Potential term used to fit solvent NOEs and solvent PRES to an
empirical measure of surface accessibility as described in
 
   Yu Wang, C.D. Schwieters, N. Tjandra, ``Parameterization of
   Solvent-Protein Interaction and Its Use on NMR Protein
   Structure Determination,'' J. Magn. Res. 221, 76-84 (2012).
 
Please use nbTargetPotTools.create_NBTargetPot to instantiate
instances of this potential term.
 
 
Constructor:
  NBTargetPot(instanceName,
              selection   ) 
 
  instanceName is a user-specified identifier
  selection is a atomSel.AtomSel object specifying the atoms to include
  when calculating sums- see below for details.
 
methods:
 
  calcEnergy()
 
  addRestraints(str) - add restraints specified in the input string
 
  rms()            - rmsd of this term
  correlation()    - correlation of calculated to target values.
  deviation()      - ensemble deviation of the restraints
  violations()     - number of restraints violated
  numRestraints()  - total number of restraints
 
 
  selection()      - atom selection specified when the term was created
  simulation()     - associated simulation.Simulation
 
  info()           - information on the term
  showViolations() - return a string which info on violated restraints.
                     if showAllRestraints()=True, info on all restraints is 
                     returned.
 
  restraints()     - return a sequence of Restraint objects.
 
 The following parameters can be set [defaults in square brackets]
 
    slope      - The slope parameter applied to the calculated values. See 
                 below. [1]
    intercept  - The intercept parameter applied to the calculated values. See 
                 below. [0]
    moveTol    - maximum distance in Angstroms any atom can move before
                 triggering a recalculation of the neighbor list [0].
    cutoffDist - cutoff distance beyond which atom contributions to
                 the sum are not evaluated [10].
    potType    - potential type, "rmsd" or "correlation"  to use in
                 energy computation [RMSD].
    aveType    - averaging type, "center" or "sum"  to use in
                 effective surface area computation [CENTER].
    aveExp     - the exponent used in averaging [6].
    invPow     - the inverse power used in the effective surface area
                 computation [3].
    excludeSameResid  - a boolean specifying whether or not to exclude
                        atoms in the same residue in the sum
                        computation [True]. 
    showAllRestraints - a boolean describing whether or not to print
                        out information on all restraints, rather than
                        only violated restraints, in the violations
                        file [False].
    ensWeights()      - return ensemble weights.
    verbose           - a boolean describing whether or not to print
                        detailed information on the neighbor lists [False].
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
 
Each Restraint contains the following members:
  
  targetSel - atom selection corresponding to one or more atoms whose
              effective surface area has been measured.
  neighbors - a list of indices of atoms which are neighbors. These
              indices correspond to atoms as listed in the associated
              simulation.Simulation.
  targetVal - effective surface area as specified in the input table.
  targetErr - effective surface area error as specified in the input table.
  calcdVal  - effective surface area as computed from the molecular structure.
  variance  - a measure of spread over ensemble members.
 
  name()    - return the restraint name - by default this in the
              string associated with the targetSel
 
 
For "sum" aveType, the effective surface area is calculated as
 
  Sacc = slope * [ \sum_{i,j} |r_i - r_j|^{-aveExp} ]^{-invPow} + intercept
 
while for "center" aveType it is
 
  Sacc = slope * [ \sum_j |r_c - r_j|^{-aveExp} ]^{-invPow} + intercept
 
where i runs over all atoms in targetSel, j runs over all neighbor
atoms, r_i is the position of atom i, and r_c is the average position
of all atoms in targetSel. For ensembleSimulation.EnsembleSimulations, the 
effective surface area is calculated as
 
  Sacc = \sum_k w_k Sacc_k
 
where Sacc_k is the effective surface area of ensemble member k, and
w_k is the associated ensemble weight.
 
For "rmsd" potType, the energy associated with restraint k is 
 
  E_k = ( Sacc - targetVal )^2 / targetErr^2
 
and the overall energy is the scaled sum:
 
  E = scale() * \sum_k E_k
 
For "correlation" potType
 
   E = scale() * correlation()
 
 
 
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

Classes
		builtins.object CDSList_NBTarget_Restraint EnsemblePot NBTargetPot_LetterClass Modified ModifiedBase NBTargetPot Restraint_NBTarget NBTarget_Restraint VarEnsWeights rc_EnsemblePot rc_ptr_NBTarget_Restraint   class CDSList_NBTarget_Restraint(builtins.object)     CDSList_NBTarget_Restraint(*args)       Methods defined here: __delitem__(self, *args, **kwargs) -> 'void' __getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< NBTarget_Restraint > >' __getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< NBTarget_Restraint > >' __init__(self, *args) Initialize self.  See help(type(self)) for accurate signature. __len__(self, *args, **kwargs) -> 'int' __repr__ = _swig_repr(self) __setitem__(self, *args, **kwargs) -> 'void' append(self, *args, **kwargs) -> 'void' help(self, *args, **kwargs) -> 'String' remove(self, *args, **kwargs) -> 'void' removeAll(self, *args, **kwargs) -> 'void' Static methods defined here: __swig_destroy__ = delete_CDSList_NBTarget_Restraint(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag   class EnsemblePot(builtins.object)     EnsemblePot(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) addEnsWeights(self, *args, **kwargs) -> 'void' calcEnergy(self, *args, **kwargs) -> 'float_type' calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type' calcWDerivs(self, *args, **kwargs) -> 'bool const' clearEnsWeights(self, *args, **kwargs) -> 'void' energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs4(self, *args, **kwargs) -> 'float_type' energyMaybeDerivsPost(self, *args, **kwargs) -> 'float_type' energyMaybeDerivsPre(self, *args, **kwargs) -> 'float_type' ensWeight(self, *args, **kwargs) -> 'float_type' ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >' ensWeightsInfo(self, *args, **kwargs) -> 'String' getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &' setCalcWDerivs(self, *args, **kwargs) -> 'void' setEnsWeights(self, *args, **kwargs) -> 'void' setUseSimEnsWeights(self, *args, **kwargs) -> 'void' simulation(self, *args) -> 'EnsembleSimulationBase const *' updateEnsWeights(self, *args, **kwargs) -> 'void' useSimEnsWeights(self, *args, **kwargs) -> 'bool const' Static methods defined here: __swig_destroy__ = delete_EnsemblePot(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag   class Modified(builtins.object)     Modified(*args, **kwargs)       Methods defined here: __call__(self, *args, **kwargs) -> 'int' Call self as a function. __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) asString(self, *args, **kwargs) -> 'String' assertClear(self, *args, **kwargs) -> 'void' clear(self, *args, **kwargs) -> 'void' set(self, *args, **kwargs) -> 'void' update(self, *args, **kwargs) -> 'void' value(self, *args, **kwargs) -> 'int' Static methods defined here: __swig_destroy__ = delete_Modified(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag Data and other attributes defined here: MOD_SELF = 1 MOD_SIMULATION = 2   class ModifiedBase(builtins.object)     ModifiedBase(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) registerTo(self, *args, **kwargs) -> 'void' unRegister(self, *args, **kwargs) -> 'void' updateValues(self, *args, **kwargs) -> 'void' Static methods defined here: __swig_destroy__ = delete_ModifiedBase(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) modified   registeredSimulations   thisown   The membership flag   class NBTargetPot_LetterClass(EnsemblePot)     NBTargetPot_LetterClass(*args, **kwargs)       Method resolution order: NBTargetPot_LetterClass EnsemblePot builtins.object Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) addRestraints(self, *args, **kwargs) -> 'void' aveExp(self, *args, **kwargs) -> 'float_type const' aveType(self, *args, **kwargs) -> 'NBTargetPot::NBTargetAveType const' correlation(self, *args, **kwargs) -> 'float_type' cutoffDist(self, *args, **kwargs) -> 'float_type const' deviation(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type' excludeSameResid(self, *args, **kwargs) -> 'bool const' info(self, *args, **kwargs) -> 'String' intercept(self, *args, **kwargs) -> 'float_type const' invPow(self, *args, **kwargs) -> 'int const' moveTol(self, *args, **kwargs) -> 'float_type const' numRestraints(self, *args, **kwargs) -> 'int' potType(self, *args, **kwargs) -> 'NBTargetPot::NBTargetPotType const' pyXplorHelp(self, *args, **kwargs) -> 'String' restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< NBTarget_Restraint > >' rms(self, *args, **kwargs) -> 'double' selection(self, *args, **kwargs) -> 'AtomSel const &' setAveExp(self, *args, **kwargs) -> 'void' setAveType(self, *args, **kwargs) -> 'void' setCutoffDist(self, *args, **kwargs) -> 'void' setExcludeSameResid(self, *args, **kwargs) -> 'void' setIntercept(self, *args, **kwargs) -> 'void' setInvPow(self, *args, **kwargs) -> 'void' setMoveTol(self, *args, **kwargs) -> 'void' setPotType(self, *args, **kwargs) -> 'void' setShowAllRestraints(self, *args, **kwargs) -> 'void' setSlope(self, *args, **kwargs) -> 'void' setVerbose(self, *args, **kwargs) -> 'void' showAllRestraints(self, *args, **kwargs) -> 'bool const' showRestraints(self, *args, **kwargs) -> 'String' showViolations(self, *args, **kwargs) -> 'String' slope(self, *args, **kwargs) -> 'float_type const' updateNeighborList(self, *args, **kwargs) -> 'void' verbose(self, *args, **kwargs) -> 'bool const' violations(self, *args, **kwargs) -> 'float_type' Static methods defined here: __swig_destroy__ = delete_NBTargetPot_LetterClass(...) Data descriptors defined here: ave_calcd   ave_obs   corr   denom   neighbors   num   restraints_   sumObs2   thisown   The membership flag Data and other attributes defined here: CENTER = 0 CORRELATION = 1 RMSD = 0 SUM = 1 Methods inherited from EnsemblePot: addEnsWeights(self, *args, **kwargs) -> 'void' calcEnergy(self, *args, **kwargs) -> 'float_type' calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type' calcWDerivs(self, *args, **kwargs) -> 'bool const' clearEnsWeights(self, *args, **kwargs) -> 'void' energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs4(self, *args, **kwargs) -> 'float_type' energyMaybeDerivsPost(self, *args, **kwargs) -> 'float_type' energyMaybeDerivsPre(self, *args, **kwargs) -> 'float_type' ensWeight(self, *args, **kwargs) -> 'float_type' ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >' ensWeightsInfo(self, *args, **kwargs) -> 'String' getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &' setCalcWDerivs(self, *args, **kwargs) -> 'void' setEnsWeights(self, *args, **kwargs) -> 'void' setUseSimEnsWeights(self, *args, **kwargs) -> 'void' simulation(self, *args) -> 'EnsembleSimulationBase const *' updateEnsWeights(self, *args, **kwargs) -> 'void' useSimEnsWeights(self, *args, **kwargs) -> 'bool const' Data descriptors inherited from EnsemblePot: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined)   class NBTarget_Restraint(Restraint_NBTarget)     NBTarget_Restraint(*args, **kwargs)       Method resolution order: NBTarget_Restraint Restraint_NBTarget builtins.object Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) calcContrib(self, *args, **kwargs) -> 'void' calcd(self, *args, **kwargs) -> 'float_type' deriv(self, *args, **kwargs) -> 'void' deviation(self, *args, **kwargs) -> 'float_type' energy(self, *args, **kwargs) -> 'float_type' err(self, *args, **kwargs) -> 'float_type' name(self, *args, **kwargs) -> 'String' obs(self, *args, **kwargs) -> 'float_type' sel(self, *args, **kwargs) -> 'AtomSel const &' updateNeighborList(self, *args, **kwargs) -> 'void' Static methods defined here: __swig_destroy__ = delete_NBTarget_Restraint(...) Data descriptors defined here: calcdVal   contrib   neighbors   targetErr   targetSel   targetVal   thisown   The membership flag variance   Methods inherited from Restraint_NBTarget: diff(self, *args, **kwargs) -> 'float_type' setName(self, *args, **kwargs) -> 'void' violated(self, *args, **kwargs) -> 'bool' Data descriptors inherited from Restraint_NBTarget: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined)   class Restraint_NBTarget(builtins.object)     Restraint_NBTarget(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) diff(self, *args, **kwargs) -> 'float_type' name(self, *args, **kwargs) -> 'String const' setName(self, *args, **kwargs) -> 'void' violated(self, *args, **kwargs) -> 'bool' Static methods defined here: __swig_destroy__ = delete_Restraint_NBTarget(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag   class VarEnsWeights(builtins.object)     VarEnsWeights(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) Static methods defined here: __swig_destroy__ = delete_VarEnsWeights(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) ensWeights   mult   thisown   The membership flag   class rc_EnsemblePot(builtins.object)     rc_EnsemblePot(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) Static methods defined here: __swig_destroy__ = delete_rc_EnsemblePot(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag   class rc_ptr_NBTarget_Restraint(builtins.object)     rc_ptr_NBTarget_Restraint(*args)       Methods defined here: __deref__(self, *args, **kwargs) -> 'NBTarget_Restraint *' __init__(self, *args) Initialize self.  See help(type(self)) for accurate signature. __ref__(self, *args, **kwargs) -> 'NBTarget_Restraint &' __repr__ = _swig_repr(self) calcContrib(self, *args, **kwargs) -> 'void' calcd(self, *args, **kwargs) -> 'float_type' count(self, *args, **kwargs) -> 'int' decr(self, *args, **kwargs) -> 'void' deriv(self, *args, **kwargs) -> 'void' deviation(self, *args, **kwargs) -> 'float_type' diff(self, *args, **kwargs) -> 'float_type' energy(self, *args, **kwargs) -> 'float_type' err(self, *args, **kwargs) -> 'float_type' forceDelete(self, *args, **kwargs) -> 'void' incr(self, *args, **kwargs) -> 'void' name(self, *args, **kwargs) -> 'String' obs(self, *args, **kwargs) -> 'float_type' ptr(self, *args, **kwargs) -> 'NBTarget_Restraint *' release(self, *args, **kwargs) -> 'NBTarget_Restraint *' reset(self, *args, **kwargs) -> 'void' sel(self, *args, **kwargs) -> 'AtomSel const &' setName(self, *args, **kwargs) -> 'void' updateNeighborList(self, *args, **kwargs) -> 'void' violated(self, *args, **kwargs) -> 'bool' Static methods defined here: __swig_destroy__ = delete_rc_ptr_NBTarget_Restraint(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) calcdVal   contrib   neighbors   targetErr   targetSel   targetVal   thisown   The membership flag variance     realNBTargetPot = class NBTargetPot(builtins.object)     realNBTargetPot(*args)       Methods defined here: __deref__(self, *args, **kwargs) -> 'NBTargetPot *' __init__(self, *args) __oldinit__ = __init__(self, *args, **kwargs) __ref__(self, *args, **kwargs) -> 'NBTargetPot &' __repr__ = _swig_repr(self) addEnsWeights(self, *args, **kwargs) -> 'void' addRestraints(self, *args, **kwargs) -> 'void' aveExp(self, *args, **kwargs) -> 'float_type const' aveType(self, *args, **kwargs) -> 'NBTargetPot::NBTargetAveType const' calcEnergy(self, *args, **kwargs) -> 'float_type' calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type' calcWDerivs(self, *args, **kwargs) -> 'bool const' clearEnsWeights(self, *args, **kwargs) -> 'void' correlation(self, *args, **kwargs) -> 'float_type' cutoffDist(self, *args, **kwargs) -> 'float_type const' decrRefCnt(self, *args, **kwargs) -> 'void' deviation(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs4(self, *args, **kwargs) -> 'float_type' energyMaybeDerivsPost(self, *args, **kwargs) -> 'float_type' energyMaybeDerivsPre(self, *args, **kwargs) -> 'float_type' ensWeight(self, *args, **kwargs) -> 'float_type' ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >' ensWeightsInfo(self, *args, **kwargs) -> 'String' excludeSameResid(self, *args, **kwargs) -> 'bool const' getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &' incrRefCnt(self, *args, **kwargs) -> 'void' info(self, *args, **kwargs) -> 'String' instanceData(self, *args, **kwargs) -> 'PyObject *' instanceName(self, *args, **kwargs) -> 'char const *' intercept(self, *args, **kwargs) -> 'float_type const' invPow(self, *args, **kwargs) -> 'int const' moveTol(self, *args, **kwargs) -> 'float_type const' numRestraints(self, *args, **kwargs) -> 'int' potName(self, *args, **kwargs) -> 'char const *' potType(self, *args, **kwargs) -> 'NBTargetPot::NBTargetPotType const' pyXplorHelp(self, *args, **kwargs) -> 'String' refCnt(self, *args, **kwargs) -> 'int' registerInstanceData(self, *args, **kwargs) -> 'void' registerTo(self, *args, **kwargs) -> 'void' resetInstanceName(self, *args, **kwargs) -> 'void' resetPotName(self, *args, **kwargs) -> 'void' restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< NBTarget_Restraint > >' rms(self, *args, **kwargs) -> 'double' scale(self, *args, **kwargs) -> 'float_type const' selection(self, *args, **kwargs) -> 'AtomSel const &' setAveExp(self, *args, **kwargs) -> 'void' setAveType(self, *args, **kwargs) -> 'void' setCalcWDerivs(self, *args, **kwargs) -> 'void' setCutoffDist(self, *args, **kwargs) -> 'void' setEnsWeights(self, *args, **kwargs) -> 'void' setExcludeSameResid(self, *args, **kwargs) -> 'void' setIntercept(self, *args, **kwargs) -> 'void' setInvPow(self, *args, **kwargs) -> 'void' setMoveTol(self, *args, **kwargs) -> 'void' setPotType(self, *args, **kwargs) -> 'void' setScale(self, *args, **kwargs) -> 'void' setShowAllRestraints(self, *args, **kwargs) -> 'void' setSlope(self, *args, **kwargs) -> 'void' setThreshold(self, *args, **kwargs) -> 'void' setUseSimEnsWeights(self, *args, **kwargs) -> 'void' setVerbose(self, *args, **kwargs) -> 'void' showAllRestraints(self, *args, **kwargs) -> 'bool const' showRestraints(self, *args, **kwargs) -> 'String' showViolations(self, *args, **kwargs) -> 'String' simulation(self, *args) -> 'EnsembleSimulationBase const *' slope(self, *args, **kwargs) -> 'float_type const' threshold(self, *args, **kwargs) -> 'float_type const' unRegister(self, *args, **kwargs) -> 'void' updateDelta(self, *args, **kwargs) -> 'void' updateEnsWeights(self, *args, **kwargs) -> 'void' updateNeighborList(self, *args, **kwargs) -> 'void' updateValues(self, *args, **kwargs) -> 'void' useSimEnsWeights(self, *args, **kwargs) -> 'bool const' verbose(self, *args, **kwargs) -> 'bool const' violations(self, *args, **kwargs) -> 'float_type' Static methods defined here: __swig_destroy__ = delete_NBTargetPot(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) ave_calcd   ave_obs   corr   denom   instanceDataCleanup   instanceDataCreate   instanceData_   modified   neighbors   num   registeredSimulations   restraints_   sumObs2   thisown   The membership flag

Functions
		NBTargetPot(*args) pyXplorHelp(*args) -> 'String'