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;;; ob-smiles.el --- Org-mode Babel support for SMILES
;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
;; Maintainer: stardiviner <numbchild@gmail.com>
;; Homepage: https://github.com/stardiviner/ob-smiles
;; Keywords: org babel SMILES
;; Version: 0.0.1
;; Package-Requires: ((smiles-mode "0.0.1") (org "8"))
;; This file is not part of GNU Emacs.
;;
;; GNU Emacs is free software: you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation, either version 3 of the License, or
;; (at your option) any later version.
;;
;; GNU Emacs is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;; GNU General Public License for more details.
;;
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs. If not, see <https://www.gnu.org/licenses/>.
;;; Commentary:
;;; I copy code from:
;;; https://kitchingroup.cheme.cmu.edu/blog/2016/03/26/A-molecule-link-for-org-mode
;;; Code:
(require 'ob)
(require 'org-element)
;; Org-mode Babel
(defun org-babel-execute:smiles (body params)
"Execute SMILES babel `BODY' with `PARAMS'."
(shell-command-to-string
(format "obabel -:\"%s\" -osvg 2> /dev/null" body)))
;; Org-mode link
(defun molecule-jump (name)
"Jump to molecule `NAME' definition."
(org-mark-ring-push)
(org-link-open-from-string (format "[[%s]]" name)))
(defun molecule-export (path desc backend)
"Export molecule to HTML format on `PATH' with `DESC' and `BACKEND'."
(let ((name (save-window-excursion
(molecule-jump path)
(org-element-property :name (org-element-context)))))
(cond
((eq 'html backend)
(format "<a href=\"#%s\">%s</a>" name name)))))
(org-link-set-parameters
"molecule"
:follow 'molecule-jump
:export 'molecule-export)
;; org-mode element
(org-element-map (org-element-parse-buffer)
'src-block
(lambda (src)
(when (string= "smiles" (org-element-property :language src))
(org-element-property :name src))))
(provide 'ob-smiles)
;;; ob-smiles.el ends here
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