contrib/lisp/ob-smiles.el

   1 ;;; ob-smiles.el --- Org-mode Babel support for SMILES.
   2 ;;; -*- coding: utf-8 -*-
   3
   4 ;; Keywords: org babel SMILES
   5 ;; Version: 0.0.1
   6 ;; Package-Requires: ((smiles-mode "0.0.1") (org "8"))
   7
   8 ;;; Commentary:
   9
  10 ;;; I copy code from:
  11 ;;; http://kitchingroup.cheme.cmu.edu/blog/2016/03/26/A-molecule-link-for-org-mode
  12
  13 ;; Author: John Kitchin [jkitchin@andrew.cmu.edu]
  14 ;; Maintainer: stardiviner [numbchild@gmail.com]
  15
  16 ;;; Code:
  17 \f
  18 ;; Org-mode Babel
  19 (defun org-babel-execute:smiles (body params)
  20   "Execute SMILES babel `BODY' with `PARAMS'."
  21   (shell-command-to-string
  22    (format "obabel -:\"%s\" -osvg 2> /dev/null" body)))
  23
  24 ;; Org-mode link
  25 (defun molecule-jump (name)
  26   "Jump to molecule `NAME' definition."
  27   (org-mark-ring-push)
  28   (org-open-link-from-string (format "[[%s]]" path)))
  29
  30 (defun molecule-export (path desc backend)
  31   "Export molecule to HTML format on `PATH' with `DESC' and `BACKEND'."
  32   (let ((name (save-window-excursion
  33                 (molecule-jump path)
  34                 (org-element-property :name (org-element-context)))))
  35     (cond
  36      ((eq 'html backend)
  37       (format "<a href=\"#%s\">%s</a>" name name)))))
  38
  39 (org-add-link-type
  40  "molecule"
  41  'molecule-jump
  42  'molecule-export)
  43
  44 ;; org-mode element
  45 (org-element-map (org-element-parse-buffer)
  46     'src-block
  47   (lambda (src)
  48     (when (string= "smiles" (org-element-property :language src))
  49       (org-element-property :name src))))
  50
  51 \f
  52 (provide 'ob-smiles)
  53
  54 ;;; ob-smiles.el ends here