Hi All,
I'm trying to map the fragment's atoms to those of the original molecule.
this is the molecule smiles:
mol =
('O=c1[nH]c(=O)n([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)cc1[N+](=O)[O-]')
and this is the fragment.
frg = 'O=C1[NH]C(=O)N([*])C=C1[N+](=O)[O-]'
I can use GetSubstructureMatches(), but, as you can see, there is a
dummy atom. So i have to remove it before the substructure match. But
I'm interested in the dummy atoms index. Any suggestion?
My final goal is to retrieve the position of the fragment (dummy atom
included). So, since the atomic coordinates are embedded in the starting
molecule, I was thinking of using GetAtomPosition(). The fragmentation
is performed by using rdMMPA.FragmentMol function which do not store the
original coordinates of the fragments.
Gabriele
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