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{
"translatorID": "e16095ae-986c-4117-9cb6-20f3b7a52f64",
"label": "Protein Data Bank",
"creator": "Philipp Zumstein",
"target": "^https?://www\\.(pdb|rcsb)\\.org/pdb/",
"minVersion": "3.0",
"maxVersion": "",
"priority": 100,
"inRepository": true,
"translatorType": 4,
"browserSupport": "gcsibv",
"lastUpdated": "2017-06-03 18:51:04"
}
/*
***** BEGIN LICENSE BLOCK *****
Copyright © 2017 Philipp Zumstein
This file is part of Zotero.
Zotero is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Zotero is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with Zotero. If not, see <http://www.gnu.org/licenses/>.
***** END LICENSE BLOCK *****
*/
function detectWeb(doc, url) {
if (url.indexOf("results.do") != -1 && getSearchResults(doc, true)) {
return "multiple";
} else if (url.indexOf("structureId") != -1) {
return "journalArticle";
}
}
function getSearchResults(doc, checkOnly) {
var items = {};
var found = false;
var rows = ZU.xpath(doc, '//li[contains(@class, "oneSearchResult")]//h3/a');
for (var i=0; i<rows.length; i++) {
var href = rows[i].href;
var title = ZU.trimInternal(rows[i].textContent);
if (!href || !title) continue;
if (checkOnly) return true;
found = true;
items[href] = title;
}
return found ? items : false;
}
function doWeb(doc, url) {
if (detectWeb(doc, url) == "multiple") {
Zotero.selectItems(getSearchResults(doc, false), function (items) {
if (!items) {
return true;
}
var articles = [];
for (var i in items) {
articles.push(i);
}
ZU.processDocuments(articles, scrape);
});
} else {
scrape(doc, url);
}
}
function scrape(doc, url) {
var translator = Zotero.loadTranslator('web');
// Embedded Metadata
translator.setTranslator('951c027d-74ac-47d4-a107-9c3069ab7b48');
translator.setDocument(doc);
translator.setHandler('itemDone', function (obj, item) {
item.DOI = ZU.xpathText(doc, '//li[strong[contains(., "DOI")]]/a');
item.tags = [];
var pdburl = ZU.xpathText(doc, '//ul/li/a[contains(., "PDB Format")]/@href');
if (pdburl) {
item.attachments.push({
url: pdburl,
title: "Protein Data Bank .pdb File",
mimeType: "chemical/x-pdb"
});
}
item.complete();
});
translator.translate();
}
/** BEGIN TEST CASES **/
var testCases = [
{
"type": "web",
"url": "http://www.rcsb.org/pdb/explore/explore.do?structureId=1COW",
"items": [
{
"itemType": "journalArticle",
"title": "The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B.",
"creators": [
{
"firstName": "M. J.",
"lastName": "van Raaij",
"creatorType": "author"
},
{
"firstName": "J. P.",
"lastName": "Abrahams",
"creatorType": "author"
},
{
"firstName": "A. G.",
"lastName": "Leslie",
"creatorType": "author"
},
{
"firstName": "J. E.",
"lastName": "Walker",
"creatorType": "author"
}
],
"date": "1996",
"DOI": "10.2210/pdb1cow/pdb",
"abstractNote": "1COW: The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B.",
"libraryCatalog": "www.rcsb.org",
"pages": "6913-6917",
"publicationTitle": "Proc.Natl.Acad.Sci.USA",
"url": "http://www.rcsb.org/pdb/explore/explore.do?structureId=1COW",
"volume": "93",
"attachments": [
{
"title": "Snapshot"
},
{
"title": "Protein Data Bank .pdb File",
"mimeType": "chemical/x-pdb"
}
],
"tags": [],
"notes": [],
"seeAlso": []
}
]
},
{
"type": "web",
"url": "http://www.rcsb.org/pdb/explore/explore.do?structureId=1VHZ",
"items": [
{
"itemType": "journalArticle",
"title": "Structural analysis of a set of proteins resulting from a bacterial genomics project",
"creators": [
{
"firstName": "J.",
"lastName": "Badger",
"creatorType": "author"
},
{
"firstName": "J. M.",
"lastName": "Sauder",
"creatorType": "author"
},
{
"firstName": "J. M.",
"lastName": "Adams",
"creatorType": "author"
},
{
"firstName": "S.",
"lastName": "Antonysamy",
"creatorType": "author"
},
{
"firstName": "K.",
"lastName": "Bain",
"creatorType": "author"
},
{
"firstName": "M. G.",
"lastName": "Bergseid",
"creatorType": "author"
},
{
"firstName": "S. G.",
"lastName": "Buchanan",
"creatorType": "author"
},
{
"firstName": "M. D.",
"lastName": "Buchanan",
"creatorType": "author"
},
{
"firstName": "Y.",
"lastName": "Batiyenko",
"creatorType": "author"
},
{
"firstName": "J. A.",
"lastName": "Christopher",
"creatorType": "author"
},
{
"firstName": "S.",
"lastName": "Emtage",
"creatorType": "author"
},
{
"firstName": "A.",
"lastName": "Eroshkina",
"creatorType": "author"
},
{
"firstName": "I.",
"lastName": "Feil",
"creatorType": "author"
},
{
"firstName": "E. B.",
"lastName": "Furlong",
"creatorType": "author"
},
{
"firstName": "K. S.",
"lastName": "Gajiwala",
"creatorType": "author"
},
{
"firstName": "X.",
"lastName": "Gao",
"creatorType": "author"
},
{
"firstName": "D.",
"lastName": "He",
"creatorType": "author"
},
{
"firstName": "J.",
"lastName": "Hendle",
"creatorType": "author"
},
{
"firstName": "A.",
"lastName": "Huber",
"creatorType": "author"
},
{
"firstName": "K.",
"lastName": "Hoda",
"creatorType": "author"
},
{
"firstName": "P.",
"lastName": "Kearins",
"creatorType": "author"
},
{
"firstName": "C.",
"lastName": "Kissinger",
"creatorType": "author"
},
{
"firstName": "B.",
"lastName": "Laubert",
"creatorType": "author"
},
{
"firstName": "H. A.",
"lastName": "Lewis",
"creatorType": "author"
},
{
"firstName": "J.",
"lastName": "Lin",
"creatorType": "author"
},
{
"firstName": "K.",
"lastName": "Loomis",
"creatorType": "author"
},
{
"firstName": "D.",
"lastName": "Lorimer",
"creatorType": "author"
},
{
"firstName": "G.",
"lastName": "Louie",
"creatorType": "author"
},
{
"firstName": "M.",
"lastName": "Maletic",
"creatorType": "author"
},
{
"firstName": "C. D.",
"lastName": "Marsh",
"creatorType": "author"
},
{
"firstName": "I.",
"lastName": "Miller",
"creatorType": "author"
},
{
"firstName": "J.",
"lastName": "Molinari",
"creatorType": "author"
},
{
"firstName": "H. J.",
"lastName": "Muller-Dieckmann",
"creatorType": "author"
},
{
"firstName": "J. M.",
"lastName": "Newman",
"creatorType": "author"
},
{
"firstName": "B. W.",
"lastName": "Noland",
"creatorType": "author"
},
{
"firstName": "B.",
"lastName": "Pagarigan",
"creatorType": "author"
},
{
"firstName": "F.",
"lastName": "Park",
"creatorType": "author"
},
{
"firstName": "T. S.",
"lastName": "Peat",
"creatorType": "author"
},
{
"firstName": "K. W.",
"lastName": "Post",
"creatorType": "author"
},
{
"firstName": "S.",
"lastName": "Radojicic",
"creatorType": "author"
},
{
"firstName": "A.",
"lastName": "Ramos",
"creatorType": "author"
},
{
"firstName": "R.",
"lastName": "Romero",
"creatorType": "author"
},
{
"firstName": "M. E.",
"lastName": "Rutter",
"creatorType": "author"
},
{
"firstName": "W. E.",
"lastName": "Sanderson",
"creatorType": "author"
},
{
"firstName": "K. D.",
"lastName": "Schwinn",
"creatorType": "author"
},
{
"firstName": "J.",
"lastName": "Tresser",
"creatorType": "author"
},
{
"firstName": "J.",
"lastName": "Winhoven",
"creatorType": "author"
},
{
"firstName": "T. A.",
"lastName": "Wright",
"creatorType": "author"
},
{
"firstName": "L.",
"lastName": "Wu",
"creatorType": "author"
},
{
"firstName": "J.",
"lastName": "Xu",
"creatorType": "author"
},
{
"firstName": "T. J.",
"lastName": "Harris",
"creatorType": "author"
}
],
"date": "2005",
"DOI": "10.2210/pdb1vhz/pdb",
"abstractNote": "1VHZ: Structural analysis of a set of proteins resulting from a bacterial genomics project",
"libraryCatalog": "www.rcsb.org",
"pages": "787-796",
"publicationTitle": "Proteins",
"url": "http://www.rcsb.org/pdb/explore/explore.do?structureId=1VHZ",
"volume": "60",
"attachments": [
{
"title": "Snapshot"
},
{
"title": "Protein Data Bank .pdb File",
"mimeType": "chemical/x-pdb"
}
],
"tags": [],
"notes": [],
"seeAlso": []
}
]
}
]
/** END TEST CASES **/
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