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