Searching PubChem from within Bioclipse

For the application note which we are about to submit, I was working on improving the PubChem Bioclipse API a bit, resulting in new download methods:

	// downloading as IMolecule or List<IMolecule>
	mol = pubchem.download(176)
	mols = pubchem.download(pubchem.search("HIV"))
	// download as String
	mol = cdk.fromString(pubchem.downloadAsString(176))

view raw NewPubChemAPI.js hosted with ❤ by GitHub

The search allows using PubChem Filters which provides many simple means to restrict the search results. For example, we can search molecules and restrict on the molecular weight:

lists = pubchem.download(pubchem.search("malaria 300:500[MW]"))

Other filters you can use in pubchem.search (provided by PubChem itself), includes (with examples):

• [el]: pubchem.search("Au[el]")
• [inchi]: pubchem.search("\"InChI=1S/CH4/h1H4\"[inchi]")
• [inchikey]: pubchem.search("VNWKTOKETHGBQD-UHFFFAOYSA-N[inchikey]")
• [mimass]: pubchem.search("375.9785:375.9786[mimass]")

And many, many more... see the linked Filters page.

Now, you surely want to look at the hits, for which we use the molecular table editor:

list = pubchem.download(pubchem.search("375.9785:375.9786[mimass]"))
cdk.saveSDFile("/Virtual/hits.sdf", list)
ui.open("/Virtual/hits.sdf")

Resulting in: