/ob-openbabel

Org-babel functions for openbabel conversions.

Primary LanguageEmacs Lisp

Readme

ob-openbabel

This is a org babel package for OpenBabel.

Header args

  • :input-format specify the input format. Default to “smi”.
  • :output-format specify the output format. Default to “svg”.
  • :other-options specify the additional options.
  • :openbabel specify the executeable of openbabel. Default to “babel”.
  • For the list of formats, see here.
  • Note: When openbabel fails, its exit code is 0. Please check the error in the shell again. You need to build openbabel with cairo for png output.

Examples

#+BEGIN_SRC openbabel :exports results :file images/C.svg
  C
#+END_SRC

./images/C.svg

#+BEGIN_SRC openbabel :exports results :file images/C-gen3d.svg :other-options --gen3d
 C
#+END_SRC

./images/C-gen3d.svg

#+BEGIN_SRC openbabel :exports results :file images/C=CO-gen3d.svg :other-options --gen3d
  C=CO
#+END_SRC

./images/C=CO-gen3d.svg

#+BEGIN_SRC openbabel :exports results :file images/caffeine-gen3d.png :output-format png :other-options --gen3d
  Cn1cnc2n(C)c(=O)n(C)c(=O)c12
#+END_SRC

./images/caffeine-gen3d.png