tagPairPot
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/tagPairPot.py

TagPairPot is an energy term consisting of restraints to one or more
target distance distributions corresponding to distances between two tags
represented by weighted sidechain rotamers.
 
 One normally creates TagPairPot objects using the create_TagPairPot
 function within the tagPairPotTools module.
 
 
Constructor:   
 
    tagPairPot(instanceName,
               nonTagSel)
  
  instanceName is a user-specified identifier. The nonTagSel argument
  is a string or atomSel.AtomSel object specifying atoms which are
  not paramagnetic tags, but which should be considered in the computation
  of tag weight due to overlap.
 
methods:
 
  calcEnergy()                 - calc energy, returns the energy value-
                                 the scaled sum of restraint energies.
  calcEnergyAndDerivs(derivs)  - calc energy, derivs, returns the energy value.
  numRestraints()              - return the number of restraints defined for
                                 this term.
  clearRestraints()            - remove all restraints.
  restraints()                 - return a sequence of restraints. See the
                                 description of the Restraint class below.
                                 Restraint properties can thus be modified.
 
  violations()      - return number of violations
  simulation()      - return the associated simulation.Simulation.
  nonTagSelection() - return atomSel.AtomSel corresponding to the
                      nonTagSel argument given when the object was created.
  tagEnv()          - return the associated tagPairDist.TagEnvironment
                      object.
  
  addRestraint(rVals,      - add one restraint with distance and target
               atomSel1,     P(r) specified in the rVals and PrObs         
               atomSel2,     arrays, respectively. The pair of tags giving 
               weight1,      rise to this trace is given by atomSel1 and   
               weight2,      atomSel2 as strings or atomSel.AtomSel 
               PrObs,        objects. Arrays weight1 and weight2 specify 
               comment="")   rotamer intrinsic weights for each selection in 
                             atomSel1 and atomSel2, resepectively, and must 
                             be of the appropriate length. An optional
                             comment may be specified.
 
accessors:
 
 The quantities below may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
   targetType - specifies one of "correlation" or "difference", and
                controls the form of the energy function. ["correlation"]
   verbose    - boolean controlling verbose output. [False]
   aWeights1  - these specify optional aWeights.AWeights objects
   aWeights2    used to vary and optimize the per-rotamer intrinsic weights
                used for all restraints. If these are not set, then rotamer
                weights are not varied.
   scale      - energy scale factor (force constant) applied to all
                restraints [1].
 
 
 
The Restraint class - returned by TagPairPot's restraints() method
 
Members:
 
 pot         - the associated instance of DEERPot
 comment     - return comment given in DEERPot.addRestraint(), if any.
 
Accessors:
 
 The quantities below may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
  scale()        - per-restraint energy scale. [1]
 
Methods:
 
  PrObs()        - the target value of Pr(r), specified at construction time.
 
  correlation()  - the correlation between observed and computed Pr(r);
                   corr = \sum_i (Pr_i - avePr) x (PrObs_i - avePrObs) /
                          [\sum_i (Pr_i-avePr)^2 \sum_i (PrObs_i-avePrObs)^2]
  energy()       - return restraint energy. For targetType="correlation", this
                   is 
                      E = scale * (1.0 - corr)
                   For targetType="difference"
                      E = 0.5 * scale * \sum_i (Pr_i-PrObs_i)^2
 
  tagPairDist()  - return the associated tagPairDist.TagPairDist
                   object describing the distance distribution arising from
                   the pair of tag ensembles.
 
       Associated short-cut methods, returning methods from tagPairDist():
         rVals()       - return the r,Pr values associated with
         Pr()          - the distance probability distribution computed from
                         atomic coordinates.
         weights1()/setWeights1(val) - return/set the intrinsic weights of 
         weights2()/setWeights2(val) - each rotamer in the two tags.
         pairDist()                  - return tagPairDist's
                                       pairDist.PairDist object.
 
 
 
 
# 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_TagPair_Restraint
Modified
ModifiedBase
Restraint_TagPairPot
TagPair_Restraint
TagEnvironment
TagPairDist
TagPairPot
TagPairPot_LetterClass
rc_ptr_TagPair_Restraint

 
class CDSList_TagPair_Restraint(builtins.object)
    CDSList_TagPair_Restraint(*args)
 

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< TagPair_Restraint > >'
__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< TagPair_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_TagPair_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 Modified(builtins.object)
    Modified(*args, **kwargs)
 

 
  Methods defined here:
__call__(self, *args, **kwargs) -> 'int'
Call self as a function.
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
clear(self, *args, **kwargs) -> 'void'
set(self, *args, **kwargs) -> 'void'
update(self, *args, **kwargs) -> 'void'
value(self, *args, **kwargs) -> 'int'

Static methods defined here:
__swig_destroy__ = delete_Modified(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

Data and other attributes defined here:
MOD_SELF = 1
MOD_SIMULATION = 2

 
class ModifiedBase(builtins.object)
    ModifiedBase(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
registerTo(self, *args, **kwargs) -> 'void'
unRegister(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_ModifiedBase(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
class Restraint_TagPairPot(builtins.object)
    Restraint_TagPairPot(*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_TagPairPot(...)

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 TagEnvironment(builtins.object)
    TagEnvironment(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
absoluteWeights(self, *args, **kwargs) -> 'bool const'
addTagAtoms(self, *args, **kwargs) -> 'void'
deltaR(self, *args, **kwargs) -> 'float_type const'
distanceSigmoidWidth(self, *args, **kwargs) -> 'float_type const'
maxR(self, *args, **kwargs) -> 'float_type const'
maxRadius(self, *args, **kwargs) -> 'float_type'
maybeUpdateNeighborList(self, *args, **kwargs) -> 'void'
minR(self, *args, **kwargs) -> 'float_type const'
moveTol(self, *args, **kwargs) -> 'float_type const'
nonTagSelection(self, *args, **kwargs) -> 'AtomSel const &'
numClosestAtoms(self, *args, **kwargs) -> 'int const'
printNeighborList(self, *args, **kwargs) -> 'void'
rValues(self, *args, **kwargs) -> 'CDSVector< float_type >'
resize(self, *args, **kwargs) -> 'void'
setAbsoluteWeights(self, *args, **kwargs) -> 'void'
setDeltaR(self, *args, **kwargs) -> 'void'
setDistanceSigmoidWidth(self, *args, **kwargs) -> 'void'
setMaxR(self, *args, **kwargs) -> 'void'
setMinR(self, *args, **kwargs) -> 'void'
setMoveTol(self, *args, **kwargs) -> 'void'
setNumClosestAtoms(self, *args, **kwargs) -> 'void'
setRadii(self, *args, **kwargs) -> 'void'
setTagRadii(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
simulation(self, *args, **kwargs) -> 'Simulation const *'
updateNeighborList(self, *args, **kwargs) -> 'void'
verbose(self, *args, **kwargs) -> 'bool const'

Static methods defined here:
__swig_destroy__ = delete_TagEnvironment(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
radii

 
thisown

 
The membership flag

 
class TagPairDist(builtins.object)
    TagPairDist(*args, **kwargs)
 

 
  Methods defined here:
Pr(self, *args, **kwargs) -> 'CDSVector< float_type >'
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
atomSel1(self, *args, **kwargs) -> 'AtomSel const &'
atomSel2(self, *args, **kwargs) -> 'AtomSel const &'
distanceWeights1(self, *args, **kwargs) -> 'CDSVector< float_type >'
distanceWeights2(self, *args, **kwargs) -> 'CDSVector< float_type >'
pairDist(self, *args, **kwargs) -> 'PairDist &'
rVals(self, *args, **kwargs) -> 'CDSVector< float_type > const &'
setWeights1(self, *args, **kwargs) -> 'void'
setWeights2(self, *args, **kwargs) -> 'void'
update(self, *args, **kwargs) -> 'void'
updateDistanceWeights(self, *args, **kwargs) -> 'void'
weights1(self, *args, **kwargs) -> 'CDSVector< float_type >'
weights2(self, *args, **kwargs) -> 'CDSVector< float_type >'

Static methods defined here:
__swig_destroy__ = delete_TagPairDist(...)
d_distanceWeight(*args, **kwargs) -> 'float_type'
distanceWeight(*args, **kwargs) -> 'float_type'

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
closestAtomIndices1

 
closestAtomIndices2

 
comment

 
d_dw1

 
d_dw2

 
distanceWeights1_

 
distanceWeights2_

 
sortedDWeights1

 
sortedDWeights2

 
tagRadii1

 
tagRadii2

 
thisown

 
The membership flag
weights1_

 
weights2_

 

 
class TagPairPot_LetterClass(builtins.object)
    TagPairPot_LetterClass(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
aWeights1(self, *args, **kwargs) -> 'AWeights *'
aWeights2(self, *args, **kwargs) -> 'AWeights *'
addRestraint(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcWeightDerivs(self, *args, **kwargs) -> 'float_type'
clearRestraints(self, *args, **kwargs) -> 'void'
nonTagSelection(self, *args, **kwargs) -> 'AtomSel const &'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< TagPair_Restraint > >'
rms(self, *args, **kwargs) -> 'float_type'
setAWeights1(self, *args, **kwargs) -> 'void'
setAWeights2(self, *args, **kwargs) -> 'void'
setTargetType(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
simulation(self, *args, **kwargs) -> 'Simulation const *'
tagEnv(self, *args, **kwargs) -> 'TagEnvironment &'
targetType(self, *args, **kwargs) -> 'TagPairPot::TagPairTargetType const'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_TagPairPot_LetterClass(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
d_dw1

 
d_dw2

 
thisown

 
The membership flag

Data and other attributes defined here:
CORRELATION = 0
DIFFERENCE = 1

 
class TagPair_Restraint(Restraint_TagPairPot)
    TagPair_Restraint(*args)
 

 
 
Method resolution order:
TagPair_Restraint
Restraint_TagPairPot
builtins.object

Methods defined here:
Pr(self, *args, **kwargs) -> 'CDSVector< float_type >'
PrObs(self, *args, **kwargs) -> 'CDSVector< float_type >'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcWeightDerivs(self, *args, **kwargs) -> 'float_type'
correlation(self, *args, **kwargs) -> 'float_type'
energy(self, *args, **kwargs) -> 'float_type'
energyAndDerivs(self, *args, **kwargs) -> 'float_type'
pairDist(self, *args, **kwargs) -> 'PairDist &'
rVals(self, *args, **kwargs) -> 'CDSVector< float_type > const &'
scale(self, *args, **kwargs) -> 'float_type const'
setScale(self, *args, **kwargs) -> 'void'
setWeights1(self, *args, **kwargs) -> 'void'
setWeights2(self, *args, **kwargs) -> 'void'
tagPairDist(self, *args, **kwargs) -> 'TagPairDist &'
updateDistanceWeights(self, *args, **kwargs) -> 'void'
weights1(self, *args, **kwargs) -> 'CDSVector< float_type >'
weights2(self, *args, **kwargs) -> 'CDSVector< float_type >'

Static methods defined here:
__swig_destroy__ = delete_TagPair_Restraint(...)

Data descriptors defined here:
PrObs_

 
ave_Pr

 
ave_PrObs

 
comment

 
d_dw1

 
d_dw2

 
denom

 
num

 
sum_PrObs2

 
thisown

 
The membership flag

Methods inherited from Restraint_TagPairPot:
diff(self, *args, **kwargs) -> 'float_type'
name(self, *args, **kwargs) -> 'String const'
setName(self, *args, **kwargs) -> 'void'
violated(self, *args, **kwargs) -> 'bool'

Data descriptors inherited from Restraint_TagPairPot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)

 
class rc_ptr_TagPair_Restraint(builtins.object)
    rc_ptr_TagPair_Restraint(*args)
 

 
  Methods defined here:
Pr(self, *args, **kwargs) -> 'CDSVector< float_type >'
PrObs(self, *args, **kwargs) -> 'CDSVector< float_type >'
__deref__(self, *args, **kwargs) -> 'TagPair_Restraint *'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ref__(self, *args, **kwargs) -> 'TagPair_Restraint &'
__repr__ = _swig_repr(self)
calcWeightDerivs(self, *args, **kwargs) -> 'float_type'
correlation(self, *args, **kwargs) -> 'float_type'
count(self, *args, **kwargs) -> 'int'
decr(self, *args, **kwargs) -> 'void'
diff(self, *args, **kwargs) -> 'float_type'
energy(self, *args, **kwargs) -> 'float_type'
energyAndDerivs(self, *args, **kwargs) -> 'float_type'
forceDelete(self, *args, **kwargs) -> 'void'
incr(self, *args, **kwargs) -> 'void'
name(self, *args, **kwargs) -> 'String const'
pairDist(self, *args, **kwargs) -> 'PairDist &'
ptr(self, *args, **kwargs) -> 'TagPair_Restraint *'
rVals(self, *args, **kwargs) -> 'CDSVector< float_type > const &'
release(self, *args, **kwargs) -> 'TagPair_Restraint *'
reset(self, *args, **kwargs) -> 'void'
scale(self, *args, **kwargs) -> 'float_type const'
setName(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setWeights1(self, *args, **kwargs) -> 'void'
setWeights2(self, *args, **kwargs) -> 'void'
tagPairDist(self, *args, **kwargs) -> 'TagPairDist &'
updateDistanceWeights(self, *args, **kwargs) -> 'void'
violated(self, *args, **kwargs) -> 'bool'
weights1(self, *args, **kwargs) -> 'CDSVector< float_type >'
weights2(self, *args, **kwargs) -> 'CDSVector< float_type >'

Static methods defined here:
__swig_destroy__ = delete_rc_ptr_TagPair_Restraint(...)

Data descriptors defined here:
PrObs_

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
ave_Pr

 
ave_PrObs

 
comment

 
d_dw1

 
d_dw2

 
denom

 
num

 
sum_PrObs2

 
thisown

 
The membership flag

 
realTagPairPot = class TagPairPot(builtins.object)
    realTagPairPot(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'TagPairPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'TagPairPot &'
__repr__ = _swig_repr(self)
aWeights1(self, *args, **kwargs) -> 'AWeights *'
aWeights2(self, *args, **kwargs) -> 'AWeights *'
addRestraint(self, *args, **kwargs) -> 'void'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
calcWeightDerivs(self, *args, **kwargs) -> 'float_type'
clearRestraints(self, *args, **kwargs) -> 'void'
decrRefCnt(self, *args, **kwargs) -> 'void'
incrRefCnt(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
nonTagSelection(self, *args, **kwargs) -> 'AtomSel const &'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char 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< TagPair_Restraint > >'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setAWeights1(self, *args, **kwargs) -> 'void'
setAWeights2(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setTargetType(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
simulation(self, *args, **kwargs) -> 'Simulation const *'
tagEnv(self, *args, **kwargs) -> 'TagEnvironment &'
targetType(self, *args, **kwargs) -> 'TagPairPot::TagPairTargetType const'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_TagPairPot(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
d_dw1

 
d_dw2

 
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
Functions
       
TagPairDist_d_distanceWeight(*args, **kwargs) -> 'float_type'
TagPairDist_distanceWeight(*args, **kwargs) -> 'float_type'
TagPairPot(*args)
pyXplorHelp(*args) -> 'String'