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:

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:

bioclipse  pubchem  VNWKTOKETHGBQD-UHFFFAOYSA-N