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pdb_plugin [2018/01/19 01:44]
pdb_plugin [2018/01/19 01:44] (現在)
ライン 1: ライン 1:
 +======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.
 +
 +|  [[https://​github.com/​iobataya/​dokuwiki-plugin-pdb|Repository at GitHUB]] ​ |  [[https://​github.com/​iobataya/​dokuwiki-plugin-pdb/​archive/​master.zip|Download]] ​ |
 +
 +
 +======Functions======
 +
 +**%%{{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|
 +
 +
 +
 +
 +
 +
 +======Caching files======
 +This plugin caches two kinds of files as media files.
 +  -Protein images from RCSB server in /​data/​media/​rcsb_image/​ directory
 +  -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)\\ ​
 +
 +/*
 +**%%{{rcsb_image:​1j7l.jpg?​150|example 1J7L}}%%**
 +{{rcsb_image:​1j7l.jpg?​150|example 1J7L}}
 +*/
 +
 +======Examples======
 +
 +
 +
 +=====small=====
 +<float left200>
 +  {{pdb>​small:​1WLA}}
 +</​float>​
 +<float left>
 +{{pdb>​small:​1WLA}}
 +</​float>​
 +
 +=====medium=====
 +<float left200>
 +  {{pdb>​medium:​1WLA}}
 +</​float>​
 +<float left>
 +{{pdb>​medium:​1WLA}}
 +</​float>​
 +=====large=====
 +  {{pdb>​large:​1WLA}}
 +
 +{{pdb>​large:​1WLA}}
 +
 +=====link=====
 +<float left200>
 +  {{pdb>​link:​1WLA}}
 +</​float>​
 +<float left>
 +{{pdb>​link:​1WLA}}
 +</​float>​
 +
 +=====short=====
 +<float left200>
 +  {{pdb>​short:​1WLA}}
 +</​float>​
 +<float left>
 +{{pdb>​short:​1WLA}}
 +</​float>​
 +=====long=====
 +<float left200>
 +  {{pdb>​long:​1WLA}}
 +</​float>​
 +<float left>
 +{{pdb>​long:​1WLA}}
 +</​float>​
 +=====serchbox=====
 +<float left200>
 +  {{pdb>​searchbox}}
 +</​float>​
 +<float left>
 +{{pdb>​searchbox}}
 +</​float>​
 +
 +
 +
 +=====structureID=====
 +This command converts from PDB ID into StructureID of NCBI.
 +
 +<float left200>
 +  {{pdb>​structureID:​1WLA}}
 +</​float>​
 +<float left>
 +{{pdb>​structureID:​1WLA}}
 +</​float>​
 +
 +=====fullSmall=====
 +Combination of an image from PDB ID and a short description from NCBI.
 +
 +  {{pdb>​fullSmall:​1WLA}}
 +
 +{{pdb>​fullSmall:​1WLA}}
 +
 +
 +=====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.
 +<float left200>
 +  {{pdb>​summaryXML:​1WLA}}
 +</​float>​
 +<float left400>
 +{{pdb>​summaryXML:​1WLA}}
 +</​float>​
 +
 +
 +====== History ======
 +  *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
 +======Links======
 +<float icon(compass)>​
 +  *[[SearchNCBI plugin]]
 +  *[[SearchDDBJ plugin]]
 +  *[[SearchEMBL plugin]]
 +  *[[PDB plugin]]
 +</​float>​
 +<​clear/>​
 +
 +{{tag>​dokuwiki plugin}}