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DokuWiki plugins

There are DokuWiki plugins for research & education which I developed. All plugins are under GPL2 license, so feel free to use them in your DokuWiki.

Dokuwiki Official

Scientific plugins

DokuWiki plugins for bioscience and biotechnology.

General plugins

pubchem_plugin

PubChem Plugin

This is a plugin for DokuWiki that creates the link or retrieve chemical structure for the compound identified by CID (Compound ID).

{{pubchem>[(COMMAND)|(COMMAND:CID)}}

COMMAND: link, small, large, clear_cache, searchbox

Functions

command function
smallDisplay a small image of chemical structure
largeDisplay a large image of chemical structure
summaryXmlDisplay a summary XML from NCBI Structure database
IUPACDisplay an IUPAC name of a compound
formulaDisplay a molecular formula of a compound
searchBoxDisplay a search box of PubChem
clearClear all PubChem cache files
remove_dirClear and remove cache directory

Examples

A syntax {{pubchem>link:6248}} creates a link like this.

6248

Images

{{pubchem>large:6248}} retrieves a large image of chemical structure.
{{pubchem>small:6248}} retrieves a small image of chemical structure.

PubChem image 6248
PubChem image 6248

You can display a search box for PubChem with {{pubchem>searchbox}}.

PubChem (NCBI)



summaryXml

{{pubchem>summaryXML:6248}} displays a summary XML from NCBI.

Formula

{{pubchem>formula:6248}} displays a chemical formula of compound.

IUPAC

{{pubchem>IUPAC:6248}} displays an IUPAC name of compound.

Clearing cache images

You can clear all image files by {{pubchem>clear_cache}}. {{pubchem>remove_dir}} will clear all files and pubchem directory.

Installation

Recent dokuwiki has Extension manager in Admin tools. It can download and install the plugin automatically.

In very old dokuwiki

  1. Install bio plugin and cache plugin if not installed.
  2. Download and extract pubchem.zip (6 KB).
  3. Upload the folder your DokuWiki at /lib/plugins/

This plugin automatically creates 'pubchem' namespace and caches images of chemical structure there.

History

  • 2016.10.24
    • URLs are changed to https: according to changes in Web API of NCBI database.
  • 2008.3.22
  • 2008.3.16
    • Vulnerability (XSS) was fixed.
  • 2007.12.08
    • Fix around creation of directory & ACL
    • 'Clear_cache' functionality
    • Append an icon image
Translations of this page:
pubchem_plugin.txt · Last modified: 2016/10/24 10:19 by swadmin