mordred.ExtendedTopochemicalAtom module¶
Extended Topochemical Atom(ETA) descriptor.
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class
mordred.ExtendedTopochemicalAtom.
EtaCoreCount
(averaged=False, reference=False)[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA core count descriptor.
α=A∑i=1Zi−ZviZvi⋅1PNi−1where Zi and Zvi are number of total and valence electons, PN is periodic number.
Parameters: Returns: reference and valence of any atoms > 4
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as_argument
¶ argument representation of descriptor
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coord
¶ get 3D coordinate
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explicit_hydrogens
= False¶
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fail
(exception)¶ raise known exception and return missing value
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kekulize
= True¶
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mol
¶ get molecule
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require_3D
= False¶
-
require_connected
= True¶
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rethrow_na
(exception)¶ treat any exceptions as known exception
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rethrow_zerodiv
()¶ treat zero div as known exception
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class
mordred.ExtendedTopochemicalAtom.
EtaShapeIndex
(type='p')[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA shape index descriptor.
shapet=αtαwhere αt is p(alpha value only atoms which bond to 1 heavy atom), y(3), or x(4).
Parameters: type (str) – one of shape_types -
shape_types
= ('p', 'y', 'x')¶
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as_argument
¶ argument representation of descriptor
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coord
¶ get 3D coordinate
-
explicit_hydrogens
= False¶
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
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class
mordred.ExtendedTopochemicalAtom.
EtaVEMCount
(type='', averaged=False)[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA VEM(valence electron mobile) count descriptor.
βs=12A∑i=1βsiβsi=A∑j=1xijσijxij={0.5(|ϵi−ϵj|≤0.3)0.75(|ϵi−ϵj|>0.3)ϵi=−αi+0.3Zvwhere σij is sigma bond count between i and j.
βnsδ=A∑i=1βnsδiwhere βnsδi is 0.5 if i-th atom is making resonance with an aromatic ring.
βns=12A∑i=1βnsiβnsi=A∑j=1yijπij+βnsδiyij={2.0(ij is aromatic bond)1.5(|ϵi−ϵj|>0.3)1.0(|ϵi−ϵj|≤0.3)where πij is pi bond count between i and j.
β=βs+βnsParameters: -
beta_types
= ('', 's', 'ns', 'ns_d')¶
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as_argument
¶ argument representation of descriptor
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coord
¶ get 3D coordinate
-
explicit_hydrogens
= False¶
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
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-
class
mordred.ExtendedTopochemicalAtom.
EtaCompositeIndex
(reference=False, local=False, averaged=False)[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA composite index descriptor.
η=∑i<j(γiγjr2ij)0.5γi=αiβiwhere rij is graph distance.
ηlocal=∑i<j,rij=1(γiγj)0.5Parameters: Returns: reference and valence of any atoms > 4
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as_argument
¶ argument representation of descriptor
-
coord
¶ get 3D coordinate
-
explicit_hydrogens
= False¶
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
-
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class
mordred.ExtendedTopochemicalAtom.
EtaFunctionalityIndex
(local=False, averaged=False)[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA functionality index descriptor.
ηF=ηR−ηwhere ηR is eta value for reference alkane.
Parameters: -
as_argument
¶ argument representation of descriptor
-
coord
¶ get 3D coordinate
-
explicit_hydrogens
= False¶
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
-
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class
mordred.ExtendedTopochemicalAtom.
EtaBranchingIndex
(ring=True, averaged=False)[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA branching index descriptor.
ηB=ηlocal,N−ηlocal,R+0.086NRwhere ηlocal,N is ηlocal for normal alkane. NR is ring count.
Parameters: Returns: NaN when A < 2
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as_argument
¶ argument representation of descriptor
-
coord
¶ get 3D coordinate
-
explicit_hydrogens
= False¶
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
-
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class
mordred.ExtendedTopochemicalAtom.
EtaDeltaAlpha
(type='A')[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA delta alpha descriptor.
ΔαA=maxParameters: type (str) – one of delta_types -
delta_types
= ('A', 'B')¶
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as_argument
¶ argument representation of descriptor
-
coord
¶ get 3D coordinate
-
explicit_hydrogens
= False¶
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
-
-
class
mordred.ExtendedTopochemicalAtom.
EtaEpsilon
(type=1)[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA epsilon descriptor.
\epsilon^i = \frac{\epsilon^i}{N^i} (i \leq 4) \epsilon^5 = \frac{\epsilon^2 + \epsilon^{\rm XH}}{N^2 + N^{\rm XH}}- types(i)
- 1
- all atoms
- 2
- heavy atoms
- 3
- all atoms of reference alkane
- 4
- all atoms of saturated carbon skeleton(reduce C-C bonds)
- XH
- hydrogens bond to hetero atoms
Parameters: type (str) – one of epsilon_types Returns: type = 3 and valence of any atoms > 4 -
explicit_hydrogens
¶
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epsilon_types
= (1, 2, 3, 4, 5)¶
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as_argument
¶ argument representation of descriptor
-
coord
¶ get 3D coordinate
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
-
class
mordred.ExtendedTopochemicalAtom.
EtaDeltaEpsilon
(type='A')[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA delta epsilon descriptor.
\begin{align}\begin{aligned}\Delta \epsilon^{\rm A} = \epsilon^1 - \epsilon^3\\\Delta \epsilon^{\rm B} = \epsilon^1 - \epsilon^4\\\Delta \epsilon^{\rm C} = \epsilon^3 - \epsilon^4\\\Delta \epsilon^{\rm D} = \epsilon^2 - \epsilon^5\end{aligned}\end{align}Parameters: type (str) – one of delta_epsilon_types -
delta_epsilon_types
= ('A', 'B', 'C', 'D')¶
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as_argument
¶ argument representation of descriptor
-
coord
¶ get 3D coordinate
-
explicit_hydrogens
= False¶
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
-
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class
mordred.ExtendedTopochemicalAtom.
EtaDeltaBeta
(averaged=False)[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA delta beta descriptor.
\Delta\beta = \beta^{\rm ns} - \beta^{\rm s}Parameters: averaged (bool) – averaged -
as_argument
¶ argument representation of descriptor
-
coord
¶ get 3D coordinate
-
explicit_hydrogens
= False¶
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
-
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class
mordred.ExtendedTopochemicalAtom.
EtaPsi
[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA psi descriptor.
\psi_1 = \frac{\alpha}{A \cdot \epsilon^2}-
as_argument
¶ argument representation of descriptor
-
coord
¶ get 3D coordinate
-
explicit_hydrogens
= False¶
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
-
-
class
mordred.ExtendedTopochemicalAtom.
EtaDeltaPsi
(type='A')[source]¶ Bases:
mordred.ExtendedTopochemicalAtom.EtaBase
ETA delta psi descriptor.
\begin{align}\begin{aligned}\Delta\psi_{\rm A} = \max\left(0.714 - \psi_1, 0\right)\\\Delta\psi_{\rm B} = \max\left(\psi_1 - 0.714, 0\right)\end{aligned}\end{align}Parameters: type (str) – one of delta_psi_types -
delta_psi_types
= ('A', 'B')¶
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as_argument
¶ argument representation of descriptor
-
coord
¶ get 3D coordinate
-
explicit_hydrogens
= False¶
-
fail
(exception)¶ raise known exception and return missing value
-
kekulize
= True¶
-
mol
¶ get molecule
-
require_3D
= False¶
-
require_connected
= True¶
-
rethrow_na
(exception)¶ treat any exceptions as known exception
-
rethrow_zerodiv
()¶ treat zero div as known exception
-