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.

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.

-Install bio plugin and cache plugin if not installed. -Download and extract pubchem.zip (6 KB). -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/>