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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

pdb_plugin

PDB plugin

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

Functions

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

Command item function
small imageShow a small image (82px in width) retrieved from RCSB database
medium imageShow a small image (252px in width) retrieved from RCSB database
large imageShow a small image (502px in width) retrieved from RCSB database
searchbox form Show a searchbox for the RCSB PDB
link link Show a link for the PDB ID
short link Show the PDB link and brief description from NCBI Structure database
long link Show the PDB link and detailed description from NCBI Structure database
structureID link Show a Structure ID for the NCBI database
fullSmall image
link
Show a combination of an image and a short description
summaryXML xml Show a XML summary data from the NCBI database using Entrez Utilities
clear_summary - Clear cached XML files in /data/media/ncbi_esummary
clear_image - Clear cached image files in /data/media/rcsb_image
remove_dir - Clear and remove directory

Caching files

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)

Examples

small

{{pdb>small:1WLA}}
PDB image

medium

{{pdb>medium:1WLA}}
PDB image

large

{{pdb>large:1WLA}}

PDB image

{{pdb>link:1WLA}}

short

{{pdb>short:1WLA}}

long

{{pdb>long:1WLA}}
1WLA - Oxygen Transport
Myoglobin (horse Heart) Recombinant Wild-type
Ligand: HEM|SO4

serchbox

{{pdb>searchbox}}
PDB (RCSB)

structureID

This command converts from PDB ID into StructureID of NCBI.

{{pdb>structureID:1WLA}}
StructureID:57663

fullSmall

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

{{pdb>fullSmall:1WLA}}

PDB image
1WLA - Oxygen Transport
Myoglobin (horse Heart) Recombinant Wild-type
Ligand: HEM|SO4

summaryXML

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.

{{pdb>summaryXML:1WLA}}
<?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>

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.
  • 2008.3.7
    • Bug fix of incorrect permission of cache files

Links

Translations of this page:
pdb_plugin.txt · Last modified: 2016/10/31 09:08 by swadmin