Molecule

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org.jscience.chemistry.gui.extended.molecule
Class Molecule

java.lang.Object
  org.jscience.chemistry.gui.extended.molecule.Molecule

public class Molecule
extends java.lang.Object
extends java.lang.Object

Tripos base molecule class

See Also:: AtomVector, BondVector, Atom, Bond, Matrix3D

Field Summary
`protected java.util.Hashtable`	`atomIdToIndex` Atom id to index map.
`protected AtomVector`	`highlightAtoms` List of highlighted atom
`protected int`	`id` Molecule id
`protected Matrix3D`	`mat` The transformation matrix
`protected AtomVector`	`myAtoms` Atom list
`protected BondVector`	`myBonds` Bond list
`protected RingVector`	`myRings` Ring list
`protected java.lang.String`	`name` Molecule name
`protected int`	`numAtoms` Number of atoms
`protected int`	`numBonds` Number of bonds
`protected int`	`numRings` Number of rings
`protected java.util.Hashtable`	`properties` Properties list
`protected static Renderer`	`rendererDefault` Default renderer so that pre-existing programs can still call Molecule.draw( Graphics )
`protected AtomVector`	`selectAtoms` List of selected atoms
`protected float`	`xmax` The bounding extents of the molecule
`protected float`	`xmin` The bounding extents of the molecule
`protected float`	`ymax` The bounding extents of the molecule
`protected float`	`ymin` The bounding extents of the molecule
`protected float`	`zmax` The bounding extents of the molecule
`protected float`	`zmin` The bounding extents of the molecule

Constructor Summary
`Molecule()` Default constructor
`Molecule(int id, java.lang.String name)` Id/Name constructor
`Molecule(Molecule jmol)` Copy constructor

Method Summary
`void`	`addAtom(Atom a)` Add an atom to this molecule
`void`	`addBond(Bond b)` Add a bond to this molecule
`void`	`addMolecule(Molecule jmol)` Add a molecule to this molecule
`void`	`addProperty(java.lang.String name, java.lang.String value)` Add a property (i.e. a "name"/"value" pair) to this molecule.
`void`	`addRing(Ring r)` Add a ring to this molecule
`void`	`calcPerpUnitVec(float x1, float y1, float x2, float y2, float[] pex, float[] pey)` Calculates 2D vector perpendicular to bond
`boolean`	`contains(Atom a)` Return true iff the atom in the parameter is one of the atoms in this molecule
`boolean`	`contains(Bond b)` Return true iff the bond in the parameter is one of the bonds in this molecule
`void`	`dehighlight()` Dehighlighted all highlighted atoms.
`void`	`deleteAtom(Atom a)` Delete an atom and its bonds from this molecule
`void`	`deleteBond(Bond b)` Delete a bond from this molecule
`void`	`deleteProperty(java.lang.String name)` Remove a property from this molecule.
`void`	`deleteRing(Ring r)` Delete a ring from this molecule
`void`	`deselect()` Deselects all `selected` atoms
`void`	`deselect(Atom a)` Deselect one `selected` atom
`void`	`draw(java.awt.Graphics g)` Draw the molecule recommend to avoid, but to use renderer approach
`boolean`	`equals(Molecule jmol)` Compares this molecule with another
`Atom`	`findAtom(float x, float y, float z, float FINDRADIUS)` Returns closest atom to point within FINDRADIUS, `null` if nothing is found,
`void`	`findBB()` Determines bounding box of a molecule (sets xmax,xmin,ymax,ymin,zmax,zmin)
`Atom`	`getAtomFromId(int atomId)` Return an atom in this molecule whose id matches the input id
`java.util.Hashtable`	`getAtomIdToIndex()` Return atomIdToIndex
`Bond`	`getBondFromId(int bondId)` Return a bond in this molecule whose id matches the input id
`AtomVector`	`getHighlightAtoms()` Return the highlighted atoms vector
`int`	`getId()` Returns id of this molecule
`Matrix3D`	`getMatrix3D()` Return 3D transformation matrix
`AtomVector`	`getMyAtoms()` Returns atom vector of this molecule
`BondVector`	`getMyBonds()` Return bond vector of this molecule
`RingVector`	`getMyRings()` Return ring vector of this molecule
`java.lang.String`	`getName()` Returns name of molecule
`int`	`getNumAtoms()` Return number of atoms in this molecule
`int`	`getNumBonds()` Return number of bonds in this molecule
`int`	`getNumRings()` Return number of rings in this molecule
`java.util.Hashtable`	`getProperties()` Return property table in this molecule
`java.lang.String`	`getPropertyValue(java.lang.String name)` Get the property value associated with specified property name.
`protected static Renderer`	`getRenderer()` Return the Renderer which draws this molecule
`AtomVector`	`getSelectAtoms()` Return the selected atoms vector
`float`	`getXmax()` Return the maxmum x coordinate
`float`	`getXmin()` Return the minimum x coordinate of this molelcule
`float`	`getYmax()` Return the maxmum y coordinate
`float`	`getYmin()` Return the minimum y coordinate
`float`	`getZmax()` Return the maxmum z coordinate
`float`	`getZmin()` Return the minimum z coordinate
`protected boolean`	`hasHighlightedAtoms()` Returns `true` if molecule has `highlighted` atoms
`boolean`	`hasSelectedAtoms()` Returns `true` if molecule has `selected` atoms
`void`	`highlight(Atom a)` Designates an atom as `highlighted`.
`void`	`highlight(AtomVector av)` Designates an atom list as `highlighted`.
`boolean`	`isAProperty(java.lang.String name)` Indicate if the molecule contains the specified property.
`boolean`	`isOuterBond(Bond b, float tx1, float ty1, float tx2, float ty2)` Returns true if bond is oriented counterclockwise with respect to the centroid of the ring, else returns false.
`void`	`select(Atom a)` Flags specified atom as `selected`
`void`	`setAtomIdToIndex(java.util.Hashtable index)` Set atomIdToIndex
`void`	`setHighlightAtoms(AtomVector av)` Set highlighted atoms vector
`void`	`setId(int id)` Set id of this molecule
`void`	`setMatrix3D(Matrix3D mat)` Set 3D transformation matrix
`void`	`setMyAtoms(AtomVector atoms)` Set atom vector
`void`	`setMyBonds(BondVector bv)` Set bond vector
`void`	`setMyRings(RingVector rv)` Set ring vector
`void`	`setName(java.lang.String s)` Set name of this molecule
`void`	`setNumAtoms(int numAtoms)` Set number of atoms
`void`	`setNumRings(int numRings)` Set number of rings
`void`	`setProperties(java.util.Hashtable prop)` Set property table
`protected static void`	`setRenderer(Renderer r)` Set renderer which draws this molecule
`void`	`setSelectAtoms(AtomVector av)` Set selected atoms vector
`void`	`setXmax(float xmax)` Set maxmum of X-coordinate
`void`	`setXmin(float xmin)` Set minimum of X-coordinate of this molecule
`void`	`setYmax(float ymax)` Set maxmum of Y-coordinate
`void`	`setYmin(float ymin)` Set minimum of Y-coordinate
`void`	`setZmax(float zmax)` Set maxmum of Z-coordinate
`void`	`setZmin(float zmin)` Set minimum of Z-coordinate
`java.lang.String`	`toString()` Returns a String representation of molecule

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Field Detail

rendererDefault

protected static Renderer rendererDefault

Default renderer so that pre-existing programs can still call Molecule.draw( Graphics )

id

protected int id

Molecule id

name

protected java.lang.String name

Molecule name

myAtoms

protected AtomVector myAtoms

Atom list

atomIdToIndex

protected java.util.Hashtable atomIdToIndex

Atom id to index map. Does not require atom ids to start at 1 or be sequential.

myBonds

protected BondVector myBonds

Bond list

myRings

protected RingVector myRings

Ring list

numAtoms

protected int numAtoms

Number of atoms

numBonds

protected int numBonds

Number of bonds

numRings

protected int numRings

Number of rings

properties

protected java.util.Hashtable properties

Properties list

mat

protected Matrix3D mat

The transformation matrix