Uses of Class
edu.sdsc.mbt.Atom

Packages that use Atom

edu.sdsc.mbt
edu.sdsc.mbt.util	This package provides classes which implement extra functionality on top of the core MBT classes (that is, capabilities that are not absolutely required by, or would otherwise overcomplicate, the core classes).
edu.sdsc.mbt.viewables	This package provides classes which enable molecular biology data to be represented as visible/renderable viewable objects, plus, this package defines a top-level StructureDocument object to encapsulate the complete state of these objects and properties.
edu.sdsc.mbt.viewers.GLViewerImpl
edu.sdsc.sirius.dialogs
edu.sdsc.sirius.io	This package provides classes which enable molecular biology data sets (such as protein structures, sequence data, etc) to be loaded into an MBT application as a Structure object.
edu.sdsc.sirius.util
edu.sdsc.sirius.viewers
edu.sdsc.sirius.viewers.TreeViewer

Uses of Atom in edu.sdsc.mbt

Fields in edu.sdsc.mbt declared as Atom

Atom	StericBumpComponent.atom1
Atom	StericBumpComponent.atom2
Atom	ResidueLabelComponent.reference
Atom	Residue.centerAtom
Atom	MonitorComponent.atom1
Atom	MonitorComponent.atom2
Atom	LabelComponent.atom
Atom	HydrogenBondComponent.atom1
Atom	HydrogenBondComponent.atom2

Methods in edu.sdsc.mbt that return Atom

Atom	StructureMap.getAtom(int atomIndex) Get the Atom at the specified index.
Atom	Residue.getAtom(int index) Return the specified Atom record contained in this Residue.
Atom	Residue.getAlphaAtom() Get the alpha (backbone) Atom (eg: "CA" or "P") for this amino acid or nucleic acid residue (or -1 for ligands).
Atom	Residue.getPolymerHeadAtom() Get the polymer "head" atom for this amino acid or nucleic acid residue (or null for ligands).
Atom	Residue.getPolymerTailAtom() Get the polymer "tail" atom for this amino acid or nucleic acid residue (or null for ligands).
Atom	Bond.getAtom(int index) Get the specified Atom record that forms this Bond.
Atom	Bond.getReferenceAtom()

Methods in edu.sdsc.mbt with parameters of type Atom

java.util.Vector	StructureMap.getAtoms(Atom atom)
int	StructureMap.getAtomIndex(Atom atom) Get the index of the specified Atom.
Residue	StructureMap.getResidue(Atom atom) Get the Residue object to which this Atom belongs.
Chain	StructureMap.getChain(Atom atom) Get the Chain object to which this Atom belongs.
void	StructureMap.addAtom(Atom added, Residue target, boolean assignName)
void	StructureMap.addAtom(Atom added, Atom bonded, Bond b, boolean assignName)
void	StructureMap.addAtom(Atom atom, Residue residue, java.lang.String chainId) Simply add an atom to the records don't assign bonds (they may be added later), and assign number based on the current numbering in the structure residue is a new Residue object that will be added to the structure (subsequent atoms may be added to the same residue from the calling method)
void	StructureMap.addAtom(Atom atom, Residue residue, int position, java.lang.String chainId) Adds a new atom with the specified position of the residue (if new)
void	StructureMap.addAtom(Atom added, Atom bonded, Bond b, int number)
java.util.Vector	StructureMap.getBonds(Atom atom) Return a Vector of all Bond objects connected to the given Atom object.
boolean	StructureMap.inRing(Atom atom, int ringSize)
void	StructureMap.removeAtom(Atom atom) This method removes an atom from the structure
int	Residue.getAtomIndex(Atom atom)
boolean	Residue.containsAtom(Atom atom) Tests whether the Residue contains a particular Atom.
void	Residue.addAtom(Atom atom) Add an Atom record to this Residue.
void	Residue.removeAtom(Atom atom)
void	Residue.setAlphaAtom(Atom atom)
static double	Bond.getDistance(Atom atom0, Atom atom1)
void	Bond.setReferenceAtom(Atom atom)

Constructors in edu.sdsc.mbt with parameters of type Atom

StericBumpComponent(Atom atom1, Atom atom2, java.lang.String label)

MonitorComponent(Atom atom1, Atom atom2, java.lang.String label)

LabelComponent(Atom atom, int dataType, int font, java.lang.String label)

LabelComponent(Atom atom, int dataType, int font, java.lang.String label, boolean selected, float[] color)

HydrogenBondComponent(Atom atom1, Atom atom2, java.lang.String label)

Bond(Atom atom0, Atom atom1)
Constructor variant used when there will likely be no atom list (eg: when only sequence data is loaded).

Uses of Atom in edu.sdsc.mbt.util

Methods in edu.sdsc.mbt.util that return Atom

static Atom	PickUtils.closestAtom(StructureComponent sc, double[] coord) Find the atom object within the specified structure component which is closest to the given coordinate.
Atom	OctreeAtomItem.getAtom() Return the Atom associated with this data item.

Methods in edu.sdsc.mbt.util with parameters of type Atom

static VectorSet	ElementProperties.getBondGeometry(Atom atom)
static double	BondFactory.distance(Atom atomA, Atom atomB) Return the coordinate distance between two Atom objects.
static Vec3d	Algebra.getAtomCoordinates(Atom atom) Returns coordinates of the given Atom in 3d space.

Constructors in edu.sdsc.mbt.util with parameters of type Atom

OctreeAtomItem(Atom atom, int index)
Construct an OctreeAtomItem from an Atom object.

Uses of Atom in edu.sdsc.mbt.viewables

Methods in edu.sdsc.mbt.viewables with parameters of type Atom

double	AtomRadiusByScaledCpk.getAtomRadius(Atom atom) Produce a radius based upon the atom element type.
double	AtomRadiusByCpk.getAtomRadius(Atom atom) Produce a radius based upon the atom element type.
double	AtomRadiusByConstant.getAtomRadius(Atom atom) Produce a radius based upon the atom element type.
double	AtomRadius.getAtomRadius(Atom atom)
java.lang.String	AtomLabelNone.getAtomLabel(Atom atom) Produce a null label.
java.lang.String	AtomLabelByChainId.getAtomLabel(Atom atom) Produce a label based upon the atom chain_id.
java.lang.String	AtomLabelByAtomName.getAtomLabel(Atom atom) Produce a label based upon the atom name.
java.lang.String	AtomLabelByAtomElement.getAtomLabel(Atom atom) Produce a label based upon the atom element.
java.lang.String	AtomLabelByAtomCompound.getAtomLabel(Atom atom) Produce a label based upon the atom name.
java.lang.String	AtomLabel.getAtomLabel(Atom atom)
void	AtomColorUniform.getAtomColor(Atom a, float[] c) Produce a color based upon the residue element type.
void	AtomColorUniform.setAtomColor(Atom a, float[] c)
void	AtomColorByElement.getAtomColor(Atom atom, float[] color) Produce a color based upon the atom element type.
void	AtomColorByCharge.getAtomColor(Atom atom, float[] color) Produce a color based upon the residue element type.
void	AtomColor.getAtomColor(Atom atom, float[] color)

Uses of Atom in edu.sdsc.mbt.viewers.GLViewerImpl

Methods in edu.sdsc.mbt.viewers.GLViewerImpl with parameters of type Atom

void	AtomLineGeometry.draw(Atom atom, StructureStyles structureStyles, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut) Please complete the missing tags for main
void	AtomGeometry.draw(Atom atom, StructureStyles structureStyles, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut)

Uses of Atom in edu.sdsc.sirius.dialogs

Fields in edu.sdsc.sirius.dialogs declared as Atom

Atom[]

StericEvent.atoms

Methods in edu.sdsc.sirius.dialogs with parameters of type Atom

static java.lang.String

AtomRenameDialog.showDialog(javax.swing.JFrame f, Atom a)

Uses of Atom in edu.sdsc.sirius.io

Fields in edu.sdsc.sirius.io declared as Atom

Atom	SideChain.CB
Atom	SideChain.HN
Atom	SideChain.CD

Uses of Atom in edu.sdsc.sirius.util

Methods in edu.sdsc.sirius.util with parameters of type Atom

static void	StructureMath.rotateStructure(double[] axis, Atom root, double angle, java.util.Vector atoms) Note that the argument is in degrees, and they get converted into radians
static double[]	StructureMath.getToOriginMatrix(Atom root)
static double[]	StructureMath.getFromOriginMatrix(Atom root)
static void	StructureMath.checkHydrogens(Atom atom, StructureViewer viewer, float pH, boolean batch)
static boolean	StructureMath.inRing(Atom root, int size) This method determines whether a given Atom is in a ring system of the specified size
static java.util.Vector	StructureMath.getRotatedAtoms(StructureMap map, Bond bond, Atom atom)
static boolean	ProteinProperties.isProteinBackbone(Atom a)
static boolean	DNAProperties.isDNABackbone(Atom a)

Uses of Atom in edu.sdsc.sirius.viewers

Methods in edu.sdsc.sirius.viewers with parameters of type Atom

void	StructureViewer.deleteHydrogen(Atom atom, boolean update) This method serves to delete hydrogens without creating any dummy atoms.
void	StructureViewer.checkDummyAtoms(Atom atom, boolean update) This method checks whether the atom should be represented as a dummy
void	StructureViewer.createMonitor(Atom atom1, Atom atom2, java.lang.String label, float[] color, boolean updateView) Creates a distance monitor
void	StructureViewer.createLabel(Atom atom, int type, int size, java.lang.String text, boolean updateView)
void	StructureViewer.createLabel(Atom atom, int type, int size, java.lang.String text, boolean selected, float[] color, boolean updateView)
void	StructureViewer.removeDummyAtom(Atom a)
void	StructureViewer.addAtom(Atom atom, boolean update) This method assumes that the necessary bookkeeping operations on StructureMap have been done, and it figures out what renderables are needed depending on the current display mode of the atom the new one gets connected to
void	StructureViewer.selectByRadius(Atom atom, float radius, boolean includeResidues)
void	StructureViewer.createBump(Atom a1, Atom a2, boolean updateView)
void	StructureViewer.createHydrogenBond(Atom atom1, Atom atom2, boolean updateView)
void	StructureViewer.computeDistance(Atom atom1, Atom atom2)
void	StructureViewer.focusView(Atom atom) this method places camera at 15 A from the specified atom and focus view on it

Uses of Atom in edu.sdsc.sirius.viewers.TreeViewer

Methods in edu.sdsc.sirius.viewers.TreeViewer with parameters of type Atom

void	StructureBrowser.addAtom(Atom atom)