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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
DokuWiki plugins for bioscience and biotechnology.
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]}}
Command | item | function |
---|---|---|
small | image | Show a small image (82px in width) retrieved from RCSB database |
medium | image | Show a small image (252px in width) retrieved from RCSB database |
large | image | Show 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 |
This plugin caches two kinds of files as media files.
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>long:1WLA}}
</float> <float left>
</float><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></float>
<float icon(compass)>
</float> <clear/>