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Python: module ccrPot

ccrPot

ccrPot For Cross-correlation relaxation and RDC correlation potentials. constructor: CCRPot(instanceName, restraints, simulation=None) -instanceName is a user-specified identifier. -restraints is an restraint table (the format is described below) -simulation is an optional simulation.Simulation. It defaults to the current Simulation. methods: addRestraints(string) - add restraints rms() - return the RMSD of calculated - observed. chi2() - return the chi-squared value. correlation() - return the correlation between calculated and observed. calcEnergy() - calc energy, returns the energy value. calcEnergyAndDerivs(derivs) - calc energy, derivs, returns the energy value. deviation() - return average of deviation of ensemble members. This is nonzero only for Ne>1 ensembleSimulations. numRestraints() - return the number of restraints. violations() - return number of violations info() - current info about the state of this instance. showViolations() - return a string listing violated restraints. showRestraints(violated) - return info on restraints. Argument violated is boolean specifying whether to return only violated restraints. restraints() - return a list of restraints. See the description of the Restraint class below. simulation() - return the associated simulation.Simulation. The following members can be read using the method named member() and set using the method setMember(val) [defaults in square brackets] scale - scale factor (force constant) [1] threshold - threshold in violation calculation [0] potType - type of potential: "harmonic", "square", or "correlation" ["harmonic"] verbose - boolean, whether to produce verbose output [False] prefactor - constant prefactor by which to multiply all restraints [1] 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] Assignment Table: The native format for the restraint is assign ( sel x1 ) ( sel x2 ) ( sel y1 ) (sel y2 ) obs err ! optional comment where the x1, x2, y1 and y2 selections specify (single) atoms involved in the interaction. The observed value is given by obs argument. The error bound is given by error argument. Restraint class methods: name() - name of this restraint. energy() - energy due to this restraint calcd() - calculated observable (ensemble average). variance() - measure of spread between different ensemble members. diff() - difference between calcd and obs atomX1() - atoms as specified in the restraint table. atomX2() - atomY1() - atomY2() - bSelection() - atomSel for atom B calced_contrib() - list of contributions due to each ensemble member. deviation() - The following members can be read using member() or set using setMember(). I.e. restraint.setObs( 1.2 ) obs - observed value err - the experimental error. comment - optional comment as specified in the restraint table. The observable is computed as delta = 1/2 * prefactor * ( 3 cosTheta^2 -1 ) where prefactor is specified as above, and cosTheta is cosTheta = dotProd( unitVec( x2-x1 ) , unitVec( y2-y1 ) The energy computation depends on the value of potType: For potType of "harmonic" and "square": E = scale * \sum_i diff_i^2 where / (calc_i - obs_i)/err_i for potType=harmonic diff_i = | (calc_i - obs_i - err) for potType=square calc_i > obs_i + err_i | 0 for potType=square abs(calc_i-obs_i)<err_i \ (calc_i - obs_i + err) for potType=square calc_i < obs_i - err_i For potType of "correlation" E = scale * (1 - correlation) with \sum_i (calcd_i-aveCalcd) * (obs_i-aveObs) correlation = ---------------------------------------------------- sqrt( \sum_i (calcd_i-aveCalcd)^2 * \sum_i (obs_i-aveObs)^2 ) and aveCalcd and aveObs the average over calculdated and experimental values, repspectively. # 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

CCRPot
CDSList_CCR_Restraint
EnsemblePot

CCRPot_LetterClass

Modified
ModifiedBase
Restraint_CCRPot

CCR_Restraint

VarEnsWeights
rc_EnsemblePot
rc_ptr_CCR_Restraint

class CCRPot_LetterClass(EnsemblePot)

    CCRPot_LetterClass(*args, **kwargs)

Method resolution order:

CCRPot_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'

chi2(self, *args, **kwargs) -> 'float_type'

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

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

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

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

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

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

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

potType(self, *args, **kwargs) -> 'CCRPot::CCRPotType'

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

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

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

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

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

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

setShowAllRestraints(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'

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

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

Static methods defined here:

__swig_destroy__ = delete_CCRPot_LetterClass(...)

Data descriptors defined here:

thisown

The membership flag

Data and other attributes defined here:

CORRELATION = 2

HARMONIC = 0

SQUARE = 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'

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 CCR_Restraint(Restraint_CCRPot)

    CCR_Restraint(*args, **kwargs)

Method resolution order:

CCR_Restraint

Restraint_CCRPot

builtins.object

Methods defined here:

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

__repr__ = _swig_repr(self)

atomX1(self, *args, **kwargs) -> 'Atom'

atomX2(self, *args, **kwargs) -> 'Atom'

atomY1(self, *args, **kwargs) -> 'Atom'

atomY2(self, *args, **kwargs) -> 'Atom'

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

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

comment(self, *args, **kwargs) -> 'String const'

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

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

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

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

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

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

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

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

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_CCR_Restraint(...)

Data descriptors defined here:

contrib

thisown

The membership flag

verbose

Methods inherited from Restraint_CCRPot:

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

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

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

Data descriptors inherited from Restraint_CCRPot:

__dict__

dictionary for instance variables (if defined)

__weakref__

list of weak references to the object (if defined)

class CDSList_CCR_Restraint(builtins.object)

    CDSList_CCR_Restraint(*args)

Methods defined here:

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

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

__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< CCR_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_CCR_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 Restraint_CCRPot(builtins.object)

    Restraint_CCRPot(*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_CCRPot(...)

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_CCR_Restraint(builtins.object)

    rc_ptr_CCR_Restraint(*args)

Methods defined here:

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

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

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

__repr__ = _swig_repr(self)

atomX1(self, *args, **kwargs) -> 'Atom'

atomX2(self, *args, **kwargs) -> 'Atom'

atomY1(self, *args, **kwargs) -> 'Atom'

atomY2(self, *args, **kwargs) -> 'Atom'

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

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

comment(self, *args, **kwargs) -> 'String const'

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'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_rc_ptr_CCR_Restraint(...)

Data descriptors defined here:

__dict__

dictionary for instance variables (if defined)

__weakref__

list of weak references to the object (if defined)

contrib

thisown

The membership flag

verbose

realCCRPot = class CCRPot(builtins.object)

    realCCRPot(*args)

Methods defined here:

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

__init__(self, *args)

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

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

__repr__ = _swig_repr(self)

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

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

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

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

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

chi2(self, *args, **kwargs) -> 'float_type'

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

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

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

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

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 > &'

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 *'

potType(self, *args, **kwargs) -> 'CCRPot::CCRPotType'

prefactor(self, *args, **kwargs) -> 'float_type 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< CCR_Restraint > >'

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

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

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

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

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

setPrefactor(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'

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

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

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

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_CCRPot(...)

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

CCRPot(*args)

pyXplorHelp(*args) -> 'String'