====== bio plugin ======

---- plugin ----
description: Class library for biology and biochemistry.
author     : Ikuo Obataya
email      : I.Obataya@gmail.com
type       : helper
lastupdate : 2008-03-22
compatible : 2006-11-06 or later
depends    : 
conflicts  : 
similar    : 
tags       : biology chemistry helper
----

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|{{http://wiki.symplus.co.jp/lib/exe/fetch.php/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.