name = 'pdb';
if (!class_exists('plugin_cache'))
@require_once(DOKU_PLUGIN.$this->name.'/classes/cache.php');
if (!class_exists('rcsb')||!class_exists('ncbi')||!class_exists('xml'))
@require_once(DOKU_PLUGIN.$this->name.'/classes/sciencedb.php');
$this->ncbi = new ncbi();
$this->rcsb = new rcsb();
$this->xmlCache = new plugin_cache("ncbi_esummary","structure","xml.gz");
$this->imgCache = new plugin_cache("rcsb_image",'',"jpg");
$this->searchBox= DOKU_PLUGIN.'pdb/pdb_search_box.htm';
$this->imageW['small'] = 80;
$this->imageW['medium'] = 250;
$this->imageW['large'] = 500;
}
function getType(){ return 'substition'; }
function getSort(){ return 158; }
function connectTo($mode) { $this->Lexer->addSpecialPattern('\{\{pdb>[^}]*\}\}',$mode,'plugin_pdb'); }
/**
* Handle the match
*/
function handle($match, $state, $pos, Doku_Handler $handler){
$match = substr($match,6,-2);
return array($state,explode(':',$match));
}
/**
* Create output
*/
function render($mode, Doku_Renderer $renderer, $data){
if($mode != 'xhtml'){return false;}
list($state, $query) = $data;
list($cmd,$pdbid) = $query;
$pdbid = urlencode($pdbid);
$cmd = strtolower($cmd);
if ($cmd=='small' || $cmd=='medium' || $cmd=='large'){
$filename = $this->imgCache->GetMediaPath($pdbid);
if ($this->rcsb->DownloadImage($pdbid,$filename)!==false)
$renderer->doc.= $this->getImageHtml($pdbid,$cmd).NL;
else
$renderer->doc.= $this->getLang('pdb_no_image').NL;
return true;
}else if($cmd=='short'||$cmd=='long'){
$summaryXML = $this->getSummaryXML($pdbid);
if(!empty($summaryXML))
$renderer->doc.= $this->getTextHtml($pdbid,$cmd,$summaryXML);
else
$renderer->doc.= $this->getLang('pdb_no_summary').NL;
return true;
}else if($cmd=='fullsmall'){
$filename = $this->imgCache->GetMediaPath($pdbid);
if ($this->rcsb->DownloadImage($pdbid,$filename)!==false)
$imageHtml = $this->getImageHtml($pdbid,"small").NL;
else
$imageHtml = $this->getLang('pdb_no_image').NL;
$renderer->doc.=''.$imageHtml.'
'.NL;
$summaryXML = $this->getSummaryXML($pdbid);
if(!empty($summaryXML))
$textHtml = $this->getTextHtml($pdbid,"long",$summaryXML);
else
$renderer->doc.= $this->getLang('pdb_no_summary').NL;
$renderer->doc.=''.$textHtml.'
'.NL;
$renderer->doc.=''.NL;
return true;
}
switch($cmd){
case 'searchbox':
$renderer->doc .= file_get_contents($this->searchBox);
return true;
case 'link':
$renderer->doc .= $this->rcsb->ExplorerLink($pdbid);
return true;
case 'summaryxml':
$summaryXML = $this->getSummaryXML($pdbid);
$renderer->doc.="".htmlspecialchars($summaryXML)."
";
return true;
case 'structureid':
$summaryXML = $this->getSummaryXML($pdbid);
$sid = $this->ncbi->GetSearchItem("Id",$summaryXML);
if (!empty($sid)){
$renderer->doc.="StructureID:".$sid;
}else{
$renderer->doc.=$pdbid." was not found.";
}
return true;
case 'clear_summary':
$renderer->doc.="Summary cleared.";
$this->xmlCache->ClearCache();
return true;
case 'clear_image':
$renderer->doc.="Image cleared.";
$this->imgCache->ClearCache();
return true;
case 'remove_dir':
$renderer->doc.="Directory removed";
$this->xmlCache->RemoveDir();
$this->imgCache->RemoveDir();
return true;
default:
// Command was not found..
$renderer->doc.=''.sprintf($this->getLang('plugin_cmd_not_found'),$cmd).'
';
$renderer->doc.=''.$this->getLang('pdb_available_cmd').'
';
return true;
}
}
/**
* Get renderered Html of Image
*/
function getImageHtml($pdbid,$type){
$pdbid = $this->rcsb->PDBformat($pdbid);
if ($pdbid===false) return NULL;
$url = $this->imgCache->GetMediaLink($pdbid);
$w = $this->imageW[$type];
$html = '';
$html.= '
';
$html.= '
';
$html.=''.$PdbAcc.'';
$html.=' - '.$PdbClass.'';
if ($type=='long'){
$html.='
'.$PdbDescr.'
';
if (!empty($LigCode)){
$html.='
';
$ss = (strpos("|",$LigCode)===false)?
$this->getLang('pdb_ligand'):$this->getlang('pdb_ligands');
$html.=$ss.$LigCode.'
';
}
}
$html.='
'.NL;
return $html;
}
/**
* Get summary XML from cache or NCBI
*/
function getSummaryXml($pdbAcc){
global $conf;
$cachedXml = $this->xmlCache->GetMediaText($pdbAcc);
if ($cachedXml!==false){ return $cachedXml; }
// convert PDB ID to Structure ID
$eSearchXml = $this->ncbi->SearchXml('structure',$pdbAcc);
$ids = $this->ncbi->GetSearchItems("Id",$eSearchXml);
$id=0;
for ($i=0;$incbi->SummaryXML('structure',$ids[$i]);
$tmpPdbId = $this->ncbi->GetSummaryItem("PdbAcc",$tmpXml);
if (strtolower($pdbAcc)==strtolower($tmpPdbId)){
$id = $ids[$i];
}
}
if ($id==0) return NULL;
// Get summary XML
$summary = $this->ncbi->SummaryXml('structure',$id);
if (!empty($summary)){
$cachePath = $this->xmlCache->GetMediaPath($pdbAcc);
if(io_saveFile($cachePath,$summary)){
chmod($cachePath,$conf['fmode']);
}
}
return $summary;
}
/*
* Convert PDB ID to Structure ID
*/
function PDBtoStructureID($pdbAcc){
$xml = $this->SearchXml('structure',$pdbAcc);
$ids = $this->GetSearchItems("Id",$xml);
for ($i=0;$iSummaryXML('structure',$ids[$i]);
$tmpPdbId = $this->GetSummaryItem("PdbAcc",$tmpXml);
if (strtolower($pdbAcc)==strtolower($tmpPdbId)){
return $ids[$i];
}
}
return 0;
}
}
?>