net.sf.octet.builder
Class AbstractMoleculeBuilder

java.lang.Object
  net.sf.octet.builder.AbstractRepresentationBuilder
      net.sf.octet.builder.AbstractMoleculeBuilder

All Implemented Interfaces:

RepresentationBuilder

public abstract class AbstractMoleculeBuilder

extends AbstractRepresentationBuilder

implements RepresentationBuilder

An extension of AbstractMoleculeBuilder intended for use in building partial or complete Molecule representations.

Author:

Richard Apodaca

Nested Class Summary

Nested classes inherited from class net.sf.octet.builder.AbstractRepresentationBuilder

AbstractRepresentationBuilder.AtomTemplate, AbstractRepresentationBuilder.BondingSystemTemplate, AbstractRepresentationBuilder.ConfigurationTemplate, AbstractRepresentationBuilder.ConformationTemplate, AbstractRepresentationBuilder.GammaSequenceTemplate, AbstractRepresentationBuilder.HalfPlaneTemplate, AbstractRepresentationBuilder.OrbitalTemplate, AbstractRepresentationBuilder.PaddleWheelTemplate

Constructor Summary

AbstractMoleculeBuilder()

Method Summary

protected BondingSystem	createBondingSystem(AbstractRepresentationBuilder.BondingSystemTemplate template) Returns a BondingSystem based on the current state of template.
protected BondingSystemCollection	createBondingSystems() Returns a BondingSystemCollection based on the current states of available BondingSystemTemplates.
protected Configuration	createConfiguration(AbstractRepresentationBuilder.ConfigurationTemplate template) Returns a Configuration based on the current state of template.
protected Conformation	createConformation() Returns a Conformation based on the state of this AbstractMoleculeBuilder.
protected GammaSequence	createGammaSequence(AbstractRepresentationBuilder.GammaSequenceTemplate template) Returns a GammaSequence based on the current state of template.
protected HalfPlane	createHalfPlane(AbstractRepresentationBuilder.HalfPlaneTemplate template) Returns a HalfPlane based on the current state of template.
protected NonbondingShell	createNonbondingShell(AbstractRepresentationBuilder.AtomTemplate template) Returns a NonbondingShell based on the current state of template.
protected Orbital	createOrbital(AbstractRepresentationBuilder.OrbitalTemplate template) Returns an Orbital based on the current state of template.
protected PaddleWheel	createPaddleWheel(AbstractRepresentationBuilder.PaddleWheelTemplate template) Returns a PaddleWheel based on the current state of template.

Methods inherited from class net.sf.octet.builder.AbstractRepresentationBuilder

addAtom, addBondingSystem, addConfiguration, addElectron, addGammaSequence, addHalfPlane, addHalfPlane, addHydrogens, addOrbital, connect, connect, constrainCenter, constrainLower, constrainUpper, createAtom, createAtomPair, flush, getAtomPairs, getAtoms, getAtomTemplates, getBondingSystemTemplates, getConformationTemplate, ionizeAntibondingElectrons, ionizeAtom, ionizeBondingElectrons

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.sf.octet.builder.RepresentationBuilder

addAtom, addBondingSystem, addConfiguration, addElectron, addGammaSequence, addHalfPlane, addHalfPlane, addHydrogens, addOrbital, connect, connect, constrainCenter, constrainLower, constrainUpper, flush, ionizeAntibondingElectrons, ionizeAtom, ionizeBondingElectrons

Constructor Detail

AbstractMoleculeBuilder

public AbstractMoleculeBuilder()

Method Detail

createBondingSystems

protected BondingSystemCollection createBondingSystems()

Returns a BondingSystemCollection based on the current states of available BondingSystemTemplates.

Returns:

a BondingSystemCollection based on the available BondingSystemTemplates

createBondingSystem

protected BondingSystem createBondingSystem(AbstractRepresentationBuilder.BondingSystemTemplate template)

Returns a BondingSystem based on the current state of template. If template only contains one AtomPair then an instance of SimpleBondingSystem is generated.

Parameters:

template - the template after which to model the BondingSystem - may not be null

Returns:

a BondingSystem based on template

createConfiguration

protected Configuration createConfiguration(AbstractRepresentationBuilder.ConfigurationTemplate template)

Returns a Configuration based on the current state of template. If template is null, then the static singleton instance of BasicConfiguration is returned.

Parameters:

template - the template after which to model the Configuration - may be null

Returns:

a Configuration based on template

createNonbondingShell

protected NonbondingShell createNonbondingShell(AbstractRepresentationBuilder.AtomTemplate template)

Returns a NonbondingShell based on the current state of template. If template is empty, then a static singleton instance of BasicNonbondingShell is returned.

Parameters:

template - the template on which to base the NonbondingShell - may be null

Returns:

a NonbondingShell based on template

createOrbital

protected Orbital createOrbital(AbstractRepresentationBuilder.OrbitalTemplate template)

Returns an Orbital based on the current state of template.

Parameters:

template - the template on which to based the Orbital - may not be null

Returns:

an Orbital based on template

createConformation

protected Conformation createConformation()

Returns a Conformation based on the state of this AbstractMoleculeBuilder.

Returns:

a Conformation based on the state of this AbstractMoleculeBuilder

createGammaSequence

protected GammaSequence createGammaSequence(AbstractRepresentationBuilder.GammaSequenceTemplate template)

Returns a GammaSequence based on the current state of template.

Parameters:

template - the template after which to model the GammaSequence

Returns:

a GammaSequence based on the current state of template

createPaddleWheel

protected PaddleWheel createPaddleWheel(AbstractRepresentationBuilder.PaddleWheelTemplate template)

Returns a PaddleWheel based on the current state of template.

Parameters:

template - the template after which to model the PaddleWheel

Returns:

a PaddleWheel based on the current state of template

createHalfPlane

protected HalfPlane createHalfPlane(AbstractRepresentationBuilder.HalfPlaneTemplate template)

Returns a HalfPlane based on the current state of template.

Parameters:

template - the template after whcih to model the HalfPlane

Returns:

a HalfPlane based on the current state of template