On Tue, Oct 2, 2018 at 10:32 PM Peter St. John <peterc.stj...@gmail.com>
wrote:
> If I store a molecule as a SMILES string, along with relevant information
> about different bonds, is it safe to annotate those bond entries by bond
> index?
>
This has already been answered (yes, you can), but to just provide a bit
more detail:
The ordering of atoms/bonds in the RDKit molecule that results from reading
a particular input is deterministic.
The atom ordering in the RDKit molecule created from a SMILES or Mol block
will always be the same and will corresponds to the ordering of the atoms
in the input.
The bond ordering in the RDKit molecule created from a SMILES or Mol block
will always be the same. The ordering of bonds from a Mol file corresponds
to the ordering in the input file. The ordering from SMILES is a bit more
complicated.[1]
For the sake of completeness: the ordering of atoms and bonds from any of
the other currently supported input types will also always be the same.
-greg
[1] Here's the story on the ordering of bonds read from SMILES:
- non "ring closure" bonds appear in the order in which they appear in the
input SMILES.
- "ring closure" bonds appear at the end of the set of bonds. their
ordering is non-trivial to describe, but it is deterministic.
Here's a relatively simple example demonstrating this:
In [6]: m = Chem.MolFromSmiles('C12ON1.F2')
In [7]: m.Debug()
Atoms:
0 6 C chg: 0 deg: 3 exp: 3 imp: 1 hyb: 4 arom?: 0 chi: 0
1 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0
2 7 N chg: 0 deg: 2 exp: 2 imp: 1 hyb: 4 arom?: 0 chi: 0
3 9 F chg: 0 deg: 1 exp: 1 imp: 0 hyb: 4 arom?: 0 chi: 0
Bonds:
0 0->1 order: 1 conj?: 0 aromatic?: 0
1 1->2 order: 1 conj?: 0 aromatic?: 0
2 2->0 order: 1 conj?: 0 aromatic?: 0
3 3->0 order: 1 conj?: 0 aromatic?: 0
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