posRMSDPot		index
posRMSDPot.py

potential terms restraining atomic positional RMSD.
 
restrains the position of selected atoms relative to those in other
members of an ensembleSimulation.EnsembleSimulation. 
 
Constructor:
 
  It is suggested that this potential term be created using the helper 
  functions posRMSDPotTools.create_BFactorPot() or
  ncsPot.NCSPot().
 
 
  PosRMSDPot(instanceName,
             restraints="",
             simulation)  - creates a potential term with the given name. 
                         restraints is an optional string of restraints.
                         simulation should specify the appropriate 
                         EnsembleSimulation (default: currentSimulation)
  
Methods:
 
 
 
  calcEnergy()                    - calcs energy
  calcEnergyAndDerivs(DerivList)  - calcs energy and derivative info
    note that these routines also update all other potential-specific data.
 
  addRestraints(restraints) - add restraints in the given string.
 
 
  rms()                      - report rmsd value for this potential term.
  numRestraints()            - report number of restraints defined for this 
                               term.
  violations()               - report number of violations for this term.
 
  info()                     - return a string giving summary info for this
                             - term.
 
  showRestraints(violated)   - return a string listing restraints. If the 
                               boolean violated is True, only violated 
                               restraints are included, else all restraints are
                               listed.
  showViolations()           - return a string listing violated restraints.
  showPositions()            - return a string containing atom position info.
 
  restraints()               - return a list of restraints.
 
  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 for potential
  potType       - potential type: 'harmonic' or 'square' [default: harmonic]
  threshold     - tolerance for violation determination.
  centerSel     - selection specifying qc. If it is empty, distances are 
                  measured with respect to the origin.
  rmsdType      - string: either "bfactor" or "rap" [default: "bfactor"]
  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. [0]
  useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
                    or to use those of the underlying EnsembleSimulation.
 
The restraint class terms have the follow members
 
  pot           - the owning potential term.
  calcd         - the most recent calculated value.
  obs           - the observed value. 
  diff          - for rmsdType='rap':
                      diff = calcd
                  for rmsdType='bfactor':
                      sqrt of V term.
                  see below.
  obsErr        - estimated error in obs 
                  (obsErrB   for rmsdType=='bfactor'
                   obsErrRAP for rmsdType=='rap'    )
  
  AtomSel sel   - atomSel.AtomSel associated with the restraint.
 
  avePos        - list of average atomic positions in each ensemble member.
  rmsd2_contrib - list of rsmd2 contributions from each ensemble member.
 
 
The potential term is defined as
 
  E = scale() * V
 
   where 
     for rmsdType='rap':
        V = calcd
     for rmsdType='bfactor':
        V = Vsq(calcd-obs,obsErrB)
     
where,
  q_{i,j} is the position of atom j in ensemble member i
  qAve_j is the ensemble-averaged position of atom j
  calcd = const sum_i w_i * rmsd2_contrib[i]
   where 
     for rmsdType='rap':
        const = 1
     for rmsdType='bfactor':
        const = 8*pi^2
  
 
  rmsd2_contrib[i] = Vsq( | (q_ij-qc) - (qAve_j-qc) | , obsErrRAP)
 
 
and
  Vsq(x,tol) = x^2             if potType=='harmonic'
               (abs(x)-tol)^2  if potType=='square'
 
 
 
# 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_PosRMSDPot_Restraint
CDSList_PosRMSDPot_RestraintPtr
Modified
ModifiedPtr
ModifiedBase
ModifiedBasePtr
PosRMSDPot
PosRMSDPotPtr
PosRMSDPot_LetterClass
PosRMSDPot_LetterClassPtr
Restraint_PosRMSDPot
PosRMSDPot_Restraint
PosRMSDPot_RestraintPtr
Restraint_PosRMSDPotPtr
rc_ptr_PosRMSDPot_Restraint
rc_ptr_PosRMSDPot_RestraintPtr

 
class CDSList_PosRMSDPot_Restraint(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_PosRMSDPot_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 0x28ad328>

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

 
list of weak references to the object (if defined)

 
class CDSList_PosRMSDPot_RestraintPtr(CDSList_PosRMSDPot_Restraint)
   
 

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

 
Methods inherited from CDSList_PosRMSDPot_Restraint:
__del__(self, destroy=<built-in function delete_CDSList_PosRMSDPot_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_PosRMSDPot_Restraint:
__dict__ = <dictproxy object at 0x28ad478>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_PosRMSDPot_Restraint' 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 0x28ad360>

 
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 0x28ad360>

 
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 0x28ad4e8>

 
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 0x28ad130>

 
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 PosRMSDPot(__builtin__.object)
   
 

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

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__mul__(*args)

 
__oldinit__ = __init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
addRestraints(*args)

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
centerSel(*args)

 
decrRefCount(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
ensWeight(*args)

 
help(*args)

 
incrRefCount(*args)

 
info(*args)

 
instanceData(*args)

 
instanceName(*args)

 
numRestraints(*args)

 
pointer(*args)

 
potName(*args)

 
potType(*args)

 
registerInstanceData(*args)

 
registerTo(*args)

 
resetPotName(*args)

 
restraints(*args)

 
rms(*args)

 
rmsdType(*args)

 
scale(*args)

 
setCenterSel(*args)

 
setEnsWeights(*args)

 
setPotType(*args)

 
setRMSDType(*args)

 
setScale(*args)

 
setShowAllRestraints(*args)

 
setThreshold(*args)

 
setUseSimEnsWeights(*args)

 
setVerbose(*args)

 
showAllRestraints(*args)

 
showPositions(*args)

 
showRestraints(*args)

 
showViolations(*args)

 
simulation(*args)

 
threshold(*args)

 
unRegister(*args)

 
updateDelta(*args)

 
updateValues(*args)

 
useSimEnsWeights(*args)

 
verbose(*args)

 
violations(*args)

 
Properties defined here:
instanceData_

 
get = PosRMSDPot_instanceData__get(...)

 
set = PosRMSDPot_instanceData__set(...)

 
modified

 
get = PosRMSDPot_modified_get(...)

 
set = PosRMSDPot_modified_set(...)

 
registeredSimulations

 
get = PosRMSDPot_registeredSimulations_get(...)

 
set = PosRMSDPot_registeredSimulations_set(...)

 
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x28ad440>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function PosRMSDPot_instanceData__get>, 'modified': <built-in function PosRMSDPot_modified_get>, 'registeredSimulations': <built-in function PosRMSDPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function PosRMSDPot_instanceData__set>, 'modified': <built-in function PosRMSDPot_modified_set>, 'registeredSimulations': <built-in function PosRMSDPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'PosRMSDPot' objects>

 
list of weak references to the object (if defined)

 
class PosRMSDPotPtr(PosRMSDPot)
   
 

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

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

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__mul__(*args)

 
__oldinit__ = __init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
addRestraints(*args)

 
calcEnergy(*args)

 
calcEnergyAndDerivs(*args)

 
centerSel(*args)

 
decrRefCount(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
ensWeight(*args)

 
help(*args)

 
incrRefCount(*args)

 
info(*args)

 
instanceData(*args)

 
instanceName(*args)

 
numRestraints(*args)

 
pointer(*args)

 
potName(*args)

 
potType(*args)

 
registerInstanceData(*args)

 
registerTo(*args)

 
resetPotName(*args)

 
restraints(*args)

 
rms(*args)

 
rmsdType(*args)

 
scale(*args)

 
setCenterSel(*args)

 
setEnsWeights(*args)

 
setPotType(*args)

 
setRMSDType(*args)

 
setScale(*args)

 
setShowAllRestraints(*args)

 
setThreshold(*args)

 
setUseSimEnsWeights(*args)

 
setVerbose(*args)

 
showAllRestraints(*args)

 
showPositions(*args)

 
showRestraints(*args)

 
showViolations(*args)

 
simulation(*args)

 
threshold(*args)

 
unRegister(*args)

 
updateDelta(*args)

 
updateValues(*args)

 
useSimEnsWeights(*args)

 
verbose(*args)

 
violations(*args)

 
Properties inherited from PosRMSDPot:
instanceData_

 
get = PosRMSDPot_instanceData__get(...)

 
set = PosRMSDPot_instanceData__set(...)

 
modified

 
get = PosRMSDPot_modified_get(...)

 
set = PosRMSDPot_modified_set(...)

 
registeredSimulations

 
get = PosRMSDPot_registeredSimulations_get(...)

 
set = PosRMSDPot_registeredSimulations_set(...)

 
Data and other attributes inherited from PosRMSDPot:
__dict__ = <dictproxy object at 0x28ad478>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function PosRMSDPot_instanceData__get>, 'modified': <built-in function PosRMSDPot_modified_get>, 'registeredSimulations': <built-in function PosRMSDPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function PosRMSDPot_instanceData__set>, 'modified': <built-in function PosRMSDPot_modified_set>, 'registeredSimulations': <built-in function PosRMSDPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'PosRMSDPot' objects>

 
list of weak references to the object (if defined)

 
class PosRMSDPot_LetterClass(__builtin__.object)
   
 

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

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
addRestraints(*args)

 
centerSel(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
help(*args)

 
info(*args)

 
numRestraints(*args)

 
potType(*args)

 
restraints(*args)

 
rms(*args)

 
rmsdType(*args)

 
setCenterSel(*args)

 
setPotType(*args)

 
setRMSDType(*args)

 
setShowAllRestraints(*args)

 
setThreshold(*args)

 
setVerbose(*args)

 
showAllRestraints(*args)

 
showPositions(*args)

 
showRestraints(*args)

 
showViolations(*args)

 
threshold(*args)

 
verbose(*args)

 
violations(*args)

 
Data and other attributes defined here:
BFACTOR = 1
HARMONIC = 0
RAP = 0
SQUARE = 1
__dict__ = <dictproxy object at 0x28ad440>

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

 
list of weak references to the object (if defined)

 
class PosRMSDPot_LetterClassPtr(PosRMSDPot_LetterClass)
   
 

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

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

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
addRestraints(*args)

 
centerSel(*args)

 
energyMaybeDerivs0(*args)

 
energyMaybeDerivs1(*args)

 
energyMaybeDerivs2(*args)

 
energyMaybeDerivs3(*args)

 
energyMaybeDerivs4(*args)

 
help(*args)

 
info(*args)

 
numRestraints(*args)

 
potType(*args)

 
restraints(*args)

 
rms(*args)

 
rmsdType(*args)

 
setCenterSel(*args)

 
setPotType(*args)

 
setRMSDType(*args)

 
setShowAllRestraints(*args)

 
setThreshold(*args)

 
setVerbose(*args)

 
showAllRestraints(*args)

 
showPositions(*args)

 
showRestraints(*args)

 
showViolations(*args)

 
threshold(*args)

 
verbose(*args)

 
violations(*args)

 
Data and other attributes inherited from PosRMSDPot_LetterClass:
BFACTOR = 1
HARMONIC = 0
RAP = 0
SQUARE = 1
__dict__ = <dictproxy object at 0x28ad130>

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

 
list of weak references to the object (if defined)

 
class PosRMSDPot_Restraint(Restraint_PosRMSDPot)
   
 

 
 
Method resolution order:
PosRMSDPot_Restraint
Restraint_PosRMSDPot
__builtin__.object
Methods defined here:
__del__(self, destroy=<built-in function delete_PosRMSDPot_Restraint>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
calcAvePos(*args)

 
calcRMSDContrib(*args)

 
deriv(*args)

 
energy(*args)

 
name(*args)

 
ok(*args)

 
showPositions(*args)

 
Properties defined here:
calcd

 
get = PosRMSDPot_Restraint_calcd_get(...)

 
set = PosRMSDPot_Restraint_calcd_set(...)

 
comment_

 
get = PosRMSDPot_Restraint_comment__get(...)

 
set = PosRMSDPot_Restraint_comment__set(...)

 
obs

 
get = PosRMSDPot_Restraint_obs_get(...)

 
set = PosRMSDPot_Restraint_obs_set(...)

 
obsErr

 
get = PosRMSDPot_Restraint_obsErr_get(...)

 
set = PosRMSDPot_Restraint_obsErr_set(...)

 
ok_

 
get = PosRMSDPot_Restraint_ok__get(...)

 
set = PosRMSDPot_Restraint_ok__set(...)

 
sel

 
get = PosRMSDPot_Restraint_sel_get(...)

 
set = PosRMSDPot_Restraint_sel_set(...)

 
verbose

 
get = PosRMSDPot_Restraint_verbose_get(...)

 
set = PosRMSDPot_Restraint_verbose_set(...)

 
Data and other attributes defined here:
__swig_getmethods__ = {'calcd': <built-in function PosRMSDPot_Restraint_calcd_get>, 'comment_': <built-in function PosRMSDPot_Restraint_comment__get>, 'obs': <built-in function PosRMSDPot_Restraint_obs_get>, 'obsErr': <built-in function PosRMSDPot_Restraint_obsErr_get>, 'ok_': <built-in function PosRMSDPot_Restraint_ok__get>, 'sel': <built-in function PosRMSDPot_Restraint_sel_get>, 'verbose': <built-in function PosRMSDPot_Restraint_verbose_get>}
__swig_setmethods__ = {'calcd': <built-in function PosRMSDPot_Restraint_calcd_set>, 'comment_': <built-in function PosRMSDPot_Restraint_comment__set>, 'obs': <built-in function PosRMSDPot_Restraint_obs_set>, 'obsErr': <built-in function PosRMSDPot_Restraint_obsErr_set>, 'ok_': <built-in function PosRMSDPot_Restraint_ok__set>, 'sel': <built-in function PosRMSDPot_Restraint_sel_set>, 'verbose': <built-in function PosRMSDPot_Restraint_verbose_set>}
Methods inherited from Restraint_PosRMSDPot:
diff(*args)

 
setName(*args)

 
violated(*args)

 
Data and other attributes inherited from Restraint_PosRMSDPot:
__dict__ = <dictproxy object at 0x28ad360>

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

 
list of weak references to the object (if defined)

 
class PosRMSDPot_RestraintPtr(PosRMSDPot_Restraint)
   
 

 
 
Method resolution order:
PosRMSDPot_RestraintPtr
PosRMSDPot_Restraint
Restraint_PosRMSDPot
__builtin__.object
Methods defined here:
__init__(self, this)

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

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
calcAvePos(*args)

 
calcRMSDContrib(*args)

 
deriv(*args)

 
energy(*args)

 
name(*args)

 
ok(*args)

 
showPositions(*args)

 
Properties inherited from PosRMSDPot_Restraint:
calcd

 
get = PosRMSDPot_Restraint_calcd_get(...)

 
set = PosRMSDPot_Restraint_calcd_set(...)

 
comment_

 
get = PosRMSDPot_Restraint_comment__get(...)

 
set = PosRMSDPot_Restraint_comment__set(...)

 
obs

 
get = PosRMSDPot_Restraint_obs_get(...)

 
set = PosRMSDPot_Restraint_obs_set(...)

 
obsErr

 
get = PosRMSDPot_Restraint_obsErr_get(...)

 
set = PosRMSDPot_Restraint_obsErr_set(...)

 
ok_

 
get = PosRMSDPot_Restraint_ok__get(...)

 
set = PosRMSDPot_Restraint_ok__set(...)

 
sel

 
get = PosRMSDPot_Restraint_sel_get(...)

 
set = PosRMSDPot_Restraint_sel_set(...)

 
verbose

 
get = PosRMSDPot_Restraint_verbose_get(...)

 
set = PosRMSDPot_Restraint_verbose_set(...)

 
Data and other attributes inherited from PosRMSDPot_Restraint:
__swig_getmethods__ = {'calcd': <built-in function PosRMSDPot_Restraint_calcd_get>, 'comment_': <built-in function PosRMSDPot_Restraint_comment__get>, 'obs': <built-in function PosRMSDPot_Restraint_obs_get>, 'obsErr': <built-in function PosRMSDPot_Restraint_obsErr_get>, 'ok_': <built-in function PosRMSDPot_Restraint_ok__get>, 'sel': <built-in function PosRMSDPot_Restraint_sel_get>, 'verbose': <built-in function PosRMSDPot_Restraint_verbose_get>}
__swig_setmethods__ = {'calcd': <built-in function PosRMSDPot_Restraint_calcd_set>, 'comment_': <built-in function PosRMSDPot_Restraint_comment__set>, 'obs': <built-in function PosRMSDPot_Restraint_obs_set>, 'obsErr': <built-in function PosRMSDPot_Restraint_obsErr_set>, 'ok_': <built-in function PosRMSDPot_Restraint_ok__set>, 'sel': <built-in function PosRMSDPot_Restraint_sel_set>, 'verbose': <built-in function PosRMSDPot_Restraint_verbose_set>}
Methods inherited from Restraint_PosRMSDPot:
diff(*args)

 
setName(*args)

 
violated(*args)

 
Data and other attributes inherited from Restraint_PosRMSDPot:
__dict__ = <dictproxy object at 0x28ad478>

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

 
list of weak references to the object (if defined)

 
class Restraint_PosRMSDPot(__builtin__.object)
   
 

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

 
__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 0x28ad440>

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

 
list of weak references to the object (if defined)

 
class Restraint_PosRMSDPotPtr(Restraint_PosRMSDPot)
   
 

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

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

 
__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_PosRMSDPot:
__dict__ = <dictproxy object at 0x28ad130>

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

 
list of weak references to the object (if defined)

 
class rc_ptr_PosRMSDPot_Restraint(__builtin__.object)
   
 

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

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__mul__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
calcAvePos(*args)

 
calcRMSDContrib(*args)

 
count(*args)

 
decr(*args)

 
deriv(*args)

 
diff(*args)

 
energy(*args)

 
incr(*args)

 
name(*args)

 
ok(*args)

 
ptr(*args)

 
reset(*args)

 
setName(*args)

 
showPositions(*args)

 
violated(*args)

 
Properties defined here:
calcd

 
get = rc_ptr_PosRMSDPot_Restraint_calcd_get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_calcd_set(...)

 
comment_

 
get = rc_ptr_PosRMSDPot_Restraint_comment__get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_comment__set(...)

 
obs

 
get = rc_ptr_PosRMSDPot_Restraint_obs_get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_obs_set(...)

 
obsErr

 
get = rc_ptr_PosRMSDPot_Restraint_obsErr_get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_obsErr_set(...)

 
ok_

 
get = rc_ptr_PosRMSDPot_Restraint_ok__get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_ok__set(...)

 
sel

 
get = rc_ptr_PosRMSDPot_Restraint_sel_get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_sel_set(...)

 
verbose

 
get = rc_ptr_PosRMSDPot_Restraint_verbose_get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_verbose_set(...)

 
Data and other attributes defined here:
__dict__ = <dictproxy object at 0x28ad440>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'calcd': <built-in function rc_ptr_PosRMSDPot_Restraint_calcd_get>, 'comment_': <built-in function rc_ptr_PosRMSDPot_Restraint_comment__get>, 'obs': <built-in function rc_ptr_PosRMSDPot_Restraint_obs_get>, 'obsErr': <built-in function rc_ptr_PosRMSDPot_Restraint_obsErr_get>, 'ok_': <built-in function rc_ptr_PosRMSDPot_Restraint_ok__get>, 'sel': <built-in function rc_ptr_PosRMSDPot_Restraint_sel_get>, 'verbose': <built-in function rc_ptr_PosRMSDPot_Restraint_verbose_get>}
__swig_setmethods__ = {'calcd': <built-in function rc_ptr_PosRMSDPot_Restraint_calcd_set>, 'comment_': <built-in function rc_ptr_PosRMSDPot_Restraint_comment__set>, 'obs': <built-in function rc_ptr_PosRMSDPot_Restraint_obs_set>, 'obsErr': <built-in function rc_ptr_PosRMSDPot_Restraint_obsErr_set>, 'ok_': <built-in function rc_ptr_PosRMSDPot_Restraint_ok__set>, 'sel': <built-in function rc_ptr_PosRMSDPot_Restraint_sel_set>, 'verbose': <built-in function rc_ptr_PosRMSDPot_Restraint_verbose_set>}
__weakref__ = <attribute '__weakref__' of 'rc_ptr_PosRMSDPot_Restraint' objects>

 
list of weak references to the object (if defined)

 
class rc_ptr_PosRMSDPot_RestraintPtr(rc_ptr_PosRMSDPot_Restraint)
   
 

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

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

 
__deref__(*args)

 
__getattr__ lambda self, name

 
__mul__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
calcAvePos(*args)

 
calcRMSDContrib(*args)

 
count(*args)

 
decr(*args)

 
deriv(*args)

 
diff(*args)

 
energy(*args)

 
incr(*args)

 
name(*args)

 
ok(*args)

 
ptr(*args)

 
reset(*args)

 
setName(*args)

 
showPositions(*args)

 
violated(*args)

 
Properties inherited from rc_ptr_PosRMSDPot_Restraint:
calcd

 
get = rc_ptr_PosRMSDPot_Restraint_calcd_get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_calcd_set(...)

 
comment_

 
get = rc_ptr_PosRMSDPot_Restraint_comment__get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_comment__set(...)

 
obs

 
get = rc_ptr_PosRMSDPot_Restraint_obs_get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_obs_set(...)

 
obsErr

 
get = rc_ptr_PosRMSDPot_Restraint_obsErr_get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_obsErr_set(...)

 
ok_

 
get = rc_ptr_PosRMSDPot_Restraint_ok__get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_ok__set(...)

 
sel

 
get = rc_ptr_PosRMSDPot_Restraint_sel_get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_sel_set(...)

 
verbose

 
get = rc_ptr_PosRMSDPot_Restraint_verbose_get(...)

 
set = rc_ptr_PosRMSDPot_Restraint_verbose_set(...)

 
Data and other attributes inherited from rc_ptr_PosRMSDPot_Restraint:
__dict__ = <dictproxy object at 0x28ad478>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'calcd': <built-in function rc_ptr_PosRMSDPot_Restraint_calcd_get>, 'comment_': <built-in function rc_ptr_PosRMSDPot_Restraint_comment__get>, 'obs': <built-in function rc_ptr_PosRMSDPot_Restraint_obs_get>, 'obsErr': <built-in function rc_ptr_PosRMSDPot_Restraint_obsErr_get>, 'ok_': <built-in function rc_ptr_PosRMSDPot_Restraint_ok__get>, 'sel': <built-in function rc_ptr_PosRMSDPot_Restraint_sel_get>, 'verbose': <built-in function rc_ptr_PosRMSDPot_Restraint_verbose_get>}
__swig_setmethods__ = {'calcd': <built-in function rc_ptr_PosRMSDPot_Restraint_calcd_set>, 'comment_': <built-in function rc_ptr_PosRMSDPot_Restraint_comment__set>, 'obs': <built-in function rc_ptr_PosRMSDPot_Restraint_obs_set>, 'obsErr': <built-in function rc_ptr_PosRMSDPot_Restraint_obsErr_set>, 'ok_': <built-in function rc_ptr_PosRMSDPot_Restraint_ok__set>, 'sel': <built-in function rc_ptr_PosRMSDPot_Restraint_sel_set>, 'verbose': <built-in function rc_ptr_PosRMSDPot_Restraint_verbose_set>}
__weakref__ = <attribute '__weakref__' of 'rc_ptr_PosRMSDPot_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.