Le 13-01-2016 à 20:58, Paul PILLOT <paulpil...@gmail.com> a écrit :
Hi Eric,
rcsb implements a REST API that you can query through Ajax to get many answers
to a lot of question.
Here is an example of code I designed to get informations from a PDB, such as
the number and names of chains, the ligands, the related pubmed abstract, etc…
PDB rest web service returns XML documents that can be easily parsed with
Jquery built in fonctions : find() to get the main node, attr() to get specific
node attributes.
My internet access is very slow at the moment, so I am not able to check which
are the nodes you are looking after, but I am convinced that you could find the
answers to your questions through this very powerful and effective channel.
Paul
$.ajax({
url: "http://www.pdb.org/pdb/rest/describePDB
<http://www.pdb.org/pdb/rest/describePDB>",
data: {
structureId: pdb
},
success: function(txt){
var $xml = $(txt);
var node = $xml.find("PDB");
if (node.length==0) {
alert(« Unknown PDB
identifier",'reponsePdb','error');
return;
}
var pId = node.attr("pubmedId");
var titre = node.attr("title");
var authors =
node.attr('citation_authors');
var txt = '<div id="article"><span
class="label label-info">Titre</span> '+titre+' ';
txt += '<span class="label
label-info">Pubmed</span> <a target="_blank"
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids='+pId+'
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids='+pId+'>">'+pId+'</a>'
txt += ' <span class="label
label-info">Auteurs</span> '+authors;
txt+= '</div><div
id="caracteristiquesMol"></div>';
$('#reponsePdb').append(txt);
$('#reponsePdb').append('<br />');
$('#auteur').val(authors);
$('#codePdb').val(pdb).triggerHandler('change');
$('#reponsePdb').data('pdb',pdb).data('pubmed_article',pId).data('auteurs_article',authors).data('titre_article',titre);
$('#imagePdb').append("<img
class='pdb-img' src='http://www.pdb.org/pdb/images/
<http://www.pdb.org/pdb/images/>"+pdb+"_bio_r_500.jpg?bioNum=1'/>");
$.ajax({
url:
"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
<http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi>",
data: {
db: "pubmed",
id: pId,
retmode: "xml",
rettype: "abstract"
},
success: function(txt){
//console.log(txt);
var $xml = $(txt);
var txt = '';
var pmc =
$xml.find("ArticleId[IdType='pmc']").text();
var volume =
$xml.find("Volume").text();
var revue =
$xml.find("Title").text();
var pages =
$xml.find("MedlinePgn").text();
var annee =
$xml.find("Year:first").text();
var doi =
$xml.find("ArticleId[IdType='doi']").text();
var abstract =
$xml.find("AbstractText").text();
txt += '<br /><span
class="label label-info">in</span> '+revue+' '+annee+' n°'+volume+ ' p'+pages+'
';
if (pmc.length>0) txt
+= '<span class="label label-info »>Full article (PubMedCentral)</span> <a
target="_blank" href="http://www.ncbi.nlm.nih.gov/pmc/articles/'+pmc+'/
<http://www.ncbi.nlm.nih.gov/pmc/articles/'+pmc+'/>">'+pmc+'</a> ';
if (doi.length>0) txt
+= '<span class="label label-info">Site de l\'éditeur</span> <a
target="_blank" href="http://dx.doi.org/'+doi+'
<http://dx.doi.org/'+doi+'>">'+revue+'</a> ';
txt += '<br /><span
class="label label-info »>Abstract</span> '+abstract+'<br />'
$('#article').append(txt);
var tiret =
pages.indexOf('-');
var pdeb =
pages.substr(0,tiret), pfin = pages.substr(tiret+1);
$('#reponsePdb').data('annee_article',annee).data( 'volume_article' , volume
).data('journal_article',revue).data('abstract_article',abstract).data('page_deb_article',pdeb).data('page_fin_article',pfin);
}
});
$.ajax({
url:
"http://www.pdb.org/pdb/rest/describeMol
<http://www.pdb.org/pdb/rest/describeMol>",
data: {
structureId: pdb
},
success: function(txt){
var $xml = $(txt);
var chaines
$xml.find("polymer").each(function(index,el){
var t = '<br
/><span class="label label-success">Chaines</span>';
$(this).find("chain").each(function(){
t+=
$(this).attr('id')+' ';
})
var nature =
$(this).attr('type');
t+= ' <span
class="label label-success">Nature</span> '+nature+' ';
var nom =
$(this).find("polymerDescription").attr('description')
t+= ' <span
class="label label-success">Nom</span> '+nom+' ';
$(this).find("accession").each(function(){
var
uniprotId = $(this).attr('id');
t+= '
<a target="_blank" href="http://www.uniprot.org/uniprot/'+uniprotId+'
<http://www.uniprot.org/uniprot/'+uniprotId+'>">'+uniprotId+'</a> '
})
var organisme =
$(this).find("Taxonomy").attr('name')
if (organisme){
t += '
<span class="label label-success">Organisme</span> '+organisme+' ';
selOrganisme(organisme)
}
$('#caracteristiquesMol').append(t);
});
var mut =
$xml.find("mutation:first").attr('desc');
if (mut) {
t = '<br/><span
class="label label-warning">Mutation</span> '+mut+' ';
$('#caracteristiquesMol').append(t);
}
}
});
$.ajax({
url:
"http://www.pdb.org/pdb/rest/ligandInfo
<http://www.pdb.org/pdb/rest/ligandInfo>",
data: {
structureId: pdb
},
success: function(txt){
var $xml = $(txt);
var chaines
$xml.find("ligand").each(function(index,el){
var t = '<br
/><span class="label label-important">Ligand</span> ';
var chId =
$(this).attr('chemicalID');
var type =
$(this).attr('type');
var nom =
$(this).find('chemicalName').text();
var smiles =
$(this).find('smiles').text();
t+= chId + ' ';
t+= ' <span
class="label label-important">Nom</span> '+nom+' ';
t+= ' <span
class="label label-important">Type</span> '+type+' ';
t+= '<br /><img
src="http://cactus.nci.nih.gov/chemical/structure/'+smiles+'/image
<http://cactus.nci.nih.gov/chemical/structure/'+smiles+'/image>"/><br />';
$('#caracteristiquesMol').append(t);
});
}
});
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