Alternative python modules to RDKit to convert SMILES to structure

Question

Python module RDKit is great, but it cannot be installed by pip, and therefore it is difficult to use it sometimes in a virtual environment.

I am wondering that if there are some alternative python modules that can convert smiles to chemical structures?

Does this answer your question? Is there a way to use free software to convert SMILES strings to structures? — Mithoron, May 25 '20 at 20:03
@Mithoron, Thanks a lot for your kind help. These tools are not suitable for me. Except Pysmiles, the rest tools are not python-based. Pysmiles cannot convert smiles to chemical structures. — Wang, May 25 '20 at 20:21
There is also the Indigo Toolkit. An example appears in an answer to this question. — BalooRM, May 25 '20 at 21:10
https://chemistry.stackexchange.com/questions/61887/portable-library-to-render-2d-structural-formulas-as-vector-graphics-from-smiles — Mithoron, May 25 '20 at 22:35

score 9 · Accepted Answer · answered May 25 '20 at 20:32

I am not aware of any other Python tool not mentioned in the question @Mithoron linked to. Openbabel is available via pip by the way.

That RDKit is not available on PyPi should not hinder you from using it in a virtual environment. RDKit is available via the conda package manager which is easy to use and combinable with pip.

If you are on Linux, the probably best solution for managing different versions of Python (also Anaconda Python) and virtual environments is pyenv. I highly recommend to check it out.

Alternative python modules to RDKit to convert SMILES to structure

1 Answers1