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org-mode/contrib/lisp/ob-smiles.el

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* ob-smiles.el (supporting SMILES in Org-mode Babel): Add. Copied version.
2018-02-09 19:25:53 -05:00
;;; ob-smiles.el --- Org-mode Babel support for SMILES.
;;; -*- coding: utf-8 -*-
;; Keywords: org babel SMILES
;; Version: 0.0.1
;; Package-Requires: ((smiles-mode "0.0.1") (org "8"))
;;; Commentary:
;;; I copy code from:
;;; http://kitchingroup.cheme.cmu.edu/blog/2016/03/26/A-molecule-link-for-org-mode
;; Author: John Kitchin [jkitchin@andrew.cmu.edu]
;; Maintainer: stardiviner [numbchild@gmail.com]
;;; Code:
;; 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)
Move link-related core functions out of "org.el" * contrib/lisp/org-wl.el (org-wl-store-link-message): * lisp/Makefile (clean-install): * lisp/ob-core.el (org-link-bracket-re): (org-babel-open-src-block-result): (org-babel-read-element): (org-babel-read-link): (org-babel-result-end): * lisp/ob-tangle.el (org-link-bracket-re): (org-babel-tangle-single-block): (org-link-analytic-bracket-re): (org-babel-detangle): (org-babel-tangle-jump-to-org): * lisp/ol.el: * lisp/org-agenda.el (org-agenda-get-some-entry-text): (org-diary): (org-agenda-format-item): (org-agenda-open-link): (org-agenda-switch-to): (org-agenda-to-appt): * lisp/org-bbdb.el (org-bbdb-store-link): * lisp/org-bibtex.el (org-bibtex-store-link): * lisp/org-capture.el (org-capture-fill-template): * lisp/org-clock.el (org-clocktable-write-default): (org-clock-get-table-data): * lisp/org-compat.el (org-doi-server-url): (org-email-link-description-format): (org-make-link-description-function): (org-from-is-user-regexp): (org-descriptive-links): (org-url-hexify-p): (org-context-in-file-links): (org-keep-stored-link-after-insertion): (org-display-internal-link-with-indirect-buffer): (org-confirm-shell-link-function): (org-confirm-shell-link-not-regexp): (org-confirm-elisp-link-function): (org-confirm-elisp-link-not-regexp): (org-file-complete-link): (org-email-link-description): (org-make-link-string): (org-store-link-props): (org-add-link-props): (org-make-link-regexps): (org-angle-link-re): (org-plain-link-re): (org-bracket-link-regexp): (org-bracket-link-analytic-regexp): (org-any-link-re): * lisp/org-docview.el (org-docview-store-link): (org-docview-complete-link): * lisp/org-element.el (org-element-link-parser): * lisp/org-eshell.el (org-eshell-store-link): * lisp/org-eww.el (org-eww-store-link): (org-eww-copy-for-org-mode): * lisp/org-footnote.el (org-footnote-next-reference-or-definition): * lisp/org-gnus.el (org-gnus-article-link): (org-gnus-store-link): * lisp/org-id.el (org-id-store-link): * lisp/org-info.el (org-info-store-link): * lisp/org-irc.el (org-irc-erc-store-link): * lisp/org-mhe.el (org-mhe-store-link): * lisp/org-pcomplete.el (pcomplete/org-mode/searchhead): * lisp/org-protocol.el (org-protocol-do-capture): * lisp/org-rmail.el (org-rmail-store-link): * lisp/org-w3m.el (org-w3m-store-link): (org-w3m-copy-for-org-mode):
2018-11-26 18:04:41 -05:00
(org-link-open-from-string (format "[[%s]]" path)))
* ob-smiles.el (supporting SMILES in Org-mode Babel): Add. Copied version.
2018-02-09 19:25:53 -05:00
(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-add-link-type
"molecule"
'molecule-jump
'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