Openbabel Alternatives

openbabel reviews and mentions

• Cheaper/free alternatives to ChemDraw?
  1 project | /r/OrganicChemistry | 18 Feb 2023

  Perhaps you are aware of openbabel as a converter between files relevant to chemistry (download page, the current documentation), and of the markup language LaTeX. (Maybe more so if you already interact with folks from physical chemistry / spectroscopy.) The official servers compile multiple packages relevant to chemistry (tag cloud chemistry). While the design of organic reactions with a GUI like ChemDraw, ChemDoodle, etc frequently is the most convenient approach (subsequent export as .pdf, or .png), chemobabel is an interesting approach to depict individual molecules for which you "only" have .mol, .sdf file or a descriptive SMILES string. Here, openbabel is working in the background to generate an illustration eventually added to your report (link to the English documentation as pdf).

• Nicely typeset chemical SMILES
  1 project | /r/LaTeX | 18 Jan 2023

  ``` %% % External assistance to generate "IUPAC traditional name" for SMILES % CC1=C(C(=O)C[C@@H]1OC(=O)[C@@H]2[C@H](C2(C)C)/C=C(\C)/C(=O)OC)C/C=C\C=C % % * converted by openbabel 3.1.1 (https://github.com/openbabel/openbabel) % on the CLI into a mol file % * this mol file was read by chemdoodle (https://web.chemdoodle.com/), % equally possible without an installation on the web on % https://web.chemdoodle.com/demos/iupac-naming % % output string (without the markup chemdoodle provides) used below: % Methyl (E)-3-[(1R,3R)-3-{(S)-3-[(2Z)-2,4-pentadienyl]-2-methyl-4-oxo-2-cyclopenten-1-yloxycarbonyl}-2,2-dimethylcyclopropyl]methacrylate % % With an input of the SMILES into ChemDraw (e.g., on % https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html# ), % the subsequent structure2name function assigns the name % (S)-2-methyl-4-oxo-3-((Z)-penta-2,4-dien-1-yl)cyclopent-2-en-1-yl (1R,3R)-3-((E)-3-methoxy-2-methyl-3-oxoprop-1-en-1-yl)-2,2-dimethylcyclopropane-1-carboxylate % % Setup around longtblr uses the example by FranekW posted in reply to % reddit "Landscape table with code snippets" by 2023-01-16, see % https://www.reddit.com/r/LaTeX/comments/10d0joc/landscape_table_with_code_snippets/ %%

• How do i preview Latex Chemfig snippets in doom emacs?
  1 project | /r/orgmode | 23 Nov 2022

  So keep an eye open on synopses like this one or an other about programs which allow to prepare the drawings and an export as .eps, .png., .svg, etc. in addition to the native file format. On occasion, there are free test sites with (somewhat reduced functionality), too, e.g., chemdraw, or marvin. And if you encounter e.g., a .mol file, openbabel (which equally may export to .png and .svg).

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