Re: [Rdkit-discuss] convert a smiles file to a xyz file

Thank you Prof. Jensen. I will study the module. Best, Chenyang On Thu, May 24, 2018 at 1:30 AM, Jan Halborg Jensen wrote: > Have a look at write_xtb_input_file in this module: https://github.com/ > jensengroup/take_elementary_step/blob/master/write_input_files.py > > The

Re: [Rdkit-discuss] convert a smiles file to a xyz file

Have a look at write_xtb_input_file in this module: https://github.com/jensengroup/take_elementary_step/blob/master/write_input_files.py The xtb input is simple an xyz file with some additional lines below if the molecule is charged. You can simply those lines in the code. Best regards, Jan

Re: [Rdkit-discuss] convert a smiles file to a xyz file

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 < bbuc...@u.northwestern.edu> wrote: > I'm not sure

Re: [Rdkit-discuss] convert a smiles file to a xyz file

In reminiscence of old times, you can do this with the Chemical Identifier Resolver, for instance with the SMILES string for ethanol, CCO: https://cactus.nci.nih.gov/chemical/structure/CCO/file?format=xyz On Wed, May 23, 2018 at 5:24 PM Chenyang Shi wrote: > Hi Everyone, >

Re: [Rdkit-discuss] convert a smiles file to a xyz file

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

Re: [Rdkit-discuss] convert a smiles file to a xyz file

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