net.sf.octet.model
Interface Conformation

All Superinterfaces:

GammaSequenceCollection, PaddleWheelCollection

All Known Implementing Classes:

BasicConformation

public interface Conformation

extends PaddleWheelCollection, GammaSequenceCollection

Representation of molecular conformation. Conformation is based on concepts first presented in a paper by Dietz (J. Chem. Inf. Comput. Sci. 1995, 35, 787). The mechanism of querying a Conformation is analogous to that for querying a Configuration.

Each instance of a conformational feature is represented by a single PaddleWheel/ GammaSequences pair. For example, a Molecule containing a trans double bond A-B will have one possible PaddleWheel/GammaSequence representation resulting from the A-B polarity and one possible representation resulting from the B-A polarity. Conformation will only capture one of these. The one that is represented is left as an implementation detail. Clients needing to compare conformational PaddleWheels should consider using PaddleWheelInvertor or an equivalent for this purpose.

Author:

Richard Apodaca

See Also:

Configuration, PaddleWheelInvertor

Method Summary

GammaSequence	getGammaSequence(PaddleWheel wheel) Returns the GammaSequence associated with the specified PaddleWheel.
PaddleWheel	getPaddleWheel(GammaSequence sequence) Returns the PaddleWheel associated with the specified GammaSequence.

Methods inherited from interface net.sf.octet.collection.PaddleWheelCollection

containsPaddleWheel, containsPaddleWheel, countPaddleWheels, getPaddleWheel, getPaddleWheel, getPaddleWheelIndex, iteratePaddleWheels, toPaddleWheelArray

Methods inherited from interface net.sf.octet.collection.GammaSequenceCollection

containsGammaSequence, containsGammaSequence, countGammaSequences, getGammaSequence, getGammaSequence, getGammaSequenceIndex, iterateGammaSequences, toGammaSequenceArray

Method Detail

getPaddleWheel

public PaddleWheel getPaddleWheel(GammaSequence sequence)

Returns the PaddleWheel associated with the specified GammaSequence.

Parameters:

sequence - the GammaSequence to search

Returns:

the PaddleWheel associated with sequence

Throws:

NoSuchGammaSequenceException - if sequence is unrecognized

getGammaSequence

public GammaSequence getGammaSequence(PaddleWheel wheel)

Returns the GammaSequence associated with the specified PaddleWheel.

Parameters:

wheel - the PaddleWheel to search

Returns:

the GammaSequence associated with wheel

Throws:

NoSuchPaddleWheelException - if wheel is unrecognized