My name is Saurabh Gupta, I am a third-year undergraduate student of the
Department of Chemistry enrolled in its integrated M.Sc. course at Indian
Institute of Technology Kharagpur. Despite majoring in chemistry I have a deep
understanding of Python, machine learning, algorithms and data
Hi Peter,
to the best of my knowledge: for a given SMILES string, you should
always end up with the same molecule object.
On the other hand, generation of (canonical / unique) SMILES often
reorders atoms and bonds (to ensure that the SMILES is unique for a
given structure). A conversion Molecule
Awesome, thanks for the tip!
Connor, that also is a great idea, I didn't know about atom-mapped SMILES
strings. That would definitely be a good method if the indexing algorithm
changes across rdkit versions.
Thanks!
-- Peter
On Tue, Oct 2, 2018 at 2:56 PM Nils Weskamp wrote:
> Hi Peter,
>
>
Hi Peter and Nils,
To supplement Nils comment I'd like to add that during writing the Mol
atoms nor bonds order is not changed, but the canonical atom mapping is
saved in molecular property "_smilesAtomOutputOrder". This does not include
bonds though, it shouldn't change, but if you wish to be
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?
I.e., if I create a new rdkit Molecule with rdkit.Chem.MolFromSmiles(xxx),
will the bond ordering always be the same? If not, does anyone know
On 10/02/2018 03:32 PM, Peter St. John wrote:
> I.e., if I create a new rdkit Molecule with rdkit.Chem.MolFromSmiles(xxx),
> will the bond ordering always be the same? If not, does anyone know a a
> robust way of specifying a bond within a molecule as a string-based
> representation?
On Tue, Oct 2, 2018 at 10:32 PM Peter St. John
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
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