Thank you all. It seems OpenBabel supports this.
Here is a tutorial I found from Dr. Kulik's group that might be useful
http://hjkgrp.mit.edu/content/geometries-strings-smiles-and-openbabel.
On Wed, May 23, 2018 at 10:59 AM, Benjamin Bucior <
[email protected]> wrote:
> 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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