mordred.Autocorrelation module

class mordred.Autocorrelation.ATS(order=0, prop='m')[source]

Bases: 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:
Returns:

NaN when any properties are NaN

since = <Version('1.0.0')>
property config
description()
explicit_hydrogens = True
classmethod from_json(obj)

Create Descriptor instance from json dict.

Parameters:

obj (dict) – descriptor dict

Returns:

descriptor

Return type:

Descriptor

get_3D_mol()
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')[source]

Bases: 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

since = <Version('1.0.0')>
property config
description()
explicit_hydrogens = True
classmethod from_json(obj)

Create Descriptor instance from json dict.

Parameters:

obj (dict) – descriptor dict

Returns:

descriptor

Return type:

Descriptor

get_3D_mol()
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')[source]

Bases: 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

since = <Version('1.0.0')>
property config
description()
explicit_hydrogens = True
classmethod from_json(obj)

Create Descriptor instance from json dict.

Parameters:

obj (dict) – descriptor dict

Returns:

descriptor

Return type:

Descriptor

get_3D_mol()
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')[source]

Bases: 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

since = <Version('1.0.0')>
property config
description()
explicit_hydrogens = True
classmethod from_json(obj)

Create Descriptor instance from json dict.

Parameters:

obj (dict) – descriptor dict

Returns:

descriptor

Return type:

Descriptor

get_3D_mol()
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')[source]

Bases: 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

since = <Version('1.0.0')>
property config
description()
explicit_hydrogens = True
classmethod from_json(obj)

Create Descriptor instance from json dict.

Parameters:

obj (dict) – descriptor dict

Returns:

descriptor

Return type:

Descriptor

get_3D_mol()
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')[source]

Bases: MATS

Geary coefficient descriptor.

Parameters:

see ATS

Returns:

NaN when

  • \(\Delta_k = 0\)

  • any properties are NaN

  • denominator = 0

since = <Version('1.0.0')>
property config
description()
explicit_hydrogens = True
classmethod from_json(obj)

Create Descriptor instance from json dict.

Parameters:

obj (dict) – descriptor dict

Returns:

descriptor

Return type:

Descriptor

get_3D_mol()
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