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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 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 | bio.zip (2.8KB) | 2008-03-22 |
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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');
This class accesses to NCBI Entrez database.
properties
eSummaryURL | String format to retrieve XML file of database and ID |
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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 $db database by using unique ID from NCBI. |
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SearchXml($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,&$xml) | Extract some items from Search XML |
This class accesses to RCSB PDB site.
properties
ImgURL | String format of URL to retrieve an image of PDB |
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LinkURL | String format to make a link to a specific PDB |
LinkFormat | String format to make a link html of PDB Explorer |
functions
DownloadImage($pdbid,$path) | Download an image to $path using PDB ID from RCSB site. |
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ExplorerURL($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 |
This class is a simple class for XML parser.
properties
tag | Tag name |
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value | Element value |
attributes | Attributes of this element |
next | Array of child classes |