mordred.ExtendedTopochemicalAtom module

Extended Topochemical Atom(ETA) descriptor.

References
class mordred.ExtendedTopochemicalAtom.EtaCoreCount(averaged=False, reference=False)[source]

Bases: mordred.ExtendedTopochemicalAtom.EtaBase

ETA core count descriptor.

α=Ai=1ZiZviZvi1PNi1

where Zi and Zvi are number of total and valence electons, PN is periodic number.

Parameters:
  • averaged (bool) – averaged by number of heavy count
  • reference (bool) – use reference alkane (same graph structure, but all atoms are carbon and all bonds are single bond)
Returns:

reference and valence of any atoms > 4

parameters()[source]
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

rtype

alias of float

class mordred.ExtendedTopochemicalAtom.EtaShapeIndex(type='p')[source]

Bases: mordred.ExtendedTopochemicalAtom.EtaBase

ETA shape index descriptor.

shapet=αtα

where 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')
parameters()[source]
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

rtype

alias of float

class mordred.ExtendedTopochemicalAtom.EtaVEMCount(type='', averaged=False)[source]

Bases: mordred.ExtendedTopochemicalAtom.EtaBase

ETA VEM(valence electron mobile) count descriptor.

βs=12Ai=1βsiβsi=Aj=1xijσijxij={0.5(|ϵiϵj|0.3)0.75(|ϵiϵj|>0.3)ϵi=αi+0.3Zv

where σij is sigma bond count between i and j.

βnsδ=Ai=1βnsδi

where βnsδi is 0.5 if i-th atom is making resonance with an aromatic ring.

βns=12Ai=1βnsiβnsi=Aj=1yijπij+βnsδiyij={2.0(ij is aromatic bond)1.5(|ϵiϵj|>0.3)1.0(|ϵiϵj|0.3)

where πij is pi bond count between i and j.

β=βs+βns
Parameters:
  • type (str) – one of beta_types
  • averaged (bool) – averaged by heavy atom count
beta_types = ('', 's', 'ns', 'ns_d')
parameters()[source]
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

rtype

alias of float

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=αiβi

where rij is graph distance.

ηlocal=i<j,rij=1(γiγj)0.5
Parameters:
  • reference (bool) – use reference alkane.
  • local (bool) – use ηlocal
  • averaged (bool) – averaged
Returns:

reference and valence of any atoms > 4

parameters()[source]
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

rtype

alias of float

class mordred.ExtendedTopochemicalAtom.EtaFunctionalityIndex(local=False, averaged=False)[source]

Bases: mordred.ExtendedTopochemicalAtom.EtaBase

ETA functionality index descriptor.

ηF=ηRη

where ηR is eta value for reference alkane.

Parameters:
  • local (bool) – use local eta
  • averaged (bool) – averaged
parameters()[source]
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

rtype

alias of float

class mordred.ExtendedTopochemicalAtom.EtaBranchingIndex(ring=True, averaged=False)[source]

Bases: mordred.ExtendedTopochemicalAtom.EtaBase

ETA branching index descriptor.

ηB=ηlocal,Nηlocal,R+0.086NR

where ηlocal,N is ηlocal for normal alkane. NR is ring count.

Parameters:
  • ring (bool) – use ring count or not
  • averaged (bool) – averaged
Returns:

NaN when A < 2

parameters()[source]
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

rtype

alias of float

class mordred.ExtendedTopochemicalAtom.EtaDeltaAlpha(type='A')[source]

Bases: mordred.ExtendedTopochemicalAtom.EtaBase

ETA delta alpha descriptor.

ΔαA=max
Parameters:type (str) – one of delta_types
delta_types = ('A', 'B')
parameters()[source]
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

rtype

alias of float

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
epsilon_types = (1, 2, 3, 4, 5)
parameters()[source]
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

rtype

alias of float

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')
parameters()[source]
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

rtype

alias of float

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
parameters()[source]
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

rtype

alias of float

class mordred.ExtendedTopochemicalAtom.EtaPsi[source]

Bases: mordred.ExtendedTopochemicalAtom.EtaBase

ETA psi descriptor.

\psi_1 = \frac{\alpha}{A \cdot \epsilon^2}
parameters()[source]
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

rtype

alias of float

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')
parameters()[source]
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

rtype

alias of float