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bio_plugin [2016/10/30 23:44] (現在)
ライン 1: ライン 1:
 +====== Bio plugin ======
 +:!: This plugin is deprecated :!:
  
 +
 +This DokuWiki plugin provides some utilities for biology and biochemistry. This plugin is a sort of class library which does not extends DokuWiki_syntax_plugin. ​
 +
 +^Download|{{computer:​source:​bio.zip|bio.zip}} (2.8KB)|2008-03-22|
 +
 +=====Classes=====
 +In order to define all classes, read '​bio.php'​. This entry script will read all classes if they don'​t ​  ​exist.
 +
 +  @require_once('​bio.php'​);​
 +
 +
 +
 +====NCBI class====
 +This class accesses to NCBI Entrez database.
 +
 +**properties**
 +^eSummaryURL|String format to retrieve XML file of database and ID|
 +^eSearchURL |String format to search in NCBI database by terms|
 +^pubchemURL |String format to retrieve XML file of PubChem|
 +^pubmedURL ​ |String format to make a link to PubMed|
 +
 +**functions**
 +^SummaryXml($db,​$id)|Retrieve a summary XML data of $db database by using unique ID from NCBI.|
 +^SearchXml($db,​$terms) |Get search result XML of terms from NCBI.|
 +^PDBtoStructureID($pdbAcc)|Convert to PDB ID to NCBI Structure ID|
 +^GetPubchemXml($cid)|Get a Pubchem summary XML data from NCBI.|
 +^GetSummaryItem($item,&​$xml)|Extract an item element from Summary XML|
 +^GetSummaryItems($item,&​$xml)|Extract some items from Summary XML|
 +^GetSearchItem($item,&​$xml)|Extract an item element from Search XML|
 +^GetSearchItem($item,&​$xml)|Extract some items from Search XML|
 +
 +
 +====RCSB class====
 +This class accesses to RCSB PDB site.
 +
 +**properties**
 +^ImgURL ​   |String format of URL to retrieve an image of PDB|
 +^LinkURL ​  ​|String format to make a link to a specific PDB|
 +^LinkFormat|String format to make a link html of PDB Explorer|
 +
 +**functions**
 +^DownloadImage($pdbid,​$path)|Download an image to $path using PDB ID from RCSB site.|
 +^ExplorerURL($pdbid) ​       |Create a URL to a specific PDB entry.|
 +^ExplorerLink($pdbid) ​      ​|Create a link html to a specific PDB entry.|
 +^PDBformat($pdbid) ​         |Check PDB ID|
 +
 +
 +
 +====XML class====
 +This class is a simple class for XML parser. ​
 +
 +**properties**
 +^tag|Tag name|
 +^value|Element value|
 +^attributes|Attributes of this element|
 +^next|Array of child classes|
 +====== History ======
 +  *2008.3.22
 +    *First version was uploaded.