mordred.Autocorrelation module

class mordred.Autocorrelation.ATS(order=0, prop=’m’)

Bases: mordred.Autocorrelation.AutocorrelationBase

Autocorrelation of Topological Structure descriptor.

a.k.a. Moreau-Broto autocorrelation descriptor

\[ \begin{align}\begin{aligned}{\rm ATS}_0 = \sum^{A}_{i=1} {\boldsymbol w}_i^2\\{\rm ATS}_k = \frac{1}{2} \left( {\boldsymbol w}^{\rm T} \cdot {}^k{\boldsymbol B} \cdot {\boldsymbol w} \right)\\\begin{split}{}^k{\boldsymbol B} = \begin{cases} 1 & (d_{ij} = k) \\ 0 & (d_{ij} \neq k) \end{cases}\end{split}\end{aligned}\end{align} \]

where \({\boldsymbol w}\) is atomic property vector, \(d_{ij}\) is graph distance(smallest number of bonds between atom i and j).

Parameters:

• order (int) – order(\(k\))
• property (str, function) – atomic properties

Returns:

NaN when any properties are NaN

explicit_hydrogens = True

from_json(obj)

create Descriptor instance from json dict.

Parameters:obj (dict) – descriptor dict Returns:descriptor Return type:Descriptor

get_parameter_dict()

kekulize = False

parameter_names = (‘order’, ‘prop’)

require_3D = False

require_connected = False

rtype

alias of float

to_json()

convert to json serializable dictionary.

Returns:dictionary of descriptor Return type:dict

class mordred.Autocorrelation.AATS(order=0, prop=’m’)

Bases: mordred.Autocorrelation.ATS

averaged ATS descriptor.

\[{\rm AATS}_k = \frac{{\rm ATS}_k}{\Delta_k}\]

where \(\Delta_k\) is number of vertex pairs at order equal to \(k\).

Parameters:see ATS Returns:NaN when

• \(\Delta_k = 0\)
• some properties are NaN

explicit_hydrogens = True

from_json(obj)

create Descriptor instance from json dict.

Parameters:obj (dict) – descriptor dict Returns:descriptor Return type:Descriptor

get_parameter_dict()

kekulize = False

parameter_names = (‘order’, ‘prop’)

require_3D = False

require_connected = False

rtype

alias of float

to_json()

convert to json serializable dictionary.

Returns:dictionary of descriptor Return type:dict

class mordred.Autocorrelation.ATSC(order=0, prop=’m’)

Bases: mordred.Autocorrelation.AutocorrelationBase

centered ATS descriptor.

ATS with \({\boldsymbol w}_{\rm c}\) property

\[{\boldsymbol w}_{\rm c} = {\boldsymbol w} - \bar{\boldsymbol w}\]

Parameters:see ATS Returns:NaN when any properties are NaN

explicit_hydrogens = True

from_json(obj)

create Descriptor instance from json dict.

Parameters:obj (dict) – descriptor dict Returns:descriptor Return type:Descriptor

get_parameter_dict()

kekulize = False

parameter_names = (‘order’, ‘prop’)

require_3D = False

require_connected = False

rtype

alias of float

to_json()

convert to json serializable dictionary.

Returns:dictionary of descriptor Return type:dict

class mordred.Autocorrelation.AATSC(order=0, prop=’m’)

Bases: mordred.Autocorrelation.ATSC

averaged ATSC descriptor.

\[{\rm AATSC}_k = \frac{{\rm ATSC}_k}{\Delta_k}\]

where \(\Delta_k\) is number of vertex pairs at order equal to \(k\).

Parameters:see ATS Returns:NaN when

• \(\Delta_k = 0\)
• any properties are NaN

explicit_hydrogens = True

from_json(obj)

create Descriptor instance from json dict.

Parameters:obj (dict) – descriptor dict Returns:descriptor Return type:Descriptor

get_parameter_dict()

kekulize = False

parameter_names = (‘order’, ‘prop’)

require_3D = False

require_connected = False

rtype

alias of float

to_json()

convert to json serializable dictionary.

Returns:dictionary of descriptor Return type:dict

class mordred.Autocorrelation.MATS(order=0, prop=’m’)

Bases: mordred.Autocorrelation.AutocorrelationBase

Moran coefficient descriptor.

\[{\rm MATS}_k = \frac{ {\rm AATSC}_k }{ \frac{1}{A} \cdot \sum {\boldsymbol w}_{\rm c}^2 }\]

Parameters:see ATS Returns:NaN when

• some properties are NaN
• denominator = 0

explicit_hydrogens = True

from_json(obj)

create Descriptor instance from json dict.

Parameters:obj (dict) – descriptor dict Returns:descriptor Return type:Descriptor

get_parameter_dict()

kekulize = False

parameter_names = (‘order’, ‘prop’)

require_3D = False

require_connected = False

rtype

alias of float

to_json()

convert to json serializable dictionary.

Returns:dictionary of descriptor Return type:dict

class mordred.Autocorrelation.GATS(order=0, prop=’m’)

Bases: mordred.Autocorrelation.MATS

Geary coefficient descriptor.

Parameters:see ATS Returns:NaN when

• \(\Delta_k = 0\)
• any properties are NaN
• denominator = 0

explicit_hydrogens = True

from_json(obj)

create Descriptor instance from json dict.

Parameters:obj (dict) – descriptor dict Returns:descriptor Return type:Descriptor

get_parameter_dict()

kekulize = False

parameter_names = (‘order’, ‘prop’)

require_3D = False

require_connected = False

rtype

alias of float

to_json()

convert to json serializable dictionary.

Returns:dictionary of descriptor Return type:dict