meshi.symmetryComplex.molecularImageElements
Class SymmetricComplex

java.lang.Object
  meshi.molecularElements.Protein
      meshi.symmetryComplex.molecularImageElements.SymmetricComplex

All Implemented Interfaces:

Updateable

Direct Known Subclasses:

SymmetricComplexCompleter

public class SymmetricComplex
extends Protein
implements Updateable

Symmetric protein, each chain is a Protein object. Chain A is "real", the others are images computed using Transformations.

Nested Class Summary

Nested classes/interfaces inherited from class meshi.molecularElements.Protein

Protein.BackboneFilter

Field Summary

private static java.lang.String	CHAIN_LETTERS
private java.lang.String	chainLetters
private ResidueList	imageResidues
private int	numberOfUpdates
protected java.util.List<Transformation>	transformations

Fields inherited from class meshi.molecularElements.Protein

angles, atoms, bonds, chains, firstResidueIndex, modelNumber, name, residues, torsions

Constructor Summary

SymmetricComplex(AtomList initialAtoms, ResidueCreator creator, SequenceAlignment alignment, Transformation[] transformations)

SymmetricComplex(AtomList initialAtoms, ResidueCreator creator, SequenceAlignment alignment, Transformation[] transformations, java.lang.String chainLetters)

SymmetricComplex(AtomList initialAtoms, ResidueCreator creator, Transformation[] transformations)

SymmetricComplex(AtomList initialAtoms, ResidueCreator creator, Transformation[] transformations, java.lang.String chainLetters, boolean freeze)

SymmetricComplex(Transformation[] transformations, java.lang.String chainLetters)

Method Summary

java.lang.String	chainLetters()
void	generateImageChains()
Chain	getSource()
java.util.List<Transformation>	getTransformations()
ResidueList	imageResidues()
void	printChainsNames()
void	resetNumberOfUpdates()
static java.lang.String	setConsecutiveChainLetters(int size)
void	setSS(ResidueList residues, SequenceAlignment alignment)
java.util.List<Transformation>	transformations()
void	update(int numberOfUpdates)
void	updateLocations()

Methods inherited from class meshi.molecularElements.Protein

addChain, allYouWantToKnow, atoms, bonds, chain, chains, defrost, firstResidueIndex, firstResidues, freeze, freeze, getAtom, getProteinName, getProteinName, getSequence, missingResidues, modelNumber, name, nowhereAtoms, printAtomsToFile, residue, residue, residueAt, residues, sequence, setName, setSS, setSS, toString

Methods inherited from class java.lang.Object

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

Field Detail

transformations

protected java.util.List<Transformation> transformations

numberOfUpdates

private int numberOfUpdates

chainLetters

private java.lang.String chainLetters

CHAIN_LETTERS

private static final java.lang.String CHAIN_LETTERS

See Also:

Constant Field Values

imageResidues

private ResidueList imageResidues

Constructor Detail

SymmetricComplex

public SymmetricComplex(Transformation[] transformations,
                        java.lang.String chainLetters)

SymmetricComplex

public SymmetricComplex(AtomList initialAtoms,
                        ResidueCreator creator,
                        Transformation[] transformations)

SymmetricComplex

public SymmetricComplex(AtomList initialAtoms,
                        ResidueCreator creator,
                        SequenceAlignment alignment,
                        Transformation[] transformations)

SymmetricComplex

public SymmetricComplex(AtomList initialAtoms,
                        ResidueCreator creator,
                        SequenceAlignment alignment,
                        Transformation[] transformations,
                        java.lang.String chainLetters)

SymmetricComplex

public SymmetricComplex(AtomList initialAtoms,
                        ResidueCreator creator,
                        Transformation[] transformations,
                        java.lang.String chainLetters,
                        boolean freeze)

Method Detail

transformations

public java.util.List<Transformation> transformations()

imageResidues

public ResidueList imageResidues()

generateImageChains

public void generateImageChains()

getSource

public Chain getSource()

getTransformations

public java.util.List<Transformation> getTransformations()

updateLocations

public void updateLocations()

update

public void update(int numberOfUpdates)

Specified by:

update in interface Updateable

resetNumberOfUpdates

public void resetNumberOfUpdates()

setSS

public void setSS(ResidueList residues,
                  SequenceAlignment alignment)

chainLetters

public java.lang.String chainLetters()

setConsecutiveChainLetters

public static java.lang.String setConsecutiveChainLetters(int size)

printChainsNames

public void printChainsNames()