Friday, August 07, 2009

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:

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 ="malaria 300:500[MW]"))
Other filters you can use in (provided by PubChem itself), includes (with examples):
  • [el]:"Au[el]")
  • [inchi]:"\"InChI=1S/CH4/h1H4\"[inchi]")
  • [inchikey]:"VNWKTOKETHGBQD-UHFFFAOYSA-N[inchikey]")
  • [mimass]:"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 ="375.9785:375.9786[mimass]"))
cdk.saveSDFile("/Virtual/hits.sdf", list)"/Virtual/hits.sdf")
Resulting in: