astex
Class Atom

java.lang.Object
  astex.Point3d
      astex.Atom

All Implemented Interfaces:

GenericInterface, Selectable

public class Atom
extends Point3d
implements Selectable, GenericInterface

A class for holding information about an atom.

Field Summary

static int	Aromatic
static int	atomsCached
static int	atomsCreated
java.lang.String	atomType The (usually sybyl) atom type of the atom.
int	attributes An integer for storing various attributes.
static int	B The B coordinate attribute.
static int	BallAndStick The property set flag.
float	ballRadius The stick radius of the atom.
static java.lang.String	BAttribute
static java.lang.String	Color
static int	CustomLabelled The property set flag.
static int	Cylinder The property set flag.
static int	Displayed The atom display flag.
static int	DisplayedMask
static int	E The energy.
static java.lang.String	Element
static int	Hetero The atom is an heteroatom.
static int	ID The ID attribute.
char	insertionCode Insertion code if any.
static int	Labelled The atom is labelled.
static int	ModellingActive Atom is active in energy calculations.
ModellingData	modellingData
static int	ModellingEnvironment Atom is environment in energy calculations.
static int	ModellingFixed Atom is fixed in energy calculations.
static int	ModellingXray Atom is xray terms in energy calculations.
static int	NameLeftJustified Atom is fixed in energy calculations.
static int	O The O coordinate attribute.
static java.lang.String	OAttribute
static java.lang.String	Opacity
static int	Property The property set flag.
static int	Q The partial charge attribute.
static java.lang.String	QAttribute
float	radius The radius of the atom.
static java.lang.String	Radius
static int	Ring
static int	Selected The atom is selected.
static int	Solvent The atom is solvent.
static int	sp
static int	sp2
static int	sp3 Hybridisation states.
static int	Surface The surfaced atom flag.
static int	SurfaceContext The surface context flag.
static int	TemporarilySelected The atom is temporarily selected.
static int	Undefined Undefined atom id.
static int	VDWSphere The sphere flag.
static int	Visited The atom visit flag.
static int	Wide The wide atom flag.
static int	X The X coordinate attribute.
static java.lang.String	XAttribute
int	xs Screen x-coordinate.
static int	Y The Y coordinate attribute.
static java.lang.String	YAttribute
int	ys Screen y-coordinate.
static int	Z The Z coordinate attribute.
static java.lang.String	ZAttribute
int	zs Screen z-coordinate.

Fields inherited from class astex.Point3d

x, y, z

Fields inherited from interface astex.generic.GenericInterface

Name

Method Summary

void	addBond(Bond bond) Add a bond to the atom.
void	addChild(GenericInterface child) Add a child.
void	addListener(GenericEventInterface geh) Add a listener.
void	addParent(GenericInterface parent) Add a parent.
boolean	connected121314(Atom otherAtom) Are these atoms connected 1,2, 1,3 or 1,4.
boolean	connected13(Atom targetAtom) Is this atom connected by two bonds to the specified atom.
boolean	connected14(Atom targetAtom) Is this atom connected by three bonds to the specified atom.
static Atom	create() Create an atom.
void	delete() Remove an atom.
void	edit(java.lang.String name, java.lang.String value)
java.lang.String	generateLabel(java.lang.String format) Generate an atom label according to a format.
java.lang.Object	get(java.lang.Object key, java.lang.Object def) Get Object representing key.
java.lang.String	getAtomLabel() Get the atom label.
java.lang.String	getAtomSymbol() Get the atomic symbol for this atom.
java.lang.String	getAtomType() Get the atomType.
double	getAttribute(int attribute) Get an attribute.
double	getBallRadius() Get the vdw radius.
double	getBFactor() Return the bFactor.
double	getBiggestDisplayedRadius() Get the biggest radius that is displayed.
Bond	getBond(Atom otherAtom) Does this atom have a bond to the specified atom.
Bond	getBond(int index) Return a specified bond or null if it doesn't exist.
int	getBondCount() Return the total number of bonds.
Atom	getBondedAtom(int index) Return the specified bonded atom.
Atom	getBondedAtom(java.lang.String nm) Get bonded atom with this name.
double	getBondingRadius() Get the bonding radius for the atom.
Bond	getBondWithOrder(int bondOrder) Return a bond with the specified order.
int	getCharge() Get the atom charge.
java.util.Enumeration	getChildren(java.lang.Object type) Get an enumeration of our children.
java.lang.Object	getClassname() Get our class description.
int	getColor() Get the atom color.
java.lang.String	getCustomLabel() Set whether the atom is solvent.
int	getElement() Get the element type of this atom.
int	getHybridisation() Return the hybridisation state of the atom.
int	getId() Get the id for this atom.
char	getInsertionCode() Get the insertion code.
double	getMass() Get the default mass for the atom.
Molecule	getMolecule() Get the molecule to which the atom belongs.
double	getOccupancy() Get the occupancy.
java.util.Enumeration	getParents(java.lang.Object type) Get an Enumeration of our parents.
float	getPartialCharge() Get the value of partialCharge.
java.util.Enumeration	getProperties() Return an enumeration of our properties.
Residue	getResidue() Get the residue to which the atom belongs.
int	getSelectedColor() Get the color or selected color if selected.
java.lang.String	getSymbol() Get the atom symbol for the element.
int	getTransparency() Get the transparency.
double	getVDWRadius() Get the VDW radius of this atom.
boolean	hasAttributes() Does the atom have any attributes set?
boolean	hasBond(Atom otherAtom) Does this atom have a bond to the other atom.
boolean	hasBondWithOrder(int bondOrder) Does this atom have a bond of the specified bond order.
boolean	hasExplicitBond() Does this atom have bonds that came from an explicit bond.
void	initialise() Initialise an atom.
boolean	isAliphaticHydrogen() Is this an aliphatic hydrogen.
boolean	isDisplayed() Has this atom been displayed.
boolean	isHBondAcceptor() Is this atom an HBond donor.
boolean	isHBondDonor() Is this atom an HBond donor.
boolean	isHeteroAtom() Is this atom a heteroatom.
boolean	isLabelled() Is this atom a solvent atom.
boolean	isSelected() Is this atom selected.
boolean	isSimpleDisplayed() Has this atom been displayed.
boolean	isSolvent() Is this atom a solvent atom.
boolean	isTemporarilySelected() Is this atom temporarily selected.
boolean	isVisited() Has this atom been visited.
boolean	isWide() Has this atom been wide.
void	release() Release an atom after we finished with it.
void	removeAllBonds() Remove all bonds.
void	removeBond(Bond b) Remove a bond from this atom.
void	removeChild(GenericInterface child) Remove a child.
void	removeListener(GenericEventInterface geh) Remove a listener.
void	removeParent(GenericInterface parent) Remove a parent.
void	resetColor() Set color back to undefined.
int	select(int state) Set the selection state.
java.lang.String	selectStatement()
java.lang.Object	set(java.lang.Object key, java.lang.Object value) Set an object value.
void	setAtomLabel(java.lang.String newLabel) Set the atom label.
void	setAtomType(java.lang.String s) Set the atomType.
void	setBallRadius(double r) Set the vdw radius.
void	setBFactor(double b) Set the bFactor.
void	setCharge(int newCharge) Set the atom charge.
void	setClassname(java.lang.String classname) Set our classname.
void	setColor(int newColor) Set the atom color.
void	setCustomLabel(java.lang.String l) Set whether the atom is solvent.
void	setDisplayed(boolean state) Set whether the atom has been displayed.
void	setElement(int newElement) Set the element of this atom.
void	setHeteroAtom(boolean state) Set whether the atom is a heteroatom.
void	setId(int newId) Set the id for this atom.
void	setInsertionCode(char c) Set the insertion code.
void	setLabelled(boolean state) Set whether the atom is solvent.
void	setOccupancy(double o) Set the occupancy.
void	setOrClearAttribute(int attribute, boolean state) Set or clear a particular attribute.
void	setParent(Residue residue) Set the residues to which the atom belongs.
void	setPartialCharge(double v) Set the value of partialCharge.
void	setSelected(boolean state) Set whether the atom is selected.
void	setSolvent(boolean state) Set whether the atom is solvent.
void	setTemporarilySelected(boolean state) Set whether the atom is temporarily selected.
void	setTransparency(int t) Set the transparency.
void	setVDWRadius(double r) Set the vdw radius.
void	setVisited(boolean state) Set whether the atom has been visited.
void	setWide(boolean state) Set whether the atom has been wide.
java.lang.String	toString() Return a string representation of this point.
void	transformToScreen(Matrix m) Transform this atom to screen coordinates.

Methods inherited from class astex.Point3d

add, angle, angleDegrees, clone, cross, cross, cross, crossNoNormalise, distance, distance, distanceSq, distanceSq, divide, dot, equal, get, getX, getY, getZ, isNullVector, length, length, max, mid, mid, min, negate, normalise, normalToLine, normalToLine, normalToLine, normalToLine, planeEquation, print, scale, set, set, set, set, setX, setY, setZ, subtract, torsion, torsion, torsionDegrees, torsionDegrees, transform, transformByMatrix, translate, translate, unitVector, unitVector, unitVector, vector, vector, zero

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

Undefined

public static int Undefined

Undefined atom id.

attributes

public int attributes

An integer for storing various attributes.

radius

public float radius

The radius of the atom.

ballRadius

public float ballRadius

The stick radius of the atom.

Solvent

public static int Solvent

The atom is solvent.

Labelled

public static int Labelled

The atom is labelled.

Selected

public static int Selected

The atom is selected.

Hetero

public static int Hetero

The atom is an heteroatom.

TemporarilySelected

public static int TemporarilySelected

The atom is temporarily selected.

Visited

public static int Visited

The atom visit flag.

Displayed

public static int Displayed

The atom display flag.

Wide

public static int Wide

The wide atom flag.

VDWSphere

public static int VDWSphere

The sphere flag.

Surface

public static int Surface

The surfaced atom flag.

SurfaceContext

public static int SurfaceContext

The surface context flag.

Property

public static int Property

The property set flag.

BallAndStick

public static int BallAndStick

The property set flag.

Cylinder

public static int Cylinder

The property set flag.

CustomLabelled

public static int CustomLabelled

The property set flag.

DisplayedMask

public static int DisplayedMask

ModellingActive

public static int ModellingActive

Atom is active in energy calculations.

ModellingEnvironment

public static int ModellingEnvironment

Atom is environment in energy calculations.

ModellingXray

public static int ModellingXray

Atom is xray terms in energy calculations.

ModellingFixed

public static int ModellingFixed

Atom is fixed in energy calculations.

NameLeftJustified

public static int NameLeftJustified

Atom is fixed in energy calculations.

Aromatic

public static final int Aromatic

See Also:

Constant Field Values

Ring

public static final int Ring

See Also:

Constant Field Values

modellingData

public ModellingData modellingData

X

public static final int X

The X coordinate attribute.

See Also:

Constant Field Values

Y

public static final int Y

The Y coordinate attribute.

See Also:

Constant Field Values

Z

public static final int Z

The Z coordinate attribute.

See Also:

Constant Field Values

B

public static final int B

The B coordinate attribute.

See Also:

Constant Field Values

O

public static final int O

The O coordinate attribute.

See Also:

Constant Field Values

ID

public static final int ID

The ID attribute.

See Also:

Constant Field Values

Q

public static final int Q

The partial charge attribute.

See Also:

Constant Field Values

E

public static final int E

The energy.

See Also:

Constant Field Values

sp3

public static final int sp3

Hybridisation states.

See Also:

Constant Field Values

sp2

public static final int sp2

See Also:

Constant Field Values

sp

public static final int sp

See Also:

Constant Field Values

xs

public transient int xs

Screen x-coordinate.

ys

public transient int ys

Screen y-coordinate.

zs

public transient int zs

Screen z-coordinate.

insertionCode

public char insertionCode

Insertion code if any.

atomType

public java.lang.String atomType

The (usually sybyl) atom type of the atom.

atomsCreated

public static int atomsCreated

atomsCached

public static int atomsCached

XAttribute

public static final java.lang.String XAttribute

See Also:

Constant Field Values

YAttribute

public static final java.lang.String YAttribute

See Also:

Constant Field Values

ZAttribute

public static final java.lang.String ZAttribute

See Also:

Constant Field Values

BAttribute

public static final java.lang.String BAttribute

See Also:

Constant Field Values

OAttribute

public static final java.lang.String OAttribute

See Also:

Constant Field Values

QAttribute

public static final java.lang.String QAttribute

See Also:

Constant Field Values

Color

public static final java.lang.String Color

See Also:

Constant Field Values

Radius

public static final java.lang.String Radius

See Also:

Constant Field Values

Opacity

public static final java.lang.String Opacity

See Also:

Constant Field Values

Element

public static final java.lang.String Element

See Also:

Constant Field Values

Method Detail

initialise

public void initialise()

Initialise an atom.

Overrides:

initialise in class Point3d

setAtomType

public void setAtomType(java.lang.String s)

Set the atomType.

getAtomType

public java.lang.String getAtomType()

Get the atomType.

setTransparency

public void setTransparency(int t)

Set the transparency.

getTransparency

public int getTransparency()

Get the transparency.

setInsertionCode

public void setInsertionCode(char c)

Set the insertion code.

getInsertionCode

public char getInsertionCode()

Get the insertion code.

create

public static Atom create()

Create an atom. This is the only public interface for creating new atoms.

release

public void release()

Release an atom after we finished with it.

setBFactor

public void setBFactor(double b)

Set the bFactor.

getBFactor

public double getBFactor()

Return the bFactor.

setOccupancy

public void setOccupancy(double o)

Set the occupancy.

getOccupancy

public double getOccupancy()

Get the occupancy.

getPartialCharge

public float getPartialCharge()

Get the value of partialCharge.

Returns:

value of partialCharge.

setPartialCharge

public void setPartialCharge(double v)

Set the value of partialCharge.

Parameters:

v - Value to assign to partialCharge.

getAttribute

public double getAttribute(int attribute)

Get an attribute.

setId

public void setId(int newId)

Set the id for this atom.

getId

public int getId()

Get the id for this atom.

setElement

public void setElement(int newElement)

Set the element of this atom.

getElement

public int getElement()

Get the element type of this atom.

getAtomSymbol

public java.lang.String getAtomSymbol()

Get the atomic symbol for this atom.

setAtomLabel

public void setAtomLabel(java.lang.String newLabel)

Set the atom label.

getAtomLabel

public java.lang.String getAtomLabel()

Get the atom label.

generateLabel

public java.lang.String generateLabel(java.lang.String format)

Generate an atom label according to a format.

getSymbol

public java.lang.String getSymbol()

Get the atom symbol for the element.

getMass

public double getMass()

Get the default mass for the atom.

getCharge

public int getCharge()

Get the atom charge.

setCharge

public void setCharge(int newCharge)

Set the atom charge.

setColor

public void setColor(int newColor)

Set the atom color.

getColor

public int getColor()

Get the atom color.

getSelectedColor

public int getSelectedColor()

Get the color or selected color if selected.

resetColor

public void resetColor()

Set color back to undefined.

getMolecule

public Molecule getMolecule()

Get the molecule to which the atom belongs.

setParent

public void setParent(Residue residue)

Set the residues to which the atom belongs.

getResidue

public Residue getResidue()

Get the residue to which the atom belongs.

addBond

public void addBond(Bond bond)

Add a bond to the atom.

getBond

public Bond getBond(int index)

Return a specified bond or null if it doesn't exist.

getBondedAtom

public Atom getBondedAtom(int index)

Return the specified bonded atom.

getBondCount

public int getBondCount()

Return the total number of bonds.

getBond

public Bond getBond(Atom otherAtom)

Does this atom have a bond to the specified atom.

getBondedAtom

public Atom getBondedAtom(java.lang.String nm)

Get bonded atom with this name.

hasBond

public boolean hasBond(Atom otherAtom)

Does this atom have a bond to the other atom.

hasExplicitBond

public boolean hasExplicitBond()

Does this atom have bonds that came from an explicit bond.

connected13

public boolean connected13(Atom targetAtom)

Is this atom connected by two bonds to the specified atom. That is are they 1,3 connected.

connected14

public boolean connected14(Atom targetAtom)

Is this atom connected by three bonds to the specified atom. That is are they 1,4 connected.

connected121314

public boolean connected121314(Atom otherAtom)

Are these atoms connected 1,2, 1,3 or 1,4.

getBondWithOrder

public Bond getBondWithOrder(int bondOrder)

Return a bond with the specified order.

hasBondWithOrder

public boolean hasBondWithOrder(int bondOrder)

Does this atom have a bond of the specified bond order.

getBondingRadius

public double getBondingRadius()

Get the bonding radius for the atom.

getVDWRadius

public double getVDWRadius()

Get the VDW radius of this atom.

getBiggestDisplayedRadius

public double getBiggestDisplayedRadius()

Get the biggest radius that is displayed.

setVDWRadius

public void setVDWRadius(double r)

Set the vdw radius.

setBallRadius

public void setBallRadius(double r)

Set the vdw radius.

getBallRadius

public double getBallRadius()

Get the vdw radius.

transformToScreen

public void transformToScreen(Matrix m)

Transform this atom to screen coordinates.

isAliphaticHydrogen

public boolean isAliphaticHydrogen()

Is this an aliphatic hydrogen.

isHBondDonor

public boolean isHBondDonor()

Is this atom an HBond donor. Only suitable for standard aminoacid names.

isHBondAcceptor

public boolean isHBondAcceptor()

Is this atom an HBond donor. Only suitable for standard aminoacid names.

hasAttributes

public boolean hasAttributes()

Does the atom have any attributes set?

setOrClearAttribute

public void setOrClearAttribute(int attribute,
                                boolean state)

Set or clear a particular attribute.

setSolvent

public void setSolvent(boolean state)

Set whether the atom is solvent.

isSolvent

public boolean isSolvent()

Is this atom a solvent atom.

setCustomLabel

public void setCustomLabel(java.lang.String l)

Set whether the atom is solvent.

getCustomLabel

public java.lang.String getCustomLabel()

Set whether the atom is solvent.

isLabelled

public boolean isLabelled()

Is this atom a solvent atom.

setLabelled

public void setLabelled(boolean state)

Set whether the atom is solvent.

setSelected

public void setSelected(boolean state)

Set whether the atom is selected.

isSelected

public boolean isSelected()

Is this atom selected.

setHeteroAtom

public void setHeteroAtom(boolean state)

Set whether the atom is a heteroatom.

isHeteroAtom

public boolean isHeteroAtom()

Is this atom a heteroatom.

setTemporarilySelected

public void setTemporarilySelected(boolean state)

Set whether the atom is temporarily selected.

isTemporarilySelected

public boolean isTemporarilySelected()

Is this atom temporarily selected.

setVisited

public void setVisited(boolean state)

Set whether the atom has been visited.

isVisited

public boolean isVisited()

Has this atom been visited.

setWide

public void setWide(boolean state)

Set whether the atom has been wide.

isWide

public boolean isWide()

Has this atom been wide. Its a bond property.

setDisplayed

public void setDisplayed(boolean state)

Set whether the atom has been displayed.

isSimpleDisplayed

public boolean isSimpleDisplayed()

Has this atom been displayed.

isDisplayed

public boolean isDisplayed()

Has this atom been displayed.

select

public int select(int state)

Set the selection state.

Specified by:

select in interface Selectable

selectStatement

public java.lang.String selectStatement()

Specified by:

selectStatement in interface Selectable

getHybridisation

public int getHybridisation()

Return the hybridisation state of the atom.

toString

public java.lang.String toString()

Description copied from class: Point3d

Return a string representation of this point.

Overrides:

toString in class Point3d

delete

public void delete()

Remove an atom.

removeBond

public void removeBond(Bond b)

Remove a bond from this atom.

removeAllBonds

public void removeAllBonds()

Remove all bonds.

getProperties

public java.util.Enumeration getProperties()

Return an enumeration of our properties.

Specified by:

getProperties in interface GenericInterface

get

public java.lang.Object get(java.lang.Object key,
                            java.lang.Object def)

Get Object representing key.

Specified by:

get in interface GenericInterface

edit

public void edit(java.lang.String name,
                 java.lang.String value)

set

public java.lang.Object set(java.lang.Object key,
                            java.lang.Object value)

Set an object value.

Specified by:

set in interface GenericInterface

getClassname

public java.lang.Object getClassname()

Get our class description.

Specified by:

getClassname in interface GenericInterface

setClassname

public void setClassname(java.lang.String classname)

Set our classname.

Specified by:

setClassname in interface GenericInterface

getParents

public java.util.Enumeration getParents(java.lang.Object type)

Get an Enumeration of our parents.

Specified by:

getParents in interface GenericInterface

addParent

public void addParent(GenericInterface parent)

Add a parent.

Specified by:

addParent in interface GenericInterface

removeParent

public void removeParent(GenericInterface parent)

Remove a parent.

Specified by:

removeParent in interface GenericInterface

getChildren

public java.util.Enumeration getChildren(java.lang.Object type)

Get an enumeration of our children.

Specified by:

getChildren in interface GenericInterface

addChild

public void addChild(GenericInterface child)

Add a child.

Specified by:

addChild in interface GenericInterface

removeChild

public void removeChild(GenericInterface child)

Remove a child.

Specified by:

removeChild in interface GenericInterface

addListener

public void addListener(GenericEventInterface geh)

Add a listener.

Specified by:

addListener in interface GenericInterface

removeListener

public void removeListener(GenericEventInterface geh)

Remove a listener.

Specified by:

removeListener in interface GenericInterface