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 | 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.