update packages

lisp/org-contrib/ob-smiles.el

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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