On Friday 17 August 2007 23:56:18 Bala B K wrote: > Hi, > > I just downloaded one sdf file from PubChem that contains 25,000 > entries > (ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF/Compound_0000 >0001_00025000.sdf.gz). I tried to read the atomcontainers using > ChemFileManipulator.getAllAtomContainers [code attached] but got an > out of memory error. Is there a way to get the atom containers one by > one? Yes. org.openscience.cdk.io.iterator.IteratingMDLReader > > Thanks, > Bala.
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