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Python: module gyrPot

gyrPot

Potential term to restrain the volume associated with the gyration tensor. This is used as an alternative to a radius of gyration resrtaint- to allow elongated structures. The target value is set in gyrPotTools.create_GyrPot based on values observed in the PDB. This term can also be used to restrain Rg values, including those due to ensembles. The Rg term can be conveniently set up using gyrPotTools.create_RgyrPot. constructor: GyrPot(instanceName, selection ) instanceName is a user-specified identifier selection is a atomSel.AtomSel object specifying the atoms to include when calculating the gyration tensor. methods calcEnergy() - calc energy, returns the energy value. calcEnergyAndDerivs(derivs) - calc energy, derivs, returns the energy value. rms() - return the magnitude of violation of this term -- abs(diff). scale() - scale factor for this energy term. selection() - return the atom selection specified in the constructor. info() - current info about the state of this instance qc() - The calculated centroid of selection(). gyrTensor() - The calculated gyration tensor. Rg() - The calculated radius of gyration ( sqrt(Tr G) ) volume() - The calculated gyration volume. eigenPairs() - The three principal moments and directions of the gyration tensor. The following parameters can be set [defaults in square brackets] targetType() - "volume" or "radius" volTarget - The target gyration volume. volRange - The +/- range about the target volume about which to evaluate zero energy (see below). rTarget - The target Rg. rRange - The +/- range about the target Rg about which to evaluate zero energy (see below). gyrWeights - a sequence specifying the relative weight to give an ensemble member's Rg. For instance, for a SAXS-derived Rg, the entries are proportional to the number of electrons of a species. For instance, [1,2] would describe a mixture of monomer and dimer. By default it is [1,1]. the above quantities may be retrieved using the member function form quantity(), while they are set using the form setQuantity(value). The gyration tensor is defined as G = 1/N sum_i (q_i - qc ) X (q_i - qc) where N is the number of selected atoms, q_i is atom i's position and qc is the centroid of the selected atoms. The ``X'' denotes outer product. The gyration volume is Vg = 4/3 pi sqrt(det G) The energy function is defined as V = scale * diff^2 where Vg - targetVol - rangeVol if Vg>targetVol+rangeVol diff = targetVol - rangeVol - Vg if Vg<targetVol-rangeVol 0 otherwise For Rg target type, Rg = sqrt( Trace G), and energy is defined as above. For an ensemble, the observed Rg is defined as Rg^2 = \sum_i w_i wg_i RG_i^2 / \sum_j w_j wg_j where w_i are ensemble weights (populations), and wg_i are specified by gyrWeights (see above). Ensemble weight gradient optimization is supported for this term. # 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

EnsemblePot

GyrPot_LetterClass

GyrPot
GyrPot_EigenPair
Modified
ModifiedBase
VarEnsWeights
rc_EnsemblePot

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 GyrPot_EigenPair(builtins.object)

    GyrPot_EigenPair(*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_GyrPot_EigenPair(...)

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

value

vector

class GyrPot_LetterClass(EnsemblePot)

    GyrPot_LetterClass(*args, **kwargs)

Method resolution order:

GyrPot_LetterClass

EnsemblePot

builtins.object

Methods defined here:

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

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

__repr__ = _swig_repr(self)

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

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

gyrTensor(self, *args, **kwargs) -> 'SymMat3'

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

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

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

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

qc(self, *args, **kwargs) -> 'Vec3'

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

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

renamed_eigenPairs(self, *args, **kwargs) -> 'FixedVector< GyrPot_EigenPair,3 >'

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

selection(self, *args, **kwargs) -> 'AtomSel'

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

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

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

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

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

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

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

targetType(self, *args, **kwargs) -> 'GyrPot::GyrTargetType const'

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

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

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

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

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

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

Static methods defined here:

__swig_destroy__ = delete_GyrPot_LetterClass(...)

Data descriptors defined here:

thisown

The membership flag

Data and other attributes defined here:

RADIUS = 0

VOLUME = 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 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 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

realGyrPot = class GyrPot(builtins.object)

    realGyrPot(*args)

Methods defined here:

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

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

__init__(self, *args)

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

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

__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'

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

eigenPairs(self, memberIndex=-1)

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 > &'

gyrTensor(self, *args, **kwargs) -> 'SymMat3'

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

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'

qc(self, *args, **kwargs) -> 'Vec3'

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

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

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

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

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

renamed_eigenPairs(self, *args, **kwargs) -> 'FixedVector< GyrPot_EigenPair,3 >'

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

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

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

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

selection(self, *args, **kwargs) -> 'AtomSel'

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

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

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

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

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

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

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

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

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

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

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

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

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

targetType(self, *args, **kwargs) -> 'GyrPot::GyrTargetType 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'

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

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

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

Static methods defined here:

__swig_destroy__ = delete_GyrPot(...)

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

GyrPot(*args)

pyXplorHelp(*args) -> 'String'

Data

__CDSVector_hh__ = 1