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org::openscience::cdk::ConformerContainer Class Reference

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List of all members.


class  CCIterator

Public Member Functions

boolean add (IAtomContainer atomContainer)
void add (int i, IAtomContainer atomContainer)
boolean addAll (Collection<?extends IAtomContainer > atomContainers)
boolean addAll (int i, Collection<?extends IAtomContainer > iAtomContainers)
void clear ()
 ConformerContainer (IAtomContainer atomContainer)
 ConformerContainer (IAtomContainer[] atomContainers)
boolean contains (Object o)
boolean containsAll (Collection<?> objects)
IAtomContainer get (int i)
String getTitle ()
int indexOf (Object o)
boolean isEmpty ()
Iterator< IAtomContaineriterator ()
int lastIndexOf (Object o)
ListIterator< IAtomContainerlistIterator ()
ListIterator< IAtomContainerlistIterator (int i)
IAtomContainer remove (int i)
boolean remove (Object o)
boolean removeAll (Collection<?> objects)
boolean retainAll (Collection<?> objects)
IAtomContainer set (int i, IAtomContainer atomContainer)
int size ()
List< IAtomContainersubList (int i, int i1)
Object[] toArray ()

Package Functions

public< IAtomContainer >
toArray (IAtomContainer[] ts)

Private Member Functions

Point3d[] getCoordinateList (IAtomContainer atomContainer)

Private Attributes

IAtomContainer atomContainer = null
List< Point3d[]> coordinates
String title = null

Detailed Description

A memory-efficient data structure to store conformers for a single molecule.

Since all the conformers for a given molecule only differ in their 3D coordinates this data structure stores a single IAtomContainer containing the atom and bond details and a List of 3D coordinate sets, each element being the set of 3D coordinates for a given conformer.

The class behaves in many ways as a List<IAtomContainer> object, though a few methods are not implemented. Though it is possible to add conformers by hand, this data structure is probably best used in combination with org.openscience.cdk.io.iterator.IteratingMDLConformerReader as

 IteratingMDLConformerReader reader = new IteratingMDLConformerReader(
          new FileReader(new File(filename)),
 while (reader.hasNext()) {
     ConformerContainer cc = (ConformerContainer) reader.next();
     for (IAtomContainer conformer : cc) {
         // do something with each conformer

.module data .githash

Rajarshi Guha
See also:

Definition at line 63 of file ConformerContainer.java.

The documentation for this class was generated from the following file:

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