Package org.openscience.cdk.io.iterator
Class IteratingMDLConformerReader
- java.lang.Object
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- org.openscience.cdk.io.iterator.IteratingMDLConformerReader
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- All Implemented Interfaces:
Iterator
public class IteratingMDLConformerReader extends Object implements Iterator
Iterate over conformers of a collection of molecules stored in SDF format. This class is analogous to theIteratingSDFReader
except that rather than return a singleIAtomContainer
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 isString 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
- Author:
- Rajarshi Guha
- See Also:
ConformerContainer
- Source code:
- main
- Belongs to CDK module:
- extra
- Keywords:
- file format SDF, conformer conformation
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Constructor Summary
Constructors Constructor Description IteratingMDLConformerReader(InputStream in, IChemObjectBuilder builder)
IteratingMDLConformerReader(Reader in, IChemObjectBuilder builder)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
hasNext()
Object
next()
void
remove()
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Detail
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IteratingMDLConformerReader
public IteratingMDLConformerReader(Reader in, IChemObjectBuilder builder)
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IteratingMDLConformerReader
public IteratingMDLConformerReader(InputStream in, IChemObjectBuilder builder)
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