Iterate over conformers of a collection of molecules stored in SDF format.
This class is analogous to the
IteratingSDFReader
except that
rather than return a single
IAtomContainer
at each iteration this
class will return all the conformers for a given molecule at each iteration.
The class assumes that the molecules are stored in SDF format and that all conformers for a given
molecule are in sequential order.
Currently, the code uses the title of each molecule in the SD file to perform te conformer check
and so it is important that all conformers for a given molecule have the same title field, but
different from the title fields of conformers of other molecules. In
the future the class will allow the user to perform the check using either the title or a more
rigorous (but more time-consuming) graph isomorphism check.
Example usage is
String filename = "/Users/rguha/conf2.sdf";
IteratingMDLConformerReader2 reader = new IteratingMDLConformerReader2(
new FileReader(new File(filename)), DefaultChemObjectBuilder.getInstance());
while (reader.hasNext()) {
ConformerContainer2 cc = (ConformerContainer2) reader.next();
}
// do something with this set of conformers