I'm not sure which flags the online tool uses, but it's based on Open Babel
so you might have some success with that tool.
http://open-babel.readthedocs.io/en/latest/3DStructureGen/Overview.html
For a quick guess at the structure, an example with the command line tool
is something like
obabel -:"[O-]C(=O)c1ccc(cc1)C(=O)[O-]" --gen3D -O structure.xyz
If your workflow is in Python, there are some make3D and addh (for
hydrogens) convenience functions in the openbabel (or its pybel) package.
As Dima mentioned, there's several challenges/nonuniqueness in going from
SMILES to 3D. Some of the conformer search tools in the link can help a
little bit, but in general it's a tricky problem.
Best,
Ben
On Wed, May 23, 2018 at 10:30 AM, Dimitri Maziuk via Rdkit-discuss <
[email protected]> wrote:
> On 5/23/2018 10:23 AM, Chenyang Shi wrote:
>
> A separate question is that is the converted molecular structure from
>> SMILES the same as that taken from a crystal structure?
>>
>
> Provided there's no undefined/different stereochemistry on SMILES side, no
> quirks with added protons, and so on and so forth... for a small simple
> molecule... maybe.
>
> Dima
>
>
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