function fix_search_items($item)
{
$data = array('chemspider:id' => $item->CSID, 'chem:molecular-formula' => preg_replace('/_\\{(\\d+)\\}/', '$1', $item->MF), 'chem:smiles' => $item->SMILES, 'iupac:inchi' => $item->InChI, 'iupac:inchikey' => $item->InChIKey, 'chem:molecular-weight' => $item->MolecularWeight, 'dc:title' => $item->CommonName, 'misc:image' => url('http://www.chemspider.com/ImagesHandler.ashx', array('w' => 200, 'h' => 200, 'id' => $item->CSID)), 'rdf:uri' => url('http://www.chemspider.com/' . urlencode($item->CSID)));
if ($data['iupac:inchi']) {
$properties = mol2stdinchi($data['iupac:inchi']);
$data['iupac:stdinchi'] = $properties['iupac:stdinchi'];
$data['iupac:stdinchikey'] = $properties['iupac:stdinchikey'];
}
return $data;
}
function parse_sdf($sdf){
$items = array();
foreach (explode('$$$$', $sdf) as $item){
if (preg_match('/^(.+?\nM\s+END\n)(.*)/s', $item, $matches)){
list(, $structure, $text) = $matches;
$item = array();
preg_match_all('/>\s+<(\w+)>(?:\r|\n)(.+?)(?:\r|\n){2}/s', $text, $meta_matches, PREG_SET_ORDER);
foreach ($meta_matches as $m)
$item['meta-' . $m[1]] = $m[2];
$item['chem:mol'] = $structure;
$item = array_merge($item, mol2stdinchi($structure));
$items[] = $item;
}
}
return $items;
}
function parse_item($item)
{
$synonyms = array();
foreach ($item->Synonyms as $name) {
$synonyms[] = $name->data;
}
$names = array();
foreach ($item->IupacNames as $name) {
$names[] = $name->data;
}
$mol = null;
if (!empty($item->ChemicalStructures)) {
foreach ($item->ChemicalStructures as $structure) {
if ($structure->defaultStructure == true) {
$mol = $structure->structure;
}
}
if (is_null($mol)) {
$mol = $item->ChemicalStructures[0]->structure;
}
$inchi = mol2stdinchi($mol);
}
return array('chebi:id' => $item->chebiId, 'dc:title' => $item->chebiAsciiName, 'iupac:inchi' => $item->inchi, 'iupac:inchikey' => preg_replace('/^InChIKey=/', '', $item->inchiKey), 'iupac:stdinchi' => $inchi['iupac:stdinchi'], 'iupac:stdinchikey' => $inchi['iupac:stdinchikey'], 'chem:molecular-formula' => $item->Formulae ? $item->Formulae[0]->data : null, 'chem:mol' => $mol, 'chem:smiles' => $item->smiles, 'misc:synonyms' => $synonyms, 'iupac:name' => $names, 'misc:image' => url('http://www.ebi.ac.uk/chebi/displayImage.do', array('defaultImage' => 'true', 'imageIndex' => 0, 'chebiId' => $item->chebiId)), 'rdf:uri' => url('http://www.ebi.ac.uk/chebi/searchId.do', array('chebiId' => $item->chebiId)));
}