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Python: module distSymmPot

distSymmPot

Potential term restraining distances expected to be symmetric. This is approximately the same functionality as that of the XPLOR NOE SYMMetry routine. The primary difference is that this term will correctly treat <n ensembleSimulation>.EnsembleSimulation averaging. Constructor: It is suggested that this potential term be created using the helper function distSymmTools.create_DistSymmPot(). DistSymmPot(instanceName, - creates a potential term with the given name. simulation ) The simulation argument is optional- it omitted simulation.defaultSimulation() will be used. Methods: addRestraint(listOfTuples) - list of two-membered tuples of atom selections, each of which specifies a distance which should be restrained. E.g. for a dimer, the list should contain two sets of distances. rms() - returns a measure of RMSD of distance symmetry violation (see below). violations() - returns number of violated distance symmetry restraints numRestraints() - return the number of restraints info() - current info about the state of this instance showViolations() - return string containing pretty-printed info on all violated restraints. restraints() - return a list of restraints. See the description of the Restraint class below. 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 (force constant) for the potential term. ensembleAveType - "none" or "average" - controls whether to enforce symmetry restraints on each ensemble member- or to enforce only overall ensemble symmetry (see below). threshold - amount of violation of restraint greater than which the restraint is considered violated [0.2 angstrom] 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] useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights or to use those of the underlying EnsembleSimulation. the above quantities may be retrieved using the member function form quantity(), while they are set using the form setQuantity(value). class DistSymmPot_Restraint: methods: public: energy() - return current energy name() - restraint name (String) raw members: tol - error tolerance for this restraint distAtom1 - list of lists of atoms. These contain atoms specified by distAtom2 addRestraints. contrib - array containing the contribution to energy from each ensemble member aveDistIntra - ave. dist. within an ensemble member deltaIntra aveDistInter - distance between atom1 in different ensemble members deltaInter1 aveDistInter2 - distance between atom2 in different ensemble members deltaInter2 The potential term is defined as E = scale() * sum_r E_r with E_r being the contribution from each restraint. For ensembleAveType="none", each restraint's energy is a sum over contributions from each ensemble member i: E_r = sum_i w_i ( ca_i + sum_i' w_i' (cr1_ii' + cr2_ii') ), with w_i being the ensemble member's weight, ca_i = < d_i^2 >_j - < d_i >_j^2 (averaged over all distances) with d_ij = |q1_ij - q2_ij| and q1_ij, the position of the atom corresponding to the first selection of the jth entry in the restraint's distAtom1 in ensemble member i. cr1_ii' = < dr1_ii'^2 >_j - < dr1_ii' >_j^2 cr2_ii' = < dr2_ii'^2 >_j - < dr2_ii' >_j^2 with dr1_ii'j = |q1_ij - q2_i'j| for ensembleAveType="average", distances are calculated using ensemble-averaged positions: E_r = ( <d^2>_k - <d>_k^2 - tol ) for <d^2>_k - <d>_k^2 > tol and zero otherwise. The average distance is <d>_k = 1/Nk sum_k |<q1_k>_e - <q2_k>_e| and variance is <d^2>_k = 1/Nk sum_k |<q1_k>_e - <q2_k>_e|^2 where the k-sums are over the restraint's distances, and <>_e denotes ensemble average. The RMSD is calculated as sqrt( sum_r E_r / N_r ) where N_r is the number of restraints. # 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_CDSList_Atom
CDSList_DistSymmPot_Restraint
DistSymmPot
EnsemblePot

DistSymmPot_LetterClass

Modified
ModifiedBase
Restraint_DistSymmPot

DistSymmPot_Restraint

VarEnsWeights
rc_EnsemblePot
rc_ptr_DistSymmPot_Restraint

class CDSList_CDSList_Atom(builtins.object)

    CDSList_CDSList_Atom(*args)

Methods defined here:

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

__getitem__(self, *args) -> 'CDSList< CDSList< Atom,10 > >'

__getslice__(self, *args, **kwargs) -> 'CDSList< CDSList< Atom,10 > >'

__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_CDSList_Atom(...)

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 CDSList_DistSymmPot_Restraint(builtins.object)

    CDSList_DistSymmPot_Restraint(*args)

Methods defined here:

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

__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< DistSymmPot_Restraint > >'

__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< DistSymmPot_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_DistSymmPot_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 DistSymmPot_LetterClass(EnsemblePot)

    DistSymmPot_LetterClass(*args, **kwargs)

Method resolution order:

DistSymmPot_LetterClass

EnsemblePot

builtins.object

Methods defined here:

__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

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

energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type'

energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type'

energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type'

ensembleAveType(self, *args, **kwargs) -> 'DistSymmPot::DistSymmEnsembleAveType'

info(self, *args, **kwargs) -> 'String'

numRestraints(self, *args, **kwargs) -> 'int'

pyXplorHelp(self, *args, **kwargs) -> 'String'

restraints(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< DistSymmPot_Restraint > >'

rms(self, *args, **kwargs) -> 'double'

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

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

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

showAllRestraints(self, *args, **kwargs) -> 'bool const'

showViolations(self, *args, **kwargs) -> 'String'

simulation2(self, *args, **kwargs) -> 'Simulation *'

verbose(self, *args, **kwargs) -> 'bool const'

violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:

__swig_destroy__ = delete_DistSymmPot_LetterClass(...)

Data descriptors defined here:

thisown

The membership flag

Data and other attributes defined here:

AVERAGE = 1

NONE = 0

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'

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 DistSymmPot_Restraint(Restraint_DistSymmPot)

    DistSymmPot_Restraint(*args, **kwargs)

Method resolution order:

DistSymmPot_Restraint

Restraint_DistSymmPot

builtins.object

Methods defined here:

__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

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

energy(self, *args, **kwargs) -> 'double'

name(self, *args, **kwargs) -> 'String'

Static methods defined here:

__swig_destroy__ = delete_DistSymmPot_Restraint(...)

Data descriptors defined here:

aveDistInter1

aveDistInter2

aveDistIntra

contrib

deltaInter1

deltaInter2

deltaIntra

distAtom1

distAtom2

thisown

The membership flag

tol

verbose

Methods inherited from Restraint_DistSymmPot:

diff(self, *args, **kwargs) -> 'float_type'

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

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

Data descriptors inherited from Restraint_DistSymmPot:

__dict__

dictionary for instance variables (if defined)

__weakref__

list of weak references to the object (if defined)

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 Restraint_DistSymmPot(builtins.object)

    Restraint_DistSymmPot(*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_DistSymmPot(...)

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_DistSymmPot_Restraint(builtins.object)

    rc_ptr_DistSymmPot_Restraint(*args)

Methods defined here:

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

__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.

__ref__(self, *args, **kwargs) -> 'DistSymmPot_Restraint &'

__repr__ = _swig_repr(self)

count(self, *args, **kwargs) -> 'int'

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

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

diff(self, *args, **kwargs) -> 'float_type'

energy(self, *args, **kwargs) -> 'double'

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

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

name(self, *args, **kwargs) -> 'String'

ptr(self, *args, **kwargs) -> 'DistSymmPot_Restraint *'

release(self, *args, **kwargs) -> 'DistSymmPot_Restraint *'

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

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

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

Static methods defined here:

__swig_destroy__ = delete_rc_ptr_DistSymmPot_Restraint(...)

Data descriptors defined here:

__dict__

dictionary for instance variables (if defined)

__weakref__

list of weak references to the object (if defined)

aveDistInter1

aveDistInter2

aveDistIntra

contrib

deltaInter1

deltaInter2

deltaIntra

distAtom1

distAtom2

thisown

The membership flag

tol

verbose

realDistSymmPot = class DistSymmPot(builtins.object)

    realDistSymmPot(*args)

Methods defined here:

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

__init__(self, *args)

__oldinit__ = __init__(self, *args, **kwargs)

__ref__(self, *args, **kwargs) -> 'DistSymmPot &'

__repr__ = _swig_repr(self)

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

addRestraint(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'

decrRefCnt(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'

ensembleAveType(self, *args, **kwargs) -> 'DistSymmPot::DistSymmEnsembleAveType'

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 *'

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< DistSymmPot_Restraint > >'

rms(self, *args, **kwargs) -> 'double'

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

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

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

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

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

setShowAllRestraints(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'

showViolations(self, *args, **kwargs) -> 'String'

simulation(self, *args) -> 'EnsembleSimulationBase const *'

simulation2(self, *args, **kwargs) -> 'Simulation *'

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

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

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

updateEnsWeights(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_DistSymmPot(...)

Data descriptors defined here:

__dict__

dictionary for instance variables (if defined)

__weakref__

list of weak references to the object (if defined)

instanceDataCleanup

instanceDataCreate

instanceData_

modified

registeredSimulations

thisown

The membership flag

Functions

DistSymmPot(*args)

pyXplorHelp(*args) -> 'String'