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

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

6248

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

<float left>

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

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

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

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

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

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

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.

• 2016.10.24
  • URLs are changed to https: according to changes in Web API of NCBI database.
• 2008.3.22
  • Some functions were parted into bio plugin and cache plugin.
• 2008.3.16
  • Vulnerability (XSS) was fixed.
• 2007.12.08
  • Fix around creation of directory & ACL
  • 'Clear_cache' functionality
  • Append an icon image

This DokuWiki plugin formats a molecular formula by using 'chem' tag.

Usage of seperation between atom-numbers and charge-numbers

You can install by using 'Manager Plugins' in Admin tools. Download URL is available at https://www.dokuwiki.org/plugin:chem.

• 2013-01-20 Source code was moved to GitHub.
• 2008-09-29 Supported the Open document format export using ODT plugin.
• 2008-03-21 Seperator implementation and bracket support

(Kibi posted bug-fix and made some extension for isotope expression in the previous system of DW. Since a 'discussion plugin' is not deployed in this current DW, I pasted his/her comment here. Thanks, Kibi — i.obataya 2009/11/11 19:17)

I've made some improvements to your plugin: now it can handle not only charge number of ion, but oxidation state: N^-3, N^-1, N⁰, N⁺¹, N⁺³, H₂⁺¹S⁺⁶O₃^-2S^-2

Fixed error with “+” in equation: 2H₂ + O₂ ⇒ 2H₂O

Fixed error with alternative formulas like Anion₂Cation₃

Added support of isotope numbers: ²³⁸U, 2²³⁹Pu

All you need is replace function getChemFormat with that:

  function getChemFormat($raw){
    $pattern = array("/([A-Za-z\]\)]+)(0)/", "/[\|]?([0-9]*)[\^]/", "/([^ ][\]\)]?)[\|]?(([\-\+][0-9]*)|([0-9]*[\-\+]))/", "/([A-Z]|[a-z]|\)|\])([1-9][0-9]*)/");
    $replace = array("\${1}<sup>\${2}</sup>", "<sup>\${1}</sup>", "\${1}<sup>\${2}</sup>","\${1}<sub>\${2}</sub>");
    return preg_replace($pattern,$replace,$raw);
  }

The examples ahead would be like this:

• oxidation state: N^-3, N^-1, N⁰, N⁺¹, N⁺³, H₂⁺¹S⁺⁶O₃^-2S^-2
• “+” in equation: 2H₂ + O₂ ⇒ 2H₂O
• alternative formulas like Anion₂Cation₃
• isotope numbers: ²³⁸U, 2²³⁹Pu

This DokuWiki plugin has several utilities accessing RCSB Protein Data Base (PDB) and NCBI Structure database to show an entry and an image.

{{pdb>[Command]:[PDB ID]}}

This plugin caches two kinds of files as media files.

1. Protein images from RCSB server in /data/media/rcsb_image/ directory
2. Structure XML summary from NCBI database in /data/media/ncbi_esummary/ directory

You can place a cached image file in the same way of that in a media file. (Find the image in rcsb_image namespace)

<float left200>

{{pdb>small:1WLA}}

</float> <float left>

<float left200>

{{pdb>medium:1WLA}}

</float> <float left>

{{pdb>large:1WLA}}

<float left200>

{{pdb>link:1WLA}}

</float> <float left> 1WLA </float>

<float left200>

{{pdb>short:1WLA}}

</float> <float left>

<float left200>

{{pdb>long:1WLA}}

</float> <float left>

<float left200>

{{pdb>searchbox}}

</float> <float left>

This command converts from PDB ID into StructureID of NCBI.

<float left200>

{{pdb>structureID:1WLA}}

</float> <float left> StructureID:57663 </float>

Combination of an image from PDB ID and a short description from NCBI.

{{pdb>fullSmall:1WLA}}

This command displays a raw data of ESummary XML data from NCBI Structure DB. The 'short' and 'long' descriptions are extracted from this file. The XML files are in /data/media/ncbi_esummary. <float left200>

{{pdb>summaryXML:1WLA}}

</float> <float left400>

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary v1 20041029//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20041029/esummary-v1.dtd">
<eSummaryResult>
<DocSum>
	<Id>57663</Id>
	<Item Name="PdbAcc" Type="String">1WLA</Item>
	<Item Name="PdbDescr" Type="String">Myoglobin (horse Heart) Recombinant Wild-type</Item>
	<Item Name="EC" Type="String"></Item>
	<Item Name="Resolution" Type="String">1.7</Item>
	<Item Name="ExpMethod" Type="String">X-Ray Diffraction</Item>
	<Item Name="PdbClass" Type="String">Oxygen Transport</Item>
	<Item Name="PdbDepositDate" Type="String">1997/09/24 00:00</Item>
	<Item Name="MMDBEntryDate" Type="String">2007/10/11 00:00</Item>
	<Item Name="OrganismList" Type="List">
		<Item Name="string" Type="String">Equus caballus</Item>
	</Item>
	<Item Name="LigCode" Type="String">HEM|SO4</Item>
	<Item Name="LigCount" Type="String">2</Item>
	<Item Name="ModProteinResCount" Type="String">0</Item>
	<Item Name="ModDNAResCount" Type="String">0</Item>
	<Item Name="ModRNAResCount" Type="String">0</Item>
	<Item Name="ProteinChainCount" Type="String"></Item>
	<Item Name="DNAChainCount" Type="String"></Item>
	<Item Name="RNAChainCount" Type="String"></Item>
</DocSum>

</eSummaryResult>

• 2016.10.24
  • URLs are changed to https according to changes in Web API of NCBI database
• 2008.3.22
  • Some functions were parted into bio plugin and cache plugin
• 2008.3.16
  • Vulnerability (XSS) was fixed.
• 2008.3.7
  • Bug fix of incorrect permission of cache files

<float icon(compass)>

• SearchNCBI plugin
• SearchDDBJ plugin
• SearchEMBL plugin
• PDB plugin

</float> <clear/>