Hi,
I've noticed that if I define a molecule as neutral, positive and negative
(depending on protonation) the EState indices calculated by RDKit reflect
the changes as expected:
m = Chem.MolFromSmiles('CCO')
m_neg = Chem.MolFromSmiles('CC[O-]')
m_pos = Chem.MolFromSmiles('CC[OH2+]')
EState indices:
m : [ 1.68055556 0.25 7.56944444]
m_neg : [ 1.56944444 0. 8.93055556]
m_pos : [ 1.79166667 0.5 6.20833333]
However, when I calculate the EState fingerprints there seems to be some
problem with the (de)protonated oxygen as its value (and even the presence
of its atoms type) fails to show up. If EState.EStateIndices() can
calculate the value for oxygen in all three states then
Fingerprinter.FingerprintMol() should also be able to handle these
notations?
I've included the output from the fingerprinter below.
Any help would be greatly appreciated.
Cheers,
Bruce
m : (array([0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0]), array([ 0. , 0. , 0.
, 0. , 0. , 0. , 1.68055556, 0. , 0.25
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. ,
0. , 0. , 0. , 0. , 0. , 0.
, 0. , 7.56944444, 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. ,
0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
]))
m_neg : (array([0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0]), array([ 0. , 0. , 0.
, 0. , 0. , 0. , 1.56944444, 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. ,
0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. ,
0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
]))
m_pos : (array([0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0]), array([ 0. , 0. , 0.
, 0. , 0. , 0. , 1.79166667, 0. , 0.5
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. ,
0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. ,
0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. , 0.
, 0. , 0. , 0. , 0. , 0. ,
0. ]))
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