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Pydoc: module tagPairPot

tagPairPot

index

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. removeTagAtoms1(sel) - remove the atoms in atomSel1 in all restraints as specified in the atomSel.AtomSel sel argument. removeTagAtoms2(sel) - remove the atoms in atomSel2 in all restraints as specified in the atomSel.AtomSel sel argument. 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. iWeights1()/setIWeights1(val) - return/set the intrinsic weights of iWeights2()/setIWeights2(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

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)

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 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 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'

removeTagAtoms1(self, *args, **kwargs) -> 'void'

removeTagAtoms2(self, *args, **kwargs) -> 'void'

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'

iWeights1(self, *args, **kwargs) -> 'CDSVector< float_type >'

iWeights2(self, *args, **kwargs) -> 'CDSVector< float_type >'

pairDist(self, *args, **kwargs) -> 'PairDist &'

rVals(self, *args, **kwargs) -> 'CDSVector< float_type > const &'

scale(self, *args, **kwargs) -> 'float_type const'

setIWeights1(self, *args, **kwargs) -> 'void'

setIWeights2(self, *args, **kwargs) -> 'void'

setScale(self, *args, **kwargs) -> 'void'

tagPairDist(self, *args, **kwargs) -> 'TagPairDist &'

updateDistanceWeights(self, *args, **kwargs) -> 'void'

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'

iWeights1(self, *args, **kwargs) -> 'CDSVector< float_type >'

iWeights2(self, *args, **kwargs) -> 'CDSVector< float_type >'

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'

setIWeights1(self, *args, **kwargs) -> 'void'

setIWeights2(self, *args, **kwargs) -> 'void'

setName(self, *args, **kwargs) -> 'void'

setScale(self, *args, **kwargs) -> 'void'

tagPairDist(self, *args, **kwargs) -> 'TagPairDist &'

updateDistanceWeights(self, *args, **kwargs) -> 'void'

violated(self, *args, **kwargs) -> 'bool'

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, **kwargs)

Methods defined here:

__deref__(self, *args, **kwargs) -> 'TagPairPot *'

__init__(self, *args, **kwargs)

__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'

removeTagAtoms1(self, *args, **kwargs) -> 'void'

removeTagAtoms2(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

TagPairPot(*args, **kwargs)

pyXplorHelp(*args) -> 'String'