mordred.Autocorrelation module¶
-
class
mordred.Autocorrelation.
ATS
(order=0, prop='m')[source]¶ 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
-
since
= StrictVersion ('1.0')¶
-
config
¶
-
description
()¶
-
explicit_hydrogens
= True¶
-
classmethod
from_json
(obj)¶ Create Descriptor instance from json dict.
- Parameters
obj (dict) – descriptor dict
- Returns
descriptor
- Return type
-
get_3D_mol
()¶
-
get_parameter_dict
()¶
-
kekulize
= False¶
-
parameter_names
= ('order', 'prop')¶
-
require_3D
= False¶
-
require_connected
= False¶
-
rtype
¶ alias of
builtins.float
-
class
mordred.Autocorrelation.
AATS
(order=0, prop='m')[source]¶ 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
-
since
= StrictVersion ('1.0')¶
-
config
¶
-
description
()¶
-
explicit_hydrogens
= True¶
-
classmethod
from_json
(obj)¶ Create Descriptor instance from json dict.
- Parameters
obj (dict) – descriptor dict
- Returns
descriptor
- Return type
-
get_3D_mol
()¶
-
get_parameter_dict
()¶
-
kekulize
= False¶
-
parameter_names
= ('order', 'prop')¶
-
require_3D
= False¶
-
require_connected
= False¶
-
rtype
¶ alias of
builtins.float
-
class
mordred.Autocorrelation.
ATSC
(order=0, prop='m')[source]¶ 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
-
since
= StrictVersion ('1.0')¶
-
config
¶
-
description
()¶
-
explicit_hydrogens
= True¶
-
classmethod
from_json
(obj)¶ Create Descriptor instance from json dict.
- Parameters
obj (dict) – descriptor dict
- Returns
descriptor
- Return type
-
get_3D_mol
()¶
-
get_parameter_dict
()¶
-
kekulize
= False¶
-
parameter_names
= ('order', 'prop')¶
-
require_3D
= False¶
-
require_connected
= False¶
-
rtype
¶ alias of
builtins.float
-
class
mordred.Autocorrelation.
AATSC
(order=0, prop='m')[source]¶ 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
-
since
= StrictVersion ('1.0')¶
-
config
¶
-
description
()¶
-
explicit_hydrogens
= True¶
-
classmethod
from_json
(obj)¶ Create Descriptor instance from json dict.
- Parameters
obj (dict) – descriptor dict
- Returns
descriptor
- Return type
-
get_3D_mol
()¶
-
get_parameter_dict
()¶
-
kekulize
= False¶
-
parameter_names
= ('order', 'prop')¶
-
require_3D
= False¶
-
require_connected
= False¶
-
rtype
¶ alias of
builtins.float
-
class
mordred.Autocorrelation.
MATS
(order=0, prop='m')[source]¶ 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
-
since
= StrictVersion ('1.0')¶
-
config
¶
-
description
()¶
-
explicit_hydrogens
= True¶
-
classmethod
from_json
(obj)¶ Create Descriptor instance from json dict.
- Parameters
obj (dict) – descriptor dict
- Returns
descriptor
- Return type
-
get_3D_mol
()¶
-
get_parameter_dict
()¶
-
kekulize
= False¶
-
parameter_names
= ('order', 'prop')¶
-
require_3D
= False¶
-
require_connected
= False¶
-
rtype
¶ alias of
builtins.float
-
class
mordred.Autocorrelation.
GATS
(order=0, prop='m')[source]¶ Bases:
mordred.Autocorrelation.MATS
Geary coefficient descriptor.
- Parameters
see
ATS
- Returns
NaN when
\(\Delta_k = 0\)
any properties are NaN
denominator = 0
-
since
= StrictVersion ('1.0')¶
-
config
¶
-
description
()¶
-
explicit_hydrogens
= True¶
-
classmethod
from_json
(obj)¶ Create Descriptor instance from json dict.
- Parameters
obj (dict) – descriptor dict
- Returns
descriptor
- Return type
-
get_3D_mol
()¶
-
get_parameter_dict
()¶
-
kekulize
= False¶
-
parameter_names
= ('order', 'prop')¶
-
require_3D
= False¶
-
require_connected
= False¶
-
rtype
¶ alias of
builtins.float