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Pydoc: module pairDist

pairDist

index

Class to generate a pairwise distance distribution and the associated gradients with respect to atomic coordinates. Constructor: PairDist(rVals, atomSel1, atomSel2, weights1, weights2, probWidth=0.5, probType="quartic", calcGradient=False) rVals - an array containing a uniform grid of distance values atomSel1, atomSel2 - atomSel.AtomSel objects containing the atoms whose positions are sed to generate the distance distribution. weights1, weights2 - arrays specifying weights for atoms in atomSel1 and and atomSel2, repsectively. probWidth - the width of the probability distribution contribution from a single pair of atoms. probType - a string describing the type of probability distribution. Currently, only "quartic" is accepted. calcGradient - specifies whether the gradient is calculated. Members: Accessors: weights1() weights2() - return/set weights. If normalize==True, setWeights1/2 will normalize input weights. probWidth - probWidth, as specified in the constructor. probType - as specified in the constructor. calcGradient - a specified in the constructor. calcWeightDerivs - calculate derivative of Pr with respect to weights1 and weights2, If True, the values are stored in the members d_dw1 and d_dw2, respectively. These are two- dimensional arrays with the first dimension denoting the atom specified in the respective atomSel, and the second specifying bin number. normalize - by default, the probability distribution is normalized by the product of the sums of the two weights arrays. Set normalize to False to disable this normalization. Methods: updateValues() - force a recalculation of the P(r) (and gradient, if the current value of calcGradient is True). Pr() - return an array containing the pairwise distance distribution the distance at the center of each bin corresponding to the associated value of rVals. Computed as <string>

Pr(r) = 1 ⁄ N∑_i, jw_iw_jPr_i, j(|q_i − q_j| − r) where the sum is over two sets of atoms with positions q_i and q_j, and associated weights w_i and w_j.

/ N_P (r^2 - r_c^2)^2 , for r<r_c Pr_{i,j}(r) = | \ 0 , for r>=r_c <string> where r_c is the probWidth member value, and N_P = 105 ⁄ (32πr⁷_c) The value N = 1 ⁄ (Δr∑_iw_i∑_jw_j), where Δr is the grid spacing of rVals, unless normalize=False, in which case N = 1 ⁄ Δr. getGradient(binNum) - return a list of (index,Vec3) pairs specifying all of the gradient contributions to binNum of the distance distribution. removeAtoms1(sel) - remove the atoms from the PairDist - specified by an removeAtoms2(sel) atomSel.AtomSel argument, along the the associated weight(s). # 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_IntVec3Pair

CDSVectorBase_Vector_float_long

CDSVector_Vector_float_0_long_int

PairDist

class CDSList_IntVec3Pair(builtins.object)

CDSList_IntVec3Pair(*args)

Methods defined here:

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

__getitem__(self, *args) -> 'CDSList< Pair< int,Vec3 > >'

__getslice__(self, *args, **kwargs) -> 'CDSList< Pair< int,Vec3 > >'

__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_IntVec3Pair(...)

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 CDSVectorBase_Vector_float_long(builtins.object)

CDSVectorBase_Vector_float_long(*args)

Methods defined here:

__call__(self, *args, **kwargs) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int > const &': Call self as a function.

__iadd__(self, *args) -> 'CDSVectorBase< CDSVector< double,0,CDS::DefaultAlloc,long,int >,CDS::DefaultAlloc,long > &'

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

__isub__(self, *args) -> 'CDSVectorBase< CDSVector< double,0,CDS::DefaultAlloc,long,int >,CDS::DefaultAlloc,long > &'

__repr__ = _swig_repr(self)

copy(self, *args) -> 'CDSVectorBase< CDSVector< double,0,CDS::DefaultAlloc,long,int >,CDS::DefaultAlloc,long > &'

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

data(self, *args) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int > const &'

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

pointer(self, *args) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int > *'

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

resize(self, *args, **kwargs) -> 'CDSVectorBase< CDSVector< double,0,CDS::DefaultAlloc,long,int >,CDS::DefaultAlloc,long > &'

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

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

size(self, *args, **kwargs) -> 'long'

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

Static methods defined here:

__swig_destroy__ = delete_CDSVectorBase_Vector_float_long(...)

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

CDSVector_Vector_float = class CDSVector_Vector_float_0_long_int(CDSVectorBase_Vector_float_long)

CDSVector_Vector_float(*args)

Method resolution order:: CDSVector_Vector_float_0_long_int; CDSVectorBase_Vector_float_long; builtins.object

Methods defined here:

__add__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__call__(self, *args) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int > const &': Call self as a function.

__getitem__(self, *args, **kwargs)

__getslice__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__iadd__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__imul__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

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

__isub__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__itruediv__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__len__(self, *args, **kwargs) -> 'long'

__mul__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__neg__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__pow__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__radd__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__repr__ = _swig_repr(self)

__rmul__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__rsub__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__rtruediv__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

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

__str__(self, *args, **kwargs) -> 'String': Return str(self).

__sub__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__truediv__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

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

fromList(s, l)

get(self, *args, **kwargs) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int >'

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

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

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

toList(self, *args, **kwargs) -> 'PyObject *'

Static methods defined here:

__swig_destroy__ = delete_CDSVector_Vector_float_0_long_int(...)

Data descriptors defined here:

thisown: The membership flag

Methods inherited from CDSVectorBase_Vector_float_long:

copy(self, *args) -> 'CDSVectorBase< CDSVector< double,0,CDS::DefaultAlloc,long,int >,CDS::DefaultAlloc,long > &'

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

data(self, *args) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int > const &'

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

pointer(self, *args) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int > *'

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

resize(self, *args, **kwargs) -> 'CDSVectorBase< CDSVector< double,0,CDS::DefaultAlloc,long,int >,CDS::DefaultAlloc,long > &'

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

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

size(self, *args, **kwargs) -> 'long'

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

Data descriptors inherited from CDSVectorBase_Vector_float_long:

__dict__: dictionary for instance variables (if defined)

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

class CDSVector_Vector_float_0_long_int(CDSVectorBase_Vector_float_long)

CDSVector_Vector_float_0_long_int(*args)

Method resolution order:: CDSVector_Vector_float_0_long_int; CDSVectorBase_Vector_float_long; builtins.object

Methods defined here:

__add__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__call__(self, *args) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int > const &': Call self as a function.

__getitem__(self, *args, **kwargs)

__getslice__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__iadd__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__imul__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

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

__isub__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__itruediv__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__len__(self, *args, **kwargs) -> 'long'

__mul__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__neg__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__pow__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__radd__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__repr__ = _swig_repr(self)

__rmul__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__rsub__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__rtruediv__(self, *args, **kwargs) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

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

__str__(self, *args, **kwargs) -> 'String': Return str(self).

__sub__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

__truediv__(self, *args) -> 'CDSVector< Vector_float,0,CDS::DefaultAlloc,long,int >'

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

fromList(s, l)

get(self, *args, **kwargs) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int >'

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

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

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

toList(self, *args, **kwargs) -> 'PyObject *'

Static methods defined here:

__swig_destroy__ = delete_CDSVector_Vector_float_0_long_int(...)

Data descriptors defined here:

thisown: The membership flag

Methods inherited from CDSVectorBase_Vector_float_long:

copy(self, *args) -> 'CDSVectorBase< CDSVector< double,0,CDS::DefaultAlloc,long,int >,CDS::DefaultAlloc,long > &'

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

data(self, *args) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int > const &'

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

pointer(self, *args) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int > *'

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

resize(self, *args, **kwargs) -> 'CDSVectorBase< CDSVector< double,0,CDS::DefaultAlloc,long,int >,CDS::DefaultAlloc,long > &'

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

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

size(self, *args, **kwargs) -> 'long'

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

Data descriptors inherited from CDSVectorBase_Vector_float_long:

__dict__: dictionary for instance variables (if defined)

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

class PairDist(builtins.object)

PairDist(*args, **kwargs)

Methods defined here:

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

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

__repr__ = _swig_repr(self)

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

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

getGradient(self, *args, **kwargs) -> 'CDSList< Pair< int,Vec3 > >'

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

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

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

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

removeAtoms1(self, *args, **kwargs) -> 'void'

removeAtoms2(self, *args, **kwargs) -> 'void'

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

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

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

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

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

setWeights1(self, *args, **kwargs) -> 'void'

setWeights2(self, *args, **kwargs) -> 'void'

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

weights1(self, *args, **kwargs) -> 'CDSVector< float_type >'

weights2(self, *args, **kwargs) -> 'CDSVector< float_type >'

Static methods defined here:

__swig_destroy__ = delete_PairDist(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

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

atomSel1

atomSel2

d_dw1

d_dw2

gradient

pairDist

rVals

thisown: The membership flag

Functions

cat(*args, **kwargs) -> 'CDSVector< CDSVector< double,0,CDS::DefaultAlloc,long,int >,0,CDS::DefaultAlloc,long,int >'

cat3(*args, **kwargs) -> 'CDSVector< CDSVector< double,0,CDS::DefaultAlloc,long,int >,0,CDS::DefaultAlloc,long,int >'

cat4(*args, **kwargs) -> 'CDSVector< CDSVector< double,0,CDS::DefaultAlloc,long,int >,0,CDS::DefaultAlloc,long,int >'

max(*args, **kwargs) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int >'

min(*args, **kwargs) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int >'

pyXplorHelp(*args) -> 'String'

sum(*args, **kwargs) -> 'CDSVector< double,0,CDS::DefaultAlloc,long,int >'

Data
		__CDSVector_hh__ = 1