noePot
index
noePot.py

potential term appropriate for ambiguous NOEs
 
constructor: NOEPot(instanceName,
                    restraintList,
                    sim1,sim2)
  instanceName is a user-specified identifier
  sim1, and sim2 are optional simulation.Simulation specifications
  [they default to the current Simulation.]
  restraintList is an optional XPLOR-style restraint table (string).
  Appropriate ensemble averaging will be performed if the sim1 argument
  is an ensembleSimulation.EnsembleSimulation.
 
methods
  addRestraints(restraintList) - add the specified XPLOR-style restraints
 
  calcEnergy()                 - calc energy, returns the energy value.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.
 
  rms()            - return the restraint rms violation
  numRestraints()  - return the numbder of restraints defined for this term.
  violations()     - return number of violations
  deviation()      - return average deviation from the mean over ensemble.
                     This is zero unless an ensembleSimulation with size 
                     greater than one is specified.
  devationSpread() - return the average devation spread over ensemble.
  restraints()     - return a list of restraints. See the description of the
                     Restraint class below.
  
  info()                    - current info about the state of this instance
  showRestraints(violated)  - return info on restraints. Argument violated is
                              boolean specifying whether to return only 
                              violated restraints.
  showViolations()          - return string containing pretty-printed info
                              on all violated restraints.
 
 
 
 The following parameters can be set [defaults in square brackets]
 
  nMono      - number of monomers [1]
  verbose    - if true, sporadically spit out info [False]
  scale      - scale factor [1]
  aveExp     - exponential to use in sum averaging [6]
  dOffset    - potential offset [0]
  hardExp    - exponential in hard region of potential [2]
  rSwitch    - distance at which to switch from hard form [0.5]
  softExp    - exponential in soft region of potential [1]
  asympSlope - slope in linear asymptotic region of pot [1]
  threshold  - threshold in violation calculation [0.5]
  potType    - type of potential: "soft" or "hard" [hard]
  aveType    - type of restraint averaging: "average", "center" or "sum" [sum]
  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]
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
 
 The energy function is defined as
 
        if pot=HARD or  r<rSwitch: 
                scale * r^hardExp
        pot=SOFT and r>rSwitch: 
                scale * (a + b / r^softExp + asympSlope * r)
 
        where
        b =  rSwitch^(softExp+1) * 
            (asympSlope - hardExp * rSwitch^(hardExp-1)) / softExp
        a = rSwitch^hardExp - b * rSwitch^(-softExp) - 
            asympSlope * rSwitch;
        
 The distance r is related to the calcualted restraint distance d by:
        if d < cdist - cMinus:      r = cdist - cMinus - d
        if d > cdist+cPlus-dOffset: r = cdist - ( d + cPlus - dOffset )
        otherwise, r = 0
 
 The restraint distance d is calculated as
   for aveType=average:
        d = [ <sum_pairs sum_ij | q_i - q_j |^(-aveExp) / Nij> ] ^(-1/aveExp)
     where q_i is the position of the i-th atom, and Nij is the number
of atom pairs in the sum. sum_pairs denotes sum over all selection pairs
introduced using the ASSIgn ... OR syntax. Note carefully the angle
brackets: they denote ensemble average. 
 
   for aveType=sum:
        d = [ <sum_pairs sum_ij | q_i - q_j |^(-aveExp) / nMono> ] ^(-1/aveExp)
     where q_i is the position of the i-th atom. sum_pairs denotes sum
over all selection pairs introduced using the ASSIgn ... OR
syntax. Note carefully the angle brackets: they denote ensemble average.
 
   for aveType=center:
        d = | sum_i q_i /N_1 - sum_j q_j /N_2 |
     where the sums are over the two selections listed in the restraint, 
and N_1, N_2 are the number of atoms in these selections. Center
averaging ignores additional selection pairs introduced using the
ASSIgn ... OR syntax: only the first pair is used in calculation of
the average positions.
      
XPLOR NOE restraint table format:
 
  ASSIgn (selection1) (selection2) <cDist> <cMinus> <cPlus> ! optional comment
      [OR (selection1) (selection2)]
      ...
 
The statement can be split across muliple lines, but the comment, if
specified, should be on the same line at cPlus. The OR keyword introduces 
additional selection pairs.
 
 
  Restraint class
 
members/methods:
  name()    - the restraint name
  comment() - the restraint comment (entered after the ! in the NOE table)
 
  sel1      - an atomSel.AtomSel corresponding to the first selection
              in the restraint table. This member is identical to
                selPairs()[0].a
  sel2      - an atomSel.AtomSel corresponding to the second selection
              in the restraint table. This member is identical to
                selPairs()[0].a
  selPairs()- a list of selection pairs, accessed through members a and b.
              The first pair corresponds to (sel1, sel2), with additional
              pairs correspond to those introduced using ASSIgn ... OR 
              assignment statements.
  d()       - the observed radius from the restraint table
  dPlus()   - the upper bound as listed in the restraint table
  dMinus()  - the lower bound as listed in the restraint table
 
  
  dist()    - the calculated average distance
 
  asString() - a string representation of the restraint.
 
  variance   - variance in dist among an 
               ensembleSimulation.EnsembleSimulation set of structures.
  
 

 
Classes
       
__builtin__.object
CDSList_NOERestraint
CDSList_NOERestraintPtr
CDSList_NOESelPair
CDSList_NOESelPairPtr
Modified
ModifiedPtr
ModifiedBase
ModifiedBasePtr
NOEPot
NOEPotPtr
NOEPot_LetterClass
NOEPot_LetterClassPtr
NOESelPair
NOESelPairPtr
Restraint_NOEPot
NOERestraint
NOERestraintPtr
Restraint_NOEPotPtr
rc_ptr_NOERestraint
rc_ptr_NOERestraintPtr

 
class CDSList_NOERestraint(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_NOERestraint>)
__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 0x129f9b8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_NOERestraint' objects>
list of weak references to the object (if defined)

 
class CDSList_NOERestraintPtr(CDSList_NOERestraint)
    
Method resolution order:
CDSList_NOERestraintPtr
CDSList_NOERestraint
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from CDSList_NOERestraint:
__del__(self, destroy=<built-in function delete_CDSList_NOERestraint>)
__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_NOERestraint:
__dict__ = <dictproxy object at 0x129f980>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_NOERestraint' objects>
list of weak references to the object (if defined)

 
class CDSList_NOESelPair(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_CDSList_NOESelPair>)
__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 0x129f8a0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_NOESelPair' objects>
list of weak references to the object (if defined)

 
class CDSList_NOESelPairPtr(CDSList_NOESelPair)
    
Method resolution order:
CDSList_NOESelPairPtr
CDSList_NOESelPair
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from CDSList_NOESelPair:
__del__(self, destroy=<built-in function delete_CDSList_NOESelPair>)
__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_NOESelPair:
__dict__ = <dictproxy object at 0x129fa60>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'CDSList_NOESelPair' 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 0x129fad0>
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 0x129f980>
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 0x129f718>
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 0x129f718>
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 NOEPot(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_NOEPot>)
__deref__(*args)
__getattr__ lambda self, name
__init__(self, *args)
__mul__(*args)
__oldinit__ = __init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
addRestraints(*args)
asympSlope(*args)
aveExp(*args)
aveType(*args)
calcDerivs(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
dOffset(*args)
deviation(*args)
deviationSpread(*args)
hardExp(*args)
help(*args)
incrRefCount(*args)
info(*args)
instanceData(*args)
instanceName(*args)
nMono(*args)
numRestraints(*args)
pointer(*args)
potName(*args)
potType(*args)
rSwitch(*args)
registerInstanceData(*args)
registerTo(*args)
resetPotName(*args)
restraints(*args)
rms(*args)
scale(*args)
setAsympSlope(*args)
setAveExp(*args)
setAveType(*args)
setDOffset(*args)
setHardExp(*args)
setNMono(*args)
setPotType(*args)
setRSwitch(*args)
setScale(*args)
setShowAllRestraints(*args)
setSoftExp(*args)
setThreshold(*args)
setVerbose(*args)
showAllRestraints(*args)
showRestraints(*args)
showViolations(*args)
simulation(*args)
simulation2(*args)
softExp(*args)
threshold(*args)
unRegister(*args)
updateValues(*args)
verbose(*args)
violations(*args)

Properties defined here:
instanceData_
get = NOEPot_instanceData__get(...)
set = NOEPot_instanceData__set(...)
modified
get = NOEPot_modified_get(...)
set = NOEPot_modified_set(...)
registeredSimulations
get = NOEPot_registeredSimulations_get(...)
set = NOEPot_registeredSimulations_set(...)

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x129ffa0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function NOEPot_instanceData__get>, 'modified': <built-in function NOEPot_modified_get>, 'registeredSimulations': <built-in function NOEPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function NOEPot_instanceData__set>, 'modified': <built-in function NOEPot_modified_set>, 'registeredSimulations': <built-in function NOEPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'NOEPot' objects>
list of weak references to the object (if defined)

 
class NOEPotPtr(NOEPot)
    
Method resolution order:
NOEPotPtr
NOEPot
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from NOEPot:
__del__(self, destroy=<built-in function delete_NOEPot>)
__deref__(*args)
__getattr__ lambda self, name
__mul__(*args)
__oldinit__ = __init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
addRestraints(*args)
asympSlope(*args)
aveExp(*args)
aveType(*args)
calcDerivs(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
dOffset(*args)
deviation(*args)
deviationSpread(*args)
hardExp(*args)
help(*args)
incrRefCount(*args)
info(*args)
instanceData(*args)
instanceName(*args)
nMono(*args)
numRestraints(*args)
pointer(*args)
potName(*args)
potType(*args)
rSwitch(*args)
registerInstanceData(*args)
registerTo(*args)
resetPotName(*args)
restraints(*args)
rms(*args)
scale(*args)
setAsympSlope(*args)
setAveExp(*args)
setAveType(*args)
setDOffset(*args)
setHardExp(*args)
setNMono(*args)
setPotType(*args)
setRSwitch(*args)
setScale(*args)
setShowAllRestraints(*args)
setSoftExp(*args)
setThreshold(*args)
setVerbose(*args)
showAllRestraints(*args)
showRestraints(*args)
showViolations(*args)
simulation(*args)
simulation2(*args)
softExp(*args)
threshold(*args)
unRegister(*args)
updateValues(*args)
verbose(*args)
violations(*args)

Properties inherited from NOEPot:
instanceData_
get = NOEPot_instanceData__get(...)
set = NOEPot_instanceData__set(...)
modified
get = NOEPot_modified_get(...)
set = NOEPot_modified_set(...)
registeredSimulations
get = NOEPot_registeredSimulations_get(...)
set = NOEPot_registeredSimulations_set(...)

Data and other attributes inherited from NOEPot:
__dict__ = <dictproxy object at 0x129f718>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'instanceData_': <built-in function NOEPot_instanceData__get>, 'modified': <built-in function NOEPot_modified_get>, 'registeredSimulations': <built-in function NOEPot_registeredSimulations_get>}
__swig_setmethods__ = {'instanceData_': <built-in function NOEPot_instanceData__set>, 'modified': <built-in function NOEPot_modified_set>, 'registeredSimulations': <built-in function NOEPot_registeredSimulations_set>}
__weakref__ = <attribute '__weakref__' of 'NOEPot' objects>
list of weak references to the object (if defined)

 
class NOEPot_LetterClass(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_NOEPot_LetterClass>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
addRestraints(*args)
asympSlope(*args)
aveExp(*args)
aveType(*args)
calcDerivs(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
dOffset(*args)
deviation(*args)
deviationSpread(*args)
hardExp(*args)
help(*args)
info(*args)
nMono(*args)
numRestraints(*args)
potType(*args)
rSwitch(*args)
restraints(*args)
rms(*args)
setAsympSlope(*args)
setAveExp(*args)
setAveType(*args)
setDOffset(*args)
setHardExp(*args)
setNMono(*args)
setPotType(*args)
setRSwitch(*args)
setShowAllRestraints(*args)
setSoftExp(*args)
setThreshold(*args)
setVerbose(*args)
showAllRestraints(*args)
showRestraints(*args)
showViolations(*args)
simulation(*args)
simulation2(*args)
softExp(*args)
threshold(*args)
updateValues(*args)
verbose(*args)
violations(*args)

Data and other attributes defined here:
AVERAGE = 0
CENTER = 1
HARD = 1
LOGNORMAL = 2
SOFT = 0
SUM = 2
__dict__ = <dictproxy object at 0x129fb08>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'NOEPot_LetterClass' objects>
list of weak references to the object (if defined)

 
class NOEPot_LetterClassPtr(NOEPot_LetterClass)
    
Method resolution order:
NOEPot_LetterClassPtr
NOEPot_LetterClass
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from NOEPot_LetterClass:
__del__(self, destroy=<built-in function delete_NOEPot_LetterClass>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
addRestraints(*args)
asympSlope(*args)
aveExp(*args)
aveType(*args)
calcDerivs(*args)
calcEnergy(*args)
calcEnergyAndDerivs(*args)
dOffset(*args)
deviation(*args)
deviationSpread(*args)
hardExp(*args)
help(*args)
info(*args)
nMono(*args)
numRestraints(*args)
potType(*args)
rSwitch(*args)
restraints(*args)
rms(*args)
setAsympSlope(*args)
setAveExp(*args)
setAveType(*args)
setDOffset(*args)
setHardExp(*args)
setNMono(*args)
setPotType(*args)
setRSwitch(*args)
setShowAllRestraints(*args)
setSoftExp(*args)
setThreshold(*args)
setVerbose(*args)
showAllRestraints(*args)
showRestraints(*args)
showViolations(*args)
simulation(*args)
simulation2(*args)
softExp(*args)
threshold(*args)
updateValues(*args)
verbose(*args)
violations(*args)

Data and other attributes inherited from NOEPot_LetterClass:
AVERAGE = 0
CENTER = 1
HARD = 1
LOGNORMAL = 2
SOFT = 0
SUM = 2
__dict__ = <dictproxy object at 0x129fd00>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'NOEPot_LetterClass' objects>
list of weak references to the object (if defined)

 
class NOERestraint(Restraint_NOEPot)
    
Method resolution order:
NOERestraint
Restraint_NOEPot
__builtin__.object

Methods defined here:
__del__(self, destroy=<built-in function delete_NOERestraint>)
__eq__(*args)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
asString(*args)
calcDistanceDiff(*args)
comment(*args)
d(*args)
dMinus(*args)
dPlus(*args)
deriv(*args)
dist(*args)
energy(*args)
logDiff(*args)
name(*args)
ok(*args)
selPairs(*args)
status(*args)

Properties defined here:
variance
get = NOERestraint_variance_get(...)
set = NOERestraint_variance_set(...)
verbose
get = NOERestraint_verbose_get(...)
set = NOERestraint_verbose_set(...)

Data and other attributes defined here:
GREATER = 1
INSIDE = 2
LESS = 0
__swig_getmethods__ = {'sel1': <function noerestraint_sel1 at 0x12a20c8>, 'sel2': <function noerestraint_sel2 at 0x12adde8>, 'variance': <built-in function NOERestraint_variance_get>, 'verbose': <built-in function NOERestraint_verbose_get>}
__swig_setmethods__ = {'variance': <built-in function NOERestraint_variance_set>, 'verbose': <built-in function NOERestraint_verbose_set>}

Methods inherited from Restraint_NOEPot:
diff(*args)
setName(*args)
violated(*args)

Data and other attributes inherited from Restraint_NOEPot:
__dict__ = <dictproxy object at 0x129fb08>
dictionary for instance variables (if defined)
__weakref__ = <attribute '__weakref__' of 'Restraint_NOEPot' objects>
list of weak references to the object (if defined)

 
class NOERestraintPtr(NOERestraint)
    
Method resolution order:
NOERestraintPtr
NOERestraint
Restraint_NOEPot
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from NOERestraint:
__del__(self, destroy=<built-in function delete_NOERestraint>)
__eq__(*args)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
asString(*args)
calcDistanceDiff(*args)
comment(*args)
d(*args)
dMinus(*args)
dPlus(*args)
deriv(*args)
dist(*args)
energy(*args)
logDiff(*args)
name(*args)
ok(*args)
selPairs(*args)
status(*args)

Properties inherited from NOERestraint:
variance
get = NOERestraint_variance_get(...)
set = NOERestraint_variance_set(...)
verbose
get = NOERestraint_verbose_get(...)
set = NOERestraint_verbose_set(...)

Data and other attributes inherited from NOERestraint:
GREATER = 1
INSIDE = 2
LESS = 0
__swig_getmethods__ = {'sel1': <function noerestraint_sel1 at 0x12a20c8>, 'sel2': <function noerestraint_sel2 at 0x12adde8>, 'variance': <built-in function NOERestraint_variance_get>, 'verbose': <built-in function NOERestraint_verbose_get>}
__swig_setmethods__ = {'variance': <built-in function NOERestraint_variance_set>, 'verbose': <built-in function NOERestraint_verbose_set>}

Methods inherited from Restraint_NOEPot:
diff(*args)
setName(*args)
violated(*args)

Data and other attributes inherited from Restraint_NOEPot:
__dict__ = <dictproxy object at 0x129f980>
dictionary for instance variables (if defined)
__weakref__ = <attribute '__weakref__' of 'Restraint_NOEPot' objects>
list of weak references to the object (if defined)

 
class NOESelPair(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_NOESelPair>)
__eq__(*args)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value

Properties defined here:
a
get = NOESelPair_a_get(...)
set = NOESelPair_a_set(...)
b
get = NOESelPair_b_get(...)
set = NOESelPair_b_set(...)

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x129fc90>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'a': <built-in function NOESelPair_a_get>, 'b': <built-in function NOESelPair_b_get>}
__swig_setmethods__ = {'a': <built-in function NOESelPair_a_set>, 'b': <built-in function NOESelPair_b_set>}
__weakref__ = <attribute '__weakref__' of 'NOESelPair' objects>
list of weak references to the object (if defined)

 
class NOESelPairPtr(NOESelPair)
    
Method resolution order:
NOESelPairPtr
NOESelPair
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from NOESelPair:
__del__(self, destroy=<built-in function delete_NOESelPair>)
__eq__(*args)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value

Properties inherited from NOESelPair:
a
get = NOESelPair_a_get(...)
set = NOESelPair_a_set(...)
b
get = NOESelPair_b_get(...)
set = NOESelPair_b_set(...)

Data and other attributes inherited from NOESelPair:
__dict__ = <dictproxy object at 0x129f980>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'a': <built-in function NOESelPair_a_get>, 'b': <built-in function NOESelPair_b_get>}
__swig_setmethods__ = {'a': <built-in function NOESelPair_a_set>, 'b': <built-in function NOESelPair_b_set>}
__weakref__ = <attribute '__weakref__' of 'NOESelPair' objects>
list of weak references to the object (if defined)

 
class Restraint_NOEPot(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_Restraint_NOEPot>)
__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 0x129fa28>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Restraint_NOEPot' objects>
list of weak references to the object (if defined)

 
class Restraint_NOEPotPtr(Restraint_NOEPot)
    
Method resolution order:
Restraint_NOEPotPtr
Restraint_NOEPot
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from Restraint_NOEPot:
__del__(self, destroy=<built-in function delete_Restraint_NOEPot>)
__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_NOEPot:
__dict__ = <dictproxy object at 0x129fbe8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {}
__swig_setmethods__ = {}
__weakref__ = <attribute '__weakref__' of 'Restraint_NOEPot' objects>
list of weak references to the object (if defined)

 
class rc_ptr_NOERestraint(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_rc_ptr_NOERestraint>)
__deref__(*args)
__eq__(*args)
__getattr__ lambda self, name
__init__(self, *args)
__mul__(*args)
__repr__(self)
__setattr__ lambda self, name, value
asString(*args)
calcDistanceDiff(*args)
comment(*args)
count(*args)
d(*args)
dMinus(*args)
dPlus(*args)
decr(*args)
deriv(*args)
diff(*args)
dist(*args)
energy(*args)
incr(*args)
logDiff(*args)
name(*args)
ok(*args)
ptr(*args)
reset(*args)
selPairs(*args)
setName(*args)
status(*args)
violated(*args)

Properties defined here:
variance
get = rc_ptr_NOERestraint_variance_get(...)
set = rc_ptr_NOERestraint_variance_set(...)
verbose
get = rc_ptr_NOERestraint_verbose_get(...)
set = rc_ptr_NOERestraint_verbose_set(...)

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x129fa98>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'sel1': <function noerestraint_sel1 at 0x12a20c8>, 'sel2': <function noerestraint_sel2 at 0x12adde8>, 'variance': <built-in function rc_ptr_NOERestraint_variance_get>, 'verbose': <built-in function rc_ptr_NOERestraint_verbose_get>}
__swig_setmethods__ = {'variance': <built-in function rc_ptr_NOERestraint_variance_set>, 'verbose': <built-in function rc_ptr_NOERestraint_verbose_set>}
__weakref__ = <attribute '__weakref__' of 'rc_ptr_NOERestraint' objects>
list of weak references to the object (if defined)

 
class rc_ptr_NOERestraintPtr(rc_ptr_NOERestraint)
    
Method resolution order:
rc_ptr_NOERestraintPtr
rc_ptr_NOERestraint
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from rc_ptr_NOERestraint:
__del__(self, destroy=<built-in function delete_rc_ptr_NOERestraint>)
__deref__(*args)
__eq__(*args)
__getattr__ lambda self, name
__mul__(*args)
__repr__(self)
__setattr__ lambda self, name, value
asString(*args)
calcDistanceDiff(*args)
comment(*args)
count(*args)
d(*args)
dMinus(*args)
dPlus(*args)
decr(*args)
deriv(*args)
diff(*args)
dist(*args)
energy(*args)
incr(*args)
logDiff(*args)
name(*args)
ok(*args)
ptr(*args)
reset(*args)
selPairs(*args)
setName(*args)
status(*args)
violated(*args)

Properties inherited from rc_ptr_NOERestraint:
variance
get = rc_ptr_NOERestraint_variance_get(...)
set = rc_ptr_NOERestraint_variance_set(...)
verbose
get = rc_ptr_NOERestraint_verbose_get(...)
set = rc_ptr_NOERestraint_verbose_set(...)

Data and other attributes inherited from rc_ptr_NOERestraint:
__dict__ = <dictproxy object at 0x129fbb0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'sel1': <function noerestraint_sel1 at 0x12a20c8>, 'sel2': <function noerestraint_sel2 at 0x12adde8>, 'variance': <built-in function rc_ptr_NOERestraint_variance_get>, 'verbose': <built-in function rc_ptr_NOERestraint_verbose_get>}
__swig_setmethods__ = {'variance': <built-in function rc_ptr_NOERestraint_variance_set>, 'verbose': <built-in function rc_ptr_NOERestraint_verbose_set>}
__weakref__ = <attribute '__weakref__' of 'rc_ptr_NOERestraint' objects>
list of weak references to the object (if defined)

 
Functions
       
help(...)
noerestraint_sel1(self)
noerestraint_sel2(self)