Python: module shapePot

shapePot

Shape Potential term This term includes potential terms to constrain the shape tensor of a atom selection. The shape tensor is defined as ( y_i^2+z_i^2 -x_i*y_i -x_i*z_i ) ( -x_i*y_i x_i^2+z_i^2 -y_i*z_i ) ( -x_i*z_i -y_i*z_i x_i^2+y_i^2 ) where (x_i,y_i,z_i) is the position of atom i relative to the center of the atom selection. Thus, the shape tensor is analogous to the inertia tensor: only it contains no mass information. There are separate potential terms which target the eigen values of this tensor (which correspond to size), and the eigenvectors of the tensor, which contain orientational information. Constructor: ShapePot(name, sel, sim) with arguments: name - a name for this potential term sel - (optional) an atomSel.AtomSel. Defaults to all atoms sim - (optional) a simulation.Simulation Object. Defaults to simulation.currentSimulation. Methods: calcEnergy() - calcs energy calcEnergyAndDerivs(DerivList) - calcs energy and derivative info note that these routines also update all other potential-specific data. 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: sizeScale - scale factor for the size term orientScale - scale factor for the orientation term targetSel - atom selection for target. Used if targetType=='molecule' sizeTol - error in size term. Used if sizePotType=='square' orientTol - error (in degrees) in orient term. Used if orientPotType=='square' targetType - specifies the target tensor 'molecule' : target specified by targetSel 'average' : target is the ensemble average of the shape tensor. 'pairwise' : the pairwise difference of the shape tensor between each ensemble member is minimized. sizePotType - potential type for size term: 'harmonic' or 'square' orientPotType - potential type for orient term: 'harmonic' or 'square' degenerateTol - if the difference between eigenvalues drops below this number, eigenvalue/eigenvector pairs are sorted such that the eigenvector overlap with the target is maximized, instead of by eigenvalue. useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights or to use those of the underlying EnsembleSimulation. Read-only accessors simulation() - simulation used by this shape term. Is an EnsembleSimulation atomSel() - atom selection defining the shape tensor. qCenter(index) - center of the atomSelection for ensemble given by index. qCenterTarget()- center position of the target selection. rotation(index)- rotation angle (in degrees) of shape tensor to target. The optional argument specifies the ensemble member (defaults to the current ensemble). getContrib(index,i) - get EigenPair for ensemble member index, number i. getTarget(i) - get EigenPair target shape tensor. EigenPair objects contain two members: value, vector info() - return string synopsis of potential info. showValues() - return pretty-printed eigenvalue info. showVectors() - return pretty-printed eigenvector info. The potential term is defined as E = sizeScale * ( V(ds_x,sizeTol) + V(ds_y,sizeTol) + V(ds_z,sizeTol) ) + orientScale * V(dTheta,orienTol) where ds_i = eigenValue(i) - target_eigenValue(i) dTheta = overall rotation of shapeTensor, relative to target and V(x,tol) = x^2 if potType=='harmonic' (abs(x)-tol)^2 if potType=='square' # 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

ShapePot_LetterClass

Modified

ModifiedBase

ShapePot

ShapePot_EigenPair

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 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'

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 ShapePot_EigenPair(builtins.object)

ShapePot_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_ShapePot_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 ShapePot_LetterClass(EnsemblePot)

ShapePot_LetterClass(*args, **kwargs)

Method resolution order:: ShapePot_LetterClass; EnsemblePot; builtins.object

Methods defined here:

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

__repr__ = _swig_repr(self)

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

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

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

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

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

energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type'

getContrib(self, *args, **kwargs) -> 'ShapePot_EigenPair'

getTarget(self, *args, **kwargs) -> 'ShapePot_EigenPair'

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

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

orientPotType(self, *args, **kwargs) -> 'ShapePot::ShapePotType'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

sizePotType(self, *args, **kwargs) -> 'ShapePot::ShapePotType'

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

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

targetSel(self, *args, **kwargs) -> 'AtomSel const'

targetType(self, *args, **kwargs) -> 'ShapePot::ShapeTargetType'

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

Static methods defined here:

__swig_destroy__ = delete_ShapePot_LetterClass(...)

Data descriptors defined here:

contrib

cosTheta

qc

qc_target

theta

thisown: The membership flag

valuesVectors

Data and other attributes defined here:

AverageTarget = 1

FixedTarget = 3

HARMONIC = 0

MoleculeTarget = 2

PairwiseTarget = 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'

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'

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 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

realShapePot = class ShapePot(builtins.object)

realShapePot(*args)

Methods defined here:

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

__init__(self, *args)

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

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

__repr__ = _swig_repr(self)

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

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

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'

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

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'

getContrib(self, *args, **kwargs) -> 'ShapePot_EigenPair'

getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &'

getTarget(self, *args, **kwargs) -> 'ShapePot_EigenPair'

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'

orientPotType(self, *args, **kwargs) -> 'ShapePot::ShapePotType'

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

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

potName(self, *args, **kwargs) -> 'char const *'

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

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

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

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'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

sizePotType(self, *args, **kwargs) -> 'ShapePot::ShapePotType'

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

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

targetSel(self, *args, **kwargs) -> 'AtomSel const'

targetType(self, *args, **kwargs) -> 'ShapePot::ShapeTargetType'

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'

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

Static methods defined here:

__swig_destroy__ = delete_ShapePot(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

contrib

cosTheta

instanceDataCleanup

instanceDataCreate

instanceData_

modified

qc

qc_target

registeredSimulations

theta

thisown: The membership flag

valuesVectors

Functions

ShapePot(*args)

pyXplorHelp(*args) -> 'String'