Uses of Class
org.proteinshader.structure.Atom

Packages that use Atom

org.proteinshader.graphics.adapter	Holds the StructureToGraphics class, which is used to manage the use of the drawing classes and OpenGL display lists.
org.proteinshader.gui	Holds all of the Swing GUI components and their associated listeners, including class Renderer, which is registered as a listener for the GLCanvas object that is used a drawing surface.
org.proteinshader.gui.components.controlpanel	Holds the JPanels used in the right-side retractable control panel of the GUI.
org.proteinshader.structure	Holds the classes that store information from a Protein Data Bank file: Structure, Model, Chain, AminoAcid, Heterogen, Water, Atom, Bond, Helix, BetaStrand, Loop, etc.
org.proteinshader.structure.visitor	Holds Visitor classes that know how to traverse the hierarchy of objects held by class Structure.
org.proteinshader.structure.visitor.modifiers	Holds helper classes for the ModifierVisitor class, which is used to modify Drawable objects (Atoms, Bonds, and Segments).

Uses of Atom in org.proteinshader.graphics.adapter

Methods in org.proteinshader.graphics.adapter with parameters of type Atom

void	StructureToGraphics.draw(GL gl, Atom atom) Draws an Atom as a sphere.

Uses of Atom in org.proteinshader.gui

Methods in org.proteinshader.gui that return Atom

Atom[]	MediatorImpl.getCurrentAtoms() Returns the current Atoms.
Atom[]	Mediator.getCurrentAtoms() Returns the current Atoms.

Methods in org.proteinshader.gui with parameters of type Atom

void	MediatorImpl.setCurrentAtoms(Atom[] atoms) Sets the current Atoms.
void	Mediator.setCurrentAtoms(Atom[] atoms) Sets the current Atoms.

Uses of Atom in org.proteinshader.gui.components.controlpanel

Methods in org.proteinshader.gui.components.controlpanel that return Atom

Atom	SelectorPanel.getSelectedAtom() Returns the currently selected Atom from the Atom list.
Atom[]	SelectorPanel.getSelectedAtoms() Returns an array of the currently selected Atoms from the Atom list.

Uses of Atom in org.proteinshader.structure

Methods in org.proteinshader.structure that return Atom

Atom	AminoAcid.addNewAtom(int serialNo, AtomEnum type, String atomID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new Atom with the type and Atom ID given as arguments, adds the Atom to the Residue's collection of Atoms, and returns a reference to the new Atom.
Atom	Residue.addNewAtom(int serialNo, AtomEnum type, String atomID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new Atom with the type and Atom ID given as arguments, adds the Atom to the Residue's collection of Atoms, and returns a reference to the new Atom.
Atom	Structure.addNewAtom(int atomSerialNo, AtomEnum atomType, String atomID, String aminoAcidType, String residueID, String chainID, String modelID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new atom with the atomID given as an argument, adds the new Atom to the requested Model-Chain-AminoAcid, and then returns a reference to the new Atom.
Atom	Structure.addNewHetAtom(int atomSerialNo, AtomEnum atomType, String atomID, String hetName, String residueID, String chainID, String modelID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new atom with the atomID given as an argument, adds the new Atom to the requested Model-Chain-(Heterogen or Water), and then returns a reference to the new Atom.
Atom	Atom.getAltAtom() Returns an alternate Atom with a lower occupancy (if it exists).
Atom	Structure.getAtom(int atomSerialNo) Returns the Atom with Atom serial number given as an argument (or null if not found).
Atom	Residue.getAtom(String atomID) Returns the Atom with the atomID given as an argument, or returns null if the Atom is not found.
Atom	Structure.getAtom(String atomID, String residueID, String chainID, String modelID) Returns the Atom with the IDs given as arguments.
Atom	AminoAcid.getC() Returns the carbon Atom of the carbonyl group if it exists.
Atom	AminoAcid.getCA() Returns the alpha carbon Atom if it exists.
Atom	Bond.getDstAtom() Returns the destination Atom for this Bond.
Atom	AminoAcid.getHAor1HA() Returns the hydrogen Atom on the alpha carbon if it exists.
Atom	AminoAcid.getHorHN() Returns the hydrogen Atom on the nitrogen of the amino group.
Atom	AminoAcid.getN() Returns the nitrogen Atom of the amino group if it exists.
Atom	AminoAcid.getO() Returns the oxygen Atom of the carbonyl group if it exists.
Atom	Water.getO() Returns the oxygen Atom (or null if not found).
Atom	AminoAcid.getOXT() Returns the Chain terminating oxygen if it exists.
Atom	Bond.getSrcAtom() Returns the source Atom for this Bond.

Methods in org.proteinshader.structure that return types with arguments of type Atom

List<Atom>	Structure.getAtomSerialNoCache() Returns the Atom serial number cache as a list.
Iterator<Atom>	Residue.iteratorAtoms() Returns an Iterator for the Atoms held by this Residue.
Iterator<Atom>	AminoAcid.iteratorBackboneAtoms() Returns an Iterator for the backbone Atoms held by this Residue.
Iterator<Atom>	AminoAcid.iteratorSideChainAtoms() Returns an Iterator for the side chain Atoms held by this Residue.

Methods in org.proteinshader.structure with parameters of type Atom

void	Atom.addNewBond(Atom dstAtom, BondEnum type, VisibilityEnum visibility) Adds a new Bond with this Atom as the source Atom and the Atom given as an argument as the destination Atom.
Bond	Atom.getBond(Atom dstAtom) Returns the Bond from this Atom (the source) to the destination Atom.
void	Atom.removeBond(Atom dstAtom) Removes the Bond from this Atom (the source) to the destination Atom.
void	Atom.setAltAtom(Atom atom) Sets the alternate Atom.

Constructors in org.proteinshader.structure with parameters of type Atom

Bond(Atom srcAtom, Atom dstAtom, BondEnum type, VisibilityEnum visibility)
Constructs a Bond for the source and destination Atoms given as arguments.

Uses of Atom in org.proteinshader.structure.visitor

Methods in org.proteinshader.structure.visitor with parameters of type Atom

Quaternion	FrenetFrameGeneratorVisitor.calculateRotation(Atom atom1, Atom atom2, Atom atom3) Calculates a rotation matrix [N B T] based on the xyz-centers of the three Atoms given as arguments, and then converts the rotation matrix into a Quaternion that is returned.
boolean	BondPredictor.isDistanceAcceptable(Atom srcAtom, Atom dstAtom) Determines if two Atoms are within an acceptable distance for a covalent Bond.
boolean	BondPredictor.isDoubleBond(Atom srcAtom, Atom dstAtom, AminoAcidEnum aminoAcidType) Uses the Atom IDs (from Atom name field in a PDB record) and the AminoAcid type to determine if the Atoms should have a double Bond (assuming that they both belong to the same AminoAcid).
void	ModifierVisitor.visit(Atom atom) If an AtomModifier has been added, it will be used to modify the Atom.
void	Visitor.visit(Atom atom) Traverses all Bonds owned by the Atom.
void	SFWriterVisitor.visit(Atom atom) Writes all information held by an Atom.
void	BoundsVisitor.visit(Atom atom) Checks xyz-coordinates to look for any new min or new max.
void	VisibilityVisitor.visit(Atom atom) Tests the visiblity of the Atom in order to determine if it should be transferred to the opaque Atoms and Bonds list or the translucent Drawables list.
void	BondDestroyerVisitor.visit(Atom atom) Removes all Bonds on the Atom.
void	BondGeneratorVisitor.visit(Atom atom) Checks if the Atom is a possible Bond destination Atom for any previously seen Atoms of the same Residue, and then adds the Atom to the list of Atoms to remember.

Uses of Atom in org.proteinshader.structure.visitor.modifiers

Methods in org.proteinshader.structure.visitor.modifiers with parameters of type Atom

void	AtomModifier.modify(Atom atom) Modifies the ball radius if requested, and then calls on modify() of the superclass, DrawableModifier, to apply any other requested modifications such as visibility, color, or radius for space-filling model.