Question: Tools for generation 3D molecule structure from 2D
0
gravatar for Katya
6 months ago by
Katya0
Russia, St.Petersburg
Katya0 wrote:

Hello, I need to generate 3D molecular structure based on 2D. I have .cdx file (it's a ChemDraw format) and I'd like to receive (for instance) .xyz file with adequate coordinates in "Z" column. By this moment, I found only Open Babel tool (and accordingly, openbabel and pybel libraries on python) that can do this. Structures, that are received using this tool for generation small molecules (e.g. CH4, ...), are nice. But I really don't like representation of structures from big molecules.

Maybe does anybody know any other (not online) tools or libraries for task like this? In principal, no matter what language, but python is better) Or maybe did someone work with Open Babel and had similar task with similar problem and found the solution? I'd be grateful for help.

P.S. I'm also searching any articles that can help me to understand conversion from 2D to 3D molecular structures algorithm, but still not enough successful.

openbabel 3d • 235 views
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