DistSymmPot_modified_set>, 'registeredSimulations': <built-in function DistSymmPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'DistSymmPot' objects>

 
list of weak references to the object (if defined)

 
class DistSymmPot_LetterClass(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_DistSymmPot_LetterClass>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
addRestraint(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
ensembleAveType(*args)

 
help(*args)

 
info(*args)

 
numRestraints(*args)

 
restraints(*args)

 
rms(*args)

 
setEnsembleAveType(*args)

 
setShowAllRestraints(*args)

 
setThreshold(*args)

 
setVerbose(*args)

 
showAllRestraints(*args)

 
showViolations(*args)

 
simulation2(*args)

 
threshold(*args)

 
verbose(*args)

 
violations(*args)

 
Data and other attributes defined here:
AVERAGE = 1
NONE = 0
__dict__ = <dictproxy object at 0x2a66fa0>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'DistSymmPot_LetterClass' objects>

 
list of weak references to the object (if defined)

 
class DistSymmPot_LetterClassPtr(DistSymmPot_LetterClass)
   
 

 
 
Method resolution order:
DistSymmPot_LetterClassPtr
DistSymmPot_LetterClass
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from DistSymmPot_LetterClass:
__del__(self, destroy=<built-in function delete_DistSymmPot_LetterClass>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
addRestraint(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
ensembleAveType(*args)

 
help(*args)

 
info(*args)

 
numRestraints(*args)

 
restraints(*args)

 
rms(*args)

 
setEnsembleAveType(*args)

 
setShowAllRestraints(*args)

 
setThreshold(*args)

 
setVerbose(*args)

 
showAllRestraints(*args)

 
showViolations(*args)

 
simulation2(*args)

 
threshold(*args)

 
verbose(*args)

 
violations(*args)

 
Data and other attributes inherited from DistSymmPot_LetterClass:
AVERAGE = 1
NONE = 0
__dict__ = <dictproxy object at 0x2a66e50>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'DistSymmPot_LetterClass' objects>

 
list of weak references to the object (if defined)

 
class DistSymmPot_Restraint(Restraint_DistSymmPot)
   
 

 
 
Method resolution order:
DistSymmPot_Restraint
Restraint_DistSymmPot
__builtin__.object
Methods defined here:
__del__(self, destroy=<built-in function delete_DistSymmPot_Restraint>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
deriv(*args)

 
energy(*args)

 
name(*args)

 
Properties defined here:
aveDistInter1

 
get = DistSymmPot_Restraint_aveDistInter1_get(...)

 
set = DistSymmPot_Restraint_aveDistInter1_set(...)

 
aveDistInter2

 
get = DistSymmPot_Restraint_aveDistInter2_get(...)

 
set = DistSymmPot_Restraint_aveDistInter2_set(...)

 
aveDistIntra

 
get = DistSymmPot_Restraint_aveDistIntra_get(...)

 
set = DistSymmPot_Restraint_aveDistIntra_set(...)

 
contrib

 
get = DistSymmPot_Restraint_contrib_get(...)

 
set = DistSymmPot_Restraint_contrib_set(...)

 
deltaInter1

 
get = DistSymmPot_Restraint_deltaInter1_get(...)

 
set = DistSymmPot_Restraint_deltaInter1_set(...)

 
deltaInter2

 
get = DistSymmPot_Restraint_deltaInter2_get(...)

 
set = DistSymmPot_Restraint_deltaInter2_set(...)

 
deltaIntra

 
get = DistSymmPot_Restraint_deltaIntra_get(...)

 
set = DistSymmPot_Restraint_deltaIntra_set(...)

 
distAtom1

 
get = DistSymmPot_Restraint_distAtom1_get(...)

 
set = DistSymmPot_Restraint_distAtom1_set(...)

 
distAtom2

 
get = DistSymmPot_Restraint_distAtom2_get(...)

 
set = DistSymmPot_Restraint_distAtom2_set(...)

 
tol

 
get = DistSymmPot_Restraint_tol_get(...)

 
set = DistSymmPot_Restraint_tol_set(...)

 
verbose

 
get = DistSymmPot_Restraint_verbose_get(...)

 
set = DistSymmPot_Restraint_verbose_set(...)

 
Data and other attributes defined here:
__swig_getmethods__ = {'aveDistInter1': <built-in function DistSymmPot_Restraint_aveDistInter1_get>, 'aveDistInter2': <built-in function DistSymmPot_Restraint_aveDistInter2_get>, 'aveDistIntra': <built-in function DistSymmPot_Restraint_aveDistIntra_get>, 'contrib': <built-in function DistSymmPot_Restraint_contrib_get>, 'deltaInter1': <built-in function DistSymmPot_Restraint_deltaInter1_get>, 'deltaInter2': <built-in function DistSymmPot_Restraint_deltaInter2_get>, 'deltaIntra': <built-in function DistSymmPot_Restraint_deltaIntra_get>, 'distAtom1': <built-in function DistSymmPot_Restraint_distAtom1_get>, 'distAtom2': <built-in function DistSymmPot_Restraint_distAtom2_get>, 'tol': <built-in function DistSymmPot_Restraint_tol_get>, ...}
__swig_setmethods__ = {'aveDistInter1': <built-in function DistSymmPot_Restraint_aveDistInter1_set>, 'aveDistInter2': <built-in function DistSymmPot_Restraint_aveDistInter2_set>, 'aveDistIntra': <built-in function DistSymmPot_Restraint_aveDistIntra_set>, 'contrib': <built-in function DistSymmPot_Restraint_contrib_set>, 'deltaInter1': <built-in function DistSymmPot_Restraint_deltaInter1_set>, 'deltaInter2': <built-in function DistSymmPot_Restraint_deltaInter2_set>, 'deltaIntra': <built-in function DistSymmPot_Restraint_deltaIntra_set>, 'distAtom1': <built-in function DistSymmPot_Restraint_distAtom1_set>, 'distAtom2': <built-in function DistSymmPot_Restraint_distAtom2_set>, 'tol': <built-in function DistSymmPot_Restraint_tol_set>, ...}
Methods inherited from Restraint_DistSymmPot:
diff(*args)

 
setName(*args)

 
violated(*args)

 
Data and other attributes inherited from Restraint_DistSymmPot:
__dict__ = <dictproxy object at 0x2a66be8>

 
dictionary for instance variables (if defined)
__weakref__ = <attribute '__weakref__' of 'Restraint_DistSymmPot' objects>

 
list of weak references to the object (if defined)

 
class DistSymmPot_RestraintPtr(DistSymmPot_Restraint)
   
 

 
 
Method resolution order:
DistSymmPot_RestraintPtr
DistSymmPot_Restraint
Restraint_DistSymmPot
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from DistSymmPot_Restraint:
__del__(self, destroy=<built-in function delete_DistSymmPot_Restraint>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
deriv(*args)

 
energy(*args)

 
name(*args)

 
Properties inherited from DistSymmPot_Restraint:
aveDistInter1

 
get = DistSymmPot_Restraint_aveDistInter1_get(...)

 
set = DistSymmPot_Restraint_aveDistInter1_set(...)

 
aveDistInter2

 
get = DistSymmPot_Restraint_aveDistInter2_get(...)

 
set = DistSymmPot_Restraint_aveDistInter2_set(...)

 
aveDistIntra

 
get = DistSymmPot_Restraint_aveDistIntra_get(...)

 
set = DistSymmPot_Restraint_aveDistIntra_set(...)

 
contrib

 
get = DistSymmPot_Restraint_contrib_get(...)

 
set = DistSymmPot_Restraint_contrib_set(...)

 
deltaInter1

 
get = DistSymmPot_Restraint_deltaInter1_get(...)

 
set = DistSymmPot_Restraint_deltaInter1_set(...)

 
deltaInter2

 
get = DistSymmPot_Restraint_deltaInter2_get(...)

 
set = DistSymmPot_Restraint_deltaInter2_set(...)

 
deltaIntra

 
get = DistSymmPot_Restraint_deltaIntra_get(...)

 
set = DistSymmPot_Restraint_deltaIntra_set(...)

 
distAtom1

 
get = DistSymmPot_Restraint_distAtom1_get(...)

 
set = DistSymmPot_Restraint_distAtom1_set(...)

 
distAtom2

 
get = DistSymmPot_Restraint_distAtom2_get(...)

 
set = DistSymmPot_Restraint_distAtom2_set(...)

 
tol

 
get = DistSymmPot_Restraint_tol_get(...)

 
set = DistSymmPot_Restraint_tol_set(...)

 
verbose

 
get = DistSymmPot_Restraint_verbose_get(...)

 
set = DistSymmPot_Restraint_verbose_set(...)

 
Data and other attributes inherited from DistSymmPot_Restraint:
__swig_getmethods__ = {'aveDistInter1': <built-in function DistSymmPot_Restraint_aveDistInter1_get>, 'aveDistInter2': <built-in function DistSymmPot_Restraint_aveDistInter2_get>, 'aveDistIntra': <built-in function DistSymmPot_Restraint_aveDistIntra_get>, 'contrib': <built-in function DistSymmPot_Restraint_contrib_get>, 'deltaInter1': <built-in function DistSymmPot_Restraint_deltaInter1_get>, 'deltaInter2': <built-in function DistSymmPot_Restraint_deltaInter2_get>, 'deltaIntra': <built-in function DistSymmPot_Restraint_deltaIntra_get>, 'distAtom1': <built-in function DistSymmPot_Restraint_distAtom1_get>, 'distAtom2': <built-in function DistSymmPot_Restraint_distAtom2_get>, 'tol': <built-in function DistSymmPot_Restraint_tol_get>, ...}
__swig_setmethods__ = {'aveDistInter1': <built-in function DistSymmPot_Restraint_aveDistInter1_set>, 'aveDistInter2': <built-in function DistSymmPot_Restraint_aveDistInter2_set>, 'aveDistIntra': <built-in function DistSymmPot_Restraint_aveDistIntra_set>, 'contrib': <built-in function DistSymmPot_Restraint_contrib_set>, 'deltaInter1': <built-in function DistSymmPot_Restraint_deltaInter1_set>, 'deltaInter2': <built-in function DistSymmPot_Restraint_deltaInter2_set>, 'deltaIntra': <built-in function DistSymmPot_Restraint_deltaIntra_set>, 'distAtom1': <built-in function DistSymmPot_Restraint_distAtom1_set>, 'distAtom2': <built-in function DistSymmPot_Restraint_distAtom2_set>, 'tol': <built-in function DistSymmPot_Restraint_tol_set>, ...}
Methods inherited from Restraint_DistSymmPot:
diff(*args)

 
setName(*args)

 
violated(*args)

 
Data and other attributes inherited from Restraint_DistSymmPot:
__dict__ = <dictproxy object at 0x2a66e88>

 
dictionary for instance variables (if defined)
__weakref__ = <attribute '__weakref__' of 'Restraint_DistSymmPot' objects>

 
list of weak references to the object (if defined)

 
class Modified(__builtin__.object)
   
 

 
  Methods defined here:
__call__(*args)

 
__del__(self, destroy=<built-in function delete_Modified>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
clear(*args)

 
set(*args)

 
update(*args)

 
value(*args)

 
Data and other attributes defined here:
MOD_SELF = 1
MOD_SIMULATION = 2
__dict__ = <dictproxy object at 0x2a66fd8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Modified' objects>

 
list of weak references to the object (if defined)

 
class ModifiedBase(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_ModifiedBase>)

 
__getattr__ lambda self, name

 
__init__(self)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
registerTo(*args)

 
unRegister(*args)

 
updateValues(*args)

 
Properties defined here:
modified

 
get = ModifiedBase_modified_get(...)

 
set = ModifiedBase_modified_set(...)

 
registeredSimulations

 
get = ModifiedBase_registeredSimulations_get(...)

 
set = ModifiedBase_registeredSimulations_set(...)

 
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x2a66fd8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'modified': <built-in function ModifiedBase_modified_get>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_get>}
__swig_setmethods__ = {'modified': <built-in function ModifiedBase_modified_set>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'ModifiedBase' objects>

 
list of weak references to the object (if defined)

 
class ModifiedBasePtr(ModifiedBase)
   
 

 
 
Method resolution order:
ModifiedBasePtr
ModifiedBase
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from ModifiedBase:
__del__(self, destroy=<built-in function delete_ModifiedBase>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
registerTo(*args)

 
unRegister(*args)

 
updateValues(*args)

 
Properties inherited from ModifiedBase:
modified

 
get = ModifiedBase_modified_get(...)

 
set = ModifiedBase_modified_set(...)

 
registeredSimulations

 
get = ModifiedBase_registeredSimulations_get(...)

 
set = ModifiedBase_registeredSimulations_set(...)

 
Data and other attributes inherited from ModifiedBase:
__dict__ = <dictproxy object at 0x2a66e88>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'modified': <built-in function ModifiedBase_modified_get>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_get>}
__swig_setmethods__ = {'modified': <built-in function ModifiedBase_modified_set>, 'registeredSimulations': <built-in function ModifiedBase_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'ModifiedBase' objects>

 
list of weak references to the object (if defined)

 
class ModifiedPtr(Modified)
   
 

 
 
Method resolution order:
ModifiedPtr
Modified
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from Modified:
__call__(*args)

 
__del__(self, destroy=<built-in function delete_Modified>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
clear(*args)

 
set(*args)

 
update(*args)

 
value(*args)

 
Data and other attributes inherited from Modified:
MOD_SELF = 1
MOD_SIMULATION = 2
__dict__ = <dictproxy object at 0x2a66e18>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Modified' objects>

 
list of weak references to the object (if defined)

 
class Restraint_DistSymmPot(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_Restraint_DistSymmPot>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
diff(*args)

 
name(*args)

 
setName(*args)

 
violated(*args)

 
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x2a66fd8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Restraint_DistSymmPot' objects>

 
list of weak references to the object (if defined)

 
class Restraint_DistSymmPotPtr(Restraint_DistSymmPot)
   
 

 
 
Method resolution order:
Restraint_DistSymmPotPtr
Restraint_DistSymmPot
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from Restraint_DistSymmPot:
__del__(self, destroy=<built-in function delete_Restraint_DistSymmPot>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
diff(*args)

 
name(*args)

 
setName(*args)

 
violated(*args)

 
Data and other attributes inherited from Restraint_DistSymmPot:
__dict__ = <dictproxy object at 0x2a66cc8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Restraint_DistSymmPot' objects>

 
list of weak references to the object (if defined)

 
class rc_ptr_DistSymmPot_Restraint(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_rc_ptr_DistSymmPot_Restraint>)

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__mul__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
count(*args)

 
decr(*args)

 
deriv(*args)

 
diff(*args)

 
energy(*args)

 
incr(*args)

 
name(*args)

 
ptr(*args)

 
reset(*args)

 
setName(*args)

 
violated(*args)

 
Properties defined here:
aveDistInter1

 
get = rc_ptr_DistSymmPot_Restraint_aveDistInter1_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_aveDistInter1_set(...)

 
aveDistInter2

 
get = rc_ptr_DistSymmPot_Restraint_aveDistInter2_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_aveDistInter2_set(...)

 
aveDistIntra

 
get = rc_ptr_DistSymmPot_Restraint_aveDistIntra_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_aveDistIntra_set(...)

 
contrib

 
get = rc_ptr_DistSymmPot_Restraint_contrib_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_contrib_set(...)

 
deltaInter1

 
get = rc_ptr_DistSymmPot_Restraint_deltaInter1_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_deltaInter1_set(...)

 
deltaInter2

 
get = rc_ptr_DistSymmPot_Restraint_deltaInter2_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_deltaInter2_set(...)

 
deltaIntra

 
get = rc_ptr_DistSymmPot_Restraint_deltaIntra_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_deltaIntra_set(...)

 
distAtom1

 
get = rc_ptr_DistSymmPot_Restraint_distAtom1_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_distAtom1_set(...)

 
distAtom2

 
get = rc_ptr_DistSymmPot_Restraint_distAtom2_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_distAtom2_set(...)

 
tol

 
get = rc_ptr_DistSymmPot_Restraint_tol_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_tol_set(...)

 
verbose

 
get = rc_ptr_DistSymmPot_Restraint_verbose_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_verbose_set(...)

 
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x2a66fd8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'aveDistInter1': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistInter1_get>, 'aveDistInter2': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistInter2_get>, 'aveDistIntra': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistIntra_get>, 'contrib': <built-in function rc_ptr_DistSymmPot_Restraint_contrib_get>, 'deltaInter1': <built-in function rc_ptr_DistSymmPot_Restraint_deltaInter1_get>, 'deltaInter2': <built-in function rc_ptr_DistSymmPot_Restraint_deltaInter2_get>, 'deltaIntra': <built-in function rc_ptr_DistSymmPot_Restraint_deltaIntra_get>, 'distAtom1': <built-in function rc_ptr_DistSymmPot_Restraint_distAtom1_get>, 'distAtom2': <built-in function rc_ptr_DistSymmPot_Restraint_distAtom2_get>, 'tol': <built-in function rc_ptr_DistSymmPot_Restraint_tol_get>, ...}
__swig_setmethods__ = {'aveDistInter1': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistInter1_set>, 'aveDistInter2': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistInter2_set>, 'aveDistIntra': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistIntra_set>, 'contrib': <built-in function rc_ptr_DistSymmPot_Restraint_contrib_set>, 'deltaInter1': <built-in function rc_ptr_DistSymmPot_Restraint_deltaInter1_set>, 'deltaInter2': <built-in function rc_ptr_DistSymmPot_Restraint_deltaInter2_set>, 'deltaIntra': <built-in function rc_ptr_DistSymmPot_Restraint_deltaIntra_set>, 'distAtom1': <built-in function rc_ptr_DistSymmPot_Restraint_distAtom1_set>, 'distAtom2': <built-in function rc_ptr_DistSymmPot_Restraint_distAtom2_set>, 'tol': <built-in function rc_ptr_DistSymmPot_Restraint_tol_set>, ...}
__weakref__ = <attribute '__weakref__' of 'rc_ptr_DistSymmPot_Restraint' objects>

 
list of weak references to the object (if defined)

 
class rc_ptr_DistSymmPot_RestraintPtr(rc_ptr_DistSymmPot_Restraint)
   
 

 
 
Method resolution order:
rc_ptr_DistSymmPot_RestraintPtr
rc_ptr_DistSymmPot_Restraint
__builtin__.object
Methods defined here:
__init__(self, this)

 
Methods inherited from rc_ptr_DistSymmPot_Restraint:
__del__(self, destroy=<built-in function delete_rc_ptr_DistSymmPot_Restraint>)

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__mul__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
count(*args)

 
decr(*args)

 
deriv(*args)

 
diff(*args)

 
energy(*args)

 
incr(*args)

 
name(*args)

 
ptr(*args)

 
reset(*args)

 
setName(*args)

 
violated(*args)

 
Properties inherited from rc_ptr_DistSymmPot_Restraint:
aveDistInter1

 
get = rc_ptr_DistSymmPot_Restraint_aveDistInter1_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_aveDistInter1_set(...)

 
aveDistInter2

 
get = rc_ptr_DistSymmPot_Restraint_aveDistInter2_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_aveDistInter2_set(...)

 
aveDistIntra

 
get = rc_ptr_DistSymmPot_Restraint_aveDistIntra_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_aveDistIntra_set(...)

 
contrib

 
get = rc_ptr_DistSymmPot_Restraint_contrib_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_contrib_set(...)

 
deltaInter1

 
get = rc_ptr_DistSymmPot_Restraint_deltaInter1_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_deltaInter1_set(...)

 
deltaInter2

 
get = rc_ptr_DistSymmPot_Restraint_deltaInter2_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_deltaInter2_set(...)

 
deltaIntra

 
get = rc_ptr_DistSymmPot_Restraint_deltaIntra_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_deltaIntra_set(...)

 
distAtom1

 
get = rc_ptr_DistSymmPot_Restraint_distAtom1_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_distAtom1_set(...)

 
distAtom2

 
get = rc_ptr_DistSymmPot_Restraint_distAtom2_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_distAtom2_set(...)

 
tol

 
get = rc_ptr_DistSymmPot_Restraint_tol_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_tol_set(...)

 
verbose

 
get = rc_ptr_DistSymmPot_Restraint_verbose_get(...)

 
set = rc_ptr_DistSymmPot_Restraint_verbose_set(...)

 
Data and other attributes inherited from rc_ptr_DistSymmPot_Restraint:
__dict__ = <dictproxy object at 0x2a66de0>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'aveDistInter1': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistInter1_get>, 'aveDistInter2': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistInter2_get>, 'aveDistIntra': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistIntra_get>, 'contrib': <built-in function rc_ptr_DistSymmPot_Restraint_contrib_get>, 'deltaInter1': <built-in function rc_ptr_DistSymmPot_Restraint_deltaInter1_get>, 'deltaInter2': <built-in function rc_ptr_DistSymmPot_Restraint_deltaInter2_get>, 'deltaIntra': <built-in function rc_ptr_DistSymmPot_Restraint_deltaIntra_get>, 'distAtom1': <built-in function rc_ptr_DistSymmPot_Restraint_distAtom1_get>, 'distAtom2': <built-in function rc_ptr_DistSymmPot_Restraint_distAtom2_get>, 'tol': <built-in function rc_ptr_DistSymmPot_Restraint_tol_get>, ...}
__swig_setmethods__ = {'aveDistInter1': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistInter1_set>, 'aveDistInter2': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistInter2_set>, 'aveDistIntra': <built-in function rc_ptr_DistSymmPot_Restraint_aveDistIntra_set>, 'contrib': <built-in function rc_ptr_DistSymmPot_Restraint_contrib_set>, 'deltaInter1': <built-in function rc_ptr_DistSymmPot_Restraint_deltaInter1_set>, 'deltaInter2': <built-in function rc_ptr_DistSymmPot_Restraint_deltaInter2_set>, 'deltaIntra': <built-in function rc_ptr_DistSymmPot_Restraint_deltaIntra_set>, 'distAtom1': <built-in function rc_ptr_DistSymmPot_Restraint_distAtom1_set>, 'distAtom2': <built-in function rc_ptr_DistSymmPot_Restraint_distAtom2_set>, 'tol': <built-in function rc_ptr_DistSymmPot_Restraint_tol_set>, ...}
__weakref__ = <attribute '__weakref__' of 'rc_ptr_DistSymmPot_Restraint' objects>

 
list of weak references to the object (if defined)

 
Functions
       
help(...)

 

 
Data
        __package__ = None
pyXplorHelp = Type help() for interactive help, or help(object) for help about object.